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Parapatrically distributed taxa pose a challenge for species delimitation due to the presence of gene flow and inherent arbitrariness of exactly defining the species boundaries in such systems. We tackled the problem of species delimitation in a parapatric species pair of Melitaea butterflies using two popular genomic methods—double digest restriction-site associated DNA sequencing (ddRAD) and target enrichment. We compared newly generated target enrichment dataset with 1733 loci to the already available ddRAD data from a previous study on the same set of specimens using a suite of phylogenetic, population genetic, and species delimitation methods. We recovered consistent phylogenetic relationships across the datasets, both demonstrating the presence of a genetically distinct Balkan lineage and paraphyly of Melitaea athalia with respect to Melitaea celadussa. Population genetic STRUCTURE analyses supported the presence of two species when using ddRAD data, but three species when using target enrichment, while a Bayes factor delimitation analysis found both two and three species scenarios equally decisive in both datasets. As the results obtained from both methods were largely congruent, we discuss some practical considerations and benefits of target enrichment over RAD sequencing. We conclude that the choice of method of genomic data collection does not influence the results of phylogenetic analyses at alpha taxonomic level, given a sufficient number of loci. Finally, we recommend a solution for delineating species in parapatric scenarios by proposing that parapatric taxa be consistently classified as subspecies or complete species, but not both, to promote taxonomic stability., This work was supported by Academy of Finland (grant no. 314702) to Marko Mutanen. Roger Vila was supported by Grant PID2019-107078GB-I00 funded by MCIN/AEI/ 10.13039/501100011033. Vlad Dincă was supported by the Academy of Finland (Academy Research Fellow, decision no. 328895).

The African Queen butterfly (Danaus chrysippus) is noted for its colour pattern polymorphism despite its aposematic and chemically defended lifestyle and for its infection with a male-killing endosymbiont (Spiroplasma). The polymorphism is largely restricted to east and central Africa where three different colour forms meet and interbreed in a large contact or hybrid zone. The primary objective of this study is to present recent data on the polymorphism, sex ratio and the incidence of male killing in D. chrysippus populations in Rwanda. We also report previously unpublished data from a random sample collected in 1914 in Bujumbura in Burundi and on the differential effects of weather on males and females in Ghana from 1972 to 1974. We sampled butterflies using butterfly nets and either marked, recorded and released them or kept specimens for subsequent examination. We used PCR/microscopy on the preserved specimens to detect Spiroplasma and the presence of a protozoan parasite (Ophryocystis). Our findings suggest that Rwanda lies close to the western edge of the joint distribution of both Spiroplasma and the polymorphism. Further biogeographical studies are recommended to test the hypothesis that male killing is restricted to the contact zone in which polymorphism is commonly observed.

Interspecific hybridization in the Cyprinidae family has been recorded worldwide, with Abramis brama (bream) and Rutilus rutilus (roach) as one of the often-reported hybridizing pairs. The only account of such an event in Bosnia and Herzegovina has been in Modrac Reservoir. Using morphological and molecular markers, the presence of hybrids was surveyed, the hybridization direction was determined and the hybrid group structure in this ecosystem was evaluated. Our findings confirmed unhindered natural hybridization between roach and bream in Modrac Reservoir. Over 50% of the hybrid specimens were classified as F2 hybrids by the NewHybrids software, while the rest were categorized as pure parental form, making it the first such finding in Europe. The analysis of mitochondrial cytochrome b showed that 90% of hybrid individuals were of bream maternal origin. The hybrid group expressed higher mean values of observed heterozygosity and gene diversity than both parental species. Signs of introgressive hybridization between parental species were detected. The hybrid zone of Modrac Reservoir appears to follow the intermediate or “flat” hybrid model based on the balanced distribution of parental and hybrid genotypes. Further investigation is needed to elucidate the factors that enable the survival and mating success of post-F1 individuals.

Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species' ranges, while putative cases of adaptive introgression had exceptionally wide clines with centers shifted towards one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per-generation dispersal between 200 and 400 meters, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range-limited species. This article is protected by copyright. All rights reserved.

Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army-ant-followers: the White-breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi.

