Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies

Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

Improving the understanding of the causes and effects of anthropogenic hybridization is fundamental to ensure species conservation, particularly in the case of hybridization between wild species and their domestic relatives. Knowledge is missing for many species also because of a lack of appropriate tools for hybrid identification. Here, coupling genotype and phenotype analysis, we carried out an extensive investigation of ongoing hybridization in Alpine ibex Capra ibex, a mountain ungulate of conservation concern from a genetic perspective. By genotyping 63 diagnostic and 465 neutral SNPs, 20 suspected hybrids and 126 Alpine ibex without suspicious phenotype, representing 8 populations across a major part of the species distribution, we found evidence for ongoing hybridization between Alpine ibex and domestic goat. We identified different levels of hybridization including backcrosses into both Alpine ibex and domestic goat. Our results suggest a lack of reproductive barriers between the two species and good survival and reproductive success of the hybrids. Hybridization was locally intense, like a hybrid swarm, but not spread across the rest of the species distribution. Most of the hybrids were discovered in two locations in the north-west of Italy, while random sampling of individuals from different areas did not provide evidence of recent hybridization. Our method, based on amplicon sequencing of 63 diagnostic SNPs specifically developed for this purpose, allowed us to identify hybrids and backcrosses up to the fourth to fifth generations and was suitable for genetic samples of different quality, although with varying levels of certainty regarding the exact number of generations passed since hybridization. Based on the paired analysis of genotype and phenotype, we provide guidelines for the first identification of hybrids in the field and suggest a procedure for the reliable identification of hybrids.

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1-2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.

Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.

Mitochondrial DNA analyses revealed distinct lineages in an alpine mammal, Siberian ibex (Capra sibirica) in Xinjiang, China

Maternal lineages of mitochondrial DNA (mtDNA) are recognized as important components of intra and interspecific biodiversity and help us to disclose the phylogeny and divergence times of many taxa. Species of the genus Capra are canonical mountain dwellers. Among these is the Siberian ibex (Capra sibirica), which is regarded as a relic species whose intraspecific classification has been controversial so far. We collected 58 samples in Xinjiang, China, and analyzed the mtDNA genes to shed light on the intraspecific relationships of the C. sibirica populations and estimate the divergence time. Intriguingly, we found that the mtDNA sequences of C. sibirica split into two main lineages in both phylogenetic and network analyses: the Southern lineage, sister to Capra falconeri, consisting of samples from Ulugqat, Kagilik (both in Xinjiang), India, and Tajikistan; and the Northern lineage further divided into four monophyletic clades A-D corresponding to their geographic origins. Samples from Urumqi, Sawan, and Arturk formed a distinct monophyletic clade C within the Northern lineage. The genetic distance between the C. sibirica clades ranges from 3.0 to 8.6%, with values of F ST between 0.839 and 0.960, indicating notable genetic differentiation. The split of the genus Capra occurred approximately 6.75 Mya during the late Miocene. The Northern lineage diverged around 5.88 Mya, followed by the divergence of Clades A-D from 3.30 to 1.92 Mya during the late Pliocene and early Pleistocene. The radiation between the Southern lineage and C. falconeri occurred at 2.29 Mya during the early Pleistocene. Our results highlight the importance of extensive sampling when relating to genetic studies of alpine mammals and call for further genomic studies to draw definitive conclusions.

A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics

Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ~14,000 year old 2.59 X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten 'Taurasian tur' likely survived Late Pleistocene climatic change in a Taurus Mountain refuge and its genomic fate is unknown.

Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19^th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.

Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.

Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats (Capra hircus)

Simple Summary

During the present decade, highly selected caprine farming has increased in popularity due to the hardiness and adaptability inherent to goats. Recent advances in genetics have enabled the improvement in goat selection efficiency. The present review explores how genetic technologies have been applied to the goat-farming sector in the last century. The main candidate genes related to economically relevant traits are reported. The major source of income in goat farming derives from the sale of milk and meat. Consequently, yield and quality must be specially considered. Meat-related traits were evaluated considering three functional groups (weight gain, carcass quality and fat profile). Milk traits were assessed in three additional functional groups (milk production, protein and fat content).

Abstract

Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.

Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey

Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.

SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats

Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.

The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat

The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.

Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA

The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching and fragmentation. Here, we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186 bp and cytochrome b 487 bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared with the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126, cytochrome b 0.0528) and high F _ST statistics (D-loop 0.725, cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.

Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers

A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.

Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment

Simple Summary

The Nubian ibex is a wild relative of the domestic goat found in hot deserts of Northern Africa and Arabia. The domestic goat is an important livestock species that is mainly found in arid and semi-arid regions of Africa and Asia. The Nubian ibex is well adapted to challenging environments in hot deserts characterized by high diurnal temperatures, intense solar radiation, and scarce water resources. It is therefore important to understand the genetic basis of its adaptation for scientific and economic importance. To identify genes with adaptive traits, the Nubian ibex genome was sequenced and compared with that of related mammals. We identified twenty-five genes under selection in the Nubian ibex that play diverse biological roles such as immune response, visual development, signal transduction, and reproduction. Three other genes under adaptive evolution involved in protective functions of the skin against damaging solar radiation in the desert were identified in Nubian ibex genome. Our finding provides valuable genomic insights into the adaptation of Nubian ibex to desert environments. The genomic information generated in this study can be used in developing appropriate breeding programs aimed at enhancing adaptation of local goats to less favorable habitats in response to changing climates.

Abstract

The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging environments in hot deserts characterized by intense solar radiation, thermal extremes, and scarce water resources. The economic importance of C. hircus breeds, as well as the current trends of global warming, highlights the need to understand the genetic basis of adaptation of C. nubiana to the desert environments. In this study, the genome of a C. nubiana individual was sequenced at an average of 37x coverage. Positively selected genes were identified by comparing protein-coding DNA sequences of C. nubiana and related species using dN/dS statistics. A total of twenty-two positively selected genes involved in diverse biological functions such as immune response, protein ubiquitination, olfactory transduction, and visual development were identified. In total, three of the twenty-two positively selected genes are involved in skin barrier development and function (ATP binding cassette subfamily A member 12, Achaete-scute family bHLH transcription factor 4, and UV stimulated scaffold protein A), suggesting that C. nubiana has evolved skin protection strategies against the damaging solar radiations that prevail in deserts. The positive selection signatures identified here provide new insights into the potential adaptive mechanisms to hot deserts in C. nubiana.

Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene

Aim:

This study is aimed at characterizing the genetic and phylogenetic structure of Lakor goats as indigenous livestock from the Southwest Maluku Regency based on mitochondrial COI gene sequences.

Materials and Methods:

The genomes of 103 follicle samples from Lakor goats, collected from Lakor Island, were analyzed. The polymerase chain reaction was used to amplify 1548 bp of the mitochondrial COI gene using two primer pairs (COIA and COIB). Following sequencing, genetic variation and phylogenetic relationship were established using MEGA version X software.

Results:

The results of multiple COI gene alignment of the total sequences identified four polymorphic nucleotides that function as genetic markers between individual animals within the Lakor goat population. These correspond to positions 228 (A-G), 519 (G-A), 900 (C-T), and 1266 (T-C). Phylogenetic signals based on the COI gene showed that Lakor goat breed is a monophyletic group or single clade with a bootstrap value of 100% by the neighbor-joining (NJ) and maximum likelihood (ML) evolutionary models. This data indicated that evolutionarily, the Lakor goat breed has a very close kinship with three goat breeds from China: The Meigu goat (KM 244714.1), Chinese Tibet (Capra hircus) (KJ 940969.1), and C. hircus (KP 677510.1). Phylogenetic information based on the cladistics system classified the Lakor goat as a single clade (monophyletic group). The low-genetic diversity within populations indicates that there has been an inbreeding depression occurring at a very high frequency.

Conclusion:

We conclude that the Lakor goat may be divided into a single clade or monophyletic group based on the COI gene sequence. Four nucleotides were identified that can be used as genetic markers among individual animals within the Lakor goat population, as well as C. hircus and others as derived from GenBank data. The Lakor goat population has a high level of inbreeding depression as a result of geographical isolation, which supports the formation of a monophyletic group with different genetic characteristics, and does not allow the introduction of males from other breeds. Phylogenetic signals indicated that Capra aegagrus (bezoar) is the ancestor of the native goats in Indonesia, including the Lakor goats.

High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor

Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats (Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region.

