Landscape and Climatic Variations Shaped Secondary Contacts amid Barn Owls of the Western Palearctic

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns

Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the north. Like most organisms, barn owls are assumed to have colonized the British Isles by crossing over Doggerland, a land bridge that connected Britain to northern Europe. However, while they are dark rufous in northern Europe, barn owls in the British Isles are conspicuously white, a contrast that could suggest selective forces are at play on the islands. Yet, our analysis of known candidate genes involved in coloration found no signature of selection. Instead, using whole genome sequences and species distribution modelling, we found that owls colonised the British Isles soon after the last glaciation, directly from a white coloured refugium in the Iberian Peninsula, before colonising northern Europe. They would have followed a hitherto unknown post-glacial colonization route to the Isles over a westwards path of suitable habitat in now submerged land in the Bay of Biscay, thus not crossing Doggerland. As such, they inherited the white colour of their Iberian founders and maintained it through low gene flow with the mainland that prevents the import of rufous alleles. Thus, we contend that neutral processes probably explain this contrasting white colour compared to continental owls. With the barn owl being a top predator, we expect future research will show this unanticipated route was used by other species from its paleo community

Genomic basis of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species

Genome structural variations to understand the adaptive anddemographic processes during domestication of small ruminants.

Les variants structuraux génomiques (SVs) composent une large part du polymorphisme observable entre les individus mais leurs impacts sur les processus micro-évolutifs restent mal connus et leur étude à large échelle est rare.La première partie de ce manuscrit est une étude de la bibliographie portant sur les SVs décrits chez les animaux domestiques. Cette partie met en avant l'importance des SVs dans la modification des gènes ou de leur régulation, impactant un grand nombre de traits sélectionnés lors de la domestication, en lien avec la productivité, la morphologie ou encore le comportement.Basée sur l’étude de données de reséquençage de 500 génomes complets de petits ruminants sauvages et domestiques, la seconde partie, ciblant trois SVs décrits dans la bibliographie, a permis (i) de réfuter l’hypothèse d’amplification en lien avec la domestication des copies endogènes protectrices du retrovirus JSRV situées dans la région 6q13 du mouton, (ii) d’identifier des duplications entourant et affectant le gène ASIP qui seraient impliquées dans les modifications de coloration du pelage en lien avec la domestication des petits ruminants, ainsi que (iii) de montrer un potentiel rôle adaptatif d'un haplotype du locus de la beta-globine lié au climat aride chez le mouton.La troisième partie se base sur une recherche sans a priori de l’ensemble des SVs présents dans des génomes complets. Au travers du développement d’une méthode de détection des SVs et de son application, cette partie permet de décrire environ 50k et 20k SVs dans les génomes des Ovis et des Capra. Parmi ces SVs, 135 chez Ovis et 70 chez Capra semblent liés à la domestication et affectent des gènes impliqués dans l’amélioration, l’immunité, la reproduction ou la survie. De plus, les distributions de 130 SVs pour les moutons et 35 SVs pour les chèvres covarient avec des variables environnementales au Maroc. Certains affectent des gènes impliqués dans la morphologie, l’immunité et le métabolisme.Ce travail met ainsi en avant de nombreux variants qui peuvent impacter des gènes et qui ont pu être ciblés lors la domestication initiale, des étapes d’amélioration ultérieure ou de l’adaptation locale des petits ruminants. Il démontre l'importance de prendre en compte les variants structuraux dans les études génomiques visant à décrire les bases génétiques de la domestication.Genomic structural variations (SVs) account for a large part of the polymorphism between individuals, but their impacts on micro-evolutionary processes remain poorly known and large-scale studies are scarce.The first part of this manuscript is a bibliographic study of SVs in domestic animals. This part highlights the importance of SVs in modifying genes or their regulation, impacting a large number of traits selected during domestication and linked to productivity, morphology or behaviour.Based on the study of resequenced data from 500 whole genomes of wild and domestic small ruminants, the second part, targeting three SVs described in the bibliography, allowed (i) to refute the hypothesis of a link between the domestication of sheep and the amplification of endogenous protective copies of the JSRV retrovirus located in the 6q13 region, l, (ii) to identify duplications surrounding and affecting the ASIP gene that could be involved in the coat color changes related to the domestication of small ruminants, as well as (iii) highlight a potential adaptive role to arid climate of an haplotype of beta-globin locus in sheep.In the third part, we conducted a whole genome survey of SVs . Through the development of a SVs detection method and its application, we could detect about 50k and 20k SVs in Ovis and Capra. Of these SVs, 135 and 70 in Ovis and Capra, respectively, appear to be linked with domestication and affect genes involved in improvement, immunity, reproduction or survival. In addition, in Morocco, the distributions of 130 SVs for sheep and 35 SVs for goats covariate with environmental variables. Some of them affect genes involved in morphology, immunity and metabolism.This work highlights that many variants impacting genes might have been targeted during initial domestication and subsequent improvement steps or during the local adaptation of sheep and goats. It demonstrates the importance of considering structural variants in genomic studies to describe the genetic basis of domestication

