Introgression Research Articles

Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes

BackgroundGene flow is crucial for enhancing economic traits of livestock. In China, breeders have used hybridization strategies for decades to improve livestock performance. Here, we performed whole-genome sequencing of a native Chinese Lijiang pig (LJP) breed. By integrating previously published data, we explored the genetic structure and introgression of genetic components from commercial European pigs (EP) into the LJP, and examined the impact of this introgression on phenotypic traits.ResultsOur analysis revealed significant introgression of EP breeds into the LJP and other domestic pig breeds in China. Using a haplotype-based approach, we quantified introgression levels and compared EP to LJP and other Chinese domestic pigs. The results show that EP introgression is widely prevalent in Chinese domestic pigs, although there are significant differences between breeds. We propose that LJP could potentially act as a mediator for the transmission of EP haplotypes. We also examined the correlation between EP introgression and the number of thoracic vertebrae in LJP and identified VRTN and STUM as candidate genes for this trait.ConclusionsOur study provides evidence of introgressed European haplotypes in the LJP breed and describes the potential role of EP introgression on phenotypic changes of this indigenous breed.

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

BackgroundThe pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown.ResultsThrough whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness.ConclusionsOur research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.

5. Introgressive hybridization and genetic barriers to interspecies gene flow in the west Pacific pen shells (genus <i>Atrina</i>)

5. Introgressive hybridization and genetic barriers to interspecies gene flow in the west Pacific pen shells (genus <i>Atrina</i>)

Traditional multilocus phylogeny fails to fully resolve Palearctic ground squirrels (Spermophilus) relationships but reveals a new species endemic to West Siberia

Previous efforts to reconstruct evolutionary history of Palearctic ground squirrels within the genus Spermophilus have primarily relied on a single mitochondrial marker for phylogenetic data. In this study, we present the first phylogeny with comprehensive taxon sampling of Spermophilus via a conventional multilocus approach utilizing five mitochondrial and five nuclear markers. Through application of the multispecies coalescent model, we constructed a species tree revealing four distinct clades that diverged during the Late Miocene. These clades are 1) S. alaschanicus and S. dauricus from East Asia; 2) S. musicus and S. pygmaeus from East Europe and northwestern Central Asia; 3) the subgenus Colobotis found across Central Asia and its adjacent regions and encompassing S. brevicauda, S. erythrogenys, S. fulvus, S. major, S. pallidicauda, S. ralli, S. relictus, S. selevini, and S. vorontsovi sp. nov.; and 4) a Central/Eastern Europe and Asia Minor clade comprising S. citellus, S. taurensis, S. xanthoprymnus, S. suslicus, and S. odessanus. The latter clade lacked strong support owing to uncertainty of taxonomic placement of S. odessanus and S. suslicus. Resolving relationships within the subgenus Colobotis, which radiated rapidly, remains challenging likely because of incomplete lineage sorting and introgressive hybridization. Most of modern Spermophilus species diversified during the Early–Middle Pleistocene (2.2–1.0 million years ago). We propose a revised taxonomic classification for the genus Spermophilus by recognizing 18 species including a newly identified one (S. vorontsovi sp. nov.), which is found only in a limited area in the southeast of West Siberia. Employing genome-wide single-nucleotide polymorphism genotyping, we substantiated the role of the Ob River as a major barrier ensuring robust isolation of this taxon from S. erythrogenys. Despite its inherent limitations, the traditional multilocus approach remains a valuable tool for resolving relationships and can provide important insights into otherwise poorly understood groups. It is imperative to recognize that additional efforts are needed to definitively determine phylogenetic relationships between certain species of Palearctic ground squirrels.

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).

Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Population genetics reveals new introgression in the nucleus herd of min pigs.

Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs. We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs. The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes. Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.

Linking Acrosome Size and Genetic Divergence in an Inter-Oceanic Mussel from the Pacific and Atlantic Coasts: A Case of Incipient Speciation?

