Abstract This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the “domestication syndrome” in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.

Citation: Theofanopoulou C, Gastaldon S, O’Rourke T, Samuels BD, Messner A, Martins PT, et al. (2017) Self-domestication in Homo sapiens: Insights from comparative genomics. PLoS ONE 12(10): e0185306. https://doi.org/10.1371/journal.pone.0185306 Editor: Michael Klymkowsky, University of Colorado Boulder, UNITED STATES Received: May 24, 2017; Accepted: September 11, 2017; Published: October 18, 2017 Copyright: © 2017 Theofanopoulou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: All relevant data are within the paper and its Supporting Information files. Funding: CB acknowledges the financial support from the Spanish Ministry of Economy and Competitiveness (grant FFI2016-78034-C2-1-P), a Marie Curie International Reintegration Grant from the European Union (PIRG-GA-2009-256413), research funds from the Fundació Bosch i Gimpera, and from the Generalitat de Catalunya (2014-SGR-200). CTh and TOR acknowledge support from the Generalitat de Catalunya in the form of doctoral (FI) fellowships. Competing interests: The authors have declared that no competing interests exist.

Introduction Recent advances in genomics, coupled with an ever-richer body of palaeoarchaeological, anatomical, and animal behavior literature, offer new opportunities to test long-standing hypotheses about human evolution. In the domain of human cognition, the retrieval of ancient DNA can, with the help of well-articulated linking hypotheses connecting genes, brain, and cognition, shed light on the emergence of ‘cognitive modernity’. It is to this end that we present data from (paleo-)genomics in support of an old hypothesis about the evolution of our species: that of self-domestication. As has been well documented elsewhere [1, 2], the idea that anatomically modern humans (AMH) are a domesticated species has long been entertained by preeminent scholars in biological and human sciences (in passing by Charles Darwin [3] and more seriously by Franz Boas [4]). We argue that such characterizations are accurate, not merely as analogies, but in identifying shared evolutionary trajectories, with accompanying convergent signatures of selection, in AMH and domesticated species. In order to explore whether our species is self-domesticated, we must first address what it means to be domesticated and whether AMH meet these criteria. We take the view, defended in more detail elsewhere [1, 5–7], that domesticated species are best categorized in terms of the phenotypic traits that they broadly share, rather than in terms of human mastery, design, or orchestration. There are inherent weaknesses in the human-mastery or conditions-based views of domestication that an account based on phenotypic traits does not face. The commonly shared traits of domesticates provide the strongest and most objective means by which these animals can be considered a single category. Furthermore, there is now evidence that many of the phenotypic traits of domesticates emerge independently of any human predispositions, intentional or otherwise [7, 8]. A broad consensus is now emerging that “commensal” and “mutualistic” processes can lead to domestication [6, 9–11], whereby both the domesticator and domesticated species seek out and benefit from cohabitation; thus, AMH were not the sole agents in all domestication events. Many of the species that have ultimately come to inhabit domestic niches are widely considered to have done so largely autonomously; in other words, to have self-domesticated. Changes in their social ecology (i.e., both their feeding niche and social organization), along with other parameters, have been recently suggested to confirm this hypothesis [12]. It has been proposed that dogs, cats, foxes [5, 7, 11, 13, 14], and even livestock species such as pigs, sheep, and cattle [6, 11, 15], may have undergone such processes. Domesticated species display a range of anatomical and behavioral phenotypes that set them apart from their wild counterparts: depigmentation; floppy, reduced ears; shorter muzzles; curly tails; smaller teeth; smaller cranial capacities (and concomitant brain size reduction); paedomorphosis; neotenous (juvenile) behavior; reduction of sexual dimorphism (feminization); docility; and more frequent estrous cycles. Of course, not all of these characteristics are found in all domesticates, but many of them are indeed present to some extent in each [16]. This constellation of features has been referred to as the “domestication syndrome” and has been hypothesized to arise from a mild deficit of neural crest cells [17]. A critical question for the present study is whether our species displays some or all of the phenotypes associated with the domestication syndrome, thus warranting comparison to determine signatures of selection shared with domesticates. Such signatures of domestication can be detected through comparisons of a domesticated species with “either their direct wild-living ancestor or close relatives if the ancestor is no longer extant” [2]. In the case of AMH, since there is no wild extant counterpart available, the obvious comparanda include our closest living relatives (i.e., the great apes) and extinct species of the genus Homo, to the extent that relevant data can be extracted from the fossil record. Many of the anatomical changes associated with domestication describe some of the well-known anatomical differences between AMH and Neanderthals (see Fig 1). The two species display different ontogenetic trajectories [18, 19] resulting in craniofacial differences that invariably lead to a more ‘gracile’, ‘juvenile’ profile in AMH relative to Neanderthals. It is