Hybrid zones provide excellent opportunities to study speciation processes and ecological interactions between recently diverged taxa. Historically, hybrid zones have been divided into those in which fitness of hybrids is independent of the environment, and those in which environmental factors influence the fitness of different genotypes. The present study investigated the temporal genetic patterns at a location within a hybrid zone between the killifish Fundulus heteroclitus and F. grandis, in an effort to determine the extent and directionality of hybridization and the fitness of different genotypes. Fishes collected over the course of three years were placed into two age classes and genotyped at three nuclear loci and one mitochondrial locus that are highly differentiated between the species, allowing for comparison of genetic patterns between different age classes of the same cohorts. Individuals of hybrid descent were prevalent at the study site, the majority of which were likely advanced generation hybrids or backcrosses to one of the parental taxa. The cohort analyses revealed decreased abundance of both single and dilocus hybrid genotypes, and directional changes in allele frequency with increased age in some, but not all cohorts. These fluctuating patterns of selection across the course of the study suggest that fitness is likely strongly influenced by environmental factors.

Euschistus heros (Hemiptera: Pentatomidae) has two allopatric strains with a hybrid zone in central Brazil. Asymmetric dispersal and gene flow between these strains of E. heros have been observed, where the South strain (SS) moves more quickly to the northern regions of the country than the North strain (NS) to the southern areas. In addition, SS generally has a bigger body size and presents dark brown coloration, and NS is usually smaller in size and presents light brown coloration. Here, we studied the reproductive behavior and tested for the presence of assortative mating and reproductive barriers between the two allopatric strains of E. heros. Nonrandom mating was observed in the SS strain based on mating choice trials and the reproductive isolation indexes. SS females and males prefer to mate with their co-specific (same strain) partner, while NS insects showed no mating preference. The insect’s pronotum width was positively associated with the mating choice suggesting size-assortative mating in E. heros. Reciprocal crosses between strains yielded similar reproductive outputs when compared with pure strain crosses, suggesting similar fitness of hybrid pure strains. The asymmetric gene flow in the hybridization zone that favors SS seems to be associated with the reproductive behavior of the species, which favors the typical phenotype found in the SS populations.

Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.

Shifting range boundaries can lead to secondary contact of closely related species, which might in turn lead to hybridization when the evolution of reproductive isolation is incomplete. We examined winter nest use of northern (Glaucomys sabrinus (Shaw, 1801)) and southern (Glaucomys volans (Linnaeus, 1758)) flying squirrels in an area of recent secondary contact and known hybridization in Ontario, Canada, to test for evidence of reinforcement due to different and diverging nesting behaviours. We radio-collared 26 flying squirrels (12 G. sabrinus and 14 G. volans) between two survey periods (winters of 2008–2009 and 2019–2020) and identified all nest trees used by individuals throughout each winter. For each nest tree, we identified the nest type and collected tree classification information to compare differences in nest use between species. We also present a novel application of habitat suitability modelling to test for evidence of divergence in nest use through time, which would suggest reinforcement. We found southern flying squirrels used a higher proportion of cavities in large, hardwood trees, whereas northern flying squirrels used more external nests and softwood trees. Conditional probabilities provided some evidence for increased differentiation in nest use by flying squirrels through time. Overall, we found relatively little overlap in winter nest use between flying squirrel species, despite evidence for hybridization at this site, and some weak evidence for increased divergence between species in nest use over 11 years.

Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (FST = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (FST = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high FST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.

Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide-ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype-environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype-environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Sincebroad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature-associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature-related barriers to gene flow and/or temperature-driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype-environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population-level sensitivity to climate change and other stressors.

Hybridization has important effects on the evolutionary trajectories of natural populations but estimates of this process in the wild and at the individual-level are lacking. Justyn et al. attempted to fill this gap using the citizen science database eBird but there are limitations to this approach. Here, we outline and directly test these limitations using literature searches, case studies, and a comparison between eBird and Birds of North America (BNA), a database that documents hybridization using the scientific literature. We use a hybrid zone between Lazuli and Indigo buntings to highlight the importance of considering geographic range when estimating rates of hybridization and two literature searches to show the importance of considering cryptic hybrids (those that cannot be identified using phenotypic traits) when quantifying these rates. We also use BNA and a case study of hybrid White-faced and Glossy Ibises to show that citizen scientists are underreporting hybrids compared with experts. Justyn et al. highlighted an important gap in the literature, but their results likely represent the lower limit of hybridization between birds and a more nuanced interpretation of their results (e.g., considering extrinsic postzygotic selection) is needed.

