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  • 1.
    Abbey-Lee, Robin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Max Planck Inst Ornithol, Germany.
    Dingemanse, Niels J.
    Ludwig Maximilians Univ Munchen, Germany.
    Adaptive individual variation in phenological responses to perceived predation levels2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 1601Article in journal (Refereed)
    Abstract [en]

    The adaptive evolution of timing of breeding (a component of phenology) in response to environmental change requires individual variation in phenotypic plasticity for selection to act upon. A major question is what processes generate this variation. Here we apply multi-year manipulations of perceived predation levels (PPL) in an avian predator-prey system, identifying phenotypic plasticity in phenology as a key component of alternative behavioral strategies with equal fitness payoffs. We show that under low-PPL, faster (versus slower) exploring birds breed late (versus early); the pattern is reversed under high-PPL, with breeding synchrony decreasing in conjunction. Timing of breeding affects reproductive success, yet behavioral types have equal fitness. The existence of alternative behavioral strategies thus explains variation in phenology and plasticity in reproductive behavior, which has implications for evolution in response to anthropogenic change.

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  • 2.
    Abbey-Lee, Robin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Uhrig, Emily
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Southern Oregon Univ, OR 97520 USA.
    Garnham, Laura
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lundgren, Kristoffer
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Child, Sarah
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Manchester, England.
    Lovlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Experimental manipulation of monoamine levels alters personality in crickets2018In: Scientific Reports, E-ISSN 2045-2322, Vol. 8, article id 16211Article in journal (Refereed)
    Abstract [en]

    Animal personality has been described in a range of species with ecological and evolutionary consequences. Factors shaping and maintaining variation in personality are not fully understood, but monoaminergic systems are consistently linked to personality variation. We experimentally explored how personality was influenced by alterations in two key monoamine systems: dopamine and serotonin. This was done using ropinirole and fluoxetine, two common human pharmaceuticals. Using the Mediterranean field cricket (Gryllus bimaculatus), we focused on the personality traits activity, exploration, and aggression, with confirmed repeatability in our study. Dopamine manipulations explained little variation in the personality traits investigated, while serotonin manipulation reduced both activity and aggression. Due to limited previous research, we created a dose-response curve for ropinirole, ranging from concentrations measured in surface waters to human therapeutic doses. No ropinirole dose level strongly influenced cricket personality, suggesting our results did not come from a dose mismatch. Our results indicate that the serotonergic system explains more variation in personality than manipulations of the dopaminergic system. Additionally, they suggest that monoamine systems differ across taxa, and confirm the importance of the mode of action of pharmaceuticals in determining their effects on behaviour.

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  • 3.
    Abul-Kasim, Kasim
    et al.
    Lund Univ, Sweden.
    Persson, Erik
    Lund Univ, Sweden.
    Levinsson, Anders
    Lund Univ, Sweden.
    Strombeck, Anita
    Lund Univ, Sweden.
    Selariu, Eufrozina
    Lund Univ, Sweden.
    Ohlin, Acke
    Region Östergötland. Skane Univ Hosp, Sweden.
    Vertebral Hemangiomas: Prevalence, New Classification and Natural History. Magnetic Resonance Imaging-Based Retrospective Longitudinal Study2023In: The Neuroradiology Journal, ISSN 1971-4009, Vol. 36, no 1, p. 23-30Article in journal (Refereed)
    Abstract [en]

    Background and purpose: To determine the prevalence of vertebral hemangiomas (VHs), establish a new classification of VHs based on their MRI-signal pattern, and study their natural history. Methods: MRI of 1000 consecutive patients who underwent at least two MRI with an interval of at least 3 years. Growth rate and change of MRI-signal pattern during the follow-up period were the parameters included in studying the natural history of VHs. Results: The prevalence of VHs was 41%. VHs were classified as type I-IV with fat-rich VHs (type I), constituted 79% of all VHs. VHs were more common among females 43 degrees/o versus males 39%, p = .22. The most affected vertebra was L1. Occurrence rates for cervical (1%), thoracic (7%), and lumbar spine (10%) differed significantly (p < .001). The prevalence of VHs increased with age regardless of gender or spinal part involved (p < .001). Only 26% of VHs changed their size and 4 degrees/o changed their signal during the average follow-up of 7 years. All VHs were slowly growing lesions (average expected growth of <3 mm/10 years). No significant difference between growth rate of VHs type I (0.25 mm/year) and other types of VHs. None of the VHs that were initially reported as "metastases cannot be rule out" showed alarming change in signal or size. Conclusions: VH can be classified into four types based on their MRI-signal pattern. Regardless of their type, VHs are slowly growing lesions. The presence of typical morphological pattern should enable radiologists to confidently differentiate them from vertebral metastases.

  • 4. Order onlineBuy this publication >>
    Agnvall, Beatrix
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Early domestication?: Phenotypic alterations of Red Junglefowl selected for divergent fear of humans2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Domestication is the process through which animals adapt to conditions provided by humans. The domesticated phenotype differs from wild ancestors in a number of traits relating to physiology, morphology and behaviour. One of the most striking differences is the animals’ fear response towards humans, and reduced fear of humans is assumed to have been an early prerequisite for the success of domestication. The early alterations seen in the domesticated phenotype may be traits developed as a correlated selection response due to tameness rather than selected upon one by one.

    This thesis summarizes a project where Red Junglefowl were selected for divergent fear of humans during six generations. In every generation, fear response to human was assessed in a standardized test and, according to fear score, the animals were bred for either high fear of humans (H) or low fear of humans (L). The animals were, above that of the standardized selection test, behaviourally phenotyped in different tests in each generation mainly focusing on fear, exploration and social behaviour. In addition to behaviour, the animals were phenotyped for body weight, egg weight, metabolism, feed intake, plumage condition, blood plasma corticosterone and peripheral serotonin. After culling, vital organs and brains were harvested and weighed.

    In paper I, we demonstrated that the selection trait has a significant genetic heritability and is genetically correlated with other behavioural responses associated with fearfulness and exploration. In paper II, we concluded that animals from the L strain had better plumage condition, higher weight, laid larger eggs and also generated larger offspring. Furthermore, when tested in a social dominance test with a limited resource, they received less and performed more aggression regardless of whether the restricted source was edible or not. In paper III, we revealed that animals from the L strain had higher basal metabolic rate as chicks, gained more weight in relation to feed intake and were bolder in a Novel Object test. Furthermore, the L males had higher plasma levels of peripheral serotonin, but the corticosterone after a restraint stress test did not differ. In paper IV and V, we concluded the project by comparing brain and organ weights as well as behaviour of the parental generation (P0) with the fifth selected generation (S5). The absolute brain weight as well as the weight specific brain weight were larger in the animals selected on H than in the L-animals. The relative weight of telencephalon was significantly higher in H whereas relative weight of cerebellum was significantly lower. Heart, liver, spleen and testes were all relatively heavier in H animals than in L. Interestingly, the behaviours assessed in P0 and S5 seemed to be rather resilient to the selection with only small differences in S5.

    To summarize, the selection on divergent tameness in Red Junglefowl has affected several phenotypic traits associated with the domesticated phenotype. The results of this project indicate that tameness in Red Junglefowl could be an underlying factor driving trait modifications towards the domesticated phenotype.

    List of papers
    1. Heritability and Genetic Correlations of Fear-Related Behaviour in Red Jungelfowl -Possible Implications for Early Domestication
    Open this publication in new window or tab >>Heritability and Genetic Correlations of Fear-Related Behaviour in Red Jungelfowl -Possible Implications for Early Domestication
    2012 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 7, no 4, p. e35162-Article in journal (Refereed) Published
    Abstract [en]

    Domesticated species differ from their wild ancestors in a number of traits, generally referred to as the domesticated phenotype. Reduced fear of humans is assumed to have been an early prerequisite for the successful domestication of virtually all species. We hypothesized that fear of humans is linked to other domestication related traits. For three generations, we selected Red Junglefowl (ancestors of domestic chickens) solely on the reaction in a standardized Fear of Human-test. In this, the birds were exposed for a gradually approaching human, and their behaviour was continuously scored. This generated three groups of animals, high (H), low (L) and intermediate (I) fearful birds. The birds in each generation were additionally tested in a battery of behaviour tests, measuring aspects of fearfulness, exploration, and sociality. The results demonstrate that the variation in fear response of Red Junglefowl towards humans has a significant genetic component and is genetically correlated to behavioural responses in other contexts, of which some are associated with fearfulness and others with exploration. Hence, selection of Red Junglefowl on low fear for humans can be expected to lead to a correlated change of other behavioural traits over generations. It is therefore likely that domestication may have caused an initial suite of behavioural modifications, even without selection on anything besides tameness.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-76833 (URN)10.1371/journal.pone.0035162 (DOI)000305336200026 ()
    Available from: 2012-04-20 Created: 2012-04-20 Last updated: 2023-12-28
    2. Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring
    Open this publication in new window or tab >>Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring
    2014 (English)In: animal, ISSN 1751-7311, Vol. 8, no 9, p. 1498-1505Article in journal (Refereed) Published
    Abstract [en]

    Many traits associated with domestication are suggested to have developed as correlated responses to reduced fear of humans. Tameness may have reduced the stress of living in human proximity and improved welfare in captivity. We selected Red Junglefowl (ancestors of all domestic chickens) for four generations on high or low fear towards humans, mimicking an important aspect of the earliest period of domestication, and tested birds from the third and fourth generation in three different social tests. Growth and plumage condition, as well as size of eggs and offspring were also recorded, as indicators of some aspects of welfare. Birds selected for low fear had higher weight, laid larger eggs and generated larger offspring, and had a better plumage condition. In a social dominance test they also performed more aggressive behaviour and received less of the same, regardless of whether the restricted resource was feed or not. Hence, dominance appeared to increase as a consequence of reduced fear of humans. Furthermore, egg size and the weight of the offspring were larger in the less fearful birds, and plumage condition better, which could be interpreted as the less fearful animals being better adapted to the environment in which they were selected.

    Place, publisher, year, edition, pages
    Cambridge University Press, 2014
    Keywords
    Red Junglefowl, domestication, fearfulness, selection, social behaviour
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-109499 (URN)10.1017/S1751731114001426 (DOI)000342219000013 ()24910136 (PubMedID)
    Available from: 2014-08-20 Created: 2014-08-20 Last updated: 2023-12-28
    3. Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)
    Open this publication in new window or tab >>Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)
    2015 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 9, article id 20150509Article in journal (Refereed) Published
    Abstract [en]

    Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44-48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication.

