Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes)

A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior

The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication.

A missense mutation in RRM1 contributes to animal tameness

The increased tameness to reduce avoidance of human in wild animals has been long proposed as the key step of animal domestication. The tameness is a complex behavior trait and largely determined by genetic factors. However, the underlying genetic mutations remain vague and how they influence the animal behaviors is yet to be explored. Behavior tests of a wild-domestic hybrid goat population indicate the locus under strongest artificial selection during domestication may exert a huge effect on the flight distance. Within this locus, only one missense mutation RRM1I241V which was present in the early domestic goat ~6500 years ago. Genome editing of RRM1I241V in mice showed increased tameness and sociability and reduced anxiety. These behavioral changes induced by RRM1I241V were modulated by the alternation of activity of glutamatergic synapse and some other synapse-related pathways. This study established a link between RRM1I241V and tameness, demonstrating that the complex behavioral change can be achieved by mutations under strong selection during animal domestication.

The brain of the silver fox (Vulpes vulpes): a neuroanatomical reference of cell-stained histological and MRI images

Although the silver fox (Vulpes vulpes) has been largely overlooked by neuroscientists, it has the potential to serve as a powerful model for the investigation of brain-behavior relationships. The silver fox is a melanistic variant of the red fox. Within this species, the long-running Russian farm-fox experiment has resulted in different strains bred to show divergent behavior. Strains bred for tameness, aggression, or without selection on behavior present an excellent opportunity to investigate neuroanatomical changes underlying behavioral characteristics. Here, we present a histological and MRI neuroanatomical reference of a fox from the conventional strain, which is bred without behavioral selection. This can provide an anatomical basis for future studies of the brains of foxes from this particular experiment, as well as contribute to an understanding of fox brains in general. In addition, this can serve as a resource for comparative neuroscience and investigations into neuroanatomical variation among the family Canidae, the order Carnivora, and mammals more broadly.

The evolutionary neuroscience of domestication

How does domestication affect the brain? This question has broad relevance. Domesticated animals play important roles in human society, and substantial recent work has addressed the hypotheses that a domestication syndrome links phenotypes across species, including Homo sapiens. Surprisingly, however, neuroscience research on domestication remains largely disconnected from current knowledge about how and why brains change in evolution. This article aims to bridge that gap. Examination of recent research reveals some commonalities across species, but ultimately suggests that brain changes associated with domestication are complex and variable. We conclude that interactions between behavioral, metabolic, and life-history selection pressures, as well as the role the role of experience and environment, are currently largely overlooked and represent important directions for future research.

What made us "hunter-gatherers of words"

This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.

The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway

Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents. Methods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques. Results: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity. Discussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.

Domestic dog lineages reveal genetic drivers of behavioral diversification

Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing a framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral, and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.

Unusual occurrence of domestication syndrome amongst African mole-rats: Is the naked mole-rat a domestic animal?

The Naked mole-rat (NMR) is becoming a prominent model organism due to its peculiar traits, such as eusociality, extreme longevity, cancer resistance, and reduced pain sensitivity. It belongs to the African mole-rats (AMR), a family of subterranean rodents that includes solitary, cooperative breeding and eusocial species. We identified and quantified the domestication syndrome (DS) across AMR, a set of morphological and behavioural traits significantly more common and pronounced amongst domesticated animals than in their wild counterparts. Surprisingly, the NMR shows apparent DS traits when compared to the solitary AMR. Animals can self-domesticate when a reduction of the fear response is naturally selected, such as in islands with no predators, or to improve the group’s harmony in cooperative breeding species. The DS may be caused by alterations in the physiology of the neural crest cells (NCC), a transient population of cells that generate a full range of tissues during development. The NCC contribute to organs responsible for transmitting the fear response and various other tissues, including craniofacial bones. Therefore, mutations affecting the NCC can manifest as behavioural and morphological alterations in many structures across the body, as seen in neurocristopathies. We observed that all social AMRs are chisel-tooth diggers, an adaption to hard soils that requires the flattening of the skull. We hypothesise that chisel-tooth digging could impose a selective pressure on the NCC that triggered the DS’s appearance, possibly facilitating the evolution of sociality. Finally, we discuss how DS traits are neutral or beneficial for the subterranean niche, strategies to test this hypothesis and report well-studied mutations in the NMR that are associated with the NCC physiology or with the control of the fear response. In conclusion, we argue that many of the NMR’s unconventional traits are compatible with the DS and provide a hypothesis about its origins. Our model proposes a novel avenue to enhance the understanding of the extraordinary biology of the NMR.