A large number of genetic variation studies have identified cases of mitochondrial genome introgression in animals, indicating that reproductive barriers among closely related species are often permeable. Because of its sheer size, the impact of hybridization on the evolution of the nuclear genome is more difficult to apprehend. Only a few studies have explored it recently thanks to recent progress in DNA sequencing and genome assembly. Here, we analysed whole-genome sequence variation among multiple individuals of two sister species of leaf beetles inside their hybrid zone, in which asymmetric mitochondrial genome introgression had previously been established. We used a machine learning approach based on computer simulations for training to identify regions of the nuclear genome that were introgressed. We inferred asymmetric introgression of ≈2% of the genome, in the same direction that was observed for the mitochondrial genome. Because a previous study based on a reduced-representation sequencing approach was not able to detect this introgression, we conclude that whole-genome sequencing is necessary when the fraction of the introgressed genome is small. We also analysed the whole-genome sequence of a hybrid individual, demonstrating that hybrids have the capacity to backcross with the species for which virtually no introgression was observed. Our data suggest that one species has recently invaded the range of the other and/or some alleles that where transferred from the invaded into the invading species could be under positive selection and may have favoured the adaptation of the invading species to the Alpine environment., SCOPUS: ar.j, info:eu-repo/semantics/published

Diploid Odontophrynus cordobae and tetraploid Odontophrynus americanus coexist in syntopy in central Argentina, and recently a hybrid zone between them with numerous triploid individuals has been reported. Furthermore, hybrid polyploids with odd numbers of chromosome sets often exhibit low viability and fertility. Our aim was to test differences in age-related life history aspects influencing fitness in hybrids and their parental species, by comparing demographic and growth-related parameters. The mean age and snout-vent length at sexual maturity and adulthood did not differ significantly among taxa. Longevity and potential reproductive lifespan were one year higher in O. cordobae than O. americanus and hybrids. We did not find significant differences in growth parameters among taxa. Our study shows similar patterns of size and demographics parameters. Triploid hybrids have a similar longevity and viability to parental species. The age structure of triploids indicates that the hybridization process has a temporal continuity. The lack of observed differences among taxa in age-related life-history aspects indicates that hybrid fitness does not seem to differ from that of the parental species, and reinforce the idea of a potential fertility of hybrids. Besides, our results suggests that hybrids do not direct their resources more to growth than to reproduction, as would be expected if they were infertile. However, further studies are necessary to determine the reproductive capacity of the hybrids.

The green odorous frog (Odorrana margaretae) displays a circular distribution around the Sichuan Basin of western China and possesses multiple replicate hybrid zones between lineages with high levels of divergence. To gain an understanding of the speciation process, we obtained 1540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: the West, North & South, and East groups. Demographic inference showed that they were initially isolated at ~2 million years ago, and subsequent post-glacial expansion produced the current circular distribution with four secondary contact zones. Hybridization in those zones involved lineages with various levels of divergence and produced greatly different patterns of introgression. Contact zones between the East and North & South groups (E-S and E-N) had contrast admixture levels but both showed a general lack of potential barrier loci. Meanwhile, the reconnection of the West and North & South groups produced two contact zones along the rim of the Basin. The S-W zone had extensive admixture while the N-W zone had limited admixture within a narrow geographic distance. Both showed substantial barrier effects, and a large number of potential barrier loci were shared. We also detected strong coupling among these loci. The N-W hybrid zone involved two highly-diverged lineages (FST = 0.704) and many loci have reached fixation around the hybrid zone. This study system offers a unique opportunity to understand the dynamics of introgression in contact zones and the architecture of reproductive isolation at different stages of speciation.