    Place, publisher, year, edition, pages
    ROYAL SOC, 2015
    Keywords
    genetics; domestication; stress
    National Category
    Zoology Evolutionary Biology
    Identifiers
    urn:nbn:se:liu:diva-123162 (URN)10.1098/rsbl.2015.0509 (DOI)000364772300009 ()26382075 (PubMedID)
    Note

    Funding Agencies|research council Formas; ERC [322206]

    Available from: 2015-12-07 Created: 2015-12-04 Last updated: 2023-12-28Bibliographically approved
    4. Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl
    Open this publication in new window or tab >>Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl
    2016 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 11, p. 1-12Article in journal (Refereed) Published
    Abstract [en]

    Domestication has caused a range of similar phenotypic changes across taxa, relating to physiology, morphology and behaviour. It has been suggested that this recurring domesticated phenotype may be a result of correlated responses to a central trait, namely increased tameness. We selected Red Junglefowl, the ancestors of domesticated chickens, during five generations for reduced fear of humans. This caused a marked and significant response in tameness, and previous studies have found correlated effects on growth, metabolism, reproduction, and some behaviour not directly selected for. Here, we report the results from a series of behavioural tests carried out on the initial parental generation (P0) and the fifth selected generation (S5), focusing on behaviour not functionally related to tameness, in order to study any correlated effects. Birds were tested for fear of humans, social reinstatement tendency, open field behaviour at two different ages, foraging/exploration, response to a simulated aerial predator attack and tonic immobility. In S5, there were no effects of selection on foraging/exploration or tonic immobility, while in the social reinstatement and open field tests there were significant interactions between selection and sex. In the aerial predator test, there were significant main effects of selection, indicating that fear of humans may represent a general wariness towards predators. In conclusion, we found only small correlated effects on behaviours not related to the tameness trait selected for, in spite of them showing high genetic correlations to fear of humans in a previous study on the same population. This suggests that species-specific behaviour is generally resilient to changes during domestication.

    Place, publisher, year, edition, pages
    PLOS, 2016
    National Category
    Developmental Biology Genetics
    Identifiers
    urn:nbn:se:liu:diva-132742 (URN)10.1371/journal.pone.0166075 (DOI)000387909300035 ()27851792 (PubMedID)
    Note

    European Research Council [322206]; FORMAS [221-2007-838]; Vetenskapsradet [621-2008-5437]

    Available from: 2016-11-22 Created: 2016-11-22 Last updated: 2023-12-28Bibliographically approved
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    Early domestication?: Phenotypic alterations of Red Junglefowl selected for divergent fear of humans
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  • 5.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bélteky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Brain size is reduced by selectionfor tameness in Red Junglefowl–correlated effects in vital organs2017In: Scientific Reports, E-ISSN 2045-2322, Vol. 7, article id 3306Article in journal (Refereed)
    Abstract [en]

    During domestication animals have undergone changes in size of brain and other vital organs. We hypothesize that this could be a correlated effect to increased tameness. Red Junglefowl (ancestors of domestic chickens) were selected for divergent levels of fear of humans for five generations. The parental (P0) and the fifth selected generation (S5) were culled when 48–54 weeks old and the brains were weighed before being divided into telencephalon, cerebellum, mid brain and optic lobes. Each single brain part as well as the liver, spleen, heart and testicles were also weighed. Brains of S5 birds with high fear scores (S5 high) were heavier both in absolute terms and when corrected for body weight. The relative weight of telencephalon (% of brain weight) was significantly higher in S5 high and relative weight of cerebellum was lower. Heart, liver, testes and spleen were all relatively heavier (% of body weight) in S5 high. Hence, selection for tameness has changed the size of the brain and other vital organs in this population and may have driven the domesticated phenotype as a correlated response.

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  • 6.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Katajamaa, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Altimiras, Jordi
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)2015In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 9, article id 20150509Article in journal (Refereed)
    Abstract [en]

    Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44-48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication.

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  • 7.
    Ali, Abshir A.
    et al.
    East Africa Univ, Somalia.
    Aalto, Mikko
    Bosaso Gen Hosp, Somalia.
    Jonasson, Jon
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Clinical genetics.
    Osman, Abdimajid
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Clinical Chemistry. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Clinical Chemistry.
    Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 5652Article in journal (Refereed)
    Abstract [en]

    African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East African and 40% West Eurasian genes in the Somali population, with a close relation to the Cushitic and Semitic speaking Ethiopian populations. We report the unique features of human leukocyte antigens (HLA) in the Somali population, which seem to differentiate from all other neighboring regions compared. Current study identified high prevalence of the diabetes type 1 (T1D) predisposing HLA DR-DQ haplotypes in Somalia. This finding may explain the increased T1D risk observed among Somali children. In addition, ethnic Somalis were found to host the highest frequencies observed thus far for several pharmacogenetic variants, including UGT1A4*2. In conclusion, we report that the Somali population displays genetic traits of significance to health and disease. The Somali dataset is publicly available and will add more information to the few genomic datasets available for African populations.

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  • 8.
    Andersson, Per
    et al.
    Linköping University, Department of Behavioural Sciences and Learning, Psychology. Linköping University, Faculty of Arts and Sciences.
    Tinghög, Gustav
    Linköping University, Department of Management and Engineering, Economics. Linköping University, Faculty of Arts and Sciences. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Health, Medicine and Caring Sciences, Division of Society and Health.
    Västfjäll, Daniel
    Linköping University, Department of Behavioural Sciences and Learning, Psychology. Linköping University, Faculty of Arts and Sciences. Decis Res, OR USA.
    The effect of herd immunity thresholds on willingness to vaccinate2022In: Humanities and Social Sciences Communications, ISSN 2662-9992, Vol. 9, no 1, article id 243Article in journal (Refereed)
    Abstract [en]

    Throughout the COVID-19 pandemic, media and policymakers openly speculated about the number of immune citizens needed to reach a herd immunity threshold. What are the effects of such numerical goals on the willingness to vaccinate? In a large representative sample (N = 1540) of unvaccinated Swedish citizens, we find that giving a low (60%) compared to a high (90%) threshold has direct effects on beliefs about reaching herd immunity and beliefs about how many others that will get vaccinated. Presenting the high threshold makes people believe that herd immunity is harder to reach (on average about half a step on a seven-point scale), compared to the low threshold. Yet at the same time, people also believe that a higher number of the population will get vaccinated (on average about 3.3% more of the population). Since these beliefs affect willingness to vaccinate in opposite directions, some individuals are encouraged and others discouraged depending on the threshold presented. Specifically, in mediation analysis, the high threshold indirectly increases vaccination willingness through the belief that many others will get vaccinated (B = 0.027, p = 0.003). At the same time, the high threshold also decreases vaccination willingness through the belief that the threshold goal is less attainable (B = -0.053, p < 0.001) compared to the low threshold condition. This has consequences for ongoing COVID-19 vaccination and future vaccination campaigns. One message may not fit all, as different groups can be encouraged or discouraged from vaccination.

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  • 9.
    Arnqvist, Göran
    et al.
    Department of Ecology and Environmental Science, Animal Ecology, University of Umeå, Umeå, Sweden.
    Edvardsson, Martin
    Department of Ecology and Environmental Science, Animal Ecology, University of Umeå, Umeå, Sweden.
    Friberg, Urban
    Department of Ecology and Environmental Science, Animal Ecology, University of Umeå, Umeå, Sweden.
    Nilsson, Tina
    Department of Ecology and Environmental Science, Animal Ecology, University of Umeå, Umeå, Sweden.
    Sexual conflict promotes speciation in insects.2000In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 97, no 19, p. 10460-10464Article in journal (Refereed)
    Abstract [en]

    Speciation rates among extant lineages of organisms vary extensively, but our understanding of the causes of this variation and, therefore, the processes of speciation is still remarkably incomplete. Both theoretical and empirical studies have indicated that sexual selection is important in speciation, but earlier discussions have focused almost exclusively on the potential role of female mate choice. Recent findings of postmating reproductive conflicts of interest between the sexes suggest a quite different route to speciation. Such conflicts may lead to perpetual antagonistic coevolution between males and females and may thus generate rapid evolutionary divergence of traits involved in reproduction. Here, we assess this hypothesis by contrasting pairs of related groups of insect species differing in the opportunity for postmating sexual conflict. Groups where females mate with many males exhibited speciation rates four times as high as in related groups where females mate only once. Our results not only highlight the general importance of postmating sexual selection in speciation, but also support the recent suggestion that sexual conflict is a key engine of speciation.

  • 10.
    Asutay, Erkin
    et al.
    Linköping University, Department of Behavioural Sciences and Learning, Psychology. Linköping University, Faculty of Arts and Sciences.
    Västfjäll, Daniel
    Linköping University, Department of Behavioural Sciences and Learning, Psychology. Linköping University, Faculty of Arts and Sciences. Decis Res, OR USA.
    The goal-relevance of affective stimuli is dynamically represented in affective experience2021In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 8, no 11, article id 211548Article in journal (Refereed)
    Abstract [en]

    Affect is a continuous and temporally dependent process that represents an individuals ongoing relationship with its environment. However, there is a lack of evidence on how factors defining the dynamic sensory environment modulate changes in momentary affective experience. Here, we show that goal-dependent relevance of stimuli is a key factor shaping momentary affect in a dynamic context. Participants (N = 83) viewed sequentially presented images and reported their momentary affective experience after every fourth stimulus. Relevance was manipulated through an attentional task that rendered each image either task-relevant or task-irrelevant. Computational models were fitted to trial-by-trial affective responses to capture the key dynamic parameters explaining momentary affective experience. The findings from statistical analyses and computational models showed that momentary affective experience was shaped by the temporal integration of the affective impact of recently encountered stimuli, and that task-relevant stimuli, independent of stimulus affect, prompted larger changes in experienced pleasantness compared with task-irrelevant stimuli. These findings clearly show that dynamics of affective experience reflect goal-relevance of stimuli in our surroundings.

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  • 11.
    Bakovic, Vid
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Nat Resources and Life Sci Vienna, Austria.
    Schuler, Hannes
    Free Univ Bozen Bolzano, Italy.
    Schebeck, Martin
    Univ Nat Resources and Life Sci Vienna, Austria.
    Feder, Jeffrey L.
    Univ Notre Dame, IN 46556 USA.
    Stauffer, Christian
    Univ Nat Resources and Life Sci Vienna, Austria.
    Ragland, Gregory J.
    Univ Colorado, CO 80202 USA.
    Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 20, p. 4648-4666Article in journal (Refereed)
    Abstract [en]

    Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher F-ST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host-related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.

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  • 12.
    Baltazar-Soares, Miguel
    et al.
    Univ Turku, Finland.
    Karell, Patrik
    Lund Univ, Sweden; Uppsala Univ, Sweden; Nov Univ Appl Sci, Finland.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Nilsson, Jan-Ake
    Lund Univ, Sweden.
    Brommer, Jon E.
    Univ Turku, Finland.
    Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls2024In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    Feathers comprise a series of evolutionary innovations but also harbour colour, a key biological trait known to co-vary with life history or complex traits. Those relationships are particularly true in melanin-based pigmentation species due to known pleiotropic effects of the melanocortin pathway - originating from melanin-associated phenotypes. Here, we explore the molecular basis of melanin colouration and expected co-variation at the molecular level in the melanin-based, colour polymorphic system of the tawny owl (Strix aluco). An extensive body of literature has revealed that grey and brown tawny owl colour morphs differ in a series of life history and behavioural traits. Thus, it is plausible to expect co-variation also at molecular level between colour morphs. To investigate this possibility, we assembled the first draft genome of the species against which we mapped ddRADseq reads from 220 grey and 150 brown morphs - representing 10 years of pedigree data from a population in Southern Finland - and explored genome-wide associations with colour phenotype. Our results revealed putative molecular signatures of cold adaptation strongly associated with the grey phenotype, namely, a non-synonymous substitution in MCHR1, plus 2 substitutions in non-coding regions of FTCD and FAM135A whose genotype combinations obtained a predictive power of up to 100% (predicting grey colour). These suggest a molecular basis of cold environment adaptations predicted to be grey-morph specific. Our results potentially reveal part of the molecular machinery of melanin-associated phenotypes and provide novel insights towards understanding the functional genomics of colour polymorphism in melanin-based pigmented species.