Etude des variants structuraux génomiques pour comprendre les processus démographiques et adaptatifs impliqués dans la domestication des petits ruminants

Genomic structural variations (SVs) account for a large part of the polymorphism between individuals, but their impacts on micro-evolutionary processes remain poorly known and large-scale studies are scarce.The first part of this manuscript is a bibliographic study of SVs in domestic animals. This part highlights the importance of SVs in modifying genes or their regulation, impacting a large number of traits selected during domestication and linked to productivity, morphology or behaviour.Based on the study of resequenced data from 500 whole genomes of wild and domestic small ruminants, the second part, targeting three SVs described in the bibliography, allowed (i) to refute the hypothesis of a link between the domestication of sheep and the amplification of endogenous protective copies of the JSRV retrovirus located in the 6q13 region, l, (ii) to identify duplications surrounding and affecting the ASIP gene that could be involved in the coat color changes related to the domestication of small ruminants, as well as (iii) highlight a potential adaptive role to arid climate of an haplotype of beta-globin locus in sheep.In the third part, we conducted a whole genome survey of SVs . Through the development of a SVs detection method and its application, we could detect about 50k and 20k SVs in Ovis and Capra. Of these SVs, 135 and 70 in Ovis and Capra, respectively, appear to be linked with domestication and affect genes involved in improvement, immunity, reproduction or survival. In addition, in Morocco, the distributions of 130 SVs for sheep and 35 SVs for goats covariate with environmental variables. Some of them affect genes involved in morphology, immunity and metabolism.This work highlights that many variants impacting genes might have been targeted during initial domestication and subsequent improvement steps or during the local adaptation of sheep and goats. It demonstrates the importance of considering structural variants in genomic studies to describe the genetic basis of domestication.Les variants structuraux génomiques (SVs) composent une large part du polymorphisme observable entre les individus mais leurs impacts sur les processus micro-évolutifs restent mal connus et leur étude à large échelle est rare.La première partie de ce manuscrit est une étude de la bibliographie portant sur les SVs décrits chez les animaux domestiques. Cette partie met en avant l'importance des SVs dans la modification des gènes ou de leur régulation, impactant un grand nombre de traits sélectionnés lors de la domestication, en lien avec la productivité, la morphologie ou encore le comportement.Basée sur l’étude de données de reséquençage de 500 génomes complets de petits ruminants sauvages et domestiques, la seconde partie, ciblant trois SVs décrits dans la bibliographie, a permis (i) de réfuter l’hypothèse d’amplification en lien avec la domestication des copies endogènes protectrices du retrovirus JSRV situées dans la région 6q13 du mouton, (ii) d’identifier des duplications entourant et affectant le gène ASIP qui seraient impliquées dans les modifications de coloration du pelage en lien avec la domestication des petits ruminants, ainsi que (iii) de montrer un potentiel rôle adaptatif d'un haplotype du locus de la beta-globine lié au climat aride chez le mouton.La troisième partie se base sur une recherche sans a priori de l’ensemble des SVs présents dans des génomes complets. Au travers du développement d’une méthode de détection des SVs et de son application, cette partie permet de décrire environ 50k et 20k SVs dans les génomes des Ovis et des Capra. Parmi ces SVs, 135 chez Ovis et 70 chez Capra semblent liés à la domestication et affectent des gènes impliqués dans l’amélioration, l’immunité, la reproduction ou la survie. De plus, les distributions de 130 SVs pour les moutons et 35 SVs pour les chèvres covarient avec des variables environnementales au Maroc. Certains affectent des gènes impliqués dans la morphologie, l’immunité et le métabolisme.Ce travail met ainsi en avant de nombreux variants qui peuvent impacter des gènes et qui ont pu être ciblés lors la domestication initiale, des étapes d’amélioration ultérieure ou de l’adaptation locale des petits ruminants. Il démontre l'importance de prendre en compte les variants structuraux dans les études génomiques visant à décrire les bases génétiques de la domestication

Etude des variants structuraux génomiques pour comprendre les processus démographiques et adaptatifs impliqués dans la domestication des petits ruminants