Hybridization is an evolutionary process with wide-ranging potential outcomes, from providing populations with important genetic variation for adaptation to being a substantial fitness cost leading to extinction. Here, we focussed on putative hybridization between two morphologically distinct species of New Zealand grasshopper. We collected Phaulacridium marginale and Phaulacridium otagoense specimens from a region where mitochondrial introgression had been detected and where their habitat has been modified by introduced mammals eating the natural vegetation and by the colonization of many non-native plant species. In contrast to observations in the 1970s, our sampling of wild pairs of grasshoppers in copula provided no evidence of assortative mating with respect to species. Geometric morphometrics on pronotum shape of individuals from areas of sympatry detected phenotypically intermediate specimens (putative hybrids), and the distribution of phenotypes in most areas of sympatry was found to be unimodal. These results suggest that hybridization associated with anthropogenic habitat changes has led to these closely related species forming a hybrid swarm, with random mating. Without evidence of hybrid disadvantage, we suggest a novel hybrid lineage might eventually result from the merging of these two species.

The importance of hybridization in generating biological diversity has been historically controversial. Previously, inference about hybridization was limited by dependence on morphological data; with the advent of the next-generation sequencing tools for nonmodel organisms, the evolutionary significance of hybridization is more evident. Here, we test classic hypotheses of hybrid origins of two species in the Phlox pilosa complex. Morphological intermediacy motivated the hypotheses that Phlox amoena lighthipei and Phlox pilosa deamii were independent homoploid hybrid lineages derived from P. amoena amoena and P. pilosa pilosa. We use double-digest restriction site-associated DNA sequencing of individuals from throughout the range of these taxa to conduct the most thorough analysis of evolutionary history in this system to date. Surprisingly, we find no support for the hybrid origin of P. pilosa deamii or P. amoena lighthipei. Our data do identify a history of admixture in individuals collected at a contemporary hybrid zone between the putative parent lineages. We show that three very different evolutionary histories, only one of which involves hybrid origin, have produced intermediate or recombinant morphological traits between P. amoena amoena and P. pilosa pilosa. Although morphological data are still an efficient means of generating hypotheses about past gene flow, genomic data are now the standard of evidence for elucidating evolutionary history.

The saltmarsh sparrow Ammospiza caudacuta and Nelson's sparrow A. nelsoni differ in ecological niche, mating behavior, and plumage, but they hybridize where their breeding distributions overlap. In this advanced hybrid zone, past interbreeding and current backcrossing result in substantial genomic introgression in both directions, although few hybrids are currently produced in most locations. However, because both species are nonterritorial and have only brief male–female interactions, it is difficult to determine to what extent assortative mating explains the low frequency of hybrid offspring. Since females often copulate with multiple males, a role of sperm as a postcopulatory prezygotic barrier appears plausible. Here, we show that sperm length differs between the two species in the hybrid zone, with low among‐male variation consistent with strong postcopulatory sexual selection on sperm cells. We hypothesize that divergence in sperm length may constitute a reproductive barrier between species, as sperm length co‐evolves with the size of specialized female sperm storage tubules. Sperm does not appear to act as a postzygotic barrier, as sperm from hybrids was unexceptional., Sperm length differs between saltmarsh and Nelson's sparrows, two species that hybridize, and length correlates with both hybrid index (based on 135 SNPs) and plumage index. This divergence in sperm phenotype may act as a reproductive barrier between species.

It is increasingly recognised that intertaxon hybridisation is more common in vertebrates than previously thought. However, recent hybridisation has rarely been reported from wild marsupials, with only three instances of first generation (F1) hybrids reported, all in macropodids. In the 1990s a chromosomally anomalous population of black-footed rock-wallaby (Petrogale lateralis) was identified in the Townsend Ridges in central eastern Western Australia. Individuals from this population had chromosomes characteristic of two P. lateralis subspecies (P. l. centralis and P. l. kimberleyensis). This unusual mixture is suggestive of a novel hybrid zone between subspecies, but it could also represent a P. l. centralis population in which a 9–10 chromosome fusion has independently arisen. To test between these hypotheses, we compared mitochondrial DNA Control Region (CR) sequence data from Townsend Ridges individuals to published data for all P. lateralis subspecies. Two divergent lineages of CR haplotypes were identified at Townsend Ridges, suggesting that it represents a novel rock-wallaby hybrid zone, the third reported in the genus. While one CR haplotype clustered with those typical of P. l. centralis, the other Townsend Ridges haplotypes clustered with those from three different P. lateralis subspecies but not with P. l. kimberleyensis. Additional studies with multiple nuclear genes will be necessary to fully understand the nature of this novel hybrid zone.