  • 13.
    Bartoszek, Krzysztof
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Phylogenetic effective sample size2016In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 407, p. 371-386Article in journal (Refereed)
    Abstract [en]

    In this paper I address the question—how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

  • 14.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Quantifying the effects of anagenetic and cladogenetic evolution2014In: Mathematical Biosciences, ISSN 0025-5564, E-ISSN 1879-3134, Vol. 254, p. 42-57Article in journal (Refereed)
    Abstract [en]

    An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.

  • 15.
    Bartoszek, Krzysztof
    Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Göteborg Sweden.
    The Laplace Motion in Phylogenetic Comparative Methods2012In: Proceedings of the 18th National Conference on Applications of Mathematics in Biology and Medicine, 2012, p. 25-30Conference paper (Refereed)
    Abstract [en]

    The majority of current phylogenetic comparative methods assume that the stochastic evolutionaryprocess is homogeneous over the phylogeny or offer relaxations of this in rather limited and usually parameter expensive ways. Here we make a preliminary investigation, bymeans of a numerical experiment, whether the Laplace motion process can offer an alternative approach.

  • 16.
    Bartoszek, Krzysztof
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Trait evolution with jumps: illusionary normality2017In: Proceedings of the XXIII National Conference on Applications of Mathematics in Biology and Medicine, 2017, p. 23-28Conference paper (Refereed)
    Abstract [en]

    Phylogenetic comparative methods for real-valued traits usually make use of stochastic process whose trajectories are continuous.This is despite biological intuition that evolution is rather punctuated thangradual. On the other hand, there has been a number of recent proposals of evolutionarymodels with jump components. However, as we are only beginning to understandthe behaviour of branching Ornstein-Uhlenbeck (OU) processes the asymptoticsof branching  OU processes with jumps is an even greater unknown. In thiswork we build up on a previous study concerning OU with jumps evolution on a pure birth tree.We introduce an extinction component and explore via simulations, its effects on the weak convergence of such a process.We furthermore, also use this work to illustrate the simulation and graphic generation possibilitiesof the mvSLOUCH package.

  • 17.
    Bartoszek, Krzysztof
    et al.
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Fuentes Gonzalez, Jesualdo
    Florida International University, Miami, USA..
    Mitov, Venelin
    IntiQuan GmbH, Basel, Switzerland..
    Pienaar, Jason
    Florida International University, Miami, USA..
    Piwczyński, Marcin
    Nicolaus Copernicus University, Toruń, Poland..
    Puchałka, Radosław,
    Nicolaus Copernicus University, Toruń, Poland..
    Spalik, Krzysztof
    University of Warsaw, Warszawa, Poland..
    Voje, Kjetil
    University of Oslo, Oslo, Norway..
    Fast mvSLOUCH: Model comparison for multivariate Ornstein--Uhlenbeck-based models of trait evolution on large phylogenies2023Data set
    Abstract [en]

    These are the Supplementary Material, R scripts and numerical results accompanying Bartoszek, Fuentes Gonzalez, Mitov, Pienaar, Piwczyński, Puchałka, Spalik and Voje "Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein–Uhlenbeck Models of Trait Evolution".

    The four data files concern two datasets. Ungulates: measurements of muzzle width, unworn lower third molar crown height, unworn lower third molar crown width and feeding style and their phylogeny; Ferula: measurements of ratio of canals, periderm thickness, wing area, wing thickness,  and fruit mass, and their phylogeny.

    Methods

    Ungulates

    The compiled ungulate dataset involves two key components: phenotypic data (Data.csv) and phylogenetic tree (Tree.tre), which consist on the following (full references for the citations presented below are provided in the paper linked to this repository, which also provides further details on the compiled dataset):The phenotypic data includes three continuous variables and one categorical variable. The continuous variables (MZW: muzzle width; HM3: unworn lower third molar crown height; WM3: unworn lower third molar crown width), measured in cm, come from Mendoza et al. (2002; J. Zool.). The categorical variable (FS, i.e. feeding style: B=browsers, G=grazers, M=mixed feeders) is based on Pérez–Barbería and Gordon (2001; Proc. R. Soc. B: Biol. Sci.). Taxonomic mismatches between these two sources were resolved based on Wilson and Reeder (2005; Johns Hopkins University Press). Only taxa with full entries for all these variables were included (i.e. no missing data allowed).

    The phylogenetic tree is pruned from the unsmoothed mammalian timetree of Hedges et al. (2015; MBE) to only include the 104 ungulate species for which there is complete phenotypic data available. Wilson and Reeder (2005; Johns Hopkins University Press) was used again to resolve taxonomic mismatches with the phenotypic data. The branch lengths of the tree are scaled to unit height and thus informative of relative time.

    Ferula

    1) The phenotypic data are divided into two data sets: first containing five continuous variables (no_ME) measured on mericarps (the dispersal unit of fruit in Apiaceae), whereas the second having the same variables together with measurement error (ME; see paper for computational details) for 75 species of Ferula and three species of Leutea. Three continuous variables were measured on anatomical cross sections (ratio_canals_ln – the proportion of oil ducts covering the space between median and lateral ribs [dimensionless], mean_gr_peri_ln_um – periderm (fruit wall) thickness [μm], thick_wings_ln_um – wing thickness [μm]); the remaining two on whole mericarps (Wings_area_ln_mm – wings area [mm2], Seed_mass_ln_mg – seed mass [mg])

    2) The phylogenetic tree was pruned from the tree obtained from the recent taxonomic revision of the genus (Panahi et al. 2018) to only include the 78 species for which the phenotypic data were generated. This tree and the associated alignment, composed of one nuclear and three plastid markers (Panahi et al. 2018), constituted an input to mcmctree software (Yang 2007) to obtain dated tree using a secondary calibration point for the root based on Banasiak et al.’s (2013) work. The branch lengths of the final tree (Ferula_fruits_tree.txt) were scaled to unit height and thus informative of relative time.

    The R setup for the manuscript was as follows:

    R version 3.6.1 (2019-09-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: openSUSE Leap 42.3

    The exact output can depend on the random seed. However, in the script we have the option of rerunning the analyses as it was in the manuscript, i.e.the random seeds that were used to generate the results are saved, included and can be read in.

    The code is divided into several directories with scripts, random seeds and result files.

    1) LikelihoodTestingDirectory contains the script test_rotation_invariance_mvSLOUCH.R that demonstrates that mvSLOUCH's likelihood calculations are rotation invariant.        

    2) Carnivorans

    Directory contains files connected to the Carnivrons' vignette in mvSLOUCH.       

    2.1) Carnivora_mvSLOUCH_objects_Full.RData

    Full output of  running the R code in the vignette.With mvSLOUCH is a very bare-minimum subset of this file that allows for the creation of the vignette.           

     2.2) Carnivora_mvSLOUCH_objects.RData              

    Reduced objects from Carnivora_mvSLOUCH_objects_Full.RData that are included with mvSLOUCH's vignette.                            

    2.3) Carnivora_mvSLOUCH_objects_remove_script.R               

    R script to reduce Carnivora_mvSLOUCH_objects_Full.RData to Carnivora_mvSLOUCH_objects.RData.     

    2.4) mvSLOUCH_Carnivorans.Rmd               

    The vignette itself.           

    2.5) refs_mvSLOUCH.bib               

    Bib file for the vignette.           

    2.6) ScaledTree.png, ScaledTree2.png, ScaledTree3.png, ScaledTree4.png   

    Plots of phylogenetic trees for vignette.

    3) SimulationStudy

    Directory contains all the output of the simulation study presented in the manuscript and scripts that allow for replication (the random number generator seeds are also provided) or running ones own simulation study, and scripts to generate graphs, and model comparison summary. This study was done using version 2.6.2 of mvSLOUCH. If one reruns using mvSLOUCH >= 2.7, then one will obtain different (corrected) values of R2 and an additional R2 version.    

    4) Ungulates

    Directory contains files connected to the "Feeding styles and oral morphology in ungulates" analyses performed for the manuscript.       

    4.1) Data.csv       

    The phenotypic data includes three continuous variables and one categorical variable. Continuous variables (MZW: muzzle width; HM3: unworn lower third molar crown height; WM3: unworn lower third molar crown width) from Mendoza et al. (2002), measured in cm. Categorical variable (FS, i.e. feeding style: B=browsers, G=grazers, M=mixed feeders) based on Pérez–Barbería and Gordon (2001). Phylogeny pruned from Hedges et al. (2015).

    Taxonomic mismatches among these sources were resolved based on Wilson and Reeder (2005). Hedges, S. B., J. Marin, M. Suleski, M. Paymer, and S. Kumar. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32:835-845. Mendoza, M., C. M. Janis, and P. Palmqvist. 2002. Characterizing complex craniodental patterns related to feeding behaviour in ungulates:a multivariate approach. Journal of Zoology 258:223-246 Pérez–Barbería, F. J., and I. J. Gordon. 2001. Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation. Proceedings of the Royal Society of London. Series B: Biological Sciences 268:1023-1032. Wilson, D. E., and D. M. Reeder. 2005. Mammal species of the world: A taxonomic and geographic reference. Johns Hopkins University Press, Baltimore, Maryland.                

    4.2) Tree.tre       

    Ungulates' phylogeny, extracted from the mammalian phylogeny of Hedges, S. B., J. Marin, M. Suleski, M. Paymer, and S. Kumar. 2015. Tree of life reveals clock–like speciation and diversification. Mol. Biol. Evol. 32:835–845.           

    4.3) OUB.R, OUF.R, OUG.R       

    R scripts for the analyses performed in the manuscript. Different files correspond to different regime setups of the feeding style variable.           

    4.4) OU1.txt, OUB.txt, OUF.txt, OUG.txt       

    Outputs of the model comparison conducted under the R scripts presented above (4.3). Different files correspond to different regime setups of the feeding style variable.        

    5) Ferula analyses

    In the models_ME directory there are input and output files from the mvSLOUCH analyzes of Ferula data with measurement error included, while in the models_no_ME directory the analyzes of data without measurement error. In each directory, one can find the following files:

    - input files: Data_ME.csv (with mesurment error) or Data_no_ME.csv (without measurement error) and tree file in Newick format (Ferula_fruits_tree.txt); the trait names in data files are abbreviated as follows: ration_canals – the proportion of oil ducts covering the space between median and lateral ribs, mean_gr_peri – periderm thickness, wings_area – wing area, thick_wings – wing thickness and seed_mass – seed mass,

    - the results for 8 analyzed models (see Fig. 2 in the main text), each in separate directory named model1, model2 and so on,

    - each model directory comprises the following files: two R scripts (for analyzes with diagonal and with upper triangular matrix Σyy; each model was run 1000 times), two csv files included information such as number of repetition (i), seed for preliminary analyzes generating starting point (seed_start_point), seed for the main analyses (seed) and AIC, AICc, SIC, BIC, R2 and loglik for each model run (these csv files are sorted according to AICc values), two directories containing results for 1000 analyzes, and two files extracted from these directories showing parameter estimation for the best models (with UpperTri and Diagonal matrix Σyy)

  • 18.
    Bartoszek, Krzysztof
    et al.
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Fuentes-Gonzalez, Jesualdo
    Florida Int Univ, FL USA; Florida Int Univ, FL USA.
    Mitov, Venelin
    IntiQuan GmbH, Switzerland.
    Pienaar, Jason
    Florida Int Univ, FL USA; Florida Int Univ, FL USA.
    Piwczynski, Marcin
    Nicolaus Copernicus Univ Torun, Poland.
    Puchalka, Radoslaw
    Nicolaus Copernicus Univ Torun, Poland.
    Spalik, Krzysztof
    Univ Warsaw, Poland.
    Voje, Kjetil Lysne
    Univ Oslo, Norway.
    Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods2023In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646Article in journal (Refereed)
    Abstract [en]

    Adams and Collyer argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution and sometimes rotation invariance can be an issue. Here we dissect the concept of rotation invariance and point out that, depending on the understanding, this can be an issue with any method that relies on numerical instead of analytical estimation approaches. We relate this to the ongoing discussion concerning phylogenetic principal component analysis. Contrary to what Adams and Collyer found, we do not observe a bias against the simpler Brownian motion process in simulations when we use the new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies and more complex model setups.

