Adaptive introgression and maintenance of a trispecies hybrid complex in range‐edge populations of Populus

Demography-driven and adaptive introgression in a hybrid zone of the Armeria syngameon

Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats.

Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.

Genomic insights into hybrid zone formation: The role of climate, landscape, and demography in the emergence of a novel hybrid lineage

Population demographic changes, alongside landscape, geographic and climate heterogeneity, can influence the timing, stability and extent of introgression where species hybridise. Thus, quantifying interactions across diverged lineages, and the relative contributions of interspecific genetic exchange and selection to divergence at the genome-wide level is needed to better understand the drivers of hybrid zone formation and maintenance. We used seven latitudinally arrayed transects to quantify the contributions of climate, geography and landscape features to broad patterns of genetic structure across the hybrid zone of Populus trichocarpa and P. balsamifera and evaluated the demographic context of hybridisation over time. We found genetic structure differed among the seven transects. While ancestry was structured by climate, landscape features influenced gene flow dynamics. Demographic models indicated a secondary contact event may have influenced contemporary hybrid zone formation with the origin of a putative hybrid lineage that inhabits regions with higher aridity than either of the ancestral groups. Phylogenetic relationships based on chloroplast genomes support the origin of this hybrid lineage inferred from demographic models based on the nuclear data. Our results point towards the importance of climate and landscape patterns in structuring the contact zones between P. trichocarpa and P. balsamifera and emphasise the value whole genome sequencing can have to advancing our understanding of how neutral processes influence divergence across space and time.

Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights

Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.

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.

Enhanced and asymmetric signatures of hybridization at climatic margins: Evidence from closely related dioecious fig species

Hybridization plays a significant role in biological evolution. However, it is not clear whether ecological contingency differentially influences likelihood of hybridization, particularly at ecological margins where parental species may exhibit reduced fitnesses. Moreover, it is unknown whether future ecosystem change will increase the prevalence of hybridization. Ficus heterostyla and F. squamosa are closely related species co-distributed from southern Thailand to southwest China where hybridization, yielding viable seeds, has been documented. As a robust test of ecological factors driving hybridization, we investigated spatial hybridization signatures based on nuclear microsatellites from extensive population sampling across a widespread contact range. Both species showed high population differentiation and strong patterns of isolation by distance. Admixture estimates exposed asymmetric interspecific gene flow. Signatures of hybridization increase significantly towards higher latitude zones, peaking at the northern climatic margins. Geographic variation in reproductive phenology combined with ecologically challenging marginal habitats may promote this phenomenon. Our work is a first systematic evaluation of such patterns in a comprehensive, latitudinally-based clinal context, and indicates that tendency to hybridize appears strongly influenced by environmental conditions. Moreover, that future climate change scenarios will likely alter and possibly augment cases of hybridization at ecosystem scales.

Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia

Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.

Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation

Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.

Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an fbranch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.

Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex

Examining the frequency and distribution of hybrids across contact zones provide insights into the factors mediating hybridization. In this study, we examined the effect of habitat and climate on hybridization patterns for three phenotypically, genetically, and ecologically distinct groups of the Canada jay (Perisoreus canadensis) in a secondary contact zone in western North America. Additionally, we tested whether the frequency of hybridization involving the three groups (referred to as Boreal, Pacific and Rocky Mountain morphotypes) is similar across the hybrid zones or whether some pairs have hybridized more frequently than others. We reanalyzed microsatellite, mtDNA and plumage data, and new microsatellite and plumage data for 526 individuals to identify putative genetic and phenotypic hybrids. The genetically and phenotypically distinct groups are associated with different habitats and occupy distinct climate niches across the contact zone. Most putative genetic hybrids (86%) had Rocky Mountain ancestry. Hybrids were observed most commonly in intermediate climate niches and in habitats where Engelmann spruce (Picea engelmannii) overlaps broadly with boreal and subalpine tree species. Our finding that hybrids occupy intermediate climate niches relative to parental morphotypes matches patterns for other plant and animal species found in this region. This study demonstrates how habitat and climate influence hybridization patterns in areas of secondary contact and adds to the growing body of research on tri-species hybrid zones.