Natural hybrid zones offer a powerful framework for understanding the genetic basis of speciation in progress because ongoing hybridization continually creates unfavorable gene combinations. Evidence indicates that postzygotic reproductive isolation is often caused by epistatic interactions between mutations in different genes that evolved independently of one another (hybrid incompatibilities). We examined the potential to detect epistatic selection against incompatibilities from genome sequence data using the site frequency spectrum (SFS) of polymorphisms by conducting individual-based simulations in SLiM. We found that the genome-wide SFS in hybrid populations assumes a diagnostic shape, with the continual input of fixed differences between source populations via migration inducing a mass at intermediate allele frequency. Epistatic selection locally distorts the SFS as non-incompatibility alleles rise in frequency in a manner analogous to a selective sweep. Building on these results, we present a statistical method to identify genomic regions containing incompatibility loci that locates departures in the local SFS compared with the genome-wide SFS. Cross-validation studies demonstrate that our method detects recessive and codominant incompatibilities across a range of scenarios varying in the strength of epistatic selection, migration rate, and hybrid zone age. Our approach takes advantage of whole genome sequence data, does not require knowledge of demographic history, and can be applied to any pair of nascent species that forms a hybrid zone.

The use of genomic and phenotypic data to scan for outliers is a mainstay for studies of hybridization and speciation. Geographic cline analysis of natural hybrid zones is widely used to identify putative signatures of selection by detecting deviations from baseline patterns of introgression. As with other outlier-based approaches, demographic histories can make neutral regions appear to be under selection and vice versa. In this study, we use a forward-time individual-based simulation approach to evaluate the robustness of geographic cline analysis under different evolutionary scenarios. We modelled multiple stepping-stone hybrid zones with distinct age, deme sizes, and migration rates, and evolving under different types of selection. We found that drift distorts cline shapes and increases false positive rates for signatures of selection. This effect increases with hybrid zone age, particularly if migration between demes is low. Drift can also distort the signature of deleterious effects of hybridization, with genetic incompatibilities and particularly underdominance prone to spurious typing as adaptive introgression. Our results suggest that geographic clines are most useful for outlier analysis in young hybrid zones with large populations of hybrid individuals. Current approaches may overestimate adaptive introgression and underestimate selection against maladaptive genotypes.

The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea,Bathymodiolusmussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of ~2500 orthologous genes, revealed that parental and hybrid mussels (F2–F4 generation) have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, redundancy analyses showed that geographic location of the mussels on the Mid-Atlantic Ridge explained most of the symbiont genetic variability compared to the other factors. We hypothesise that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels.

The exploration of hybrid zones and the intergenomic conflicts exposed through hybridization provide windows into the processes of divergence and speciation. Sex chromosomes and mitonuclear incompatibilities have strong associations with the genetics of hybrid dysfunction. In ZW sex-determining systems, maternal co-inheritance of the mitochondrial and W chromosomes immediately exposes incompatibilities between these maternal contributions of one species and the Z chromosome of another. We analyze mitochondrial and Z chromosome admixture in the long-tailed finch (Poephila acuticauda) of Australia, where hybridizing subspecies differ prominently in Z chromosome genotype and in bill color, yet the respective centers of geographic admixture for these two traits are offset by 350 km. We report two well-defined mitochondrial clades that diverged ∼0.5 million years ago. Mitochondrial contact is geographically co-located within a hybrid zone of Z chromosome admixture and is displaced from bill color admixture by nearly 400 km. Consistent with Haldane's rule expectations, hybrid zone females are significantly less likely than males to carry an admixed Z chromosome or have mismatched Z-mitochondrial genotypes. Furthermore, there are significantly fewer than expected mitonuclear mismatches in hybrid zone females and paternal backcross males. Results suggest a potential for mitonuclear/sex chromosome incompatibilities in the emergence of reproductive isolation in this system.

