Genetic architecture of tameness in a rat model of animal domestication

The role of G protein-coupled receptors and their ligands in animal domestication

The domestication of plants and animals has resulted in one of the most significant cultural and socio-economical transitions in human history. Domestication of animals, including human-supervised reproduction, largely uncoupled particular animal species from their natural, evolutionary history driven by environmental and ecological factors. The primary motivations for domesticating animals were, and still are, producing food and materials (e.g. meat, eggs, honey or milk products, wool, leather products, jewelry and medication products) to support plowing in agriculture or in transportation (e.g. horse, cattle, camel and llama) and to facilitate human activities (for hunting, rescuing, therapeutic aid, guarding behavior and protecting or just as a companion). In recent years, decoded genetic information from more than 40 domesticated animal species have become available; these studies have identified genes and mutations associated with specific physiological and behavioral traits contributing to the complex genetic background of animal domestication. These breeding-altered genomes provide insights into the regulation of different physiological areas, including information on links between e.g. endocrinology and behavior, with important pathophysiological implications (e.g. for obesity and cancer), extending the interest in domestication well beyond the field. Several genes that have undergone selection during domestication and breeding encode specific G protein-coupled receptors, a class of membrane-spanning receptors involved in the regulation of a number of overarching functions such as reproduction, development, body homeostasis, metabolism, stress responses, cognition, learning and memory. Here we summarize the available literature on variations in G protein-coupled receptors and their ligands and how these have contributed to animal domestication.

Scleral appearance is not a correlate of domestication in mammals

Numerous hypotheses try to explain the unusual appearance of the human eye with its bright sclera and transparent conjunctiva and how it could have evolved from a dark-eyed phenotype, as is present in many non-human primates. Recently, it has been argued that pigmentation defects induced by self-domestication may have led to bright-eyed ocular phenotypes in humans and some other primate lineages, such as marmosets. However, it has never been systematically studied whether actual domesticated mammals consistently deviate from wild mammals in regard to their conjunctival pigmentation and if this trait might therefore be part of a domestication syndrome. Here, we test this idea by drawing phylogenetically informed comparisons from a photographic dataset spanning 13 domesticated mammal species and their closest living wild relatives (n ≥ 15 photos per taxon). We did not recover significant differences in scleral appearance or irido-scleral contrast between domesticated and wild forms, suggesting that conjunctival depigmentation, unlike cutaneous pigmentation disorders, is not a general correlate of domestication. Regardless of their domestication status, macroscopically depigmented conjunctivae were observed in carnivorans and lagomorphs, whereas ungulates generally displayed darker eyes. For some taxa, we observed pronounced intraspecific variation, which should be addressed in more exhaustive future studies. Based on our dataset, we also present preliminary evidence for a general increase of conjunctival pigmentation with eye size in mammals. Our findings suggest that conjunctival depigmentation in humans is not a byproduct of self-domestication, even if we assume that our species has undergone such a process in its recent evolutionary history.

On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves

The evolution of RNA-seq technologies has yielded datasets of scientific value that are often generated as condition associated biological replicates within expression studies. With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abundance, a source of ambiguity is transcript level intra-condition count variation; as indicated by disjointed results between analysis tools. We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis. Initially iterative differential expression analysis involving simulated counts, where levels of intra-condition variation and sets of over represented transcripts are explicitly specified, was performed. Then counts derived from inter- and intra-study data representing brain samples of dogs, wolves and foxes (wolves vs. dogs and aggressive vs. tame foxes) were used. For simulations, the sensitivity in detecting differentially expressed transcripts increased after removing hyper-variable transcripts, although at levels of intra-condition variation above 5% detection became unreliable. For real data, prior to applying TVscript, ≈20% of the transcripts identified as being differentially expressed were associated with high levels of intra-condition variation, an over representation relative to the reference set. As transcripts harbouring such variation were removed pre-analysis, a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. The removal of transcripts possessing intra-condition variation values within (and above) the 97^th and 95^th percentiles, for wolves vs. dogs and aggressive vs. tame foxes, maximized the sensitivity in detecting differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through analysis of our real data the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at: https://sourceforge.net/projects/tvscript/.

Self-Domestication Underground? Testing for Social and Morphological Correlates of Animal Personality in Cooperatively-Breeding Ansell’s Mole-Rats (Fukomys anselli)

Ansell’s mole-rats (Fukomys anselli) are sexually dimorphic subterranean rodents that live in families consisting of a single breeding pair and their late-dispersing non-breeding offspring. Most individuals exhibit a conspicuous white head patch, which results from integumental depigmentation. Alongside other morphological, physiological, and social characteristics, skin depigmentation in these social rodents mirrors traits that presumably evolved as byproducts from selection against aggression in domestic animals, making them a potential candidate species for a self-domesticated wild mammal. Here we explored whether the expression of the white head patch, sexual dimorphism, and reproductive division of labor are reflected by different personalities in Ansell’s mole-rats. We tested locomotory activity and risk-taking as well as aggression and affiliative behavior in 51 individuals originating from nine captive families in various experimental set-ups. In line with the concept of animal personality, we recovered consistent individual responses over time. While sex had no influence on any tested variable, reproductive status was found to affect risk-taking behavior but not other personality dimensions. Discriminant function analysis revealed that family members clustered more closely together than expected by chance, suggesting that group affiliation rather than sex or social status determines behavioral profiles in this species. Finally, we failed to recover any consistent correlation between head patch expression and behavior, which conflicts with predictions of the self-domestication hypothesis. We argue that many domestication-like traits in Ansell’s mole-rat and its congeners evolved in the framework of subterranean adaptation and call for a cautious application of the self-domestication concept to wild mammals.