well-established that prognathism is significantly reduced in our species [19, 20]. Brow ridges and nasal projections are smaller in AMH than in our most closely related (extinct) relatives [21], as are our teeth [22, 23] and our cranial capacity [24]. This profile is sometimes called ‘feminized’ [21], and is associated with an overall reduction of sexual dimorphism, which is also associated with domestication [25]. The process of ‘feminization’ (reduction of androgen levels and rise in estrogen levels [21]) is often associated with reduced reactivity of the hypothalamus-pituitary-adrenal axis [26], a physiological trait thought to be critical for domestication [17, 27]. Evidence from digit ratio comparisons—a measure of prenatal androgen exposure [28]—further suggests that Neanderthals had higher prenatal androgen exposure than AMH [29]. Additional differences in other traits associated with domestication may exist, but there are either obvious confounding factors involved (e.g., geography for pigmentation), or the data are more controversial (as in the case of reproductive cycle changes [30]). PPT PowerPoint slide

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larger image TIFF original image Download: Fig 1. Salient craniofacial differences between AMH and Neanderthals (top) and between dogs and wolves (bottom). https://doi.org/10.1371/journal.pone.0185306.g001 In light of these differences, we contend (contra [21]) that self-domestication coincided with the emergence of AMH (sensu [31]: specimens sharing a significant number of derived features in the skeleton with extant members of our species), since the critical phenotypic changes are already present in the first specimens, although this self-domestication process may have intensified as our species expanded geographically and demographically. Having laid out the case that AMH exhibit characteristics typical of the domestication syndrome, it remains to be clarified how our self-domestication event may have occurred. An obvious difference between AMH and other (self-)domesticated species is that the selective pressures leading to our domestication must have been intraspecific, although it has been suggested that the bonobo (Pan paniscus), a species that displays some of the traits of the domestication syndrome, has undergone a similar self-domestication process [25]. But even interspecific domestication events suggest that the selective pressures for our self-domestication need not have been qualitatively different from those experienced by other species. The recent domestication of the silver fox (Vulpes vulpes) demonstrates this: In the experimental breeding program started by Dmitry Belyaev [7, 8, 26, 32], foxes were intensively selected and bred over more than half a century based on only one criterion, tameness towards humans. Within twenty years of selection for this trait, a range of traits typical of the domestication syndrome had emerged [8]. Crucially, this suggests that selection for tameness is enough to bring about a constellation of domestic traits (see [33]), many of which humans share. The domesticated traits exhibited by AMH plausibly emerged following similar intraspecific selective pressures for prosocial behaviors: in other words, tameness towards fellow humans. Similarly, it has been claimed that reduced emotional reactivity and increased prosociality among humans were keys to our self-domestication [34]. So, what, if anything, differentiates prosociality from self-domestication? Certainly, reduced reactivity or increased prosocial behaviors seem to be necessary precursors of self-domestication, but these are not sufficient to describe the full-blown suite of traits associated with the domestication syndrome. Only consistent selection for such behaviors has been shown experimentally to bring about the far more extensive phenotype of domestication (i.e., in the silver fox experiment), although selection for tameness exclusively does not seem to be the only pressure at work in some cases of domestication (cf. the ‘socioecological’ factor that may have shaped dog domestication [12]). Intriguingly, there is evidence that domestication can enable the development of complex behaviors beyond those discussed so far for the domestication syndrome. For example, both dogs and domesticated foxes outperform all non-human primates in tests of cooperative communication [34]. The Bengalese finch, domesticated from its wild ancestor, the white-rumped munia [35, 36], has developed a complex song that is preferred by both female finches and munias over the stereotyped song of the male munia [37]. There are tempting parallels to be drawn here regarding the potential effects of self-domestication on the emergence of human language, relating to the emergence of a fully modern ‘language-ready’ brain [38–40], or the triggering of our capacity for complex iterative learning, necessary for the cultural transmission of language [2, 41]. The self-domestication hypothesis is, then, a strong contender to account for key aspects of modern human cognition. The central claim of the present paper is that (paleo-)genomic data can provide evidence to complement the anatomical and behavioral data outlined above, which suggest that AMH underwent a process of self-domestication. Crucially, we now have high-quality genomes for our closest extinct relatives, the Neanderthals and Denisovans, allowing for genomic comparison with AMH [42], as well as genomes of several domesticated species, which can be compared with their wild counterparts [43]. This information offers the opportunity to test for the existence of significant overlapping regions showing signatures of positive selection and putatively associated with (self-)domestication.