Genetic evidence for allopatric speciation of the Siberian ibex Capra sibirica in India

Montane systems, formed by a series of climatic oscillations and temporal topographic metamorphoses, have broken up the contiguous distribution of widespread species and accelerated allopatric speciation. We used a partial fragment of the mitochondrial cytochrome b (cytb) gene to address speciation across the entire range of the Siberian ibex Capra sibirica. We demonstrated that the Siberian ibex is a polytypic species, plausibly formed by a combination of at least 2 species and/or 3 to 4 sub-species. Bayesian phylogeny showed that the Indian-Tajikistan (I-T) clade is adequately diverged from the other clades based on the mean intra-specific distance criterion, and warrants recognition as a distinct species. We provide pragmatic evidence for the endorsement of the I-T clade as a distinct species of Siberian ibex and urge prioritization of the conservation of this species at global and regional scales.

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.

Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds

The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation.

Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.

Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces

Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.

DENTAL ENAMEL FORMATION AND IMPLICATIONS FOR ORAL HEALTH AND DISEASE

Dental enamel is the hardest and most mineralized tissue in extinct and extant vertebrate species and provides maximum durability that allows teeth to function as weapons and/or tools as well as for food processing. Enamel development and mineralization is an intricate process tightly regulated by cells of the enamel organ called ameloblasts. These heavily polarized cells form a monolayer around the developing enamel tissue and move as a single forming front in specified directions as they lay down a proteinaceous matrix that serves as a template for crystal growth. Ameloblasts maintain intercellular connections creating a semi-permeable barrier that at one end (basal/proximal) receives nutrients and ions from blood vessels, and at the opposite end (secretory/apical/distal) forms extracellular crystals within specified pH conditions. In this unique environment, ameloblasts orchestrate crystal growth via multiple cellular activities including modulating the transport of minerals and ions, pH regulation, proteolysis, and endocytosis. In many vertebrates, the bulk of the enamel tissue volume is first formed and subsequently mineralized by these same cells as they retransform their morphology and function. Cell death by apoptosis and regression are the fates of many ameloblasts following enamel maturation, and what cells remain of the enamel organ are shed during tooth eruption, or are incorporated into the tooth's epithelial attachment to the oral gingiva. In this review, we examine key aspects of dental enamel formation, from its developmental genesis to the ever-increasing wealth of data on the mechanisms mediating ionic transport, as well as the clinical outcomes resulting from abnormal ameloblast function.

Utility of several microsatellite markers for the genetic characterisation of three ex situ populations of threatened caprine taxa (<i>Capra aegagrus</i>, <i>C. cylindricornis</i> and <i>C. falconeri</i>)

Abstract. Caprines belong to the most endangered group of mammals and artiodactyls suffering from many negative human impacts. Fortunately, many of them are protected and managed by national and international legislation and in situ and ex situ conservation actions. Although many microsatellite markers have been developed for wild and domestic caprines, they remain uninvestigated in respect of their utility for some taxa. We examined the utility of the International Society for Animal Genetics microsatellite set for genetic characterisations of three wild and one domestic Capra species from captive or semi-captive ex situ populations in Europe. Our data suggest the utility of this microsatellite set for detecting shared and species-specific alleles, characterising the genetic variability, and determining phylogenetic relationships and intraspecific structures in investigated taxa. We detected a depleted genetic variability in Capra falconeri and Capra cylindricornis in European ex situ populations; unrelated individuals are therefore needed for improving genetic variability parameters, as they are for the extralimital population of Capra aegagrus in the Vřísek game reserve (Czech Republic), for which we identified no genetic introgression from the domestic goat and great dissimilarity with some analysed individuals from European zoos. Current results here indicate some difficulties with the historical evidence, for example with respect to the origin and purity of particular individuals under breeding programmes.

Y-chromosomal variation of local goat breeds of Turkey close to the domestication centre

Genetic variations in chromosome Y are enabling researchers to identify paternal lineages, which are informative for introgressions and migrations. In this study, the male-specific region markers, sex-determining region-Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honamlı, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illustrate that Y-chromosomal variants have a more breed-dependent distribution than mitochondrial or autosomal DNA. This probably reflects male founder effects, but a role in adaptation cannot be excluded.

Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages

Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.

A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

BACKGROUND

Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species.

RESULTS

The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record.

CONCLUSIONS

The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.

Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete

The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.