Domestication of farmed fish via the attenuation of stress responses mediated by the hypothalamus-pituitary-inter-renal endocrine axis

Human-directed domestication of terrestrial animals traditionally requires thousands of years for breeding. The most prominent behavioral features of domesticated animals include reduced aggression and enhanced tameness relative to their wild forebears, and such behaviors improve the social tolerance of domestic animals toward both humans and crowds of their own species. These behavioral responses are primarily mediated by the hypothalamic-pituitary-adrenal (inter-renal in fish) (HPA/I) endocrine axis, which is involved in the rapid conversion of neuronal-derived perceptual information into hormonal signals. Over recent decades, growing evidence implicating the attenuation of the HPA/I axis during the domestication of animals have been identified through comprehensive genomic analyses of the paleogenomic datasets of wild progenitors and their domestic congeners. Compared with that of terrestrial animals, domestication of most farmed fish species remains at early stages. The present review focuses on the application of HPI signaling attenuation to accelerate the domestication and genetic breeding of farmed fish. We anticipate that deeper understanding of HPI signaling and its implementation in the domestication of farmed fish will benefit genetic breeding to meet the global demands of the aquaculture industry.

From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management

Simple Summary

Horses were domesticated later than any other major livestock species. Their role in shaping ancient civilizations cannot be overestimated. As a primary means of transportation, an essential asset in warfare, and later one of the key elements of circus entertainment, horses quickly became luxurious goods. Vast amounts of money were invested in the horse industry resulted resulting in the rapid development of horse breeding and husbandry. This review examines paleogenetic, archeological, and classical studies on managing horses in antiquity. Many ancient approaches and practices in horse management are still relevant today and some of them, now abandoned, are worth re-examination.

Abstract

The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.

Genetic Liability for Internalizing Versus Externalizing Behavior Manifests in the Developing and Adult Hippocampus: Insight From a Meta-analysis of Transcriptional Profiling Studies in a Selectively Bred Rat Model

BACKGROUND

For more than 16 years, we have selectively bred rats for either high or low levels of exploratory activity within a novel environment. These bred high-responder (bHR) and bred low-responder (bLR) rats model temperamental extremes, exhibiting large differences in internalizing and externalizing behaviors relevant to mood and substance use disorders.

METHODS

We characterized persistent differences in gene expression related to bHR/bLR phenotype across development and adulthood in the hippocampus, a region critical for emotional regulation, by meta-analyzing 8 transcriptional profiling datasets (microarray and RNA sequencing) spanning 43 generations of selective breeding (postnatal day 7: n = 22; postnatal day 14: n = 49; postnatal day 21: n = 21; adult: n = 46; all male). We cross-referenced expression differences with exome sequencing within our colony to pinpoint candidates likely to mediate the effect of selective breeding on behavioral phenotype. The results were compared with hippocampal profiling from other bred rat models.

RESULTS

Genetic and transcriptional profiling results converged to implicate multiple candidate genes, including two previously associated with metabolism and mood: Trhr and Ucp2. Results also highlighted bHR/bLR functional differences in the hippocampus, including a network essential for neurodevelopmental programming, proliferation, and differentiation, centering on Bmp4 and Mki67. Finally, we observed differential expression related to microglial activation, which is important for synaptic pruning, including 2 genes within implicated chromosomal regions: C1qa and Mfge8.

CONCLUSIONS

These candidate genes and functional pathways may direct bHR/bLR rats along divergent developmental trajectories and promote a widely different reactivity to the environment.

Combined change of behavioral traits for domestication and gene-networks in mice selectively bred for active tameness

Tameness is a major element of animal domestication and involves two components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). To understand the behavioral and genetic mechanisms of active tameness in mice, we had previously conducted selective breeding for long durations of contact and heading toward human hands in an active tameness test using a wild-derived heterogeneous stock. Although the study showed a significant increase in contacting and heading with the 12th generation of breeding, the effect on other behavioral indices related to tameness and change of gene expression levels underlying selective breeding was unclear. Here, we analyzed nine tameness-related traits at a later stage of selective breeding and analyzed how gene expression levels were changed by the selective breeding. We found that five traits, including contacting and heading, showed behavioral change in the selective groups comparing to the control through the generations. Furthermore, we conducted cluster analyses to evaluate the relationships among the nine traits and found that contacting and heading combined in an independent cluster in the selected groups, but not in the control groups. RNA-Seq of hippocampal tissue revealed differential expression of 136 genes between the selection and control groups, while the pathway analysis identified the networks associated with these genes. These results suggest that active tameness was hidden in the control groups but became apparent in the selected populations by selective breeding, potentially driven by changes in gene expression networks.