  • 19.
    Bartoszek, Krzysztof
    et al.
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences. Uppsala University, Sweden.
    Glemin, Sylvain
    Uppsala University, Sweden; CNRS University of Montpellier IRD EPHE, France.
    Kaj, Ingemar
    Uppsala University, Sweden.
    Lascoux, Martin
    Uppsala University, Sweden.
    Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations2017In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 429, p. 35-45Article in journal (Refereed)
    Abstract [en]

    The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.(C) 2017 Elsevier Ltd. All rights reserved.

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  • 20.
    Bartoszek, Krzysztof
    et al.
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Gonzalez, Jesualdo Fuentes
    Department of Biological Sciences, Florida International University, Miami, Fl 33199, USA.
    Mitov, Venelin
    IntiQuan GmbH, Basel, Switzerland.
    Pienaar, Jason
    Department of Biological Sciences and the Institute of Environment, Florida International University, Miami, Fl 33199, USA.
    Piwczyński, Marcin
    Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland.
    Puchałka, Radosław
    Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland.
    Spalik, Krzysztof
    Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warszawa, Poland.
    Voje, Kjetil Lysne
    Natural History Museum, University of Oslo, Oslo, Norway.
    Model Selection Performance in Phylogenetic Comparative Methods Under Multivariate Ornstein–Uhlenbeck Models of Trait Evolution2023In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 72, no 2, p. 275-293Article in journal (Refereed)
    Abstract [en]

    The advent of fast computational algorithms for phylogenetic comparative methods allows for considering multiple hypotheses concerning the co-adaptation of traits and also for studying if it is possible to distinguish between such models based on contemporary species measurements. Here we demonstrate how one can perform a study with multiple competing hypotheses using mvSLOUCH by analyzing two data sets, one concerning feeding styles and oral morphology in ungulates, and the other concerning fruit evolution in Ferula (Apiaceae). We also perform simulations to determine if it is possible to distinguish between various adaptive hypotheses. We find that Akaikes information criterion corrected for small sample size has the ability to distinguish between most pairs of considered models. However, in some cases there seems to be bias towards Brownian motion or simpler Ornstein-Uhlenbeck models. We also find that measurement error and forcing the sign of the diagonal of the drift matrix for an Ornstein-Uhlenbeck process influences identifiability capabilities. It is a cliche that some models, despite being imperfect, are more useful than others. Nonetheless, having a much larger repertoire of models will surely lead to a better understanding of the natural world, as it will allow for dissecting in what ways they are wrong. [Adaptation; AICc; model selection; multivariate Ornstein-Uhlenbeck process; multivariate phylogenetic comparative methods; mvSLOUCH.]

  • 21.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Jones, Graham
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden / Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden.
    Oxelman, Bengt
    Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden.
    Sagitov, Serik
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Time to a single hybridization event in a group of species with unknown ancestral history2013In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 322, p. 1-6Article in journal (Refereed)
    Abstract [en]

    We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.

  • 22.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Sweden.
    Krzeminski, Michal
    Gdansk University of Technology.
    Critical case stochastic phylogenetic tree model via the Laplace transform2014In: Demonstratio Matematicae, ISSN 0420-1213, Vol. 47, no 2, p. 474-481Article in journal (Refereed)
    Abstract [en]

    Birth-and-death models are now a common mathematical tool to describe branching patterns observed in real-world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth-and-death model that is compatible with phylogenetic trees of both in uenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the death rate. This is a non-trivial situation and to study its asymptotic behaviour we employed the Laplace transform. With this we correct the proof of Liggett and Schinazi (2009) in the critical case.

  • 23.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Pienaar, Jason
    Department of Genetics, University of Pretoria, Pretoria 0002, South Africa.
    Mostad, Petter
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Andersson, Staffan
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Hansen, Thomas F.
    CEES, Department of Biology, University of Oslo, Oslo, Norway.
    A phylogenetic comparative method for studying multivariate adaptation2012In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 314, p. 204-215Article in journal (Refereed)
    Abstract [en]

    Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptationbetween traits. Based on Ornstein-Uhlenbeck (OU) models of adaptive evolution, we present a method,with R implementation, in which multiple traits evolve both in response to each other and, as inprevious OU models, to fixed or randomly evolving predictor variables. We present the interpretation ofthe model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antlerand body-size evolution in deer (Cervidae).

  • 24.
    Bartoszek, Krzysztof
    et al.
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Pietro, Lio'
    Computer Laboratory , University of Cambridge, Cambridge, Un ited Kingdom.
    A novel algorithm to reconstruct phylogenies using gene sequences and expression data2014In: International Proceedings of Chemical, Biological & Environmental Engineering; Environment, Energy and Biotechnology III, 2014, Vol. 70, p. 8-12Conference paper (Refereed)
    Abstract [en]

    Phylogenies based on single loci should be viewed with caution and the best approach for obtaining robust trees is to examine numerous loci across the genome. It often happens that for the same set of species trees derived from different genes are in conflict between each other. There are several methods that combine information from different genes in order to infer the species tree. One novel approach is to use informationfrom different -omics. Here we describe a phylogenetic method based on an Ornstein–Uhlenbeck process that combines sequence and gene expression data. We test our method on genes belonging to the histidine biosynthetic operon. We found that the method provides interesting insights into selection pressures and adaptive hypotheses concerning gene expression levels.

  • 25.
    Bartoszek, Krzysztof
    et al.
    Uppsala universitet, Tillämpad matematik och statistik.
    Sagitov, Serik
    A consistent estimator of the evolutionary rate2015In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 371, p. 69-78Article in journal (Refereed)
    Abstract [en]

    We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.

  • 26.
    Bartoszek, Krzysztof
    et al.
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Sagitov, Serik
    Chalmers University of Technology and the Unversity of Gothenburg, Sweden.
    Phylogenetic confidence intervals for the optimal trait value2015In: Journal of Applied Probability, ISSN 0021-9002, E-ISSN 1475-6072, Vol. 52, no 4, p. 1115-1132Article in journal (Refereed)
    Abstract [en]

    We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree ismodelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein–Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the samplemean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean isapproximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

  • 27.
    Bergfeldt, Nora
    et al.
    Stockholm Univ, Sweden; Swedish Museum Nat Hist, Sweden.
    Kirdok, Emrah
    Mersin Univ, Turkiye.
    Oskolkov, Nikolay
    Lund Univ, Sweden.
    Mirabello, Claudio
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Unneberg, Per
    Uppsala Univ, Sweden.
    Malmstrom, Helena
    Uppsala Univ, Sweden.
    Fraser, Magdalena
    Uppsala Univ, Sweden.
    Sanchez-Quinto, Federico
    Uppsala Univ, Sweden.
    Jorgensen, Roger
    Univ Tromso, Norway.
    Skar, Birgitte
    NTNU Univ Museum, Norway.
    Liden, Kerstin
    Stockholm Univ, Sweden.
    Jakobsson, Mattias
    Uppsala Univ, Sweden.
    Stora, Jan
    Stockholm Univ, Sweden.
    Goetherstrom, Anders
    Stockholm Univ, Sweden.
    Identification of microbial pathogens in Neolithic Scandinavian humans2024In: Scientific Reports, E-ISSN 2045-2322, Vol. 14, no 1, article id 5630Article in journal (Refereed)
    Abstract [en]

    With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

  • 28.
    Bohlin, Gustav
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Göransson, Andreas C.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Tibell, Lena A. E.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Diverse use of threshold concepts - A content analysis of online dynamic visualizations describing evolution.2015Conference paper (Refereed)
    Abstract [en]

    There is an abundance of dynamic visualizations (animations, videos and simulations) that claim to explain evolution available on the Internet. The present study explores what aspects of evolution that are represented in these potential learning tools. A criteria catalogue covering 40 operationalized variables was used as a content analysis grid in the analysis of 71 dynamic visualizations. The concepts, derived from research literature, were operationalized into variables sorted into four different categories: (a) content-specific concepts (such as limited resources or inherited variation), (b) threshold concepts (core concepts that transform and integrate understanding within a subject), (c) alternative conceptions (such as teleological explanations or anthropomorphism), and (d) model organism. The results indicate that some concepts are dominantly communicated while others are seldom or never included in online visualizations. Regarding the proposed threshold concepts, evolutionary events happening on small time- and spatial scales, such as subcellular processes, were seldom observed. Rather, the focus was on events happening at a population level in time scales spanning from years and longer. This echoes with an observed lack of explanations regarding randomly occurring mutations providing the basis for variation. Implications include that there are components of evolution that would benefit from being addressed with an increased focus in biology teaching and science education research. The results may also serve as a useful toolkit in the design of new educational material.

  • 29.
    Bravo, Gustavo A.
    et al.
    Harvard Univ, MA 02138 USA.
    Antonelli, Alexandre
    Harvard Univ, MA 02138 USA; Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden; Gothenburg Bot Garden, Sweden.
    Bacon, Christine D.
    Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden.
    Bartoszek, Krzysztof
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Blom, Mozes P. K.
    Swedish Museum Nat Hist, Sweden.
    Huynh, Stella
    Univ Neuchatel, Switzerland.
    Jones, Graham
    Univ Gothenburg, Sweden.
    Knowles, L. Lacey
    Univ Michigan, MI 48109 USA.
    Lamichhaney, Sangeet
    Harvard Univ, MA 02138 USA.
    Marcussen, Thomas
    Univ Oslo, Norway.
    Morlon, Helene
    Ecole Normale Super Paris, France.
    Nakhleh, Luay K.
    Rice Univ, TX USA.
    Oxelman, Bengt
    Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden.
    Pfeil, Bernard
    Univ Gothenburg, Sweden.
    Schliep, Alexander
    Chalmers Univ Technol, Sweden; Univ Gothenburg, Sweden.
    Wahlberg, Niklas
    Lund Univ, Sweden.
    Werneck, Fernanda P.
    Inst Nacl de Pesquisas da Amazonia, Brazil.
    Wiedenhoeft, John
    Chalmers Univ Technol, Sweden; Univ Gothenburg, Sweden; Rutgers State Univ, NJ USA.
    Willows-Munro, Sandi
    Univ Kwazulu Natal, South Africa.
    Edwards, Scott V
    Harvard Univ, MA 02138 USA; Univ Gothenburg, Sweden; Chalmers Univ Technol, Sweden.
    Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics2019In: PeerJ, E-ISSN 2167-8359, Vol. 7, article id e6399Article in journal (Refereed)
    Abstract [en]

    Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

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  • 30.
    Brengdahl, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Differentiation of dispersive traits under a fluctuating range distribution in Asellus aquaticus2014Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Knowledge about dispersion is of utmost importance for understanding populations’ reaction to changes in the environment. Expansion of a population range brings with it both spatial sorting and over time, spatial selection. This means that dispersion rates increases over time at the expanding edge. Most studies have so far been performed on continuously expanding populations. This study aims to bring more knowledge about dispersal biology in dynamic systems. I studied dispersal traits in two permanent and two seasonal vegetation habitats of an isopod (Asellus aquaticus), for which differentiation between habitat types has previously been shown. I quantified differences in displacement (dispersal rate) and three morphological traits, head angle (body streamline) and leg of the third and seventh pair of legs. Isopods from the seasonal vegetation had higher displacement rates than animals from permanent vegetation. This inclines that mechanisms driving spatial selection in expanding population ranges also exist in dynamic systems. The more streamlined isopods found in seasonal sites further points towards spatial sorting by dispersion capability. Because no effect of permanence was found on leg length and there was no correlation between streamlining and displacement, the higher dispersion among animals from seasonal habitats most likely derives from behavioral differences.