Admixture mapping and selection scans identify genomic regions associated with stomatal patterning and disease resistance in hybrid poplars

Variation in fitness components can be linked in some cases to variation in key traits. Metric traits that lie at the intersection of development, defense, and ecological interactions may be expected to experience environmental selection, informing our understanding of evolutionary and ecological processes. Here, we use quantitative genetic and population genomic methods to investigate disease dynamics in hybrid and non-hybrid populations. We focus our investigation on morphological and ecophysiological traits which inform our understanding of physiology, growth, and defense against a pathogen. In particular, we investigate stomata, microscopic pores on the surface of a leaf that regulate gas exchange during photosynthesis and are sites of entry for various plant pathogens. Stomatal patterning traits were highly predictive of disease risk. Admixture mapping identified a polygenic basis of disease resistance. Candidate genes for stomatal and disease resistance map to the same genomic regions and experienced positive selection. Genes with functions to guard cell homeostasis, the plant immune system, components of constitutive defenses, and growth-related transcription factors were identified. Our results indicate positive selection acted on candidate genes for stomatal patterning and disease resistance, potentially acting in concert to structure their variation in naturally formed backcrossing hybrid populations.

A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan-Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai-Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.

Population genomics of an emergent tri-species hybrid zone

Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is, however, evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression probably occurred before the formation of this tri-species hybrid zone, and might result from bridge hybridization, vagrancies, or other three-species interactions.

Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges

The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.

The Syngameon Enigma

Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.

Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation

The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.

Complex introgression among three diverged largemouth bass lineages

Hybrid zones between diverged lineages offer a unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships among these Mobile Delta bass populations, M. salmoides and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.

Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence

BACKGROUND

Natural hybridization can influence the adaptive response to selection and accelerate species diversification. Understanding the composition and structure of hybrid zones may elucidate patterns of hybridization processes that are important to the formation and maintenance of species, especially for taxa that have experienced rapidly adaptive radiation. Here, we used morphological traits, ddRAD-seq and plastid DNA sequence data to investigate the structure of a Rhododendron hybrid zone and uncover the hybridization patterns among three sympatric and closely related species.

RESULTS

Our results show that the hybrid zone is complex, where bi-directional hybridization takes place among the three sympatric parental species: R. spinuliferum, R. scabrifolium, and R. spiciferum. Hybrids between R. spinuliferum and R. spiciferum (R. ×duclouxii) comprise multiple hybrid classes and a high proportion of F₁ generation hybrids, while a novel hybrid taxon between R. spinuliferum and R. scabrifolium dominated the F₂ generation, but no backcross individuals were detected. The hybrid zone showed basically coincident patterns of population structure between genomic and morphological data.

CONCLUSIONS

Natural hybridization exists among the three Rhododendron species in the hybrid zone, although patterns of hybrid formation vary between hybrid taxa, which may result in different evolutionary outcomes. This study represents a unique opportunity to dissect the ecological and evolutionary mechanisms associated with adaptive radiation of Rhododendron species in a biodiversity hotspot.

Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin—probably Russian—of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration–selection balance underlying the genetic architecture of key adaptive quantitative traits.

Hybridization and introgression in sympatric and allopatric populations of four oak species

BACKGROUND

Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization.

RESULTS

Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844-0.944) and moderate differentiation (FST = 0.037-0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize.

CONCLUSIONS

Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.

Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization

Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.

Four Species Linked by Three Hybrid Zones: Two Instances of Repeated Hybridization in One Species Group (Genus Liolaemus)

Hybridization is an evolutionary process that can generate diverse outcomes, such as reinforcing species boundaries, generating new species, or facilitating the introgression of locally-adapted alleles into new genomic backgrounds. Liolaemus is a highly diverse clade of South American lizards with ~260 species and as many as ten new species are described each year. Previous Liolaemus studies have detected gene flow and introgression among species using phylogenetic network methods and/or through comparisons of nuclear and mitochondrial DNA patterns, yet no study has systematically studied hybrid zones between Liolaemus species. Here, we compared three hybrid zones between four species in the Liolaemus fitzingerii group of lizards in Central Argentina where two species, L. melanops and L. xanthoviridis, each hybridize with two other species (L. shehuen and L. fitzingerii). We sampled three transects that were each ~120 km in length and sequenced both mitochondrial and genome-wide SNP data for 267 individuals. In our analyses of nuclear DNA, we also compared bi-allelic SNPs to phased alleles (50 bp RAD loci). Population structure analyses confirmed that boundaries separating species are sharp, and all clines are &lt;65 km wide. Cline center estimates were consistent between SNPs and phased alleles, but cline width estimates were significantly different with the SNPs producing wider estimates. The mitochondrial clines are narrower and shifted 4–20 km southward in comparison to the nuclear clines in all three hybrid zones, indicating that either each of the species has sex-biased dispersal (males northward or females southward), the population densities are unequal, or that the hybrid zones are moving north over time. These comparisons indicate that some patterns of hybridization are similar across hybrid zones (mtDNA clines all narrower and shifted to the south), whereas cline width is variable. Hybridization in the L. fitzingerii group is common and geographically localized; further studies are needed to investigate whether hybrid zones act as hard species boundaries or promoters of speciation through processes such as reinforcement. Nonetheless, this study provides insights into both biotic and abiotic mechanisms helping to maintain species boundaries within the speciose Liolaemus system.

Growth-defense trade-offs masked in unadmixed populations are revealed by hybridization

Organisms are constantly challenged by pathogens and pests, which can drive the evolution of growth-defense strategies. Plant stomata are essential for gas exchange during photosynthesis and conceptually lie at the intersection of the physiological demands of growth and exposure to foliar fungal pathogens. Generations of natural selection for locally adapted growth-defense strategies can eliminate variation between traits, potentially masking trade-offs and selection conflicts that may have existed in the past. Hybrid populations offer a unique opportunity to reset the clock on selection and to study potentially maladaptive trait variation before selection removes it. We study the interactions of growth, stomatal, ecopysiological, and disease resistance traits in poplars (Populus) after infection by the leaf rust Melampsora medusae. Phenotypes were measured in a common garden and genotyped at 227K SNPs. We isolate the effects of hybridization on trait variance, discover correlations between stomatal, ecophysiology, and disease resistance, examine trade-offs and selection conflicts, and explore the evolution of growth-defense strategies potentially mediated by selection for stomatal traits on the upper leaf surface. These results suggest an important role for stomata in determining growth-defense strategies in organisms susceptible to foliar pathogens, and reinforces the contribution of hybridization studies toward our understanding of trait evolution.

Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis

Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.

Range and niche expansion through multiple interspecific hybridization: a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)

BACKGROUND

Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species.

RESULTS

The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap.

CONCLUSIONS

The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.

Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa

Comparing gene expression patterns and genetic polymorphisms between populations is of central importance for understanding the origin and maintenance of biodiversity. Based on population-specific gene expression levels and allele frequency differences, we sought to identify population divergence (PD) genes across the introgression-resistant genomic regions of Populus trichocarpa. Genes containing highly diverged loci [i.e., genetic divergence (GD)] or showing expression divergence (ED) between populations were widely distributed in the genome and substantially enriched in functional categories related to stress responses, disease resistance, timing of flowering, cell cycle regulation, plant growth, and development. Nine genomic regions showing evidence of strong positive selection were overlapped with GD genes, which had significant differences between Oregon (a southernmost peripheral deme) and the other demes. However, we did not find evidence that genes under positive selection show an enrichment for ED. PD genes and genes under selection pertained to the same gene classes, such as SERINE/CYSTEINE PROTEASE, ABC TRANSPORTER, GLYCOSYLTRANSFERASE and other transferases. Our analysis also revealed that GD genes were polymorphic within the species (41.9 ± 3.66 biallelic variants per gene), as previously reported in herbaceous plants. By contrast, ED genes contained less genetic variants (10.73 ± 1.14) and were likely highly expressed. In addition, we found that trans- rather than cis-acting variants considerably contribute to the evolution of >90% PD genes. Overall, this study elucidates that cohorts of PD genes agree with the general attributes of known speciation genes and GD genes will provide substrates for positive selection to operate on.

Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species

Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.

Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants

Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.

RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

Genetic adaptation of Tibetan poplar (Populus szechuanica var. tibetica) to high altitudes on the Qinghai-Tibetan Plateau

Plant adaptation to high altitudes has long been a substantial focus of ecological and evolutionary research. However, the genetic mechanisms underlying such adaptation remain poorly understood. Here, we address this issue by sampling, genotyping, and comparing populations of Tibetan poplar, Populus szechuanica var. tibetica, distributed from low (~2,000 m) to high altitudes (~3,000 m) of Sejila Mountain on the Qinghai-Tibet Plateau. Population structure analyses allow clear classification of two groups according to their altitudinal distributions. However, in contrast to the genetic variation within each population, differences between the two populations only explain a small portion of the total genetic variation (3.64%). We identified asymmetrical gene flow from high- to low-altitude populations. Integrating population genomic and landscape genomic analyses, we detected two hotspot regions, one containing four genes associated with altitudinal variation, and the other containing ten genes associated with response to solar radiation. These genes participate in abiotic stress resistance and regulation of reproductive processes. Our results provide insight into the genetic mechanisms underlying high-altitude adaptation in Tibetan poplar.

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.

Patterns of hybridization and cryptic introgression among one- and four-needled pinyon pines

BACKGROUND AND AIMS

Pinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex.

METHODS

We address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves.

KEY RESULTS

We found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression.

CONCLUSIONS

Our detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.

Oaks: an evolutionary success story

The genus Quercus is among the most widespread and species-rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro- and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.

Recent hybrids recapitulate ancient hybrid outcomes

Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z chromosome in both the old and contemporary hybrids. The same pattern of reduced L. melissa ancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in old or ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection and recombination affect hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown.

Complex patterns of differentiation and gene flow underly the divergence of aposematic phenotypes in Oophaga poison frogs

Hybridization and introgression can have complex consequences for both species evolution and conservation. Here, we investigated the origin and characteristics of a putative hybrid zone between two South American poison dart frog species, Oophaga anchicayensis and the critically endangered Oophaga lehmanni, which are heavily sought after on the illegal pet market. Using a combination of phenotypic (49 traits) and genomic (ddRADseq) data, we found that the putative hybrids are morphologically distinct from their parental species and confirmed genomic signatures of admixture in these populations. Several lines of evidence (hybrid indices, interspecific hybrid heterozygosity, genomic clines, comparisons with simulated hybrids and demographic modelling) support the conclusion that these populations are not comprised of early-generation hybrids and thus, they probably did not arise as a result of illegal translocations associated with wildlife trafficking. Instead, they probably represent an independent lineage which has persisted through isolation and has only relatively recently re-established gene flow with both parental species. Furthermore, we detected signals of differential introgression from parental species into these hybrid populations which suggest relaxed stabilizing selection on these aposematic colour morphs, potentially via context-dependent female choice. These populations thus provide a fascinating window into the role of hybridization, isolation and female choice in the diversification of South American poison dart frogs. In addition, our results underline the importance of landscape conservation measures to protect, not only known localities of nominal species, but also the phenotypic and genomic variation harbored by admixed lineages which represent crucial repositories for the impressive diversity in this system.

Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Applying whole-transcriptome sequencing and population genetic analyses, we present an example of ancient introgression from a cypress species (Cupressus gigantea) that occurs at higher latitude and elevation on the Qinghai-Tibet Plateau into a related species (C. duclouxiana), which has likely aided the latter species to extend its range by colonizing cooler and drier mountain habitats during postglacial periods. We show that 16 introgressed candidate adaptive loci could have played pivotal roles in response to diverse stresses experienced in a high-elevation environment. Our findings provide new insights into the evolutionary history of Qinghai-Tibet Plateau plants and the importance of introgression in the adaptation of species to climate change.

Influence of a climatic gradient on genetic exchange between two oak species

PREMISE

In plant groups with limited intrinsic barriers to gene flow, it is thought that environmental conditions can modulate interspecific genetic exchange. Oaks are known for limited barriers to gene flow among closely related species. Here, we use Quercus as a living laboratory in which to pursue a fundamental question in plant evolution: Do environmental gradients restrict or promote genetic exchange between species?

METHODS

We focused on two North American oaks, the rare Quercus dumosa and the widespread Q. berberidifolia. We sampled intensively along a contact zone in California, USA. We sequenced restriction site-associated DNA markers and measured vegetative phenotype. We tested for genetic exchange, the association with climate, and the effect on phenotype.

RESULTS

There is evidence for genetic exchange between the species. Admixed plants are found in areas of intermediate climate, while less admixed plants are found at the extremes of the climatic gradient. Genetic and phenotypic patterns are out of phase in the contact zone; some plants display the phenotype of one species but are genetically associated with another.

CONCLUSIONS

Our results support the hypothesis that a strong climatic gradient can promote genetic exchange between species. The overall weak correlation between genotype and phenotype in the contact zone between the species suggests that genetic exchange can lead to the breakdown of trait combinations used to define species. This incongruency predicts ongoing problems for conservation of Q. dumosa, with implications for conservation of other oaks.

The role of interspecific hybridization in adaptive potential at range margins

Is interspecific hybridization an ordinary part of species biology? And if so, how evolutionarily important is it? These questions have been discussed in the botanical literature, in one form or another, at least since J.P. Lotsy early in the last century. He coined the term syngameon, now defined as "a group of otherwise distinct species interconnected by limited gene exchange, i.e. the most inclusive interbreeding evolutionary unit" (Suarez-Gonzalez, Lexer, & Cronk, Biology Letters, 14, 20170688, ). North American poplars (Populus, Salicaceae) form one such syngameon. In this issue of Molecular Ecology, a new study (Chhatre, Evans, DiFazio, & Keller, Molecular Ecology, 27, ) uses three species from the North American poplar syngameon to tackle the twin issues of (a) the extent of gene exchange and (b) the significance of this gene exchange to the biology of these trees. They demonstrate that a hybrid zone exists where the ranges of Populus angustifolia and Populus balsamifera overlap in the Rocky Mountains, and postulate that this hybridization may facilitate population survival at the range edges. Indeed, the authors show that a remarkable number of loci are introgressing under selection. Very remarkably, they detect additional hybridity (making a trihybrid zone) with Populus trichocarpa (a species that does not occur in the area). Intriguingly, there is some genomic evidence of ancient introgression events. This suggests a model of episodic species divergence and hybridization, in which the syngameon is dynamic and behaving as a supraspecific metapopulation over geological time.

Hybridization and introgression during density-dependent range expansion: European wildcats as a case study

Interbreeding between historically allopatric species with incomplete reproductive barriers may result when species expand their range. The genetic consequences of such hybridization depend critically on the dynamics of the range expansion. Hybridization models during range expansion have been developed but assume dispersal to be independent from neighboring population densities. However, organisms may disperse because they are attracted by conspecifics or because they prefer depopulated areas. Here, through spatially explicit simulations, we assess the effect of various density-dependent dispersal modes on the introgression between two species. We find huge introgression from the local species into the invasive one with all dispersal modes investigated, even when the hybridization rate is relatively low. This represents a general expectation for neutral genes even if the dispersal modes differ in colonization times and amount of introgression. Invasive individuals attracted by conspecifics need more time to colonize the whole area and are more introgressed by local genes, whereas the opposite is found for solitary individuals. We applied our approach to a recent expansion of European wildcats in the Jura Mountains and the hybridization with domestic cats. We show that the simulations explained better the observed level of introgression at nuclear, mtDNA, and Y chromosome markers, when using solitary dispersal for wildcats instead of random or gregarious dispersal, in accordance with ecological knowledge. Thus, use of density-dependent dispersal models increases the predictive power of the approach.