Age-Related Changes in the Behaviour of Domestic Horses as Reported by Owners

Simple Summary

Some treatments for common problem behaviours in domestic horses can compromise horse welfare. Such behaviours can be the manifestation of pain, confusion and conflict. In contrast, among the desirable attributes in horses, boldness and independence are two important behavioural traits that affect the fearfulness, assertiveness and sociability of horses when interacting with their environment, objects, conspecifics and humans. Shy and socially dependent horses are generally more difficult to manage and train than their bold and independent counterparts. Previous studies have shown how certain basic temperament traits predict the behavioural output of horses, but few have investigated how the age of the horse and the age it was when started being trained under saddle affect behaviour. Using 1940 responses to the Equine Behaviour Assessment and Research Questionnaire (E-BARQ), the current study explored the behavioural evidence of boldness and independence in horses and how these related to the age of the horse. Results revealed age-related effects on boldness and independence of horses. Older horses were bolder than younger horses, but horses started under saddle at an older age were less bold and independent than those started at a younger age. Additionally, significant differences in boldness and independence relating to specific breeds and primary equestrian disciplines also emerged. Finally, riders with eight or more years of riding experience reported having more independent horses than those who had ridden their whole lives. Understanding how horses’ ages affect behavioural traits can improve horse–rider matching and potentially also optimise welfare.

Abstract

The broad traits of boldness and independence in domestic horses can affect their usefulness and, indirectly, their welfare. The objective of the current study was to explore associations between attributes that reflect equine boldness and independence with both the age of horses and the age at which they were started under saddle, as well as other variables including breed, colour and primary equestrian discipline. All data were sourced from responses (n = 1940) to the 97-question online Equine Behaviour Assessment and Research Questionnaire (E-BARQ). Twenty E-BARQ items from the dataset were selected to reflect boldness and independence and were tested for univariate significance at p < 0.2. Multivariable modelling of the effect of age on remaining traits was assessed by an ordinal logistic regression, using a cumulative log odds model. This revealed that older horses were bolder (p = 0.012). However, horses started under saddle at an older age were less bold and less independent (p = 0.040 and p = 0.010, respectively). Australian Stock Horses were bolder and more independent (p = 0.014 and p = 0.007, respectively) than crossbreed horses. Horses used for breeding conformation (p = 0.039), working equitation (p = 0.045), eventing (p = 0.044) and traditional working horses (p = 0.034) were bolder than those used for other disciplines. Dressage (p = 0.039) and therapy (p = 0.040) horses were less bold than horses used for other disciplines. Stallions were bolder (p = −0.034) than geldings. Brown (p = 0.049) and chestnut (p = 0.027) horses were less bold than bay horses. Compared to crossbreed horses, Thoroughbreds (p = 0.000) and companion horses (p = 0.017) were less bold whilst heavy horses (p = 0.029) and ponies (p = 0.044) were bolder. Compared to pleasure horses, mounted games horses (p = 0.033) were less independent whereas working equitation horses (p = 0.020) were more independent. Riders with more than eight years’ experience reported more independence in their horses (p = 0.015) than those who had ridden their whole lives. The study findings suggest that boldness and independence are separate traits and only boldness was associated with the age of the horse. Factors that relate to desirable boldness and independence are important in ridden horses because they can affect rider safety. Results from this study should improve horse–rider matching and thereby potentially enhance horse welfare.

Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome

Background

In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best conditions. This concept links quality of life and longevity of an individual with disease susceptibilities encoded by his/her genome. Female reproductive potential has been investigated deeply, widely, and comprehensively in the past, but the male one has not received an equal amount of attention. Therefore, here we focused on the human Y chromosome and found candidate single-nucleotide polymorphism (SNP) markers of male reproductive potential.

Results

Examining in silico (i.e., using our earlier created Web-service SNP_TATA_Z-tester) all 1206 unannotated SNPs within 70 bp proximal promoters of all 63 Y-linked genes, we found 261 possible male-reproductive-potential SNP markers that can significantly alter the binding affinity of TATA-binding protein (TBP) for these promoters. Among them, there are candidate SNP markers of spermatogenesis disorders (e.g., rs1402972626), pediatric cancer (e.g., rs1483581212) as well as male anxiety damaging family relationships and mother’s and children’s health (e.g., rs187456378). First of all, we selectively verified in vitro both absolute and relative values of the analyzed TBP–promoter affinity, whose Pearson’s coefficients of correlation between predicted and measured values were r = 0.84 (significance p <  0.025) and r = 0.98 (p <  0.025), respectively. Next, we found that there are twofold fewer candidate SNP markers decreasing TBP–promoter affinity relative to those increasing it, whereas in the genome-wide norm, SNP-induced damage to TBP–promoter complexes is fourfold more frequent than SNP-induced improvement (p <  0.05, binomial distribution). This means natural selection against underexpression of these genes. Meanwhile, the numbers of candidate SNP markers of an increase and decrease in male reproductive potential were indistinguishably equal to each other (p <  0.05) as if male self-domestication could have happened, with its experimentally known disruptive natural selection. Because there is still not enough scientific evidence that this could have happened, we discuss the human diseases associated with candidate SNP markers of male reproductive potential that may correspond to domestication-related disorders in pets.

Conclusions

Overall, our findings seem to support a self-domestication syndrome with disruptive natural selection by male reproductive potential preventing Y-linked underexpression of a protein.