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  • 31.
    Brengdahl, Martin
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Dispersive trait expression of Asellus aquaticus from a rare cave habitat2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Dispersal influences several ecological and evolutionary processes, such as intraspecific competition, genetic drift and inbreeding. It can lead to phenotypic mismatch with the habitat when a locally adapted individual winds up in an environment with a divergent selection regime compared to the source habitat. The aim of this project was to compare dispersive traits in the freshwater isopod Asellus aquaticus from a cave habitat, with surface dwelling isopods collected upstream and downstream from the cave system. The subterranean stream (cave) represents a rare, geographically limited habitat which has a divergent selective pressure compared to the surrounding habitats. Experiments on dispersal were performed in the laboratory, in darkness with IR-equipment for visualization. Displacement was measured using one-dimensional test arenas. Compared to the surface phenotype, the cave phenotype was expected to have reduced fitness outside of the cave and unlikely to successfully disperse to new areas of similar suitable conditions. The results did not follow my main hypothesis that isopods from the cave would be less dispersive than individuals from the surface. The inconclusive results might derive from large variation in the data and divergent adaptations which yield similar expression of dispersal.

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    Dispersive trait expression of Asellus aquaticus from a rare cave habitat
  • 32.
    Brengdahl, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Kimber, Christopher
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Maguire-Baxter, Jack
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Friberg, Urban
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Sex differences in life span: Females homozygous for the X chromosome do not suffer the shorter life span predicted by the unguarded X hypothesis2018In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, no 3, p. 568-577Article in journal (Refereed)
    Abstract [en]

    Life span differs between the sexes in many species. Three hypotheses to explain this interesting pattern have been proposed, involving different drivers: sexual selection, asymmetrical inheritance of cytoplasmic genomes, and hemizygosity of the X(Z) chromosome (the unguarded X hypothesis). Of these, the unguarded X has received the least experimental attention. This hypothesis suggests that the heterogametic sex suffers a shortened life span because recessive deleterious alleles on its single X(Z) chromosome are expressed unconditionally. In Drosophila melanogaster, the X chromosome is unusually large (approximate to 20% of the genome), providing a powerful model for evaluating theories involving the X. Here, we test the unguarded X hypothesis by forcing D. melanogaster females from a laboratory population to express recessive X-linked alleles to the same degree as males, using females exclusively made homozygous for the X chromosome. We find no evidence for reduced life span or egg-to-adult viability due to X homozygozity. In contrast, males and females homozygous for an autosome both suffer similar, significant reductions in those traits. The logic of the unguarded X hypothesis is indisputable, but our results suggest that the degree to which recessive deleterious X-linked alleles depress performance in the heterogametic sex appears too small to explain general sex differences in life span.

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  • 33.
    Brengdahl, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Kimber, Christopher
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Maguire-Baxter, Jack
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Malacrinò, Antonino
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Friberg, Urban
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetic Quality Affects the Rate of Male and Female Reproductive Aging Differently in Drosophila melanogaster2018In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 192, no 6, p. 761-772Article in journal (Refereed)
    Abstract [en]

    Males and females often maximize fitness by pursuing different reproductive strategies, with males commonly assumed to benefit more from increased resource allocation into current reproduction. Such investment should trade off with somatic maintenance and may explain why males frequently live shorter than females. It also predicts that males should experience faster reproductive aging. Here we investigate whether reproductive aging and life span respond to condition differently in male and female Drosophila melanogaster, as predicted if sexual selection has shaped male and female resource-allocation patterns. We manipulate condition through genetic quality by comparing individuals inbred or outbred for a major autosome. While genetic quality had a similar effect on condition in both sexes, condition had a much larger general effect on male reproductive output than on female reproductive output, as expected when sexual selection on vigor acts more strongly on males. We find no differences in reproductive aging between the sexes in low condition, but in high condition reproductive aging is relatively faster in males. No corresponding sex-specific change was found for life span. The sex difference in reproductive aging appearing in high condition was specifically due to a decreased aging rate in females rather than any change in males. Our results suggest that females age slower than males in high condition primarily because sexual selection has favored sex differences in resource allocation under high condition, with females allocating relatively more toward somatic maintenance than males.

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  • 34.
    Brommesson, Peter
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Sellman, Stefan
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Beck-Johnson, Lindsay
    Colorado State Univ, CO 80523 USA.
    Hallman, Clayton
    Colorado State Univ, CO 80523 USA.
    Murrieta, Deedra
    Colorado State Univ, CO 80523 USA.
    Webb, Colleen T.
    Colorado State Univ, CO 80523 USA.
    Miller, Ryan S.
    US Dept Agr Vet Serv, CO 80526 USA.
    Portacci, Katie
    US Dept Agr Vet Serv, CO 80526 USA.
    Lindström, Tom
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Assessing intrastate shipments from interstate data and expert opinion2021In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 8, no 3, article id 192042Article in journal (Refereed)
    Abstract [en]

    Live animal shipments are a potential route for transmitting animal diseases between holdings and are crucial when modelling spread of infectious diseases. Yet, complete contact networks are not available in all countries, including the USA. Here, we considered a 10% sample of Interstate Certificate of Veterinary Inspections from 1 year (2009). We focused on distance dependence in contacts and investigated how different functional forms affect estimates of unobserved intrastate shipments. To further enhance our predictions, we included responses from an expert elicitation survey about the proportion of shipments moving intrastate. We used hierarchical Bayesian modelling to estimate parameters describing the kernel and effects of expert data. We considered three functional forms of spatial kernels and the inclusion or exclusion of expert data. The resulting six models were ranked by widely applicable information criterion (WAIC) and deviance information criterion (DIC) and evaluated through within- and out-of-sample validation. We showed that predictions of intrastate shipments were mildly influenced by the functional form of the spatial kernel but kernel shapes that permitted a fat tail at large distances while maintaining a plateau-shaped behaviour at short distances better were preferred. Furthermore, our study showed that expert data may not guarantee enhanced predictions when expert estimates are disparate.

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  • 35. Order onlineBuy this publication >>
    Bélteky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Chicken domestication: Effects of tameness on brain gene expression and DNA methylation2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Domestication greatly increases phenotypic variation in a short time span, with selection for a single phenotype and a plethora of associated phenotypic changes as an outcome of the process. The domestication process influences the underlying genomic architecture of a species, and the success and speed of the process is likely influenced by it. The main aims of my thesis was to study how domestication affects the brain of chickens: specifically changes in morphology, gene expression, and DNA methylation. Differences in gene expression and DNA methylation between White Leghorn and Red Junglefowl chickens were mapped, and inheritance of these patterns were quantified, indicating a faithful transmission of breed-specific epigenetic markers. Selection on the behavioral trait fearfulness, generated high and low fearful lines of Red Junglefowl. Both the parental population and the fifth selected generation were used for the analyses in this thesis. One experiment studied morphological changes in the brain and other vital organs, and found that relative total brain size increased in high fearful birds, as a consequence of an increase in cerebral hemisphere size in high fearful birds and not in low fearful birds. Also, the relative heart, liver, spleen and testis size increased in high fearful birds, indicating correlated morphological changes with selection for fearfulness. Two additional experiments examined differential gene expression in the hypothalamus and the anterior cerebral hemisphere. The hypothalamus differed in expression of genes with reproductive and immunological functions, whilst the cerebral hemisphere differed in expression of genes related to social behaviors and neurological functions especially those upregulated in low fearful birds.  These results indicate the occurrence of tissue- and species-specific changes in gene expression as overlap with other domestication events were nearly nonexistent. A fourth experiment sought to associate the change in fear levels and gene expression differences with DNA methylation. Chromosomal regions with differential DNA methylation between high and low fearful birds were identified, and genes in these regions had annotated functions relevant to phenotypic differences between the selection lines. This thesis is the first to study the genetic alterations of domestication using the wild ancestor of an already domesticated species to repeat the domestication process selecting against fear of humans. The findings corroborate results from previous comparisons of wild and domestic animals, and further support the theory that rigorous selection for a behavioral trait can cause a cascade of genetic and epigenetic changes facilitating the domestication of a population.

    List of papers
    1. Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens
    Open this publication in new window or tab >>Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens
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    2012 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 13, no 59Article in journal (Refereed) Published
    Abstract [en]

    Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation. Here, we show that in Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differ substantially from that of a domesticated egg laying breed. Expression as well as methylation differences are largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences are tissue-specific, and the differential methylation at specific loci are little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication. Hence, our results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.

    Place, publisher, year, edition, pages
    BioMed Central, 2012
    Keywords
    Domestication, gene expression, tiling array, behaviour, methylation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-70159 (URN)10.1186/1471-2164-13-59 (DOI)000301440800001 ()
    Note

    funding agencies|Swedish Research Council| 2008-14496-59340-36 |Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning| 221 2007 838 |

    Available from: 2011-08-22 Created: 2011-08-22 Last updated: 2024-01-17Bibliographically approved
    2. Domestication and tameness: brain geneexpression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology
    Open this publication in new window or tab >>Domestication and tameness: brain geneexpression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology
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    2016 (English)In: Royal Society Open Science, E-ISSN 2054-5703, no 3, article id 160033Article in journal (Refereed) Published
    Abstract [en]

    The domestication of animals has generated a set of phenotypicmodifications, affecting behaviour, appearance, physiologyand reproduction, which are consistent across a range ofspecies. We hypothesized that some of these phenotypes couldhave evolved because of genetic correlation to tameness,an essential trait for successful domestication. Starting froman outbred population of red junglefowl, ancestor of alldomestic chickens, we selected birds for either high or lowfear of humans for five generations. Birds from the fifthselected generation (S5) showed a divergent pattern of growthand reproduction, where low fear chickens grew larger andproduced larger offspring. To examine underlying geneticmechanisms, we used microarrays to study gene expressionin thalamus/hypothalamus, a brain region involved in fearand stress, in both the parental generation and the S5. Whileparents of the selection lines did not show any differentiallyexpressed genes, there were a total of 33 genes with adjustedp-values below 0.1 in S5. These were mainly related to spermfunction,immunological functions, with only a few known tobe relevant to behaviour. Hence, five generations of divergentselection for fear of humans produced changes in hypothalamicgene expression profiles related to pathways associated withmale reproduction and to immunology. This may be linked to the effects seen on growth and size of offspring. These results support the hypothesis thatdomesticated phenotypes may evolve because of correlated effects related to reduced fear of humans.