Sex chromosomes often bear distinct patterns of genetic variation due to unique patterns of inheritance and demography. The processes of mutation, recombination, genetic drift and selection also influence rates of evolution on sex chromosomes differently than autosomes. Measuring such differences provides information about how these processes shape genomic variation and their roles in the origin of species. To test hypotheses and predictions about patterns of autosomal and sex-linked genomic diversity and differentiation, we measured population genetic statistics within and between populations and subspecies of the barn swallow (Hirundo rustica) and performed explicit comparisons between autosomal and Z-linked genomic regions. We first tested for evidence of low Z-linked genetic diversity and high Z-linked population differentiation relative to autosomes, then for evidence that the Z chromosome bears greater ancestry information due to faster lineage sorting. Finally, we investigated geographical clines across hybrid zones for evidence that the Z chromosome is resistant to introgression due to selection against hybrids. We found evidence that the barn swallow mating system, demographic history and linked selection each contribute to low Z-linked diversity and high Z-linked differentiation. While incomplete lineage sorting is rampant across the genome, our results indicate faster sorting of ancestral polymorphism on the Z. Finally, hybrid zone analyses indicate barriers to introgression on the Z chromosome, suggesting that sex-linked traits are important in reproductive isolation, especially in migratory divide regions. Our study highlights how selection, gene flow and demography shape sex-linked genetic diversity and underlines the relevance of the Z chromosome in speciation.

The genetic diversity of Syphacia nematodes (intestinal parasites of rodents) was studied in the hybrid zone of two sister species of common voles, Microtus arvalis and Microtus obscurus, in the Oka River valley, east of Moscow. Syphacia nematodes of other rodent species (Microtus rossiaemeridionalis, Alexandromys oeconomus, Sylvaemus uralensis, and Apodemus agrarius) that inhabit the area were also studied. Phylogenetic trees for the studied nematodes were inferred from the analysis of nuclear ITS1+5.8S+ITS2, LSU rDNA, and mitochondrial CO1 gene partial sequences. Syphacia nematodes of the studied area form three well-defined clades in the phylogenetic tree of this genus. Morphological analysis revealed similarities between the obtained sequences with those of known Syphacia species from the GenBank database, which enabled identifying these three clades up to the species level: S. montana, S. agraria, and S. frederici. Russian haplotypes of Syphacia are different from West European and East Asian haplotypes with pronounced genetic distances. A high level of specificity was reported for two of these three species (S. frederici, only in Sylvaemus uralensis; S. agraria, only in Apodemus agrarius). S. montana was found in different species of voles. Remarkably, S. montana specimens from M. arvalis and M. obscurus were genetically uniform, while S. montana, specimens from hybrids between these two species formed a separate clade distant from those originating from non-hybridised hosts.

Populations or species exploiting different habitats can differ in sensory perception as a result of divergent adaptation. In bony fish, the water current is perceived via neuromasts, the end organ of the lateral line system. Although fish in different habitats are known to vary in neuromasts, we know little about the genetic basis for such variation. Here, we investigate the genetic basis for variation in supraorbital neuromasts in a hybrid zone between the Japanese gobies Gymnogobius breunigii and Gymnogobius castaneus. The former has supraorbital canal neuromasts with six cephalic pores, whereas the latter has only superficial neuromasts with no canals or pores in the supraorbital region. Our genomic analysis showed that G. breunigii and G. castaneus occur mainly in the lower and mid/upper reaches, respectively. In a river in northern Japan, hybrids were found at the sites between the habitats of the two species. These hybrids exhibited anomalies of cephalic pores. Using this hybrid zone, we conducted genome-wide association studies and identified one locus significantly associated with the number of pores. Genomic cline analysis in the hybrid zone demonstrated that this locus exhibited a higher introgression rate compared with the genomic background, indicating the possibility of adaptive introgression.

Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental‐selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid‐Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate‐driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species’ postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long‐term, west‐to‐east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.