Genomic structural variations (SVs) account for a large part of the polymorphism between individuals, but their impacts on micro-evolutionary processes remain poorly known and large-scale studies are scarce.The first part of this manuscript is a bibliographic study of SVs in domestic animals. This part highlights the importance of SVs in modifying genes or their regulation, impacting a large number of traits selected during domestication and linked to productivity, morphology or behaviour.Based on the study of resequenced data from 500 whole genomes of wild and domestic small ruminants, the second part, targeting three SVs described in the bibliography, allowed (i) to refute the hypothesis of a link between the domestication of sheep and the amplification of endogenous protective copies of the JSRV retrovirus located in the 6q13 region, l, (ii) to identify duplications surrounding and affecting the ASIP gene that could be involved in the coat color changes related to the domestication of small ruminants, as well as (iii) highlight a potential adaptive role to arid climate of an haplotype of beta-globin locus in sheep.In the third part, we conducted a whole genome survey of SVs . Through the development of a SVs detection method and its application, we could detect about 50k and 20k SVs in Ovis and Capra. Of these SVs, 135 and 70 in Ovis and Capra, respectively, appear to be linked with domestication and affect genes involved in improvement, immunity, reproduction or survival. In addition, in Morocco, the distributions of 130 SVs for sheep and 35 SVs for goats covariate with environmental variables. Some of them affect genes involved in morphology, immunity and metabolism.This work highlights that many variants impacting genes might have been targeted during initial domestication and subsequent improvement steps or during the local adaptation of sheep and goats. It demonstrates the importance of considering structural variants in genomic studies to describe the genetic basis of domestication.Les variants structuraux génomiques (SVs) composent une large part du polymorphisme observable entre les individus mais leurs impacts sur les processus micro-évolutifs restent mal connus et leur étude à large échelle est rare.La première partie de ce manuscrit est une étude de la bibliographie portant sur les SVs décrits chez les animaux domestiques. Cette partie met en avant l'importance des SVs dans la modification des gènes ou de leur régulation, impactant un grand nombre de traits sélectionnés lors de la domestication, en lien avec la productivité, la morphologie ou encore le comportement.Basée sur l’étude de données de reséquençage de 500 génomes complets de petits ruminants sauvages et domestiques, la seconde partie, ciblant trois SVs décrits dans la bibliographie, a permis (i) de réfuter l’hypothèse d’amplification en lien avec la domestication des copies endogènes protectrices du retrovirus JSRV situées dans la région 6q13 du mouton, (ii) d’identifier des duplications entourant et affectant le gène ASIP qui seraient impliquées dans les modifications de coloration du pelage en lien avec la domestication des petits ruminants, ainsi que (iii) de montrer un potentiel rôle adaptatif d'un haplotype du locus de la beta-globine lié au climat aride chez le mouton.La troisième partie se base sur une recherche sans a priori de l’ensemble des SVs présents dans des génomes complets. Au travers du développement d’une méthode de détection des SVs et de son application, cette partie permet de décrire environ 50k et 20k SVs dans les génomes des Ovis et des Capra. Parmi ces SVs, 135 chez Ovis et 70 chez Capra semblent liés à la domestication et affectent des gènes impliqués dans l’amélioration, l’immunité, la reproduction ou la survie. De plus, les distributions de 130 SVs pour les moutons et 35 SVs pour les chèvres covarient avec des variables environnementales au Maroc. Certains affectent des gènes impliqués dans la morphologie, l’immunité et le métabolisme.Ce travail met ainsi en avant de nombreux variants qui peuvent impacter des gènes et qui ont pu être ciblés lors la domestication initiale, des étapes d’amélioration ultérieure ou de l’adaptation locale des petits ruminants. Il démontre l'importance de prendre en compte les variants structuraux dans les études génomiques visant à décrire les bases génétiques de la domestication

Sequencing depth for one re-sequenced individual (ID: IC17) of Tyto alba aligned to the trimmed reference (with only one repeat of each repeated region).

(A) Depth along the complete genome. (B) Close up on the non-coding region where the repeats are located. The vertical lines represent the delimitation of the plateau where the mean depth for the repeated regions. The horizontal straight line represents the median depth for all base pairs in the two panels. (TIF)</p

Correlation between the number of repeats in both regions of the control region of the mtDNA of the resequenced individuals of Tyto alba and the difference between tissues used for the extraction.

Convex hulls were drawn to show the distribution of number of repeats between the different tissues. There is a strong correlation between both numbers of repeats r = 0.65, r2 = 0.42, p = 2x10-16. (TIF)</p