    Place, publisher, year, edition, pages
    Royal Society Publishing, 2016
    Keywords
    artificial selection, gene expression, microarray, chicken, fearfulness
    National Category
    Ecology
    Identifiers
    urn:nbn:se:liu:diva-130501 (URN)10.1098/rsos.160033 (DOI)000384411000002 ()
    Note

    Funding agencies:  Research council Formas; Vetenskapsradet; ERC [322206]

    Available from: 2016-08-11 Created: 2016-08-11 Last updated: 2023-12-28
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  • 36.
    Cauchoix, M.
    et al.
    CNRS, France; Inst Adv Study Toulouse, France.
    Chow, P. K. Y.
    Univ Exeter, England; Hokkaido Univ, Japan.
    van Horik, J. O.
    Univ Exeter, England.
    Atance, C. M.
    Univ Ottawa, Canada.
    Barbeau, E. J.
    UPS, France.
    Barragan-Jason, G.
    Inst Adv Study Toulouse, France.
    Bize, P.
    Univ Aberdeen, Scotland.
    Boussard, A.
    Stockholm Univ, Sweden.
    Buechel, S. D.
    Stockholm Univ, Sweden.
    Cabirol, A.
    Univ Paul Sabatier, France.
    Cauchard, L.
    Univ Montreal, Canada.
    Claidiere, N.
    Aix Marseille Univ, France.
    Dalesman, S.
    Aberystwyth Univ, Wales.
    Devaud, J. M.
    Univ Paul Sabatier, France.
    Didic, M.
    AP HM Timone, France; Inst Neurosci Syst, France.
    Doligez, B.
    Univ Lyon 1, France.
    Fagot, J.
    Aix Marseille Univ, France.
    Fichtel, C.
    German Primate Ctr, Germany; Univ Gottingen, Germany; Leibniz Sci Campus Primate Cognit, Germany.
    Henke-von der Malsburg, J.
    German Primate Ctr, Germany; Univ Gottingen, Germany; Leibniz Sci Campus Primate Cognit, Germany.
    Hermer, E.
    Univ Gottingen, Germany.
    Huber, L.
    Leibniz Sci Campus Primate Cognit, Germany.
    Huebner, F.
    German Primate Ctr, Germany; Univ Gottingen, Germany; Leibniz Sci Campus Primate Cognit, Germany.
    Kappeler, P. M.
    German Primate Ctr, Germany; Univ Gottingen, Germany; Leibniz Sci Campus Primate Cognit, Germany.
    Klein, S.
    Univ Paul Sabatier, France.
    Langbein, J.
    Leibniz Inst Farm Anim Biol, Germany.
    Langley, E. J. G.
    Univ Exeter, England.
    Lea, S. E. G.
    Univ Exeter, England.
    Lihoreau, M.
    Univ Paul Sabatier, France.
    Lovlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Matzel, L. D.
    Rutgers State Univ, NJ USA.
    Nakagawa, S.
    Univ New South Wales, Australia; Univ New South Wales, Australia.
    Nawroth, C.
    Leibniz Inst Farm Anim Biol, Germany.
    Oesterwind, S.
    Univ Rostock, Germany.
    Sauce, B.
    Rutgers State Univ, NJ USA.
    Smith, E. A.
    Univ Lincoln, England.
    Sorato, Enrico
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Tebbich, S.
    Univ Vienna, Austria.
    Wallis, L. J.
    Univ Vienna, Austria; Eotvos Lorand Univ, Hungary.
    Whiteside, M. A.
    Univ Exeter, England.
    Wilkinson, A.
    Univ Lincoln, England.
    Chaine, A. S.
    CNRS, France; Inst Adv Study Toulouse, France.
    Morand-Ferron, J.
    Univ Ottawa, Canada.
    The repeatability of cognitive performance: a meta-analysis2018In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 373, no 1756, article id 20170281Article in journal (Refereed)
    Abstract [en]

    Behavioural and cognitive processes play important roles in mediating an individuals interactions with its environment. Yet, while there is a vast literature on repeatable individual differences in behaviour, relatively little is known about the repeatability of cognitive performance. To further our understanding of the evolution of cognition, we gathered 44 studies on individual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repeatable. We compared repeatability (R) in performance (1) on the same task presented at different times (temporal repeatability), and (2) on different tasks that measured the same putative cognitive ability (contextual repeatability). We also addressed whether R estimates were influenced by seven extrinsic factors (moderators): type of cognitive performance measurement, type of cognitive task, delay between tests, origin of the subjects, experimental context, taxonomic class and publication status. We found support for both temporal and contextual repeatability of cognitive performance, with mean R estimates ranging between 0.15 and 0.28. Repeatability estimates were mostly influenced by the type of cognitive performance measures and publication status. Our findings highlight the widespread occurrence of consistent inter-individual variation in cognition across a range of taxa which, like behaviour, may be associated with fitness outcomes. This article is part of the theme issue Causes and consequences of individual differences in cognitive abilities.

  • 37.
    Dingemanse, Niels J.
    et al.
    Ludwig Maximilians Univ Munchen, Germany.
    Moiron, Maria
    Max Planck Inst Ornithol, Germany; UMR 5175 Campus CNRS, France.
    Araya-Ajoy, Yimen G.
    Max Planck Inst Ornithol, Germany; Norwegian Univ Sci and Technol, Norway.
    Mouchet, Alexia
    Ludwig Maximilians Univ Munchen, Germany; Max Planck Inst Ornithol, Germany.
    Abbey-Lee, Robin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Max Planck Inst Ornithol, Germany.
    Individual variation in age-dependent reproduction: Fast explorers live fast but senesce young?2020In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 89, no 2, p. 601-613Article in journal (Refereed)
    Abstract [en]

    Adaptive integration of life history and behaviour is expected to result in variation in the pace-of-life. Previous work focused on whether risky phenotypes live fast but die young, but reported conflicting support. We posit that individuals exhibiting risky phenotypes may alternatively invest heavily in early-life reproduction but consequently suffer greater reproductive senescence. We used a 7-year longitudinal dataset with amp;gt;1,200 breeding records of amp;gt;800 female great tits assayed annually for exploratory behaviour to test whether within-individual age dependency of reproduction varied with exploratory behaviour. We controlled for biasing effects of selective (dis)appearance and within-individual behavioural plasticity. Slower and faster explorers produced moderate-sized clutches when young; faster explorers subsequently showed an increase in clutch size that diminished with age (with moderate support for declines when old), whereas slower explorers produced moderate-sized clutches throughout their lives. There was some evidence that the same pattern characterized annual fledgling success, if so, unpredictable environmental effects diluted personality-related differences in this downstream reproductive trait. Support for age-related selective appearance was apparent, but only when failing to appreciate within-individual plasticity in reproduction and behaviour. Our study identifies within-individual age-dependent reproduction, and reproductive senescence, as key components of life-history strategies that vary between individuals differing in risky behaviour. Future research should thus incorporate age-dependent reproduction in pace-of-life studies.

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  • 38.
    Eklöf, Anna
    et al.
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
    Helmus, Matthew R.
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
    Moore, M.
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
    Allesina, Stefano
    Department of Ecology and Evolution, and Computation Institute, University of Chicago, Chicago, IL 60637, USA.
    Relevance of evolutionary history for food web structure2012In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 279, no 1733, p. 1588-1596Article in journal (Refereed)
    Abstract [en]

    Explaining the structure of ecosystems is one of the great challenges of ecology. Simple models for foodweb structure aim at disentangling the complexity of ecological interaction networks and detect the main forces that are responsible for their shape. Trophic interactions are influenced by species traits, which in turn are largely determined by evolutionary history. Closely related species are more likely to share similar traits, such as body size, feeding mode and habitat preference than distant ones. Here, we present a theoretical framework for analysing whether evolutionary history—represented by taxonomic classification—provides valuable information on food web structure. In doing so, we measure which taxonomic ranks better explain species interactions. Our analysis is based on partitioning of the species into taxonomic units. For each partition, we compute the likelihood that a probabilistic model for food web structurere produces the data using this information. We find that taxonomic partitions produce significantly higher likelihoods than expected at random. Marginal likelihoods (Bayes factors) are used to perform model selection among taxonomic ranks. We show that food webs are best explained by the coarser taxonomic ranks (kingdom to class). Our methods provide a way to explicitly include evolutionary history in models for food web structure.

  • 39. Order onlineBuy this publication >>
    Fallahshahroudi, Amir
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Domestication Effects on the Stress Response in Chickens: Genetics, Physiology, and Behaviour2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Animal domestication, the process where animals become adapted to living in proximity to humans, is associated with the alteration of multiple traits, including decreased fearfulness and stress response. With an estimated population of 50 billion, the domesticated chicken is the most populous avian species in the world. Hundreds of chicken breeds have been developed for meat and egg production, hobby or research purposes. Multidirectional selection and the relaxation of natural selection in captivity have created immense phenotypic diversity amongst domesticates in a relatively short evolutionary time. The extensive phenotypic diversity, existence of the wild ancestor, and feasibility of intercrossing various breeds makes the chicken a suitable model animal for deciphering genetic determinants of complex traits such as stress response. We used chicken domestication as a model to gain insights about the mechanisms that regulate stress response in an avian species. We studied behavioural and physiological stress response in the ancestral Red Junglefowl and one of its domesticated progenies, White Leghorn. An advanced intercross between the aforementioned breeds was later used to map genetic loci underlying modification of stress response. The general pattern of the stress response in chickens was comparable with that reported in mammals, however we identified distinctive differences in the stress modulatory pathways in chickens. We showed that changes in the expression levels of several stress modulatory genes in the brain, the pituitary and the adrenal glands underlie the observed modified stress response in domesticated chickens. Using quantitative trait loci (QTL) mapping, several QTL underlying stress induced corticosterone, aldosterone and baseline dehydroepiandrosterone (DHEA) levels were detected. As a next step, we combined QTL mapping with gene expression (eQTL) mapping and narrowed two QTL down to the putative causal genes, SERPINA10 and PDE1C. Both of these genes were differentially expressed in the adrenal glands of White Leghorn and the Red Junglefowl, had overlapping eQTL with hormonal QTL, and their expression levels in the adrenal glands were correlated with plasma levels of corticosterone and al-dosterone. These two genes thus serve as strong candidates for further functional investigation concerning modification of the stress response during domestication. This dissertation increase the knowledge about genetics and physiology of the stress response in an avian species and its modification during domestication. Our findings expand the basic knowledge about the stress response in chicken, which can potentially be used to improve welfare through appropriate genetic selection.