Discussion As already mentioned in the Introduction, several scholars have pointed out that there are several routes to domestication. We should therefore expect genes targeted by domestication processes to differ considerably across species. Nevertheless, reviewing the molecular events associated with domestication reveals common themes, with significant numbers of genes related to brain function and behavior, anatomy, and diet, across domesticates. This is consistent with the view that domestication may be best represented as a spectrum or continuum [120], with a polygenic basis and non-uniform symptomatology. This state of affairs is reflected in significant brain gene expression differences across domesticates, with the majority of these changes being species-specific [121]. Because of these findings, we find the overlaps listed in S1 and S2 Tables and the associated functions and pathways discussed in the Results section all the more relevant, especially because they converge to a large extent with what is to be expected from the neural crest-based hypothesis [17] put forth to capture the common mechanistic basis of domestication events. A disruption in neural crest developmental programs might be the source of changes spanning multiple organ systems and morphological structures [17], and the genes examined here seem to broadly support this view. It is quite possible that a neural crest-based explanation won’t apply to all domesticates [16], but it is interesting that this hypothesis finds its strongest support in species like dogs (see also [122]), which have been argued to be self-domesticated [34]. Recall that the goal of the present study was not to provide molecular evidence for a general theory of domestication, but rather to identify domestication-related pathways that could be suggestive of a self-domestication process in AMH. The fact that we find neural crest-related changes in AMH compared to Neanderthals/Denisovans, and that such changes are also found in another species hypothesized to have undergone a self-domestication process, reinforces our hypothesis that self-domestication took place in our species. Apart from neural crest-related genes and pathways, we identified common themes pertaining to neuronal development, synaptic plasticity, and enhanced learning. These categories are often mentioned in studies on selective sweeps in AMH (e.g., [46]). These results are in line with claims in other studies on domestication [49, 123–125], where categories like ‘neurological process’ frequently stand out strongly in gene ontology category enrichment analyses. This potentially lends credence to claims pairing domestication and a certain type of intelligence [126]. It is also not unreasonable to suspect that byproducts of the domestication process, such as enhanced sensory-motor perceptual and learning pathways, may provide a foundation for more complex communicative abilities, including vocal learning abilities [39, 127]. In a similar vein, among the genes under selection in both AMH and one or more domesticates, as well as in those under selection in multiple domesticates though not AMH, one finds multiple strong candidates for neurodevelopmental diseases and syndromes (see also [128]). This could be seen as an additional piece of evidence suggestive of a self-domestication process in AMH. A build-up of deleterious alleles is documented across domesticated species when compared to their wild counterparts. For instance, there is a higher frequency of non-synonymous substitutions in the nuclear DNA of domesticated dogs relative to gray wolves [129], and the same is true of their mitochondrial DNA [130]. A higher frequency of non-synonymous substitutions in domesticated yaks compared to the wild yaks has also been reported [131]. This build-up of deleterious alleles has been described as the ‘cost of domestication’ [132], which, if true, could be a byproduct of self-domestication in AMH, too. A study like the present one suffers from several limitations. While we have tried to make our comparisons as fair as possible, we have relied on genomic data that necessarily reflect the current state of the art for the various species we examined. The lists of genes associated with signals of positive selection are derived from the literature, and were generated using different analytical tools. While we have done our best to minimize the number of simplifying assumptions (see Methods), we must point out that even within a single species (e.g., AMH), no two studies completely agree on a definitive list. Indeed, in some cases, they produce lists of very different sizes. In addition, we may have missed important genes of interest due to the lack of information on them in the various databases we consulted. While it is to be hoped that some of these limitations will be overcome in the future, we think that the overlaps discussed in this study should encourage further detailed examination of these genes and the processes in which they take part. Last, but not least, it remains to be determined experimentally that the overlaps discovered here are indeed associated with mutations that led to similar functional effects across species. We could have been more strict about our notion of convergence, and restrict our attention to genes where the exact same difference (e.g., the same amino acid substitution) could be detected across species (for an early attempt along these lines, see [133]). But given that convergent evolution is often hypothesized to occur in the absence of this very strict notion of convergence—for instance, convergent evolution in the domain of vocal learning is related to non-identical changes in FOXP2 across vocal learners [134]—we feel justified in our approach.

