Fig 1 - uploaded by Andrew Rubio
Content may be subject to copyright.
An evolutionary tree representing the 15 domesticated mammals (indicated with gray terminal branches) and their closely related wild relatives (indicated with black terminal branches) that were studied. The tree is based on multiple genes, as described in Upham et al. 2019. The tree was obtained as a "phylogeny subset" from the VertLife website (https://vertlife.org/data/). See text and S2 Table for species names. All mammal silhouettes were taken from http://phylopic.org and are under a public domain license. The pertinent information concerning each silhouette is available as a S1 File). https://doi.org/10.1371/journal.pone.0263830.g001
Source publication
Neural crest cell genes control the migration of neural crest cells to multiple parts of developing vertebrate embryos. A recent hypothesis posits that the “domestication syndrome” characteristic of domesticated animals is driven by selection for tameness acting on neural crest cell genes, particularly those affecting cell migration. This is posite...
Contexts in source publication
Context 1
... pairs of taxa (each domesticate and a closely related wild species) formed the basis for our comparative analysis, in a phylogenetic context. Fig 1 shows the phylogenetic tree of relationships of the taxa included in this study, which is based on Upham et al. [13]. ...
Context 2
... analyze patterns of selection, we took a comparative approach. First, we obtained a phylogenetic tree (Fig 1) for the 30 species of mammals investigated with a topology based on up-todate (maximum likelihood and Bayesian) methods of DNA sequence data analysis [13], using the interactive phylogeny subsets function for the mammalian phylogenetic tree available on the VertLife website (vertlife.org/data: [13]). ...
Similar publications
Background
Persistent high-risk Human papillomavirus (HPV) subtypes infection has been implicated as a causative of cervical cancer. Distribution and genotypes of HPV infection among females and their variations would assist in the formulation of preventive strategy for cervical cancer. The purpose of the present study is to investigate the prevale...
Citations
... This work was started by D.K. Belyaev back in 1958 on farm foxes [1]; later, it was continued on minks and gray rats and is unique in duration, scale, and complexity. It has been shown that alterations of behavior from the "wild" to "tame" type follow general patterns and are on the spectrum of manifestations of so-called domestication syndrome [2][3][4]. ...
... The distribution of brain region samples from tame and aggressive rats by levels of DEGs' expression (112 genes in total) in these samples with the first (PC1) and second (PC2) principal components as coordinates. The right-hand cluster of the graph combines brain samples from three aggressive rats (samples numbered [1][2][3][4][5][6][7][8][9][10][11][12], and the left-hand cluster contains brain samples from three tame rats (samples numbered 13-24). ...
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.
... Cluster 1 (blue): includes genes associated with melanogenesis (anxa2, ap1s1, rab32), iridophore development (fhl1), and carotenoid metabolism (adh1b, aldh2). Cluster 2 (green): includes genes associated with melanogenesis (ctbp2, dct, irf4, lef1, rab38, tyrp1), iridophore development (prps1), keratin metabolism (ovol1), pteridine synthesis (xdh) and carotenoid metabolism (rdh16) Rubio and Summers 2022). Although the field has made considerable progress in identifying key candidate genes associated with the production of aposematic coloration in poison frogs (Posso-Terranova and Andrés 2017; Stuckert et al. 2019Stuckert et al. , 2021Rodríguez et al. 2020;Twomey et al. 2020a, b), very little is known about whether these color related genes are under positive selection, with the exception of two studies (Rodríguez et al. 2020;Linderoth et al. 2023). ...
Aposematic organisms rely on their bright conspicuous coloration to communicate to potential predators that they are toxic and unpalatable. These aposematic phenotypes are strongly tied to survival and therefore make excellent opportunities to investigate the genetic underpinning of coloration. The genus Ranitomeya includes phenotypically diverse members of Neotropical aposematic poison frogs native to South America. Significant progress has been made in elucidating the molecular mechanisms responsible for aposematic coloration in poison frogs, which have paved the way for future studies to test hypotheses of the evolution of coloration across aposematic vertebrates. However, very little is known about whether these color related genes are under positive selection. We assembled transcriptomes from publicly available data reads sets for 9 different color morphs of poison frogs in the Ranitomeya genus that display bright conspicuous coloration (four morphs of R. imitator, two morphs of R. variabilis, two morphs of R. fantastica, one morph of R. summersi) to identify protein-coding genes responsible for color production that are under positive selection. Our results show that there are multiple genes under strong positive selection that are predicted to play roles in melanin synthesis (dct, tyrp1, irf4), iridophore development (fhl1), keratin metabolism (ovol1), pteridine synthesis (prps1, xdh), and carotenoid metabolism (adh1b, aldh2). The identification of positive selection affecting candidate color-pattern genes is consistent with the possibility that these genes mediate (in part) the molecular evolution of coloration. This may be attributed to aposematic phenotypes being directly tied to survival and reproduction in poison frogs.
... Wilkins et al. [44] listed several candidate NCC-related genes that could be involved in the DS syndrome. In a recent study, a comparative analysis of selection was carried out for most of these candidate genes [50]. The results highlighted signals of positive selection on these key genes in domesticated compared to wild species, which is consistent with the hypothesis of an important role for co-selection of genes in the DS. ...