    List of papers
    1. Domestication effects on behavioural and hormonal responses to acute stress in chickens
    Open this publication in new window or tab >>Domestication effects on behavioural and hormonal responses to acute stress in chickens
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    2014 (English)In: Physiology and Behavior, ISSN 0031-9384, E-ISSN 1873-507X, Vol. 133, p. 161-169Article in journal (Refereed) Published
    Abstract [en]

    Comparative studies have shown that alterations in physiology, morphology and behaviour have arisen due tothe domestication. A driving factor behind many of the changes could be a shift in stress responses,withmodifiedendocrine and behavioural profiles. In the present study we compared two breeds of chicken (Gallus gallus), thedomesticWhite Leghorn (WL) egg laying breed and its ancestor, the Red Junglefowl (RJF). Birds were exposed toan acute stress event, invoked by 3 or 10 min of physical restraint. Theywere then continuouslymonitored for theeffects on a wide range of behaviours during a 60 min recovery phase. Blood samples were collected from thechicken at baseline, and after 10 and 60 min following a similar restraint stress, and the samples wereanalyzed for nine endogenous steroids of the HPA and HPG axes. Concentration of the steroids was determinedusing validated liquid chromatography tandem mass spectrometry methods. In RJF, an immediate behaviouralresponse was observed after release from restraint in several behaviours, with a relatively fast return to baselinewithin 1 h. In WL, somebehaviourswere affected for a longer period of time, and others not at all. Concentrationsof corticosterone increasedmore in RJF, but returned faster to baseline compared toWL. A range of baseline levelsfor HPG-related steroids differed between the breeds, and they were generally more affected by the stress in WLthan in RJF. In conclusion, RJF reacted stronger both behaviourally and physiologically to the restraint stress, butalso recovered faster. This would appear to be adaptive under natural conditions, whereas the stress recovery ofdomesticated birds has been altered by domestication and breeding for increased reproductive output.

    Place, publisher, year, edition, pages
    Elsevier, 2014
    Keywords
    Corticosterone Recovery Restraint White Leghorn Red Junglefowl
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-107167 (URN)10.1016/j.physbeh.2014.05.024 (DOI)000340315100022 ()
    Note

    Funders: Swedish Research Council (VR) [621-2011-4731]; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) [221-2011-1088]; ERC (project Genewell) [322206]; Swedish Centre of Excellence in Animal Welfare; ARUP Institute for Clinical and Experimental Pathology

    Available from: 2014-06-09 Created: 2014-06-09 Last updated: 2023-12-28
    2. Domestication Effects on Stress Induced Steroid Secretion and Adrenal Gene Expression in Chickens
    Open this publication in new window or tab >>Domestication Effects on Stress Induced Steroid Secretion and Adrenal Gene Expression in Chickens
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    2015 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 5, p. 1-10, article id 15345Article in journal (Refereed) Published
    Abstract [en]

    Understanding the genetic basis of phenotypic diversity is a challenge in contemporary biology. Domestication provides a model for unravelling aspects of the genetic basis of stress sensitivity. The ancestral Red Junglefowl (RJF) exhibits greater fear-related behaviour and a more pronounced HPA-axis reactivity than its domesticated counterpart, the White Leghorn (WL). By comparing hormones (plasmatic) and adrenal global gene transcription profiles between WL and RJF in response to an acute stress event, we investigated the molecular basis for the altered physiological stress responsiveness in domesticated chickens. Basal levels of pregnenolone and dehydroepiandrosterone as well as corticosterone response were lower in WL. Microarray analysis of gene expression in adrenal glands showed a significant breed effect in a large number of transcripts with over-representation of genes in the channel activity pathway. The expression of the best-known steroidogenesis genes were similar across the breeds used. Transcription levels of acute stress response genes such as StAR, CH25 and POMC were upregulated in response to acute stress. Dampened HPA reactivity in domesticated chickens was associated with changes in the expression of several genes that presents potentially minor regulatory effects rather than by means of change in expression of critical steroidogenic genes in the adrenal.

    Place, publisher, year, edition, pages
    Nature Publishing Group, 2015
    National Category
    Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:liu:diva-122305 (URN)10.1038/srep15345 (DOI)000362885300001 ()26471470 (PubMedID)
    Note

    Funding agencies: Swedish Research Council (VR) [621-2011-4731]; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) [221-2011-1088]; SRC [621-2011-5523]; ERC [322206]; Swedish Centre of Excellence in Animal Welfare

    Available from: 2015-10-28 Created: 2015-10-28 Last updated: 2023-12-28
    3. Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication.
    Open this publication in new window or tab >>Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication.
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    2017 (English)In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 7, no 2Article in journal (Refereed) Published
    Abstract [en]

    The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic-pituitary-adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in chickens. Improved understanding of the genes associated with HPA-axis reactivity can provide insights into the pathways and mechanisms causing stress-related pathologies.

    Place, publisher, year, edition, pages
    The Genetics Society, 2017
    Keywords
    animal, domestication, quantitative trait, genes, corticosterone, aldosterone
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-134649 (URN)10.1534/g3.116.037721 (DOI)000394357100015 ()27974436 (PubMedID)
    Note

    Funding agencies: Swedish Research Council (SRC) (Vetenskapsradet) [621-2011-4731]; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Forskningsradet for Miljo, Areella Naringar och Samhallsbyggande) [221-2011-1088]; European Research Co

    Available from: 2017-02-21 Created: 2017-02-21 Last updated: 2024-01-17
    4. QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.
    Open this publication in new window or tab >>QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.
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    2017 (English)In: Molecular and Cellular Endocrinology, ISSN 0303-7207, E-ISSN 1872-8057, Vol. 446, p. 52-58, article id S0303-7207(17)30090-4Article in journal (Refereed) Published
    Abstract [en]

    Domestication of animals is associated with numerous alterations in physiology, morphology, and behavior. Lower reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and reduced fearfulness is seen in most studied domesticates, including chickens. Previously we have shown that the physiological stress response as well as expression levels of hundreds of genes in the hypothalamus and adrenal glands are different between domesticated White Leghorn and the progenitor of modern chickens, the Red Junglefowl. To map genetic loci associated with the transcription levels of genes involved in the physiological stress response, we conducted an eQTL analysis in the F12 generation of an inter-cross between White Leghorn and Red Junglefowl. We selected genes for further studies based on their known function in the regulation of the HPA axis or sympathoadrenal (SA) system, and measured their expression levels in the hypothalamus and the adrenal glands after a brief stress exposure (physical restraint). The expression values were treated as quantitative traits for the eQTL mapping. The plasma levels of corticosterone were also assessed. We analyzed the correlation between gene expression and corticosterone levels and mapped eQTL and their potential effects on corticosterone levels. The effects on gene transcription of a previously found QTL for corticosterone response were also investigated. The expression levels of the glucocorticoid receptor (GR) in the hypothalamus and several genes in the adrenal glands were correlated with the post-stress levels of corticosterone in plasma. We found several cis- and trans-acting eQTL for stress-related genes in both hypothalamus and adrenal. In the hypothalamus, one eQTL for c-FOS and one QTL for expression of GR were found. In the adrenal tissue, we identified eQTL for the genes NR0B1, RGS4, DBH, MAOA, GRIN1, GABRB2, GABRB3, and HSF1. None of the found eQTL were significant predictors of corticosterone levels. The previously found QTL for corticosterone was associated with GR expression in hypothalamus. Our data suggests that domestication related modification in the stress response is driven by changes in the transcription levels of several modulators of the HPA and SA systems in hypothalamus and adrenal glands and not by changes in the expression of the steroidogenic genes. The presence of eQTL for GR in hypothalamus combined with the negative correlation between GR expression and corticosterone response suggests GR as a candidate for further functional studies regarding modification of stress response during chicken domestication.

    Keywords
    Animal domestication, HPA axis, QTL, Stress response, eQTL
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-136027 (URN)10.1016/j.mce.2017.02.010 (DOI)000399509600006 ()28189567 (PubMedID)
    Note

    Funding agencies: Swedish Research Council (VR) [621-2011-4731]; Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) [221-2011-1088]; ERC [Genewell 322206]; SRC grant [VR 621-2011-4423, 2015-4870]; Swedish Centre of Excellence in A

    Available from: 2017-03-27 Created: 2017-03-27 Last updated: 2023-12-28
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    Domestication Effects on the Stress Response in Chickens: Genetics, Physiology, and Behaviour
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  • 40.
    Favati, Anna
    et al.
    Stockholm University, Sweden.
    Leimar, Olof
    Stockholm University, Sweden.
    Radesäter, Tommy
    Stockholm University, Sweden.
    Løvlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology. Stockholm University, Sweden.
    Social status and personality: stability in social state can promote consistency of behavioural responses2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1774, p. 20132531-Article in journal (Refereed)
    Abstract [en]

    Stability of ‘state’ has been suggested as an underlying factor explainingbehavioural stability and animal personality (i.e. variation among, andconsistency within individuals in behavioural responses), but the possibilitythat stable social relationships represent such states remains unexplored.Here, we investigated the influence of social status on the expression andconsistency of behaviours by experimentally changing social status betweenrepeated personality assays. We used male domestic fowl (Gallus gallusdomesticus), a social species that forms relatively stable dominance hierarchies,and showed that behavioural responses were strongly affected bysocial status, but also by individual characteristics. The level of vigilance,activity and exploration changed with social status, whereas boldnessappeared as a stable individual property, independent of status. Furthermore,variation in vocalization predicted future social status, indicatingthat individual behaviours can both be a predictor and a consequence ofsocial status, depending on the aspect in focus. Our results illustrate thatsocial states contribute to both variation and stability in behaviouralresponses, and should therefore be taken into account when investigatingand interpreting variation in personality.

    Download full text (pdf)
    fulltext
  • 41.
    Favati, Anna
    et al.
    Stockholm Univ, Sweden.
    Lovlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Leimar, Olof
    Stockholm Univ, Sweden.
    Effects of social experience, aggressiveness and comb size on contest success in male domestic fowl2021In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 8, no 2, article id 201213Article in journal (Refereed)
    Abstract [en]

    The ability to dominate conspecifics and thereby gain access to resources depends on a number of traits and skills. Experience of dominance relationships during development is a potential source of learning such skills. We here study the importance of social experience, aggressiveness and morphological traits for competitiveness in social interactions (contest success) in male domestic fowl (Gallus gallus domesticus). We let males grow up either as a single (dominant) male or as an intermediately ranked male in a group of males, and measured their success in duels against different opponents. We found that single-raised males had lower contest success than group-raised males, and that aggression and comb size correlated positively with contest success. This indicates that experience of dominance interactions with other males increases future success in duels. We similarly studied the consequences of growing up as a dominant or subordinate in a pair of males, finding no statistically significant effect of the dominance position on contest success. Finally, we found that males were consistent over time in contest success. We conclude that social experience increases contest success in male domestic fowl, but that certain behavioural and morphological characteristics have an equal or even stronger covariation with contest success.

    Download full text (pdf)
    fulltext
  • 42.
    Favati, Anna
    et al.
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Zidar, Josefina
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Thorpe, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Lovlie, Hanne
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    The ontogeny of personality traits in the redjunglefowl, Gallus gallus2016In: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 27, no 2, p. 484-493Article in journal (Refereed)
    Abstract [en]

    Consistent behavioral differences among individuals, that is, personality, are described in numerous species. Nevertheless, thedevelopment of behavioral consistency over ontogeny remains unclear, including whether the personality of individuals is consistentthroughout life, and if adult personality can be predicted already at young age. We investigated the ontogeny of personality in thered junglefowl (Gallus gallus) by scoring personality of hatchlings at 5 time points through adulthood, including before and after themajor developmental stages of becoming independent and sexual mature. We use the conceptual framework laid out by Stamps andGroothuis (2010a) to holistically investigate the observed changes in behavioral response over ontogeny. We demonstrate that meanvalues of behavioral responses changed across ontogeny and stabilized after independence. Rank-order consistencies of behavioralresponses were overall low across independence and sexual maturation. Only in 1 case could low rank-order consistencies potentiallybe explained by different phenotypes displaying different amounts of change in behavior; more explorative individuals decreased inexploration after independence, while less explorative individuals remained so. Correlations among behavior varied across ontogenyand weakened after sexual maturation. Our results demonstrate that both absolute values and consistency of behavioral traits maychange across ontogeny and that individual developmental trajectories and adult personality only to some extent can be predictedearly in life. These results have implications for future studies on personality, highlighting that the life stage at which individuals arescored affects the observed consistency of behavioral responses.