Methods Data To identify signatures of a self-domestication process in AMH, we first constructed a list of genes associated with signs of positive selection in AMH compared to Neanderthals and Denisovans, which yielded a total of 742 genes. We then compared this list to the genes independently argued to be associated with positive selection in domesticated species versus their wild counterparts, which numbered 691 in total, and examined the overlap between these two gene lists. For AMH-Neanderthal/Denisovan comparisons, we made use of findings based on high-quality genome reconstructions, specifically: the list of genes in regions of putative selective sweeps, together with pathway and disease annotation, of Prüfer et al. [44]; the list of genes from the top 20 candidate regions for the modern human ancestral branch in the work of Racimo [48]; and the extended list of genomic regions predicted to underlie positively selected human specific traits by Peyrégne et al. [46]. We included in our study a range of domesticated species for which detailed genetic information is available. These species offer representative examples of the various routes to domestication [11], as well as different temporal windows for domestication. The species include: dog (Canis familiaris) [49, 50, 52], cat (Felis catus) [47], horse (Equus caballus) [45], and taurine cattle (Bos taurus) [51]. We homogenized the nomenclature across gene sets as best we could. We also examined other species, including the rabbit (Oryctolagus cuniculus) [125], and bonobo (Pan paniscus) [135]. In the end, the lists of genes under selection for these species (compared to their wild counterparts) were too small to draw any firm conclusions. To help us understand domestication-related changes better, we made use of the comparison of two lines of rats (Rattus norvegicus) selected for tame and aggressive behaviour to identify genetic loci that differ between the lines [136], the comparison of gene expression levels in the brains of domesticated and wild animals [121], genomic signatures of domestication in neurogenetic genes in Drosophila melanogaster (in which neurogenetic genes have been claimed to be associated with signs of positive selection [123]), and the genetic divergence between foxes (Vulpes vulpes) that were selected for tame and aggressive behavior [67]. For the Great Ape comparison—chimpanzee (Pan t. troglodytes), orangutan (Pongo abelii), and gorilla (G. g. gorilla)—we made use of positive and balancing selection and selective sweep data from Cagan et al. [137] (Tables S6, S18(68), S19(69), S20(70), S24(74), and S97). For AMH comparisons with the Eurasian wolf (Canis lupus lupus) we used data from Stronen et al. [54] (Tables 2, S3, and S5: genes under selection associated with environmental and geographic variables or with no obvious spatial patterns) and Pilot et al. [53] (Table S4: genes adjacent to loci putatively under selection in European wolves). For the wisent (Bison bonasus) we used data from Gautier et al. [55] (Table S3: genes under positive selection between the wisent and bovine lineages) and Wang et al. [56] (Table S14: genes under positive selection in the wisent). Methods In order to test the significance of the overlap between domestication-related genes and genes showing signals of positive selection and selective sweep in AMH, a hypergeometric intersection test was performed using the R software [138] and the R package hint [139]. A hypergeometric intersection distribution can be employed to compute the probability of picking an intersection of size v when drawing independently and without replacement from two sets A and B composed of objects of n categories, with a and b number of draws, respectively (where a ≠ b) [139]. As a model of our data we chose as a simplifying assumption n = 19,500 as the average number of protein-coding genes for all the species taken into consideration. From the original lists, we removed antisense RNA genes (non coding), miRNAs, and other non-coding transcripts/products listed in the original tables. From this modeled genome, a total of a = 691 genes were drawn from the domesticate pool (comprising cat, dog, cattle, and horse), while b = 742 genes were drawn from the total AMH pool. The resulting intersection size (i.e., the number of genes associated with positive selection signals both in AMH and in one or more domesticate) was v = 41. The hint.test function was then employed to test the significance of this intersection, obtaining p < 0.01. A Monte Carlo simulation was performed using Matlab (MathWorks, Natick, MA) to confirm these results. Two random samples, of lengths 691 and 742 (with no replacement), were drawn from a pool representing 