The domestication of animals started around 12,000 years ago in the Near East region. This “endless process” is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today’s domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.
... The study included the "bonobo, the sister species of the chimpanzee, which is thought to be self-domesticated." [58] Modern humans are closely related to chimpanzees and like the bonobo exhibit a number of domesticated traits, including reduced brains during the last 50,000 years; changes in dentition; reduction of aggressiveness; and retention of juvenile characteristics; and most of these features are generally attenuated in autism spectrum disorder (ASD). According to Antonio Benítez-Burraco, Wanda Lattanzi, and Elliot Murphy, and as their figure below illustrates: shown. ...
... It has been described as the first work of science fiction and in its central episode featuring the animation of a giant man-made humanoid Creature arouses paranoid reactions to science and technology which have since become commonplace: notably in relation to eugenics, robotics, and "designer babies"-not to mention "Frankenfood". 58 Frankenstein is an iconic work of Gothic literature, which Mary Shelley was also reading at the time. If, as critics have claimed, "an anxiety with no possibility of escape is the main theme of the Gothic tales," then they self-evidently belong on the psychotic, paranoid side of the mentalistic spectrum. ...
... Evolutionary tree representing 15 domesticated mammals (gray terminal branches) and their closely related wild relatives (black terminal branches).[58] ...
This pre-print is a sequel to my The Diametric Mind. See the Preface for details.
... Wilkins et al. (2014) [8] have shown that the selection for tameness acts specifically on genes, which influence the formation, differentiation and migration patterns of neural crest cells. This NCC hypothesis has been confirmed in the genetic study by Rubio and Summers (2022) [56] on differences in NCC genes between 15 domesticated mammalian species, including the dromedary and their wild relatives. ...
Being in an advanced stage of domestication is a newly proposed requirement to decide which animals can be safely kept by humans. Dutch legislators were the first to apply it and other European countries may be tempted to adopt a similar approach. Unexpectedly, the Dutch assessors considered the dromedary (Camelus dromedarius) as being insufficiently domesticated and this species will therefore no longer be able to be kept as a production animal from 2024 onwards. In a recent publication on this topic, we showed that the domestication of the dromedary is actually very advanced. In this paper, we apply the same criteria that were used by the Dutch assessors to determine the degree of domestication, taking into account the most recent scientific developments in this area, even though it should be noted that these criteria have neither been peer-reviewed, nor published in an international scientific journal. For the sake of comparison, and in order to validate the procedure, we also applied these criteria to the house cat. The results confirm that the dromedary is highly domesticated, but also that the house cat (Felis silvestris catus) is at most semi-domesticated. Obviously, we agree with the decision of the Dutch legislators to place the house cat on the positive list, but our analysis demonstrates that this was decided on false grounds. Our analysis makes it clear that the requirement of being in an advanced stage of domestication is not suitable. Instead of maintaining this requirement, we recommend implementing evidence-based, peer-reviewed methods to decide which animals can be kept by humans, and to include species specific-guidelines in the legislation on how this can be achieved safely.
... Hence, via altering the migration of neural crest cells and their differentiation in organs mediating stress responses, morphological changes in other neural crest-derived structures may follow as a byproduct of selection for tameness. Although there is compelling genetic evidence for pronounced alterations of the neural crest being correlated with domestication across mammalian lineages [26], no consensus has been reached on exactly which traits are comprised by the domestication syndrome [20]. A recent review found that, apart from tameness and docility, skin depigmentation is the only trait that is universally expressed in domesticated mammals, calling the scope of the syndrome into question [18]. ...
Numerous hypotheses try to explain the unusual appearance of the human eye with its bright sclera and transparent conjunctiva and how it could have evolved from a dark-eyed phenotype, as is present in many non-human primates. Recently, it has been argued that pigmentation defects induced by self-domestication may have led to bright-eyed ocular phenotypes in humans and some other primate lineages, such as marmosets. However, it has never been systematically studied whether actual domesticated mammals consistently deviate from wild mammals in regard to their conjunctival pigmentation and if this trait might therefore be part of a domestication syndrome. Here, we test this idea by drawing phylogenetically informed comparisons from a photographic dataset spanning 13 domesticated mammal species and their closest living wild relatives ( n ≥ 15 photos per taxon). We did not recover significant differences in scleral appearance or irido-scleral contrast between domesticated and wild forms, suggesting that conjunctival depigmentation, unlike cutaneous pigmentation disorders, is not a general correlate of domestication. Regardless of their domestication status, macroscopically depigmented conjunctivae were observed in carnivorans and lagomorphs, whereas ungulates generally displayed darker eyes. For some taxa, we observed pronounced intraspecific variation, which should be addressed in more exhaustive future studies. Based on our dataset, we also present preliminary evidence for a general increase of conjunctival pigmentation with eye size in mammals. Our findings suggest that conjunctival depigmentation in humans is not a byproduct of self-domestication, even if we assume that our species has undergone such a process in its recent evolutionary history.