Tameness correlates with domestication related traits in a Red Junglefowl intercross

Early animal domestication may have been driven by selection on tameness. Selection on only tameness can bring about correlated selection responses in other traits, not intentionally selected upon, which may be one cause of the domesticated phenotype. We predicted that genetically reduced fear towards humans in Red Junglefowl, ancestors of domesticated chickens, would be correlated to other traits included in the domesticated phenotype. Fear level was determined by a standardised behaviour test, where the reaction towards an approaching human was recorded. We first selected birds for eight generations for either high or low fear levels in this test, to create two divergent selection lines. An F3 intercross, with birds from the eighth generation as parentals, was generated to study correlations between fear‐of‐human scores and other unselected phenotypes, possibly caused by pleiotropy or linkage. Low fear‐of‐human scores were associated with higher body weight and growth rates, and with increased activity in an open field test, indicating less general fearfulness. In females, low fear‐of‐human scores were also associated with more efficient fear habituation and in males with an increased tendency to emit food calls in a mirror test, indicating increased social dominance. Low fear‐of‐human scores were also associated with smaller brain relative to body weight, and with larger cerebrum relative to total brain weight in females. All these effects are in line with the changes observed in domesticated chickens compared to their ancestors, and we conclude that tameness may have been a driving factor underlying some aspects of the domesticated phenotype.

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

Selection for reduced fear in red junglefowl changes brain composition and affects fear memory

Brain size reduction is a common trait in domesticated species when compared to wild conspecifics. This reduction can happen through changes in individual brain regions as a response to selection on specific behaviours. We selected red junglefowl for 10 generations for diverging levels of fear towards humans and measured brain size and composition as well as habituation learning and conditioned place preference learning in young chicks. Brain size relative to body size as well as brainstem region size relative to whole brain size were significantly smaller in chicks selected for low fear of humans compared to chicks selected for high fear of humans. However, when including allometric effects in the model, these differences disappear but a tendency towards larger cerebra in low-fear chickens remains. Low-fear line chicks habituated more effectively to a fearful stimulus with prior experience of that same stimulus, whereas high-fear line chicks with previous experience of the stimulus had a response similar to naive chicks. The phenotypical changes are in line with previously described effects of domestication.

Morphology does not covary with predicted behavioral correlations of the domestication syndrome in dogs

Domesticated animals display suites of altered morphological, behavioral, and physiological traits compared to their wild ancestors, a phenomenon known as the domestication syndrome (DS). Because these alterations are observed to co-occur across a wide range of present day domesticates, the traits within the DS are assumed to covary within species and a single developmental mechanism has been hypothesized to cause the observed co-occurrence. However, due to the lack of formal testing it is currently not well-resolved if the traits within DS actually covary. Here, we test the hypothesis that the presence of the classic morphological domestication traits white pigmentation, floppy ears, and curly tails predict the strength of behavioral correlations in support of the DS in 78 dog breeds. Contrary to the expectations of covariation among DS traits, we found that morphological traits did not covary among themselves, nor did they predict the strength of behavioral correlations among dog breeds. Further, the number of morphological traits in a breed did not predict the strength of behavioral correlations. Our results thus contrast with the hypothesis that the DS arises due to a shared underlying mechanism, but more importantly, questions if the morphological traits embedded in the DS are actual domestication traits or postdomestication improvement traits. For dogs, it seems highly likely that strong selection for breed specific morphological traits only happened recently and in relation to breed formation. Present day dogs therefore have limited bearing of the initial selection pressures applied during domestication and we should reevaluate our expectations of the DS accordingly.

How Natural Genetic Variation Shapes Behavior

Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds to years. Behavior is further shaped at intergenerational timescales by genetic variation, drift, and selection. This sophistication and flexibility of behavior makes it challenging to measure behavior consistently in individual subjects and to compare it across individuals. In spite of these challenges, careful behavioral observations in nature and controlled measurements in the laboratory, combined with modern technologies and powerful genetic approaches, have led to important discoveries about the way genetic variation shapes behavior. A critical mass of genes whose variation is known to modulate behavior in nature is finally accumulating, allowing us to recognize emerging patterns. In this review, we first discuss genetic mapping approaches useful for studying behavior. We then survey how variation acts at different levels-in environmental sensation, in internal neuronal circuits, and outside the nervous system altogether-and then discuss the sources and types of molecular variation linked to behavior and the mechanisms that shape such variation. We end by discussing remaining questions in the field.

Sex differences in adult mood and in stress-induced transcriptional coherence across mesocorticolimbic circuitry

Women are approximately two times as likely to be diagnosed with major depressive disorder (MDD) compared to men. While sex differences in MDD might be driven by circulating gonadal hormones, we hypothesized that developmental hormone exposure and/or genetic sex might play a role. Mice were gonadectomized in adulthood to isolate the role of developmental hormones. We examined the effects of developmental gonadal and genetic sex on anhedonia-/depressive-like behaviors under non-stress and chronic stress conditions and performed RNA-sequencing in three mood-relevant brain regions. We used an integrative network approach to identify transcriptional modules and stress-specific hub genes regulating stress susceptibility, with a focus on whether these differed by sex. After identifying sex differences in anhedonia-/depressive-like behaviors (female > male), we show that both developmental hormone exposure (gonadal female > gonadal male) and genetic sex (XX > XY) contribute to the sex difference. The top biological pathways represented by differentially expressed genes were related to immune function; we identify which differentially expressed genes are driven by developmental gonadal or genetic sex. There was very little overlap in genes affected by chronic stress in males and females. We also identified highly co-expressed gene modules affected by stress, some of which were affected in opposite directions in males and females. Since all mice had equivalent hormone exposure in adulthood, these results suggest that sex differences in gonadal hormone exposure during sensitive developmental periods program adult sex differences in mood, and that these sex differences are independent of adult circulating gonadal hormones.