Evolutionary endocrinology and the problem of Darwin's tangled bank

Like Darwin's tangled bank of biodiversity, the endocrine mechanisms that give rise to phenotypic diversity also exhibit nearly endless forms. This tangled bank of mechanistic diversity can prove problematic as we seek general principles on the role of endocrine mechanisms in phenotypic evolution. A key unresolved question is therefore: to what degree are specific endocrine mechanisms re-used to bring about replicated phenotypic evolution? Related areas of inquiry are booming in molecular ecology, but behavioral traits are underrepresented in this literature. Here, I leverage the rich comparative tradition in evolutionary endocrinology to evaluate whether and how certain mechanisms may be repeated hotspots of behavioral evolutionary change. At one extreme, mechanisms may be parallel, such that evolution repeatedly uses the same gene or pathway to arrive at multiple independent (or, convergent) origins of a particular behavioral trait. At the other extreme, the building blocks of behavior may be unique, such that outwardly similar phenotypes are generated via lineage-specific mechanisms. This review synthesizes existing case studies, phylogenetic analyses, and experimental evolutionary research on mechanistic parallelism in animal behavior. These examples show that the endocrine building blocks of behavior have some elements of parallelism across replicated evolutionary events. However, support for parallelism is variable among studies, at least some of which relates to the level of complexity at which we consider sameness (i.e. pathway vs. gene level). Moving forward, we need continued experimentation and better testing of neutral models to understand whether, how - and critically, why - mechanism A is used in one lineage and mechanism B is used in another. We also need continued growth of large-scale comparative analyses, especially those that can evaluate which endocrine parameters are more or less likely to undergo parallel evolution alongside specific behavioral traits. These efforts will ultimately deepen understanding of how and why hormone-mediated behaviors are constructed the way that they are.

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/.

Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia

BACKGROUND

The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).

RESULTS

The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance.

CONCLUSIONS

Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.

Identification of Functional Single Nucleotide Polymorphisms in the Porcine SLC6A4 Gene Associated with Aggressive Behavior in Weaned Pigs after Mixing

Variation in genes of the serotonergic system influence aggressive behavior by affecting serotonin levels in the central and cortical nervous system. SLC6A4 (serotonin transporter) is a master regulator of 5-HT signaling and involved in the regulation of aggressive behavior in humans and rodents. To identify potential functional single nucleotide polymorphisms (SNPs) for the porcine SLC6A4 gene associated with aggressive behavior, a total of 500 pigs (268 barrows and 232 gilts) were selected and mixed in 51 pens. Their behavior was recorded and observed for 72 h after mixing. Based on a composite aggressive score (CAS), the most aggressive and the least aggressive pigs within each pen were selected separately (a total of 204 pigs). Ear tissue was sampled to extract genomic DNA. Eight SNPs in the 5'-flanking region, coding region, and 3'-untranslated region (3'-UTR) of SLC6A4 were genotyped, of which 6 SNPs had significant differences (P < 0.05) in allele frequency between the most aggressive and least aggressive pigs. Luciferase activity was greater in plasmids of genotype GG than plasmids of genotype CC of rs345058216 (P < 0.01). Computational analysis nominated MAZ as putative transcription factor (TF) with higher probability to bind the SLC6A4 promoter at the SNP (rs345058216) site. Also, we demonstrated that MAZ overexpression modulates SLC6A4 promoter activity in allele-specific manner with an in vitro assay. In addition, we demonstrated that SLC6A4 was a direct target of miR-671-5p. The dual luciferase reporter gene assay and cell transfection were performed to examine the role of miR-671-5p in regulating SLC6A4 expression. The luciferase assays revealed that the SNP rs332335871 affects regulation of miR-671-5p in SLC6A4 expression. After overexpression of miR-671-5p in porcine primary neural cells, the SLC6A4 mRNA levels can be significantly reduced. In conclusion, we here found that miR-671-5p and MAZ mediated porcine SLC6A4 expression level, which provides the possible molecular mechanism of aggressive behavior.