In recent years, advances in analyses of the sperm morphology and genetics of Perumytilus purpuratus have allowed to two evolutionary scenarios for this mussel to be suggested: (1) the scenario of cryptic species and (2) the scenario of incipient or in progress speciation. For a better understanding of the evolutionary history of P. purpuratus, we performed extensive sampling along a latitudinal gradient of ca. 7180 km of coastline-from the Southern Pacific Ocean to the Atlantic Ocean-and we delved deeper into the sperm morphology of P. purpuratus, exploring its association with the phylogeny and population genetics to determine whether the variability in sperm traits between the northern and southern regions was a signal of cryptic or incipient species. Overall, our results showed that sperm sizes were strongly correlated with the genetic structure in males of P. purpuratus. We identified at 37° S on the Pacific coast a coincident break of both sperm size and genetic disruption that can be explained by historical events and postglacial recolonization as causal phenomena for the observed divergences. Furthermore, evidence of genetic admixture between lineages was found at 38° S, suggesting the presence of an introgressive hybridization zone and incomplete reproductive isolation in an in fraganti or incipient speciation process.

Mottled ducks, feral mallards, and their hybrids in Florida

AbstractThe nonmigratory and endemic Florida mottled duck (Anas fulvigula fulvigula) is facing conservation threats from the combined effects of urbanization and introgressive hybridization with feral mallards (Anas platyrhynchos) and mallard x mottled duck hybrids. In the past, the status of the Florida mottled duck population was assessed during annual aerial surveys and most brown ducks (mottled ducks, mallards, and hybrids of them) detected during the survey would have been mottled ducks. But the release of domesticated mallards for aesthetic purposes has led to increases in the prevalence of mallards‐hybrids (mallards or mallard x mottled duck hybrids) throughout peninsular Florida, USA, and because it is impossible to differentiate among mottled ducks, female mallards, and hybrids during aerial surveys, helicopter surveys were halted in 2009 until state researchers could conduct a range‐wide study to determine what proportion of brown ducks are mottled ducks versus mallards‐hybrids. We used plumage keys and high‐resolution photography to categorize brown ducks from 557 wetland grid points as either mottled ducks or mallards‐hybrids. Of the 5,179 brown ducks categorized, 40.1% were mottled ducks and 59.9% were mallards‐hybrids. We used logistic regression analysis to model the interactive effect of a site's latitude and level of urbanization (urban gradient value within a 2‐km buffer) to generate a predictive raster surface (1‐km resolution) of the study area with values corresponding to the probability that a brown duck observed within a cell is a pure mottled duck. Predicted values will be used as correction factors when estimating final mottled duck population abundance from brown‐duck survey data. Additionally, the predictive raster surface will be used to identify wetlands where mottled ducks remain predominant so that these sites can be targeted for preservation. Overall, mallards‐hybrids outnumbered mottled ducks throughout most of peninsular Florida, especially in more urbanized regions, and their current prevalence rate presents a serious conservation threat, via hybridization, to extant mottled duck populations.

Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species.

Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.

Determining the Matrilineal Origin of Indonesian Kerinci Duck Breed (Anas platyrhynchos) Based on MT-ND2 Gene Diversity

The Kerinci duck (Anas platyrhynchos), hailing from Jambi Province, represents one of the local duck breeds of Indonesia. This study aimed to ascertain the matrilineal origin of Kerinci ducks through analysis of the mitochondrial NADH Dehydrogenase subunit 2 (MT-ND2) gene. In this pursuit, forward sequences of the MT-ND2 gene (490 bp) were extracted from unsexed Kerinci ducks, totalling forty-eight (48) sequences, procured from blood samples. The findings demonstrated the identification of fifteen (15) distinct haplotypes within the MT-ND2 gene, with corresponding haplotype diversity (Hd) and nucleotide diversity (pi) values of 0.74 and 0.003, respectively. The resulting phylogenetic tree unveiled that Kerinci ducks exhibit two matrilineal origins: an Asian and an independent Kerinci lineage. Moreover, most Kerinci ducks were categorised within the H4 group (24 birds) of the Asian lineage. Nevertheless, this study also revealed the existence of an independent Kerinci lineage comprising eight (8) duck haplotypes. In conclusion, the analysis of the MT-ND2 gene underscored the genetic introgression of A. zonorhyncha and A. poecilorhyncha in Kerinci ducks.

Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks.

Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.

Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation

The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.

The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon)

The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three ‘pure’ species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an ‘evolutionary syngameon’ where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.