The History of Farm Foxes Undermines the Animal Domestication Syndrome

The Russian Farm-Fox Experiment is the best known experimental study in animal domestication. By subjecting a population of foxes to selection for tameness alone, Dimitry Belyaev generated foxes that possessed a suite of characteristics that mimicked those found across domesticated species. This 'domestication syndrome' has been a central focus of research into the biological pathways modified during domestication. Here, we chart the origins of Belyaev's foxes in eastern Canada and critically assess the appearance of domestication syndrome traits across animal domesticates. Our results suggest that both the conclusions of the Farm-Fox Experiment and the ubiquity of domestication syndrome have been overstated. To understand the process of domestication requires a more comprehensive approach focused on essential adaptations to human-modified environments.

Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific

Populations of vertebrate species introduced onto islands regularly develop similar phenotypic changes, e.g., larger or smaller body size, shortened limbs, duller coats, as well as behavioural changes such as increased tameness and reduced flight-initiation distance. These changes overlap in part with those associated with the 'domestication syndrome', especially tameness and changes in coat patterns, and might indicate a similar neural crest involvement in the concurrent development of multiple phenotypic traits. Here I examine long-term data on free-living populations of wild Polynesian rats from seven mainland countries and 117 islands (n = 3,034), covering the species' native and introduced range. Mainland populations showed no aberrant coat patterns, with the exception of one albino, whereas aberrant coat patterns were found in 12 island populations. Observed coat colour polymorphisms consisted of leucistic (including singular white patches), melanistic (darkly pigmented) and piebald (mixed) coat patterns. After isolation for at least seven centuries, wild Polynesian rat populations on islands seem to exhibit a trend towards a higher incidence of aberrant coat patterns. These phenotypic changes are here explained as a neutral, non-adaptive process, likely part of the 'domestication syndrome' (via the commensal pathway of domestication), in combination with genetic drift, little or no gene flow between the islands and/or the mainland and a relaxed selection (as a result of the weakening or removal of competitor/predator pressure) under commensality.

Activity, social and sexual behaviour in Red Junglefowl selected for divergent levels of fear of humans

The domesticated phenotype is a set of behavioural, morphological and physiological traits that is common for domesticated species. Previous research has found that selection for tameness only can give rise to correlated selection responses that resemble the domesticated phenotype. It has therefore been suggested that tameness may drive the domesticated phenotype as correlated traits. We selected Red Junglefowl for divergent levels of fear of human for eight generations and assessed possible correlated selection responses in other behaviours in semi-natural settings. Behavioural studies were carried out on birds from generations six to eight, and at different ages, in order to study possible effects on general activity, social behaviour and male courtship behaviour. We found that the differences between selection lines changed with age. Adult low fear birds were generally more active and high fear males showed a more intense courtship behaviour. Our study shows that several behaviours can be modified through correlated selection responses by selection on reduced fear of humans only, emphasising the putative role of tameness as a driver of domestication related phenotypes.

Measuring Active and Passive Tameness Separately in Mice

Domesticated animals such as dogs and laboratory mice show a high level of tameness, which is important for humans to handle them easily. Tameness has two behavioral components: a reluctance to avoid humans (passive tameness) and a motivation to approach humans (active tameness). To quantify these components in mice, we previously developed behavioral tests for active tameness, passive tameness, and the willingness to stay on a human hand, each designed to be completed within 3 min. The data obtained were used for selective breeding, with a large number of mice analyzed per generation. The active tameness test measures the movement of the mouse toward a human hand and the contact it engages in. The passive tameness test measures the duration of time that a mouse tolerates human touch. In the stay-on-hand test, a mouse is placed on a human hand and touched slowly using the thumb of that hand; the duration of time that the animal remains on the hand is measured. Here, we describe the test set-up and apparatus, explain the procedures, and discuss the appropriate data analysis. Finally, we explain how to interpret the results.

Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

BACKGROUND

Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe.

RESULTS

Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs.

CONCLUSIONS

In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids.

Revisiting the famous farm foxes: A psychological perspective

Five decades ago, Dmitry Belyaev, Lyudmila Trut, and colleagues began a now-famous experiment, selectively breeding foxes based on one criterion: perceived tame behavior. Over generations, the fox population changed in behavior (as predicted) but, intriguingly, also changed markedly in appearance-for example, many had wider mouths, curlier tails, different fur coloring, and floppy ears. These researchers concluded that the morphological changes that appeared in their foxes were a by-product of the researchers' selecting for genetic variants that are implicated both in behavior and in appearance. For decades, scientists have largely accepted this "shared genetic variants" interpretation to fully account for the co-occurrence of behavioral and morphological phenotypes in these foxes and in other domesticated animals. However, several decades of psychological research on human social cognition, human-canine interaction, and canine behavior strongly suggest that such an account may be incomplete. I forward a supplementary perspective, based on psychological research, that the covariation of appearance and behavior among these foxes may be partly an artifact of human psychological processes at play in selection. These processes include humans' tendency to infer individuals' traits based on their physical features; trait inferences, in turn, influence how humans treat those individuals. If accurate, this account bears on our understanding of these famous foxes, human-canine interactions, as well as humans' role in domestication.