Y chromosome phylogeny for cutthroat trout (Oncorhynchus clarkii) subspecies is generally concordant with those of other markers

Sequence divergence was evaluated in the non-recombining, male-specific OmyY1 region of the Y chromosome among the subspecies of cutthroat trout (Oncorhynchus clarkii) in the western United States. This evaluation identified subspecies-discriminating OmyY1-haplotypes within a ∼1200bp region of the OmyY1 locus and localized the region to the end of the Y chromosome by FISH analysis. OmyY1 sequences were aligned and used to reconstruct a phylogeny of the cutthroat trout subspecies and related species via maximum-parsimony and Bayesian analyses. In the Y-haplotype phylogeny, clade distributions generally corresponded to the geographic distributions of the recognized subspecies. This phylogeny generally corresponded to a mitochondrial tree obtained for these subspecies in a previous study. Both support a clade of trout vs. Pacific salmon, of rainbow trout, and of a Yellowstone cutthroat group within the cutthroat trout. In our OmyY1 tree, however, the cutthroat "clade", although present topologically, was not statistically significant. Some key differences were found between trees obtained from the paternally-inherited OmyY1 vs. maternally-inherited mitochondrial haplotypes in cutthroat trout compared to rainbow trout. Other findings are: The trout OmyY1 region evolves between 3 and 13 times slower than the trout mitochondrial regions that have been studied. The Lahontan cutthroat trout had a fixed OmyY1 sequence throughout ten separate populations, suggesting this subspecies underwent a severe population bottleneck prior to its current dispersal throughout the Great Basin during the pluvial phase of the last ice age. The Yellowstone group is the most derived among the cutthroat trout and consists of the Yellowstone, Bonneville, Colorado, Rio Grande and greenback subspecies. Identification of subspecies and sex with this Y-chromosome marker may prove useful in conservation efforts.

Expectation-maximization algorithm for determining natural selection of Y-linked genes through two-sex branching processes

A two-dimensional bisexual branching process has recently been presented for the analysis of the generation-to-generation evolution of the number of carriers of a Y-linked gene. In this model, preference of females for males with a specific genetic characteristic is assumed to be determined by an allele of the gene. It has been shown that the behavior of this kind of Y-linked gene is strongly related to the reproduction law of each genotype. In practice, the corresponding offspring distributions are usually unknown, and it is necessary to develop their estimation theory in order to determine the natural selection of the gene. Here we deal with the estimation problem for the offspring distribution of each genotype of a Y-linked gene when the only observable data are each generation's total numbers of males of each genotype and of females. We set out the problem in a non parametric framework and obtain the maximum likelihood estimators of the offspring distributions using an expectation-maximization algorithm. From these estimators, we also derive the estimators for the reproduction mean of each genotype and forecast the distribution of the future population sizes. Finally, we check the accuracy of the algorithm by means of a simulation study.

A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons

Background

The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs).

Results

To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade.

Conclusions

Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance.

Y-chromosome phylogeny in the evolutionary net of chamois (genus Rupicapra)

Background

The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. The study of matrilineal mitochondrial DNA (mtDNA) and biparentally inherited microsatellites showed that the two species are paraphyletic and indicated alternate events of population contraction and dispersal-hybridization in the diversification of chamois. Here we investigate the pattern of variation of the Y-chromosome to obtain information on the patrilineal phylogenetic position of the genus Rupicapra and on the male-specific dispersal of chamois across Europe.

Results

We analyzed the Y-chromosome of 87 males covering the distribution range of the Rupicapra genus. We sequenced a fragment of the SRY gene promoter and characterized the male specific microsatellites UMN2303 and SRYM18. The SRY promoter sequences of two samples of Barbary sheep (Ammotragus lervia) were also determined and compared with the sequences of Bovidae available in the GenBank. Phylogenetic analysis of the alignment showed the clustering of Rupicapra with Capra and the Ammotragus sequence obtained in this study, different from the previously reported sequence of Ammotragus which groups with Ovis. Within Rupicapra, the combined data define 10 Y-chromosome haplotypes forming two haplogroups, which concur with taxonomic classification, instead of the three clades formed for mtDNA and nuclear microsatellites. The variation shows a west-to-east geographical cline of ancestral to derived alleles.

Conclusions

The phylogeny of the SRY-promoter shows an association between Rupicapra and Capra. The position of Ammotragus needs a reinvestigation. The study of ancestral and derived characters in the Y-chromosome suggests that, contrary to the presumed Asian origin, the paternal lineage of chamois originated in the Mediterranean, most probably in the Iberian Peninsula, and dispersed eastwards through serial funding events during the glacial-interglacial cycles of the Quaternary. The diversity of Y-chromosomes in chamois is very low. The differences in patterns of variation among Y-chromosome, mtDNA and biparental microsatellites reflect the evolutionary characteristics of the different markers as well as the effects of sex-biased dispersal and species phylogeography.