Association between host genetics of sheep and the rumen microbial composition

A synergy between the rumen microbiota and the host genetics has created a symbiotic relationship, beneficial to the host's health. In this study, the association between the host genetics and rumen microbiome of Damara and Meatmaster sheep was investigated. The composition of rumen microbiota was estimated through the analysis of the V3-V4 region of the 16S rRNA gene, while the sheep blood DNA was genotyped with Illumina OvineSNP50 BeadChip and the genome-wide association (GWA) was analyzed. Sixty significant SNPs dispersed in 21 regions across the Ovis aries genome were found to be associated with the relative abundance of seven genera: Acinetobacter, Bacillus, Clostridium, Flavobacterium, Prevotella, Pseudomonas, and Streptobacillus. A total of eighty-four candidate genes were identified, and their functional annotations were mainly associated with immunity responses and function, metabolism, and signal transduction. Our results propose that those candidate genes identified in the study may be modulating the composition of rumen microbiota and further indicating the significance of comprehending the interactions between the host and rumen microbiota to gain better insight into the health of sheep.

Genetic approaches for increasing fitness in endangered species

The global rate of wildlife extinctions is accelerating, and the persistence of many species requires conservation breeding programs. A central paradigm of these programs is to preserve the genetic diversity of the founder populations. However, this may preserve original characteristics that make them vulnerable to extinction. We introduce targeted genetic intervention (TGI) as an alternative approach that promotes traits that enable species to persist in the face of threats by changing the incidence of alleles that impact on fitness. The TGI toolkit includes methods with established efficacy in model organisms and agriculture but are largely untried for conservation, such as synthetic biology and artificial selection. We explore TGI approaches as a species-restoration tool for intractable threats including infectious disease and climate change.

Can domestication shape Canidae brain morphology? The accessory olfactory bulb of the red fox as a case in point

BACKGROUND

The accessory olfactory bulb (AOB) is the first integrative center of the vomeronasal system (VNS), and the general macroscopic, microscopic, and neurochemical organizational patterns of the AOB differ fundamentally among species. Therefore, the low degree of differentiation observed for the dog AOB is surprising. As the artificial selection pressure exerted on domestic dogs has been suggested to play a key role in the involution of the dog VNS, a wild canid, such as the fox, represents a useful model for studying the hypothetical effects of domestication on the AOB morphology.

METHODS

A comprehensive histological, lectin-histochemical, and immunohistochemical study of the fox AOB was performed. Anti-Gαo and anti-Gαi2 antibodies were particularly useful, as they label the transduction cascade of the vomeronasal receptor types 1 (V1R) and 2 (V2R), respectively. Other employed antibodies included those against proteins such as microtubule-associated protein 2 (MAP-2), tubulin, glial fibrillary acidic protein, growth-associated protein 43 (GAP-43), olfactory marker protein (OMP), calbindin, and calretinin.

RESULTS

The cytoarchitecture of the fox AOB showed a clear lamination, with neatly differentiated layers; a highly developed glomerular layer, rich in periglomerular cells; and large inner cell and granular layers. The immunolabeling of Gαi2, OMP, and GAP-43 delineated the outer layers, whereas Gαo and MAP-2 immunolabeling defined the inner layers. MAP-2 characterized the somas of AOB principal cells and their dendritic trees. Anti-calbindin and anti-calretinin antibodies discriminated neural subpopulations in both the mitral-plexiform layer and the granular cell layer, and the lectin Ulex europeus agglutinin I (UEA-I) showed selectivity for the AOB and the vomeronasal nerves.

CONCLUSION

The fox AOB presents unique characteristics and a higher degree of morphological development compared with the dog AOB. The comparatively complex neural basis for semiochemical information processing in the fox compared with that observed in dogs suggests loss of AOB anatomical complexity during the evolutionary history of dogs and opens a new avenue of research for studying the effects of domestication on brain structures.

The association of C789A polymorphism in the dopamine beta-hydroxylase gene (DBH) and aggressive behaviour in dogs

The genetic basis of aggressive behaviour has been examined extensively, including analysis of genes encoding neurotransmitters, signalling molecules and regulatory enzymes, as well as their synthesis and degradation. Dopamine beta-hydroxylase, an enzyme catalysing the conversion of dopamine into norepinephrine in synaptic endings, significantly affects the modulation of emotional states and behaviour. The aim of this study was to determine the association of C789A polymorphism in the canine dopamine beta-hydroxylase gene (DBH) and aggressive behaviour in dogs. A total of 110 dogs of different breeds were analysed. All animals were classified according to their individual behavioural characteristics, defined by a veterinary interview and observation. Polymorphism was analysed using ACRS-PCR (amplification created restriction site-polymerase chain reaction) method. Significant differences in DBH genotypes and allele frequency between aggressive and non-aggressive dogs were observed (χ2 = 16,232, P = 0.0003). In aggressive dogs, the CC genotype (0.788) and C allele (0.815) were most frequent while in non-aggressive dogs, their frequencies were significantly lower (0.361 and 0.404, respectively). The obtained results indicate that DBH is a promising candidate gene for canine behavioural study.

Human-modified canids in human-modified landscapes: The evolutionary consequences of hybridization for grey wolves and free-ranging domestic dogs

Introgressive hybridization between domestic animals and their wild relatives is an indirect form of human-induced evolution, altering gene pools and phenotypic traits of wild and domestic populations. Although this process is well documented in many taxa, its evolutionary consequences are poorly understood. In this study, we assess introgression patterns in admixed populations of Eurasian wolves and free-ranging domestic dogs (FRDs), identifying chromosomal regions with significantly overrepresented hybrid ancestry and assessing whether genes located within these regions show signatures of selection. Although the dog admixture proportion in West Eurasian wolves (2.7%) was greater than the wolf admixture proportion in FRDs (0.75%), the number and average length of chromosomal blocks showing significant overrepresentation of hybrid ancestry were smaller in wolves than FRDs. In wolves, 6% of genes located within these blocks showed signatures of positive selection compared to 23% in FRDs. We found that introgression from wolves may provide a considerable adaptive advantage to FRDs, counterbalancing some of the negative effects of domestication, which can include reduced genetic diversity and excessive tameness. In wolves, introgression from FRDs is mostly driven by drift, with a small number of positively selected genes associated with brain function and behaviour. The predominance of drift may be the consequence of small effective size of wolf populations, which reduces efficiency of selection for weakly advantageous or against weakly disadvantageous introgressed variants. Small wolf population sizes result largely from human-induced habitat loss and hunting, thus linking introgression rates to anthropogenic processes. Our results imply that maintenance of large population sizes should be an important element of wolf management strategies aimed at reducing introgression rates of dog-derived variants.

Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness

Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.

Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Background

While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus).

Results

Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases.

Conclusions

The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07899-2.

Neuromorphological Changes following Selection for Tameness and Aggression in the Russian Farm-Fox experiment

The Russian farm-fox experiment is an unusually long-running and well-controlled study designed to replicate wolf-to-dog domestication. As such, it offers an unprecedented window onto the neural mechanisms governing the evolution of behavior. Here we report evolved changes to gray matter morphology resulting from selection for tameness versus aggressive responses toward humans in a sample of 30 male fox brains. Contrasting with standing ideas on the effects of domestication on brain size, tame foxes did not show reduced brain volume. Rather, gray matter volume in both the tame and aggressive strains was increased relative to conventional farm foxes bred without deliberate selection on behavior. Furthermore, tame- and aggressive-enlarged regions overlapped substantially, including portions of motor, somatosensory, and prefrontal cortex, amygdala, hippocampus, and cerebellum. We also observed differential morphologic covariation across distributed gray matter networks. In one prefrontal-cerebellum network, this covariation differentiated the three populations along the tame-aggressive behavioral axis. Surprisingly, a prefrontal-hypothalamic network differentiated the tame and aggressive foxes together from the conventional strain. These findings indicate that selection for opposite behaviors can influence brain morphology in a similar way.SIGNIFICANCE STATEMENT Domestication represents one of the largest and most rapid evolutionary shifts of life on earth. However, its neural correlates are largely unknown. Here we report the neuroanatomical consequences of selective breeding for tameness or aggression in the seminal Russian farm-fox experiment. Compared with a population of conventional farm-bred control foxes, tame foxes show neuroanatomical changes in the PFC and hypothalamus, paralleling wolf-to-dog shifts. Surprisingly, though, aggressive foxes also show similar changes. Moreover, both strains show increased gray matter volume relative to controls. These results indicate that similar brain adaptations can result from selection for opposite behavior, that existing ideas of brain changes in domestication may need revision, and that significant neuroanatomical change can evolve very quickly, within the span of <100 generations.

Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis

BACKGROUND AND AIM

Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times.

METHODS

In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans.

RESULTS

We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups.

CONCLUSION

We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.

Capturing the Effects of Domestication on Vocal Learning Complexity

Domesticated and vocal learning species can serve as informative model organisms for the reduction of reactive aggression and emergence of speech in our lineage. Amidst mounting evidence that domestication modifies vocal repertoires across different species, we focus on the domesticated Bengalese finch, which has a more complex song than the wild-type white-rumped munia. Our explanation for this effect revolves around the glutamate neurotransmitter system. Glutamate signaling (i) is implicated in birdsong learning, (ii) controls dopamine activity in neural circuits crucial for vocal learning, (iii) is disproportionately targeted in the evolution of domesticates, and (iv) regulates stress responses and aggressive behaviors attenuated under domestication. We propose that attenuated excitation of stress-related neural circuits potentiates vocal learning via altered dopaminergic signaling.

Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective

The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.

Association between temperament related traits and single nucleotide polymorphisms in the serotonin and oxytocin systems in Merino sheep

Animal temperament is defined as the consistent behavioral and physiological differences that are seen between individuals in response to the same stressor. Neurotransmitter systems, like serotonin and oxytocin in the central nervous system, underlie variation in behavioral traits in humans and other animals. Variations like single nucleotide polymorphisms (SNPs) in the genes for tryptophan 5-hydroxylase (TPH2), the serotonin transporter (SLC6A4), the serotonin receptor (HTR2A), and the oxytocin receptor (OXTR) are associated with behavioral phenotype in humans. Thus, the objective of this study was to identify SNPs in those genes and to test if those variations are associated with the temperament in Merino sheep. Using ewes from the University of Western Australia temperament flock, which has been selected on emotional reactivity for more than 20 generations, eight SNPs (rs107856757, rs107856818, rs107856856 and rs107857156 in TPH2, rs20917091 in SLC6A4, rs17196799 and rs17193181 in HTR2A, and rs17664565 in OXTR) were found to be distributed differently between calm and nervous sheep. These eight SNPs were then genotyped in 260 sheep from a flock that has never been selected on emotional reactivity, followed by the estimation of the behavioral traits of those 260 sheep using an arena test and an isolation box test. We found that several SNPs in TPH2 (rs107856757, rs107856818, rs107856856 and rs107857156) were in strong linkage disequilibrium, and all were associated with behavioral phenotype in the nonselected sheep. Similarly, rs17196799 in HTR2A was also associated with the behavioral phenotype.

Whole-genome resequencing reveals loci under selection during silkworm improvement

Breeding or genetic improvement refers to the process of artificial selection following domestication; as such, it has had a major influence on modern agriculture and animal production. Improvement generally focuses on traits that greatly affect the economic performance. Therefore, understanding the genetic basis underlying improvement will contribute to the identification of genes controlling economic traits and will facilitate future crop and animal breeding. However, genome-wide study of the molecular basis underlying improvement remains rare. The silkworm is a unique, entirely domesticated economically important invertebrate; genetic improvement has had a huge effect on the silkworm regarding silk-related traits. Herein, we performed whole-genomic sequencing on local and genetically improved silkworm lines to identify the genomic regions under strong selection in silkworm breeding/improvement. By genomic-wide selective sweeping analysis, we identified 24 genomic regions with strong selection signals, eight of which contained 13 candidate genes underlying silkworm breeding. Interestingly, six of these genes were annotated with functions related to neural signal response. Among the six genes, BGIBMGA004050 encodes silkworm CREB-regulated_transcription_coactivator_1 (BmCRTC1), which was reported to be involved in energy-sensing pathways. These results suggested that improvement may have affected the nervous system of the silkworm. This research will provide new insights into the genetic basis underlying the genetic improvement of silkworms and possibly of other species.

Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioral traits

Strong selection has resulted in substantial morphological and behavioral diversity across modern dog breeds, which makes dogs interesting model animals to study the underlying genetic architecture of these traits. However, results from between-breed analyses may confound selection signatures for behavior and morphological features that were coselected during breed development. In this study, we assess population genetic differences in a unique resource of dogs of the same breed but with systematic behavioral selection in only one population. We exploit these different breeding backgrounds to identify signatures of recent selection. Selection signatures within populations were found on chromosomes 4 and 19, with the strongest signals in behavior-related genes. Regions showing strong signals of divergent selection were located on chromosomes 1, 24, and 32, and include candidate genes for both physical features and behavior. Some of the selection signatures appear to be driven by loci associated with coat color (Chr 24; ASIP) and length (Chr 32; FGF5), while others showed evidence of association with behavior. Our findings suggest that signatures of selection within dog breeds have been driven by selection for morphology and behavior. Furthermore, we demonstrate that combining selection scans with association analyses is effective for dissecting the traits under selection.

Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions

Given their remarkable phenotypic diversity, dogs present a unique opportunity for investigating the genetic bases of cognitive and behavioral traits. Our previous work demonstrated that genetic relatedness among breeds accounts for a substantial portion of variation in dog cognition. Here, we investigated the genetic architecture of breed differences in cognition, seeking to identify genes that contribute to variation in cognitive phenotypes. To do so, we combined cognitive data from the citizen science project Dognition.com with published breed-average genetic polymorphism data, resulting in a dataset of 1654 individuals with cognitive phenotypes representing 49 breeds. We conducted a breed-average genome-wide association study to identify specific polymorphisms associated with breed differences in inhibitory control, communication, memory, and physical reasoning. We found five single nucleotide polymorphisms (SNPs) that reached genome-wide significance after Bonferroni correction, located in EML1, OR52E2, HS3ST5, a U6 spliceosomal RNA, and a long noncoding RNA. When we combined results across multiple SNPs within the same gene, we identified 188 genes implicated in breed differences in cognition. This gene set included more genes than expected by chance that were (1) differentially expressed in brain tissue and (2) involved in nervous system functions including peripheral nervous system development, Wnt signaling, presynapse assembly, and synaptic vesicle exocytosis. These results advance our understanding of the genetic underpinnings of complex cognitive phenotypes and identify specific genetic variants for further research.

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.

Fear and Foxes: An Educational Primer for Use with "Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes"

The way genes contribute to behavior is complicated. Although there are some single genes with large contributions, most behavioral differences are due to small effects from many interacting genes. This makes it hard to identify the genes that cause behavioral differences. Mutagenesis screens in model organisms, selective breeding experiments in animals, comparisons between related populations with different behaviors, and genome-wide association studies in humans are promising and complementary approaches to understanding the heritable aspects of complex behaviors. To connect genes to behaviors requires measuring behavioral differences, locating correlated genetic changes, determining when, where, and how these candidate genes act, and designing causative confirmatory experiments. This area of research has implications from basic discovery science to human mental health.

How human behavior can impact the evolution of genetically-mediated behavior in wild non-human species

Humans intensely modify the ecosystems we inhabit. Many of the impacts that this behavior can have on other species also sharing these spaces are obvious. A prime example is the devastating current extinction crisis. Yet some populations of non-human, non-domesticated species survive or even appear to thrive in heavily disturbed or human-built habitats. Theoretically, this apparent paradox could be facilitated partly by the evolution of genetically-mediated trait adaptations to the impacts of human behavior. At the least, persistence in strongly modified habitats would provide requisite selection pressures for this process to potentially occur in the future. In fact, we have a growing number of well-characterized examples of morphological trait adaptations to human behavior. However, our knowledge of genetically-mediated behavioral adaptations in similar contexts is less well developed. In this review I set up and discuss several evolutionary scenarios by which human behavior might have impacted the evolution of genetically mediated behavior in non-human, non-domestic species and highlight several approaches that could be used in future studies of this process.

Human Social Evolution: Self-Domestication or Self-Control?

The self-domestication hypothesis suggests that, like mammalian domesticates, humans have gone through a process of selection against aggression - a process that in the case of humans was self-induced. Here, we extend previous proposals and suggest that what underlies human social evolution is selection for socially mediated emotional control and plasticity. In the first part of the paper we highlight general features of human social evolution, which, we argue, is more similar to that of other social mammals than to that of mammalian domesticates and is therefore incompatible with the notion of human self-domestication. In the second part, we discuss the unique aspects of human evolution and propose that emotional control and social motivation in humans evolved during two major, partially overlapping stages. The first stage, which followed the emergence of mimetic communication, the beginnings of musical engagement, and mimesis-related cognition, required socially mediated emotional plasticity and was accompanied by new social emotions. The second stage followed the emergence of language, when individuals began to instruct the imagination of their interlocutors, and to rely even more extensively on emotional plasticity and culturally learned emotional control. This account further illustrates the significant differences between humans and domesticates, thus challenging the notion of human self-domestication.

Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions

The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothalamus is an essential part of the hypothalamic-pituitary-adrenal axis and regulates the fight-or-flight response, and thus, we hypothesized that selective breeding for tameness/aggressiveness has shaped the hypothalamic transcriptomic profile. RNA-seq analysis identified 70 differentially expressed genes (DEGs). Seven of these genes, DKKL1, FBLN7, NPL, PRIMPOL, PTGRN, SHCBP1L and SKIV2L, showed the same direction expression differences in the hypothalamus, basal forebrain and prefrontal cortex. The genes differentially expressed across the three tissues are involved in cell division, differentiation, adhesion and carbohydrate processing, suggesting an association of these processes with selective breeding. Additionally, 159 transcripts from the hypothalamus demonstrated differences in the abundance of alternative spliced forms between the tame and aggressive foxes. Weighted gene coexpression network analyses also suggested that gene modules in hypothalamus were significantly associated with tame vs aggressive behavior. Pathways associated with these modules include signal transduction, interleukin signaling, cytokine-cytokine receptor interaction and peptide ligand-binding receptors (eg, G-protein coupled receptor [GPCR] ligand binding). Current studies show the selection for tameness vs aggressiveness in foxes is associated with unique hypothalamic gene profiles partly shared with other brain regions and highlight DEGs involved in biological processes such as development, differentiation and immunological responses. The role of these processes in fox and dog domestication remains to be determined.

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.

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

Rapid behavioral assay using handling test provides breed and sex differences in tameness of chickens

BACKGROUND

Japanese indigenous chicken breeds are often used to improve meat quality rather than broilers in the Jidori industry. There are sometimes severe crowding accidents caused by many birds frightened by environmental stimuli. To prevent the economic loss, the chickens need to be more gentle, tame, and imperturbable.

METHODS

In this study, a new handling test for tameness in adult chickens in individual cages was performed with 100 birds from each sex of Shamo, Rhode Island Red, Nagoya, Australorp, and Ukokkei, as well as 10 hens of F1 hybrid between Shamo and Rhode Island Red, to measure both active and passive tameness. We counted the number heading toward human hands (heading) and retreating in other directions (avoiding) in both active and passive tameness phases, as well as the number of steps taken (step) during the handling test.

RESULTS

Male chickens exhibited higher avoidance behavior than females. Nagoya females displayed the lowest level of avoidance behavior, which implies passive tameness. In terms of active tameness, a variety of phenotypes can be obtained in different combinations of breed and sex. These results suggested the handling test will be good method for rapid screening of individual differences in tameness. In addition, there were heterosis effects on avoidance and locomotive behaviors. Since F1 is often used in the Jidori industry, the breeders should be tested not only for meat production but also for tameness.

CONCLUSIONS

In the future, combining both the behavioral screening and the population genomics will establish typical evidence about mechanisms of tameness and domestication in animals.

Artificial selection for male winners in the Siamese fighting fish Betta splendens correlates with high female aggression

In Southeast Asia, males of the Siamese fighting fish Betta splendens have been selected across centuries for paired-staged fights. During the selection process, matched for size males fight in a small tank until the contest is resolved. Breeders discard losing batches and reproduce winner batches with the aim of increasing fight performance. We assessed the results of this long-term selection process by comparing under standard laboratory conditions male and female aggressive behaviour of one strain selected for staged fights ("fighters") and one strain of wild-types. The aggressive response of adult fish was tested against their mirror image or a size-matched conspecific. Fighter males were more aggressive than wild-type males for all measured behaviours. Differences were not only quantitative but the pattern of fight display was also divergent. Fighter males had an overall higher swimming activity, performing frequent fast strikes in the direction of the intruder and displaying from a distance. Wild-type males were less active and exhibited aggressive displays mostly in close proximity to the stimuli. Females of the fighter strain, which are not used for fights, were also more aggressive than wild-type females. Aggressive behaviours were correlated across male and female fighter siblings, suggesting common genetic and physiological mechanisms to male and female aggression in this species. The study further shows that results were largely independent of the stimulus type, with the mirror test inducing similar and less variable responses than the live conspecific presentation. These results suggest that selection for male winners co-selected for high-frequency and metabolic demanding aggressive display in males and also enhanced female aggression, opening a wide range of testable hypothesis about the ultimate and proximate mechanisms of male and female aggression in B. splendens.

Identifying loci under positive selection in complex population histories

Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.