A longitudinal study of phenotypic changes in early domestication of house mice

Similar phenotypic changes occur across many species as a result of domestication, e.g. in pigmentation and snout size. Experimental studies of domestication have concentrated on intense and directed selection regimes, while conditions that approximate the commensal and indirect interactions with humans have not been explored. We examine long-term data on a free-living population of wild house mice that have been indirectly selected for tameness by regular exposure to humans. In the course of a decade, this mouse population exhibited significantly increased occurrence of white patches of fur and decreased head length. These phenotypic changes fit to the predictions of the 'domestication syndrome'.

Selective breeding and selection mapping using a novel wild-derived heterogeneous stock of mice revealed two closely-linked loci for tameness

Tameness is a major behavioral factor for domestication, and can be divided into two potential components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). We identified genetic loci for active tameness through selective breeding, selection mapping, and association analysis. In previous work using laboratory and wild mouse strains, we found that laboratory strains were predominantly selected for passive tameness but not active tameness during their domestication. To identify genetic regions associated with active tameness, we applied selective breeding over 9 generations for contacting, a behavioural parameter strongly associated with active tameness. The prerequisite for successful selective breeding is high genetic variation in the target population, so we established and used a novel resource, wild-derived heterogeneous stock (WHS) mice from eight wild strains. The mice had genetic variations not present in other outbred mouse populations. Selective breeding of the WHS mice increased the contacting level through the generations. Selection mapping was applied to the selected population using a simulation based on a non-selection model and inferred haplotype data derived from single-nucleotide polymorphisms. We found a genomic signature for selection on chromosome 11 containing two closely linked loci.

Gene expression of behaviorally relevant genes in the cerebral hemisphere changes after selection for tameness in Red Junglefowl

The process of domestication in animals has led to alterations in behavior, physiology and phenotypic traits, changes that may be driven by correlations with reduced fear of humans. We used Red Junglefowl, ancestors of all domesticated chickens selected for either high or low fear of humans for five generations to study the effects of selection on gene transcription in the cerebral hemisphere, which is heavily involved in behaviour control. A total of 24 individuals from the parental generation as well as from the fifth selected generation were used. Twenty-two genes were significantly differentially expressed at p < 0.05 after false discovery rate (FDR) correction. Those genes that were upregulated in the low fearful animals were found to be involved in neural functions. Gene ontology and pathway analysis revealed enrichment for terms associated with behavioural processes. We conclude that five generations of divergent selection for high or low tameness has significantly changed gene expression patterns in the cerebral hemisphere in the Red Junglefowl population used here, which could underlie a range of changes in the domestic phenotype.

QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl

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.

Facial shape differences between rats selected for tame and aggressive behaviors

Domestication has been consistently accompanied by a suite of traits called the domestication syndrome. These include increased docility, changes in coat coloration, prolonged juvenile behaviors, modified function of adrenal glands and reduced craniofacial dimensions. Wilkins et al recently proposed that the mechanistic factor underlying traits that encompass the domestication syndrome was altered neural crest cell (NCC) development. NCC form the precursors to a large number of tissue types including pigment cells, adrenal glands, teeth and the bones of the face. The hypothesis that deficits in NCC development can account for the domestication syndrome was partly based on the outcomes of Dmitri Belyaev's domestication experiments initially conducted on silver foxes. After generations of selecting for tameness, the foxes displayed phenotypes observed in domesticated species. Belyaev also had a colony of rats selected over 64 generations for either tameness or defensive aggression towards humans. Here we focus on the facial morphology of Belyaev's tame, 'domesticated' rats to test whether: 1) tameness in rats causes craniofacial changes similar to those observed in the foxes; 2) facial shape, i.e. NCC-derived region, is distinct in the tame and aggressive rats. We used computed-tomography scans of rat skulls and landmark-based geometric morphometrics to quantify and analyze the facial skeleton. We found facial shape differences between the tame and aggressive rats that were independent of size and which mirrored changes seen in domesticated animals compared to their wild counterparts. However, there was no evidence of reduced sexual dimorphism in the face of the tame rats. This indicates that not all morphological changes in NCC-derived regions in the rats follow the pattern of shape change reported in domesticated animals or the silver foxes. Thus, certain phenotypic trends that are part of the domestication syndrome might not be consistently present in all experimental animal models.

CRISPR/Cas9-mediated genome editing in wild-derived mice: generation of tamed wild-derived strains by mutation of the a (nonagouti) gene

Wild-derived mice have contributed to experimental mouse genetics by virtue of their genetic diversity, which may help increase the chance of identifying novel modifier genes responsible for specific phenotypes and diseases. However, gene targeting using wild-derived mice has been unsuccessful because of the unavailability of stable embryonic stem cells. Here, we report that CRISPR/Cas9-mediated gene targeting can be applied to the Japanese wild-derived MSM/Ms strain (Mus musculus molossinus). We targeted the nonagouti (a) gene encoding the agouti protein that is localized in hair and the brain. We obtained three homozygous knockout mice as founders, all showing black coat colour. While homozygous knockout offspring were physiologically indistinguishable from wild-type litter-mates, they showed specific domesticated behaviours: hypoactivity in the dark phase and a decline in the avoidance of a human hand. These phenotypes were consistent over subsequent generations. Our findings support the empirical hypothesis that nonagouti is a domestication-linked gene, the loss of which might repress aggressive behaviour.

Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl

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.

Taming the Past: Ancient DNA and the Study of Animal Domestication

During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.

Genetics of Interactive Behavior in Silver Foxes (Vulpes vulpes)

Individuals involved in a social interaction exhibit different behavioral traits that, in combination, form the individual's behavioral responses. Selectively bred strains of silver foxes (Vulpes vulpes) demonstrate markedly different behaviors in their response to humans. To identify the genetic basis of these behavioral differences we constructed a large F₂ population including 537 individuals by cross-breeding tame and aggressive fox strains. 98 fox behavioral traits were recorded during social interaction with a human experimenter in a standard four-step test. Patterns of fox behaviors during the test were evaluated using principal component (PC) analysis. Genetic mapping identified eight unique significant and suggestive QTL. Mapping results for the PC phenotypes from different test steps showed little overlap suggesting that different QTL are involved in regulation of behaviors exhibited in different behavioral contexts. Many individual behavioral traits mapped to the same genomic regions as PC phenotypes. This provides additional information about specific behaviors regulated by these loci. Further, three pairs of epistatic loci were also identified for PC phenotypes suggesting more complex genetic architecture of the behavioral differences between the two strains than what has previously been observed.

Generalized CNS arousal: An elementary force within the vertebrate nervous system

Why do animals and humans do anything at all? Arousal is the most powerful and essential function of the brain, a continuous function that accounts for the ability of animals and humans to respond to stimuli in the environment by producing muscular responses. Following decades of psychological, neurophysiological and molecular investigations, generalized CNS arousal can now be analyzed using approaches usually applied to physical systems. The concept of "criticality" is a state that illustrates an advantage for arousal systems poised near a phase transition. This property provides speed and sensitivity and facilitates the transition of the system into different brain states, especially as the brain crosses a phase transition from less aroused to more aroused states. In summary, concepts derived from applied mathematics of physical systems will now find their application in this area of neuroscience, the neurobiology of CNS arousal.

Interplay between aggression, brain monoamines and fur color mutation in the American mink

Domestication of wild animals alters the aggression towards humans, brain monoamines and coat pigmentation. Our aim is the interplay between aggression, brain monoamines and depigmentation. The Hedlund white mutation in the American mink is an extreme case of depigmentation observed in domesticated animals. The aggressive (-2.06 ± 0.03) and tame (+3.5 ± 0.1) populations of wild-type dark brown color (standard) minks were bred during 17 successive generations for aggressive or tame reaction towards humans, respectively. The Hedlund mutation was transferred to the aggressive and tame backgrounds to generate aggressive (-1.2 ± 0.1) and tame (+3.0 ± 0.2) Hedlund minks. Four groups of 10 males with equal expression of aggressive (-2) or tame (+5) behavior, standard or with the Hedlund mutation, were selected to study biogenic amines in the brain. Decreased levels of noradrenaline in the hypothalamus, but increased concentrations of the serotonin metabolite, 5-hydroxyindoleacetic acid and dopamine metabolite, homovanillic acid, in the striatum were measured in the tame compared with the aggressive standard minks. The Hedlund mutation increased noradrenaline level in the hypothalamus and substantia nigra, serotonin level in the substantia nigra and striatum and decreased dopamine concentration in the hypothalamus and striatum. Significant interaction effects were found between the Hedlund mutation and aggressive behavior on serotonin metabolism in the substantia nigra (P < 0.001), dopamine level in the midbrain (P < 0.01) and its metabolism in the striatum (P < 0.05). These results provide the first experimental evidence of the interplay between aggression, brain monoamines and the Hedlund mutation in the American minks.

Domestication and tameness: brain gene expression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology

The domestication of animals has generated a set of phenotypic modifications, affecting behaviour, appearance, physiology and reproduction, which are consistent across a range of species. We hypothesized that some of these phenotypes could have evolved because of genetic correlation to tameness, an essential trait for successful domestication. Starting from an outbred population of red junglefowl, ancestor of all domestic chickens, we selected birds for either high or low fear of humans for five generations. Birds from the fifth selected generation (S₅) showed a divergent pattern of growth and reproduction, where low fear chickens grew larger and produced larger offspring. To examine underlying genetic mechanisms, we used microarrays to study gene expression in thalamus/hypothalamus, a brain region involved in fear and stress, in both the parental generation and the S₅. While parents of the selection lines did not show any differentially expressed genes, there were a total of 33 genes with adjusted p-values below 0.1 in S₅. These were mainly related to sperm-function, immunological functions, with only a few known to be relevant to behaviour. Hence, five generations of divergent selection for fear of humans produced changes in hypothalamic gene expression profiles related to pathways associated with male reproduction and to immunology. This may be linked to the effects seen on growth and size of offspring. These results support the hypothesis that domesticated phenotypes may evolve because of correlated effects related to reduced fear of humans.