Taxonomic status of hares (Lepus spp.) in Xinjiang, China (Lagomorpha: Leporidae): An integrative approach

AbstractThe taxonomic status and interspecies relationships of hares (genus Lepus) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome‐wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. Lepus yarkandensis and Lepus timidus, which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of Lepus tolai, namely, Lepus tolai lehmanni and Lepus tolai centrasiaticus. Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from L. tolai by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of Lepus tibetanus, Lepus tibetanus pamirensis. Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between L. yarkandensis and L. tibetanus pamirensis, L. yarkandensis and L. tolai centrasiaticus, and L. tolai lehmanni and L. timidus.

The marine fishes from southern Mindanao, Philippines, including a DNA barcode reference library of commercially important species

The Philippines has been long known for its multispecies fisheries, and while there is a growing effort to document fish diversity, collections-based species inventories remain insufficient in southern Mindanao. Market survey efforts conducted in Pujada Bay, Davao Gulf, and Sarangani Bay in the last ten years resulted in documenting 556 species of marine fishes from 82 families, while underwater fish visual census (FVC) surveys conducted in Davao Gulf from 2019 to 2022 revealed 365 species in 42 families. Combining the data from market surveys, FVC, and published literature, we present 771 species of marine fishes (770 teleosts, 1 elasmobranch) belonging to 94 families. Of the 771 species documented, 130 are deep reef and deepwater species, while 20 species await further taxonomic investigations for species-level identifications.Moreover, 498 cytochrome oxidase I (COI) genetic barcodes were produced representing 357 species from 59 families, which covers 46% of the total number of species reported and 63% of the market survey data. Genetic distances based on taxonomic ranks were concordant with other barcoding studies on marine fishes. Samples (20 species) with pairwise genetic distances that did not conform with the expected intra- and interspecific threshold suggest cases that also need to be investigated further (e.g., incomplete lineage sorting, introgressive hybridization, crypticspeciation). All market survey data used in genetic barcoding correspond to tissue samples, live-color photographs, and preserved specimens. This work complements the DNA barcode libraries reported recently in the country, and this serves as an additional reference for future biodiversity management and conservation efforts.

From microcosm to macrocosm: adaptive radiation of Darwin’s finches

Abstract In this Perspective we show the value of studying living organisms in the field to understand their history. Darwin’s finches are an iconic example of the early stages of speciation in a young adaptive radiation that produced 18 species in little more than a million years. The question they pose is how and why so many species originated and diversified rapidly. A long-term study of four species of finches on the small island of Daphne Major, combined with genomic investigations, provide some answers in terms of extrinsic and intrinsic factors. Beak size and shape, as well as body size, are key heritable features involved in both ecological and reproductive isolation, and their evolution by natural selection was caused by competitor species during prolonged droughts. Introgressive hybridization of related species is rare but recurring, apparently widespread, increases genetic variation, and does not incur a fitness cost. Hybridization can produce a new species. We use a phylogeny based on whole genome sequences of the four finches to infer morphological transitions in their radiation. Several lines of evidence indicate that some species are missing from the early phase of the radiation due to extinction. Combining these results, we re-cast the classical allopatry-then-sympatry theory of adaptive radiation as a competition-selection-hybridization process that generates a diversity of species.

Limited gene flow in adjacent valleys and genetic introgression in a mountain hybrid zone between <i>Aconitum</i> (Ranunculaceae) species

The number of polyploid plants in angiosperms is estimated at about 30-80%, depending on the study, but hybridization between diploids and tetraploids is not a common phenomenon. In this study, our aim was to determine the extent of hybridization and introgression between <i>Aconitum</i> species in a mountainous hybrid zone in the Tatra Mountains (Western Carpathians). We hypothesized that topography would affect their populations’ genetic structure. For this purpose, inter simple sequence repeat (ISSR) molecular markers and chloroplast DNA (cpDNA, region <i>trn</i>L(UAG)–<i>ndh</i>F) sequencing were used. The results revealed that diploid and tetraploid <i>Aconitum</i> species had specific cpDNA haplotypes, while the spontaneous hybrid species harbored a cpDNA haplotype typical for tetraploids. Bayesian STRUCTURE analysis showed that introgression occurred between diploid and tetraploid species above the tree line, where a spontaneous hybrid, a putative triploid <i>A. ×berdaui</i>, originated, probably via the triploid bridge mechanism. Molecular analysis of variance, principal coordinate analysis, and neighbor-net clustering revealed different genetic profiles of the diploids between neighboring mountain valleys. Hence, mountain topography, ridges, and valleys can form an effective geographical barrier, preventing gene flow over longer distances. Introgression happens near or above the tree line, where the hybridization zone is formed. In the introgressants, however, no morphological alterations were discernible.

Diversity of MHC class II DRB alleles and mitochondrial DNA in northern and eastern European pine marten, Martes martes (Mammalia: Mustelidae)

Abstract Four mitochondrial phylogroups are distinguished in the European pine marten (Martes martes), two of which, FNR1/2, are shared with the more easterly sister species, the sable (Martes zibellina). Here, we found that the phylogroup frequencies differed markedly between the southern Finland and western Russia populations in the eastern part of the range of Martes martes, suggesting differential introgression from M. zibellina in these regions. We also examined the diversity of a protein-coding gene, MHC class II DRB, in these two Martes species. We detected 16 functional Martes martes DRB alleles (Mama-DRBs), including several codons that seem to have undergone positive selection, and eight presumed pseudogenes (Mama-DRB*PSs); some alleles/pseudogenes were geographically widespread and others restricted. In a broader carnivoran DRB tree, all Mama-DRBs grouped within a mustelid clade, four in a basal group comprising alleles from early-diverged species and the others in a derived group containing alleles from more recently diverged species. Many alleles showed trans-species polymorphism, suggesting that Mama-DRBs have evolved under pathogen-driven balancing selection. Three of six Mama-DRBs and one of four pseudogenes shared with Martes zibellina were restricted to the FNR1/2 mitochondrial DNA phylogroups, pointing to the possibility that genetic introgression from Martes zibellina might have contributed to Mama-DRB diversity and thus adaptability.

Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae).

Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.

The application of Vavilov's approaches to the phylogeny and evolution of cultivated species of the genus Avena L.

The central problem that Vavilov was investigating was the overall concept of global plant genetic resources. The theoretical basis of this concept consisted of the law of homologous series in variation, research on the problem of species as a system, botanical and geographical bases of plant breeding, and the key theory of the centers of origin of cultivated plants. The VIR global collection of plant genetic resources collected by Vavilov and his associates from all over the world reflects the fullness of botanical, morphological and genetic diversity, and can be used for historical, evolutionary, phylogenetic and applied breeding research aimed at unlocking the potential of all the collection material. The whole diversity of cultivated oats, as was proved by Vavilov, had originated from segetal weeds. This process can be clearly traced in Spain on the example of the cultivated diploid species A. strigosa, A. abyssinica in Ethiopia, A. byzantina in Turkey and Iran, and on segetal forms of A. sativa. The studies of the morphological features as a whole do not yield a complete picture of the evolutionary and systematic status of some oat species and forms. The methods and approaches that use DNA markers and genomic technologies, and are promising for the study of oat polymorphism and phylogeny have been actively researched recently. A number of works devoted to the molecular aspects of the evolution and phylogeny of the genus Avena have recently appeared. The research uses various markers of genes, gene regions, intergenic spacers (internal and external), both nuclear and chloroplast and mitochondrial, genomic approaches and other modern methods. On the basis of a comprehensive study of the complete intraspecific diversity from different zones of the distribution range of cultivated oat species as well as on the basis of an analysis of data on the geography of forms and species distribution ranges, it was established that the process of hexaploid species formation also took place in the western part of the Mediterranean, and subsequently, when moving eastward, these forms started occupying all the vast spaces in the region of the Southwest Asian center, forming a large intraspecific diversity of wild forms and weedy ones in transit to cultivated hexaploid oat species. An analysis of the intraspecific diversity of landraces has specified the centers of morphogenesis of all cultivated oat species. The phylogenetic analysis of the representative intraspecific diversity of cultivated and wild Avena species carried out using next generation sequencing (NGS) showed that diploid species with A-genome variants are in fact not primary diploids, but a peculiar Mediterranean introgressive hybridization complex of species that sporadically enter into interspecific hybridization. It was established that the tetraploid cultivated species A. abyssinica had most likely originated from the wild A. vaviloviana. An analysis of the ways of A. sativa and A. byzantina domestication showed that the most widespread ribotype of the A. sativa hexaploid was inherited from A. ludoviciana, and the second most widespread one, from A. magna, while A. byzantina has two unique ribotype families, most likely inherited from an extinct oat species or a still undiscovered cryptospecies.