Hybridization in nature offers unique insights into the process of natural selection in incipient species and their hybrids. In order to evaluate the patterns and targets of selection, we examine a recently discovered baboon hybrid zone in the Kafue River Valley of Zambia, where Kinda baboons (Papio kindae) and grey-footed chacma baboons (P. ursinus griseipes) coexist with hybridization. We genotyped baboons at 14,962 variable genome-wide autosomal markers using double-digest RADseq. We compared ancestry patterns from this genome-wide data set to previously reported ancestry from mitochondrial-DNA and Y-chromosome sources. We also fit a Bayesian genomic cline model to scan for genes with extreme patterns of introgression. We show that the Kinda baboon Y chromosome has penetrated the species boundary to a greater extent than either mitochondrial DNA or the autosomal chromosomes. We also find evidence for overall restricted introgression in the JAK/STAT signalling pathway. Echoing results in other species including humans, we find evidence for enhanced and/or directional introgression of immune-related genes or pathways including the toll-like receptor pathway, the blood coagulation pathway, and the LY96 gene. Finally we show enhanced introgression and excess chacma baboon ancestry in the sperm tail gene ODF2. Together, our results elucidate the dynamics of introgressive hybridization in a primate system while identifying genes and pathways possibly under selection.

Genetic exchange between independently evolving lineages may give rise to the formation of new taxa, and hypotheses for this have been derived from species with intermediate phenotypes, when compared to potential parental species. Goulet-Scott and collaborators (2021) evaluate such a hypothesis in a wildflower species complex by integrating genomic and trait information. They find no support for hybrid speciation, despite detecting signatures of genetic admixture in some individuals resulting from interspecific gene flow in a hybrid zone.

Identifying factors that create and maintain a hybrid zone is of great interest to ecology, evolution and, more recently, conservation biology. Here, we investigated the role of environmental features in shaping the spatial dynamics of a hybrid zone between the southern tigrina, Leopardus guttulus, and Geoffroy's cat, L. geoffroyi, testing for exogenous selection as the main force acting on its maintenance. These Neotropical felid species are mainly allopatric, with a restricted area of sympatry in the ecotone between the Atlantic Forest and Pampa biomes. As both biomes have experienced high rates of anthropogenic habitat alteration, we also analysed the influence of habitat conversion on the hybrid zone structure. To do this, we used 13 microsatellite loci to identify potential hybrids and generated ecological niche models for them and their parental species. We compared the influence of variables on parental species and hybrid occurrence and calculated the amount of niche overlap among them. Parental species showed different habitat requirements and predicted co-occurrence was restricted to the forest-grassland mosaic of the ecotone. However, hybrids were found beyond this area, mainly in the range of L. geoffroyi. Hybrids demonstrated higher tolerance to habitat alteration than parental types, with a probability of occurrence that was positively related with mosaics of cropland areas and remnants of natural vegetation. These results indicate that exogenous selection alone does not drive the dynamics of the hybrid zone, and that habitat conversion influences its structure, potentially favouring hybrids over parental species.

Mauldin et al. (2014) examined 103 woodrats collected in 1988 from a putative contact zone located in Major County, Oklahoma, and provided evidence for a substantial level of hybridization between Neotoma floridana and N. micropus. This site was resampled in 2010, with 42 woodrats collected, and again in 2011, when an additional 88 woodrats were collected from 11 localities along a transect extending northwest to southeast of the center of the hybrid zone. These specimens were examined to: 1) serve as independent data sets, separated by 22 years, for a temporal comparison of hybrid zone characteristics and 2) determine the geographic extent of genetic introgression between the two species. All individuals were genotyped at 11 genetic markers (eight microsatellite loci, one mitochondrial gene—Cytochrome b, and two nuclear introns—intron 2 of the vertebrate alcohol dehydrogenase gene and intron 7 of the beta-fibrinogen gene) that were shown to be informative in the original study. Levels of allelic introgression were assessed at 12 localities (11 new localities, as well as the previously sampled putative contact zone) to determine size and continuity of the hybrid zone. Expanded geographic sampling revealed evidence of genetic introgression at 11 of 12 localities, although only two localities were determined to be active areas of hybridization in 2011. The temporal comparison revealed that characteristics of the hybrid zone (i.e., frequency of hybridization, directionality, location of the zone, and ratios of hybrid classes) remained similar between sampling events. These findings suggest hybridization between these species is ongoing but is intermittent and potentially ephemeral in this region.