19,500 genes using Matlab’s random number generation function. These simulated draws were performed 1,000,000 times and the percentage of trials in which the intersection was ≥41 was calculated. The results revealed that 0.33% of trials had intersections of this size. Since we pooled data for positive selection and selective sweep in AMH from different sources, hypergeometric intersection tests were carried out between the domestication pool and the pool of each AMH dataset used in this study. A significant intersection was found with the data in [44] (a = 691, b = 108, v = 9; p < 0.05) and with the combined data from [44] and [48] (a = 691, b = 419, v = 24, p < 0.05). Overlaps with domesticates were tested for Great Apes, using data from Cagan et al. [137]. For chimpanzee (Pan t. troglodytes), b = 415 with v = 16; for orangutan (Pongo abelii), b = 500 with v = 20; for gorilla (G. g. gorilla), b = 426 with v = 12. The hypergeometric intersection tests yielded non-significant results for all these intersections. Monte Carlo simulations, performed as described above, mutatis mutandis, showed that intersections of these sizes occurred in a large fraction of trials (40.11% of trials for chimpanzee; 32% for orangutan; 82.89% for gorilla). As in the case of AMH, overlaps with individual domesticates were tested, with no significant results. We tested overlaps with the Eurasian wolf (Canis lupus lupus) using data from Stronen et al. [54] (Table 2: b = 32 with v = 3, S3: b = 70 with v = 0, S5: b = 33 with v = 1) and [140] (b = 32 with v = 1). For the wisent (Bison bonasus) we tested overlaps using data from Gautier et al. [55] (b = 425 with v = 11) and Wang et al. [56] (b = 72 with v = 3). None of the overlaps between these non-domesticated species and AMH were significant. For synteny analysis, we used the genomic data available for each species in the NCBI (https://www.ncbi.nlm.nih.gov/) and Ensemble (http://www.ensembl.org/index.html) databases. In S1 Table, for each of the 41 overlapping genes we included the 4 protein-coding genes flanking the region of interest. We added more flanking protein-coding genes only in the instances where some event (e.g., gene insertion or local duplication) rendered the synteny less clear. We also used NCBI Gene Search and BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to confirm that some of the genes surrounding the genes of interest were the same genes across taxa, with different names in some species’ assemblies. We then examined the functions of the genes in S1, S2 and S3 Tables, paying close attention to the pathways in which they are involved, and to their interactions with other genes already highlighted in the domestication literature. In addition to performing an exhaustive PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search on each of the genes, we drew upon the information available in Genecards (http://genecards.org), Uniprot (http://www.uniprot.org/), String 10.0 (http://string-db.org), and Biogrid 3.4 (http://thebiogrid.org) to identify potential protein-protein interactions and Gene Ontology category enrichment signals. Additionally, we fed the gene lists in S1 and S2 Tables into Ingenuity Pathway Analysis software (QIAGEN, Redwood City, CA) and used the Core Analysis tools to study the associated gene networks and functions. The two major networks generated by these analyses, in which the centrality of the ERK pathway is visible, are provided S1 Fig. Furthermore, we gathered information about the expression patterns of these genes, concentrating on those genes with relatively high expression in tissues such as brain, bone, and adrenal glands. For this, we relied on the following resources: Brainspan (http://www.brainspan.org), Human Brain Transcriptome (http://hbatlas.org), Bgee (http://bgee.org), Proteomics DB (https://proteomicsdb.org), Human Protein Atlas (http://www.proteinatlas.org), Gene Enrichment Profiler (http://xavierlab2.mgh.harvard.edu/EnrichmentProfiler/index.html), and GTex (http://www.gtexportal.org). For the information presented in the Supplementary Material, we consulted the following databases: KEGG Pathways and Disease (http://www.kegg.jp/kegg/), PANTHER (http://www.pantherdb.org), Reactome Pathway Database (http://www.reactome.org), OMIM (http://omim.org), and MalaCards (http://www.malacards.org/).

Acknowledgments We acknowledge the help of Nina Riddell in generating graph (c) in Fig 2. The Homo skull drawings in Fig 1 were done by Francisco Peña, who granted us permission to use them here. The wolf and dog skulls in Fig 1 were adapted from DigiMorph.org, with kind permission from Dr. Timothy Rowe. We thank Kay Sušelj for assistance with the Monte Carlo simulations.