  • 43.
    Friberg, Urban
    Department of Ecology and Environmental Science, Section of Animal Ecology, Umeå University, Umeå , Sweden.
    Genetic variation in male and female reproductive characters associated with sexual conflict in Drosophila melanogaster2005In: Behavior Genetics, ISSN 0001-8244, E-ISSN 1573-3297, Vol. 35, no 4, p. 455-462Article in journal (Refereed)
    Abstract [en]

    Recent studies have shown that elevated mating, courtship and seminal substances affect female fitness negatively in Drosophila melanogaster. It has also been shown that males vary with respect to these characters and that male harm to females correlates positively with components of male fitness. These results suggest that there is sexual conflict over the effect of such male characters. An important component of this scenario is that females have evolved counteradaptations to male harm, but so far there is limited evidence for this. Here I define female resistance as the ability to withstand an increased exposure to males. Across 10 genetically differentiated lines of D. melanogaster, I found genetic variation among females in the reduction of lifespan that followed from exposure to males of different durations. There was also genetic variation among males with regards to the degree to which they decrease the lifespan of their mates. These results suggest that genetic variation for female ability to endure male sexually antagonistic adaptations exists and may play an important role in male–female coevolution.

  • 44.
    Friberg, Urban
    et al.
    Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden / Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA.
    Lew, Timothy
    Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA.
    Byrne, Pillip
    Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA / School of Botany and Zoology, Australian National University, Canberra, Australian Capital Territory 0200, Australia.
    Rice, William
    Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA.
    Assessing the potential for an ongoing arms race within and between the sexes: selection and heritable variation2005In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 59, no 7, p. 1540-1551Article in journal (Refereed)
    Abstract [en]

    In promiscuous species, sexual selection generates two opposing male traits: offense (acquiring new mates and supplanting stored sperm) and defense (enforcing fidelity on one's mates and preventing sperm displacement when this fails). Coevolution between these traits requires both additive genetic variation and associated natural selection. Previous work with Drosophila melanogaster found autosomal genetic variation for these traits among inbred lines from a mixture of populations, but only nonheritable genetic variation was found within a single outbred population. These results do not support ongoing antagonistic coevolution between offense and defense, nor between either of these male traits and female reproductive characters. Here we use a new method (hemiclonal analysis) to study genomewide genetic variation in a large outbred laboratory population of D. melanogaster. Hemiclonal analysis estimates the additive genetic variation among random, genomewide haplotypes taken from a large, outbred, locally adapted laboratory population and determines the direction of the selection gradient on this variation. In contrast to earlier studies, we found low but biologically significant heritable variation for defensive and offensive offspring production as well as all their components (P1, fidelity, P2, and remating). Genetic correlations between these traits were substantially different from those reported for inbred lines. A positive genetic correlation was found between defense and offense, demonstrating that some shared genes influence both traits. In addition to this common variation, evidence for unique genetic variation for each trait was also found, supporting an ongoing coevolutionary arms race between defense and offense. Reproductive conflict between males can strongly influence female fitness. Correspondingly, we found genetic variation in both defense and offense that affected female fitness. No evidence was found for intersexual conflict in the context of male defense, but we found substantial intersexual conflict in the context of male offensive sperm competitive ability. These results indicate that conflict between competing males also promotes an associated arms race between the sexes.

  • 45.
    Friesen, Christopher R.
    et al.
    University of Sydney, Australia; Oregon State University, OR 97330 USA.
    Uhrig, Emily
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Oregon State University, OR 97330 USA.
    Bentz, Ehren J.
    Oregon State University, OR 97330 USA.
    Blakemore, Leslie A.
    Oregon State University, OR 97330 USA.
    Mason, Robert T.
    Oregon State University, OR 97330 USA.
    Correlated evolution of sexually selected traits: interspecific variation in ejaculates, sperm morphology, copulatory mate guarding, and body size in two sympatric species of garter snakes2017In: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 71, no 12, article id UNSP 180Article in journal (Refereed)
    Abstract [en]

    Male reproductive success is dependent on a correlated suite of traits related to a species ecology and mating system dynamics. Closely related species differing in their mating systems and ecology, such as the garter snakes (Thamnophis), are ideal for studying the correlated evolution of sexually selected traits. Here, we compare the degree of sexual size dimorphism (SSD), copulatory behavior, copulatory plug size, and traits associated with sperm competition between two sympatric and closely related Thamnophis species, T. sirtalis and T. radix with divergent mating aggregation size and density. Our findings indicate that T. sirtalis has greater female-biased SSD, shorter copulations, and larger, more strongly adhering copulatory plugs than T. radix. Our finding that T. sirtalis have longer sperm and higher numbers of sperm per ejaculate is further evidence of more intense sperm competition in this species than in T. radix. However, this reduced number of sperm in the ejaculate means that T. radix males are likely capable of more matings per season than T. sirtalis. This result may reflect differences in feeding during the breeding season (obligate aphagy in T. sirtalis) and the potential for sperm loss in T. radix during prolonged copulations that are prevented in T. sirtlais by their substantial copulatory plugs. Our findings demonstrate that ecological and mating system dynamics have the capacity to strongly influence correlated selection of pre- and postcopulatory traits.

  • 46.
    Gavrilets, Sergey
    et al.
    Departments of Ecology and Evolutionary Biology and Mathematics, University of Tennessee, Knoxville,USA.
    Arnqvist, Göran
    Department of Ecology and Environmental Science, University of Umeå, Sweden.
    Friberg, Urban
    Department of Ecology and Environmental Science, University of Umeå, Sweden.
    The evolution of female mate choice by sexual conflict2001In: Proceedings of the Royal Society of London Series B, ISSN 0080-4649, Vol. 268, no 1466, p. 531-539Article in journal (Refereed)
    Abstract [en]

    Although empirical evidence has shown that many male traits have evolved via sexual selection by female mate choice, our understanding of the adaptive value of female mating preferences is still very incomplete. It has recently been suggested that female mate choice may result from females evolving resistance rather than attraction to males, but this has been disputed. Here, we develop a quantitative genetic model showing that sexual conflict over mating indeed results in the joint evolution of costly female mate choice and exaggerated male traits under a wide range of circumstances. In contrast to traditional explanations of costly female mate choice, which rely on indirect genetic benefits, our model shows that mate choice can be generated as a side–effect of females evolving to reduce the direct costs of mating.

  • 47.
    Gering, E.
    et al.
    Nova Southeastern Univ, FL USA.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Theunissen, Doortje
    Linköping University, Department of Physics, Chemistry and Biology, Ecological and Environmental Modeling. Linköping University, Faculty of Science & Engineering.
    Martin Cerezo, Maria Luisa
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Steep, A.
    Michigan State Univ, MI USA.
    Getty, T.
    Michigan State Univ, MI USA.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Ecological and Environmental Modeling. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Signals of selection and ancestry in independently feral Gallus gallus populations2024In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    Recent work indicates that feralisation is not a simple reversal of domestication, and therefore raises questions about the predictability of evolution across replicated feral populations. In the present study we compare genes and traits of two independently established feral populations of chickens (Gallus gallus) that inhabit archipelagos within the Pacific and Atlantic regions to test for evolutionary parallelism and/or divergence. We find that feral populations from each region are genetically closer to one another than other domestic breeds, despite their geographical isolation and divergent colonisation histories. Next, we used genome scans to identify genomic regions selected during feralisation (selective sweeps) in two independently feral populations from Bermuda and Hawaii. Three selective sweep regions (each identified by multiple detection methods) were shared between feral populations, and this overlap is inconsistent with a null model in which selection targets are randomly distributed throughout the genome. In the case of the Bermudian population, many of the genes present within the selective sweeps were either not annotated or of unknown function. Of the nine genes that were identifiable, five were related to behaviour, with the remaining genes involved in bone metabolism, eye development and the immune system. Our findings suggest that a subset of feralisation loci (i.e. genomic targets of recent selection in feral populations) are shared across independently established populations, raising the possibility that feralisation involves some degree of parallelism or convergence and the potential for a shared feralisation 'syndrome'.

  • 48.
    Gering, E.
    et al.
    Kellogg Biological Station, Michigan State Universiry, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Willis, P.
    Department of Biology, University of Victoria, Cunningham 202, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada.
    Getty, T.
    Kellogg Biological Station, Michigan State Universiry, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reserviors2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 9, p. 2112-2124Article in journal (Refereed)
    Abstract [en]

    A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.

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  • 49.
    Gering, Eben
    et al.
    Michigan State Univ, MI 48824 USA; Nova Southeastern Univ, FL 33314 USA.
    Incorvaia, Darren
    Michigan State Univ, MI 48824 USA.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Conner, Jeffrey
    Michigan State Univ, MI 49060 USA.
    Getty, Thomas
    Michigan State Univ, MI 48824 USA.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Getting Back to Nature: Feralization in Animals and Plants2019In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 34, no 12, p. 1137-1151Article, review/survey (Refereed)
    Abstract [en]

    Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how domestication genes act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.

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  • 50.
    Gering, Eben
    et al.
    Michigan State Univ, MI 48824 USA.
    Incorvaia, Darren
    Michigan State Univ, MI 48824 USA.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Getty, Thomas
    Michigan State Univ, MI 48824 USA.
    Maladaptation in feral and domesticated animals2019In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 12, no 7, p. 1274-1286Article, review/survey (Refereed)
    Abstract [en]

    Selection regimes and population structures can be powerfully changed by domestication and feralization, and these changes can modulate animal fitness in both captive and natural environments. In this review, we synthesize recent studies of these two processes and consider their impacts on organismal and population fitness. Domestication and feralization offer multiple windows into the forms and mechanisms of maladaptation. Firstly, domestic and feral organisms that exhibit suboptimal traits or fitness allow us to identify their underlying causes within tractable research systems. This has facilitated significant progress in our general understandings of genotype-phenotype relationships, fitness trade-offs, and the roles of population structure and artificial selection in shaping domestic and formerly domestic organisms. Additionally, feralization of artificially selected gene variants and organisms can reveal or produce maladaptation in other inhabitants of an invaded biotic community. In these instances, feral animals often show similar fitness advantages to other invasive species, but they are also unique in their capacities to modify natural ecosystems through introductions of artificially selected traits. We conclude with a brief consideration of how emerging technologies such as genome editing could change the tempos, trajectories, and ecological consequences of both domestication and feralization. In addition to providing basic evolutionary insights, our growing understanding of mechanisms through which artificial selection can modulate fitness has diverse and important applications-from enhancing the welfare, sustainability, and efficiency of agroindustry, to mitigating biotic invasions.

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