The taming of the neural crest: a developmental perspective on the origins of morphological covariation in domesticated mammals

Studies on domestication are blooming, but the developmental bases for the generation of domestication traits and breed diversity remain largely unexplored. Some phenotypic patterns of human neurocristopathies are suggestive of those reported for domesticated mammals and disrupting neural crest developmental programmes have been argued to be the source of traits deemed the 'domestication syndrome'. These character changes span multiple organ systems and morphological structures. But an in-depth examination within the phylogenetic framework of mammals including domesticated forms reveals that the distribution of such traits is not universal, with canids being the only group showing a large set of predicted features. Modularity of traits tied to phylogeny characterizes domesticated mammals: through selective breeding, individual behavioural and morphological traits can be reordered, truncated, augmented or deleted. Similarly, mammalian evolution on islands has resulted in suites of phenotypic changes like those of some domesticated forms. Many domesticated mammals can serve as valuable models for conducting comparative studies on the evolutionary developmental biology of the neural crest, given that series of their embryos are readily available and that their phylogenetic histories and genomes are well characterized.

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers.

The Genetic Architecture of Domestication in Animals

Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the “domestication phenotype.” In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.

Domestication affects the structure, development and stability of biobehavioural profiles

Domestication is an evolutionary process during which the biobehavioural profile (comprising e.g. social and emotional behaviour, cognitive abilities, as well as hormonal stress responses) is substantially reshaped. Using a comparative approach, and focusing mainly on the domestic and wild guinea pig, an established model system for the study of domestication, we review (a) how wild and domestic animals of the same species differ in behaviour, emotion, cognition, and hormonal stress responses, (b) during which phases of life differences in biobehavioural profiles emerge and (c) whether or not animal personalities exist in both the wild and domestic form. Concerning (a), typical changes with domestication include increased courtship, sociopositive and maternal behaviours as well as decreased aggression and attentive behaviour. In addition, domestic animals display more anxiety-like and less risk-taking and exploratory behaviour than the wild form and they show distinctly lower endocrine stress responsiveness. There are no indications, however, that domestic animals have diminished cognitive abilities relative to the wild form. The different biobehavioural profiles of the wild and domestic animals can be regarded as adaptations to the different environmental conditions under which they live, i.e., the natural habitat and artificial man-made housing conditions, respectively. Concerning (b), the comparison of infantile, adolescent and adult wild and domestic guinea pigs shows that the typical biobehavioural profile of the domestic form is already present during early phases of life, that is, during early adolescence and weaning. Thus, differences between the domestic and the wild form can be attributed to genetic alterations resulting from artificial selection, and likely to environmental influences during the pre- and perinatal phase. Interestingly, the frequency of play behaviour does not differ between the domestic and wild form early in life, but is significantly higher in domesticated guinea pigs at later ages. Concerning (c), there is some evidence that personalities occur in both wild and domestic animals. However, there may be differences in which behavioural domains – social and sexual behaviour, emotionality, stress-responsiveness – are consistent over time. These differences are probably due to changing selection pressures during domestication.

Aggressive behavior, brain size and domestication in clonal rainbow trout lines

Domestication causes behavior and brain size changes in many species. We addressed three questions using clonal rainbow trout lines: What are the mirror-elicited aggressive tendencies in lines with varying degrees of domestication? How does brain size relate to genotype and domestication level? Finally, is there a relationship between aggressive behavior and brain size? Clonal lines, although sampling a limited subset of the species variation, provide us with a reproducible experimental system with which we can develop hypotheses for further research. We performed principal component analyses on 12 continuous behavior and brain/body size variables and one discrete behavioral variable ("yawn") and detected several aggression syndromes. Two behaviors, "freeze" and "escape", associated with high domestication; "display" and "yawn" behavior associated with wild lines and "swim against the mirror" behavior associated with semi-wild and domestic lines. Two brain size traits, total brain and olfactory volume, were significantly related to domestication level when taking total body size into account, with domesticated lines having larger total brain volume and olfactory regions. The aggression syndromes identified indicate that future QTL mapping studies on domestication-related traits would likely be fruitful.

Adding ‘epi-’ to behaviour genetics: implications for animal domestication

In this review, it is argued that greatly improved understanding of domestication may be gained from extending the field of behaviour genetics to also include epigenetics. Domestication offers an interesting framework of rapid evolutionary changes caused by well-defined selection pressures. Behaviour is an important phenotype in this context, as it represents the primary means of response to environmental challenges. An overview is provided of the evidence for genetic involvement in behavioural control and the presently used methods for finding so-called behaviour genes. This shows that evolutionary changes in behaviour are to a large extent correlated to changes in patterns of gene expression, which brings epigenetics into the focus. This area is concerned with the mechanisms controlling the timing and extent of gene expression, and a lot of focus has been placed on methylation of cytosine in promoter regions, usually associated with genetic downregulation. The review considers the available evidence that environmental input, for example stress, can modify methylation and other epigenetic marks and subsequently affect behaviour. Furthermore, several studies are reviewed, demonstrating that acquired epigenetic modifications can be inherited and cause trans-generational behaviour changes. In conclusion, epigenetics may signify a new paradigm in this respect, as it shows that genomic modifications can be caused by environmental signals, and random mutations in DNA sequence are therefore not the only sources of heritable genetic variation.

Mining the pig genome to investigate the domestication process

Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.

Genetic influences on brain gene expression in rats selected for tameness and aggression

Interindividual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior toward humans for >64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40, and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals.