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

Whole-Genome Sequencing-Based Population Genetic Analysis of Wild and Domestic Rabbit Breeds

The European rabbit exists in the wild and has several highly bred domesticated forms. There are well-separated wild European rabbit populations, and intensive breeding has resulted in various forms and utilizations. In this work, we aimed to carry out an extended WGS-based population genomics study on several wild European rabbit populations and selected breeds. Utilizing multiple methods, we showed that although domestic and wild populations were clearly separated, there was evidence of admixture between them in France and Hungary. The populations showed various levels of inbreeding, with one of the Hungarian subpopulations having excess runs of homozygosity. We identified numerous variants fixed in either domestic or wild animals, two of which were found to be fixed at different alleles in the two populations. Some putatively selected regions did not overlap with any known genes in the rabbit genome, suggesting some importance to these intergenic sites. The enrichment of selected regions in certain types of transcription factor binding sites suggests a possible role for these regulatory elements during domestication. In addition, the new high-coverage rabbit whole-genome sequences may provide helpful material for further population genetics analyses.

Gene expression comparisons between captive and wild shrew brains reveal captivity effects

Compared with their free-ranging counterparts, wild animals in captivity experience different conditions with lasting physiological and behavioural effects. Although shifts in gene expression are expected to occur upstream of these phenotypes, we found no previous gene expression comparisons of captive versus free-ranging mammals. We assessed gene expression profiles of three brain regions (cortex, olfactory bulb and hippocampus) of wild shrews (Sorex araneus) compared with shrews kept in captivity for two months and undertook sample dropout to examine robustness given limited sample sizes. Consistent with captivity effects, we found hundreds of differentially expressed genes in all three brain regions, 104 overlapping across all three, that enriched pathways associated with neurodegenerative disease, oxidative phosphorylation and genes encoding ribosomal proteins. In the shrew, transcriptomic changes detected under captivity resemble responses in several human pathologies, including major depressive disorder and neurodegeneration. While interpretations of individual genes are tempered by small sample sizes, we propose captivity influences brain gene expression and function and can confound analyses of natural processes in wild individuals under captive conditions.

The evolution of human music in light of increased prosocial behavior: a new model

Together with language, music is perhaps our most distinctive behavioral trait. Following the lead of evolutionary linguistic research, different hypotheses have been proposed to explain why only humans perform music and how this ability might have evolved in the species. In this paper, we advance a new model of music evolution that builds on the theory of self-domestication, according to which the human phenotype is, at least in part, the outcome of a process similar to mammal domestication, triggered by a progressive reduction in reactive aggression levels in response to environmental changes. In the paper, we specifically argue that changes in aggression management through the course of human cultural evolution can account for the behaviors conducive to the emergence and evolution of music. We hypothesize 4 stages in the evolutionary development of music under the influence of environmental changes and evolution of social organization: starting from musilanguage, 1) proto-music gave rise to 2) personal and private forms of timbre-oriented music, then to 3) small-group ensembles of pitch-oriented music, at first of indefinite and then definite pitch, and finally to 4) collective (tonal) music. These stages parallel what has been hypothesized for languages and encompass the diversity of music types and genres described worldwide. Overall, music complexity emerges in a gradual fashion under the effects of enhanced abilities for cultural niche construction, resulting from the stable trend of reduction in reactive aggression towards the end of the Pleistocene, leading to the rise of hospitality codes, and succeeded by the increase in proactive aggression from the beginning of the Holocene onward. This paper addresses numerous controversies in the literature on the evolution of music by providing a clear structural definition of music, identifying its structural features that distinguish it from oral language, and summarizing the typology of operational functions of music and formats of its transmission. The proposed framework of structural approach to music arms a researcher with means to identify and comparatively analyze different schemes of tonal organization of music, placing them in the context of human social and cultural evolution. Especially valuable is the theory of so-called "personal song", described and analyzed here from ethological, social, cultural, cognitive, and musicological perspectives. Personal song seems to constitute a remnant of the proto-musical transition from animal communication to human music as we know it today. We interlink the emergence of personal song with the evolution of kinship, placing both of them on the timeline of cultural evolution - based on totality of ethnographic, archaeological, anthropological, genetic, and paleoclimatic data.

Candidate SNP Markers Significantly Altering the Affinity of the TATA-Binding Protein for the Promoters of Human Genes Associated with Primary Open-Angle Glaucoma

Primary open-angle glaucoma (POAG) is the most common form of glaucoma. This condition leads to optic nerve degeneration and eventually to blindness. Tobacco smoking, alcohol consumption, fast-food diets, obesity, heavy weight lifting, high-intensity physical exercises, and many other bad habits are lifestyle-related risk factors for POAG. By contrast, moderate-intensity aerobic exercise and the Mediterranean diet can alleviate POAG. In this work, we for the first time estimated the phylostratigraphic age indices (PAIs) of all 153 POAG-related human genes in the NCBI Gene Database. This allowed us to separate them into two groups: POAG-related genes that appeared before and after the phylum Chordata, that is, ophthalmologically speaking, before and after the camera-type eye evolved. Next, in the POAG-related genes' promoters, we in silico predicted all 3835 candidate SNP markers that significantly change the TATA-binding protein (TBP) affinity for these promoters and, through this molecular mechanism, the expression levels of these genes. Finally, we verified our results against five independent web services-PANTHER, DAVID, STRING, MetaScape, and GeneMANIA-as well as the ClinVar database. It was concluded that POAG is likely to be a symptom of the human self-domestication syndrome, a downside of being civilized.

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.

Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection

Atherosclerosis is a systemic disease in which focal lesions in arteries promote the build-up of lipoproteins and cholesterol they are transporting. The development of atheroma (atherogenesis) narrows blood vessels, reduces the blood supply and leads to cardiovascular diseases. According to the World Health Organization (WHO), cardiovascular diseases are the leading cause of death, which has been especially boosted since the COVID-19 pandemic. There is a variety of contributors to atherosclerosis, including lifestyle factors and genetic predisposition. Antioxidant diets and recreational exercises act as atheroprotectors and can retard atherogenesis. The search for molecular markers of atherogenesis and atheroprotection for predictive, preventive and personalized medicine appears to be the most promising direction for the study of atherosclerosis. In this work, we have analyzed 1068 human genes associated with atherogenesis, atherosclerosis and atheroprotection. The hub genes regulating these processes have been found to be the most ancient. In silico analysis of all 5112 SNPs in their promoters has revealed 330 candidate SNP markers, which statistically significantly change the affinity of the TATA-binding protein (TBP) for these promoters. These molecular markers have made us confident that natural selection acts against underexpression of the hub genes for atherogenesis, atherosclerosis and atheroprotection. At the same time, upregulation of the one for atheroprotection promotes human health.

The human fear paradox turns out to be less paradoxical when global changes in human aggression and language evolution are considered

Our commentary focuses on the interaction between Grossmann's fearful ape hypothesis (FAH) and the human self-domestication hypothesis (HSDH), also taking into account language acquisition and evolution. Although there is considerable overlap between the two hypotheses, there are also some discrepancies, and our goal is to consider the extent to which HSDH can explain the phenomena identified by FAH without invoking fearfulness as directly adaptive.

Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases

Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log₂ values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log₂ values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.

Social status mediated variation in hypothalamic transcriptional profiles of male mice

Animals of different social status exhibit variation in aggression, territorial and reproductive behavior as well as activity patterns, feeding, drinking and status signaling. This behavioral and physiological plasticity is coordinated by underlying changes in brain gene transcription. Using Tag-based RNA sequencing (Tag-seq), we explore RNA transcriptomes from the medial preoptic area (mPOA) and ventral hypothalamus (vHYP) of male mice of different social ranks in a dominance hierarchy and detect candidate genes and cellular pathways that underlie status-related plasticity. Within the mPOA, oxytocin (Oxt) and vasopressin (Avp) are more highly expressed in subdominant mice compared to other ranks, while nitric oxide synthase (Nos1) has lower expression in subdominant mice. Within the vHYP, we find that both orexigenic and anorexigenic genes involved in feeding behavior, including agouti-related peptide (Agrp), neuropeptide-Y (Npy), galanin (Gal), proopiomelanocortin (Pomc), and Cocaine- and Amphetamine-Regulated Transcript Protein prepropeptide (Cartpt), are less expressed in dominant animals compared to more subordinate ranks. We suggest that this may represent a reshaping of feeding circuits in dominant compared to subdominant and subordinate animals. Furthermore, we determine several genes that are positively and negatively associated with the level of despotism (aggression) in dominant males. Ultimately, we identify hypothalamic genes controlling feeding and social behaviors that are differentially transcribed across animals of varying social status. These changes in brain transcriptomics likely support phenotypic variation that enable animals to adapt to their current social status.

Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients

Although half of hypertensive patients have hypertensive parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% of hypertension heredity. Therefore, mainstream transcriptome profiling of hypertensive subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating patients according to their symptoms, individual lifestyle, and genetic background. Within this mainstream paradigm, here, we determined whether, among the known hypertension-related DEGs that we could find, there is any genome-wide hypertension theranostic molecular marker applicable to everyone, everywhere, anytime. Therefore, we sequenced the hippocampal transcriptome of tame and aggressive rats, corresponding to low and high stress reactivity, an increase of which raises hypertensive risk; we identified stress-reactivity-related rat DEGs and compared them with their known homologous hypertension-related animal DEGs. This yielded significant correlations between stress reactivity-related and hypertension-related fold changes (log2 values) of these DEG homologs. We found principal components, PC1 and PC2, corresponding to a half-difference and half-sum of these log2 values. Using the DEGs of hypertensive versus normotensive patients (as the control), we verified the correlations and principal components. This analysis highlighted downregulation of β-protocadherins and hemoglobin as whole-genome hypertension theranostic molecular markers associated with a wide vascular inner diameter and low blood viscosity, respectively.

A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential

One of the greatest achievements of genetics in the 20th century is D.K. Belyaev’s discovery of destabilizing selection during the domestication of animals and that this selection affects only gene expression regulation (not gene structure) and inf luences systems of neuroendocrine control of ontogenesis in a stressful environment. Among the experimental data generalized by Belyaev’s discovery, there are also f indings about accelerated extinc tion of testes’ hormonal function and disrupted seasonality of reproduction of domesticated foxes in comparison with their wild congeners. To date, Belyaev’s discovery has already been repeatedly conf irmed, for example, by independent observations during deer domestication, during the use of rats as laboratory animals, after the reintroduction of endangered species such as Przewalski’s horse, and during the creation of a Siberian reserve population of the Siberian grouse when it had reached an endangered status in natural habitats. A genome-wide comparison among humans, several domestic animals, and some of their wild congeners has given rise to the concept of self-domestication syndrome, which includes autism spectrum disorders. In our previous study, we created a bioinformatic model of human self-domestication syndrome using differentially expressed genes (DEGs; of domestic animals versus their wild congeners) orthologous to the human genes (mainly, nervous-system genes) whose changes in expression affect reproductive potential, i. e., growth of the number of humans in the absence of restrictions caused by limiting factors. Here, we applied this model to 68 human genes whose changes in expression alter the reproductive health of women and men and to 3080 DEGs of domestic versus wild animals. As a result, in domestic animals, we identif ied 16 and 4 DEGs, the expression changes of which are codirected with changes in the expression of the human orthologous genes decreasing and increasing human reproductive potential, respectively. The wild animals had 9 and 11 such DEGs, respectively. This difference between domestic and wild animals was signif icant according to Pearson’s χ2 test (p < 0.05) and Fisher’s exact test (p < 0.05). We discuss the results from the standpoint of restoration of endangered animal species whose natural habitats are subject to an anthropogenic impact.

Unraveling patterns of disrupted gene expression across a complex tissue

Whole tissue RNASeq is the standard approach for studying gene expression divergence in evolutionary biology and provides a snapshot of the comprehensive transcriptome for a given tissue. However, whole tissues consist of diverse cell types differing in expression profiles, and the cellular composition of these tissues can evolve across species. Here, we investigate the effects of different cellular composition on whole tissue expression profiles. We compared gene expression from whole testes and enriched spermatogenesis populations in two species of house mice, Mus musculus musculus and M. m. domesticus, and their sterile and fertile F1 hybrids, which differ in both cellular composition and regulatory dynamics. We found that cellular composition differences skewed expression profiles and differential gene expression in whole testes samples. Importantly, both approaches were able to detect large-scale patterns such as disrupted X chromosome expression, although whole testes sampling resulted in decreased power to detect differentially expressed genes. We encourage researchers to account for histology in RNASeq and consider methods that reduce sample complexity whenever feasible. Ultimately, we show that differences in cellular composition between tissues can modify expression profiles, potentially altering inferred gene ontological processes, insights into gene network evolution, and processes governing gene expression evolution.

Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes

The silver fox and blue fox are economically important fur species and were domesticated by humans from their wild counterparts, the arctic fox and red fox, respectively. Farmed foxes show obvious differences from their wild counterparts, including differences in physiology, body size, energy metabolism, and immunity. However, the molecular mechanisms underlying these differences are presently unclear. In this study, we built transcriptome libraries from multiple pooled tissues for each species of farmed fox, used RNA-seq to obtain a comprehensive dataset, and performed selection analysis and sequence-level analyses of orthologous genes to identify the genes that may be influenced by human domestication. More than 153.3, 248.0, 81.6, and 65.8 million clean reads were obtained and assembled into a total of 118,577, 401,520, 79,900, and 186,988 unigenes with an average length range from 521 to 667 bp for AF, BF, RF, and SF, respectively. Selective pressure analysis showed that 11 and 14 positively selected genes were identified, respectively, in the two groups (AF vs. BF and RF vs. SF). Several of these genes were associated with natural immunity (CFI and LRRFIP1), protein synthesis (GOLGA4, CEP19 and SLC35A2), and DNA damage repair (MDC1). Further functional enrichment analyses demonstrated that two positively selected genes (ACO1 and ACAD10) were involved in metabolic process (GO:0008152, p-value = .032), representing a significant enrichment. Sequence analysis of 117 orthologous genes shared by the two groups showed that the LEMD2, RRBP1, and IGBP1 genes might be affected by artificial selection in farmed foxes, with mutation sites located within sequences that are otherwise highly conserved across most mammals. Our results provide a valuable transcriptomic resource for future genetic studies and improvement in the assisted breeding of foxes and other farmed animals.

Evolutionary linguistics can help refine (and test) hypotheses about how music might have evolved

Both the music and social bonding (MSB) hypothesis and the music as a credible signal hypothesis emerge as solid views of how human music and human musicality might have evolved. Nonetheless, both views could be improved (and tested in better ways) with the consideration of the way in which human language(s) might have evolved under the effects of our self-domestication.

Did Dog Domestication Contribute to Language Evolution?

Different factors seemingly account for the emergence of present-day languages in our species. Human self-domestication has been recently invoked as one important force favoring language complexity mostly via a cultural mechanism. Because our self-domestication ultimately resulted from selection for less aggressive behavior and increased prosocial behavior, any evolutionary or cultural change impacting on aggression levels is expected to have fostered this process. Here, we hypothesize about a parallel domestication of humans and dogs, and more specifically, about a positive effect of our interaction with dogs on human self-domestication, and ultimately, on aspects of language evolution, through the mechanisms involved in the control of aggression. We review evidence of diverse sort (ethological mostly, but also archeological, genetic, and physiological) supporting such an effect and propose some ways of testing our hypothesis.

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Belyaev's concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).

Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing

BACKGROUND

Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation.

METHODS

In this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks.

RESULTS

Using fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions.

CONCLUSIONS

A wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.