... In defence of the NCC hypothesis, Wilkins et al. [5] discussed apparent misrepresentations in Johnsson et al. [6], and emphasized the demonstrable promotion of scientific interest and activity, especially via support from multiple findings of past selection on NCC candidate-genes in ancient domesticates (e.g. [66,67,77]). Despite this, however, Johnsson et al. [6] had argued evidence of past selection on genes associated with NCCs is not necessarily evidence for the specific pleiotropic mechanisms implied by the NCC hypothesis to explain domestication syndrome. ...
Altered neural crest cell (NCC) behaviour is an increasingly cited explanation for the domestication syndrome in animals. However, recent authors have questioned this explanation, while others cast doubt on whether domestication syndrome even exists. Here, we review published literature concerning this syndrome and the NCC hypothesis, together with recent critiques of both. We synthesize these contributions and propose a novel interpretation, arguing shared trait changes under ancient domestication resulted primarily from shared disruption of wild reproductive regimes. We detail four primary selective pathways for 'reproductive disruption' under domestication and contrast these succinct and demonstrable mechanisms with cryptic genetic associations posited by the NCC hypothesis. In support of our perspective, we illustrate numerous important ways in which NCCs contribute to vertebrate reproductive phenotypes, and argue it is not surprising that features derived from these cells would be coincidentally altered under major selective regime changes, as occur in domestication. We then illustrate several pertinent examples of Darwin's 'unconscious selection' in action, and compare applied selection and phenotypic responses in each case. Lastly, we explore the ramifications of reproductive disruption for wider evolutionary discourse, including links to wild 'self-domestication' and 'island effect', and discuss outstanding questions.
... Hence, via altering the migration of neural crest cells and their differentiation in the adrenal medulla, morphological changes in other neural crest-derived structures may follow as a byproduct of selection for tameness. Although there is compelling genetic evidence for pronounced alterations of the neural crest being correlated with domestication across mammalian lineages [24], no consensus has been reached on exactly which traits are comprised by the domestication syndrome. A recent review found that, apart from tameness and docility, skin depigmentation is the only trait that is universally expressed in domesticated mammals, calling the scope of the syndrome into question [18]. ...
Numerous hypotheses try to explain the unusual appearance of the human eye with its bright sclera and transparent conjunctiva and how it could have evolved from a dark-eyed phenotype, as is present in many non-human primates. Recently, it has been argued that pigmentation defects induced by self-domestication may have led to bright-eyed ocular phenotypes in humans and some other primate lineages, such as marmosets. However, it has never been systematically studied whether actual domesticated mammals consistently deviate from wild mammals in regard to their conjunctival pigmentation and if this trait might therefore be part of a domestication syndrome. Here, we test this idea by drawing phylogenetically informed comparisons from a photographic dataset spanning 13 domesticated mammal species and their closest living wild relatives. We did not recover significant differences in scleral appearance or irido-scleral contrast between domesticated and wild forms, suggesting that conjunctival depigmentation, unlike cutaneous pigmentation disorders, is not a general correlate of domestication. Regardless of their domestication status, macroscopically depigmented conjunctivae were observed in carnivorans and lagomorphs, whereas ungulates generally displayed darker eyes. Based on our dataset, we also present preliminary evidence for a general increase of conjunctival pigmentation with eye size in mammals. Our findings suggest that conjunctival depigmentation in humans is not a byproduct of self-domestication, even if we assume that our species has undergone such a process in its recent evolutionary history.
... It suggests that minor deficiencies in the migration and proliferation of neural crest cells underlie trait formation in domestic animals. Recent comparative work on neural crest genes in domestic and wild animals by Rubio et al. [7] provides support for this hypothesis. A reduced number of neural crest cells arriving at their target sites is directly reflected in the structures that depend on these cells (6]. ...
Morphological traits, such as white patches, floppy ears and curly tails, are ubiquitous in domestic animals and are referred to as the 'domestication syndrome'. A commonly discussed hypothesis that has the potential to provide a unifying explanation for these traits is the 'neural crest/domestication syndrome hypothesis'. Although this hypothesis has the potential to explain most traits of the domestication syndrome, it only has an indirect connection to the reduction of brain size, which is a typical trait of domestic animals. We discuss how the expensive-tissue hypothesis might help explain brain-size reduction in domestication.
The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have significant public affection due to their stunning appearance, although the green peafowl is currently endangered. Some studies have suggested introgression between these the two species, although evidence is mixed. In this study, we successfully assembled a high-quality chromosome-level reference genome of the blue peafowl, including the autosomes, Z and W sex chromosomes as well as a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes and 33 peahen W chromosomes genomes provide the first substantial genetic evidence for recent hybridization between green and blue peafowl. We found three hybrid green peafowls in zoo samples rather than in the wild samples, with blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that two of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Hybridization of endangered species with its relatives is extremely detrimental to conservation. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, in order to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to preventing the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in four Zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP2 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for white feather color of blue peafowl (also called white peafowl), which prevents melanocytes from being transported into feathers, such that melanin cannot be deposited.