Secondary contact between closely related species can lead to the formation of hybrid zones, allowing for interspecific gene flow. Hybrid zone movement can take place if one of the species possesses a competitive advantage over the other, ultimately resulting in species replacement. Such hybrid zone displacement is predicted to leave a genomic footprint across the landscape in the form of asymmetric gene flow (or introgression) of selectively neutral alleles from the displaced to the advancing species. Hybrid zone movement has been suggested for marbled newts in the Iberian Peninsula, supported by asymmetric gene flow and a distribution relict (i.e., an enclave) of Triturus marmoratus in the range of T. pygmaeus. We developed a panel of nuclear and mitochondrial SNP markers to test for the presence of a T. marmoratus genomic footprint in the Lisbon peninsula, south of the enclave. We found no additional populations of T. marmoratus. Analysis with the software Structure showed no genetic traces of T. marmoratus in T. pygmaeus. A principal component analysis showed some variation within the local T. pygmaeus, but it is unclear if this represents introgression from T. marmoratus. The results may be explained by (a) species replacement without introgressive hybridization and (b) displacement with hybridization followed by the near‐complete erosion of the footprint by purifying selection. We predict that testing for a genomic footprint north of the reported enclave would confirm that species replacement in these marbled newts occurred with hybridization., Hybrid zone movement has been suggested in the marbled newts, supported by the discovery of a Triturus marmoratus enclave. Here, we tested for a genomic footprint of species replacement of the receding T. marmoratus by the advancing T. pygmaeus, employing 54 newly developed nuclear SNPs and one mitochondrial DNA marker. In the absence of genetic traces of T. marmoratus in T. pygmaeus, we propose two biogeographic scenarios of species replacement.

Significance In Baja California, the deserts meet the coastal dunes in a narrow transition visible even from satellite images. We study two species pairs of desert shrubs (Encelia) that occur across this transition. Although these species can interbreed, they remain distinct. Using a combination of genetics, field experiments, three-dimensional imaging, and physiological measurements, we show that natural selection helps counteract homogenizing effects of gene exchange. Different habitats of these species create multiple mechanisms of selection—drought, salinity, herbivory, and burial, which together maintain these species in their native habitats and their hybrids in intermediate habitats. This study illustrates how environmental factors influence traits and fitness and how these in turn can maintain species, highlighting the importance of natural selection in speciation., Natural selection is an important driver of genetic and phenotypic differentiation between species. For species in which potential gene flow is high but realized gene flow is low, adaptation via natural selection may be a particularly important force maintaining species. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of Encelia species hybridize at ecologically divergent parapatric boundaries, such mechanisms may maintain species boundaries throughout Encelia.

We studied the population genetic structure underlying the geographic variation in the structural colour of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colours of different reflectance wavelengths perceived as red, green and indigo. These forms occur parapatrically in an area of Japan. The colour variation was not related to variation in climatic factors. Using single nucleotide polymorphisms (SNPs) from restriction-site-associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red and east/red) by a combination of genetic clusters (west, south and east) and three colour forms. There were three transition zones for the colour forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colours. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident colour changes, which implies regionally specific selection on the different colours. In a genomewide association study, we identified four SNPs that were associated with the red/green or indigo colour and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different colour range. These loci may have controlled the transitions between different combinations of colours. Our study demonstrates that geographic colour variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colours, and the effects of different colour loci.

We examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most likely the result of human-mediated long-distance dispersal. For N. helvetica, we identified a southern and a northern population cluster, connected by broad-scale gene flow in a unimodal hybrid zone running across France. This pattern either reflects genetic divergence caused by allopatry in two microrefuges and subsequent secondary contact or introgression of foreign alleles into the southern cluster.

The dynamic biogeography of glacial refugia may cause complex patterns of genetic admixture between parapatric taxa, which in turn can mislead their systematics, diversity, and distributions. We investigated this issue for green toads (Bufotes) inhabiting the circum-Aegean region, a biodiversity hotspot of the Eastern Mediterranean. A previous phylogeographic study based on mitochondrial and microsatellite loci identified the hybrid zone between the European (viridis) and Anatolian (sitibundus) lineages of B. viridis all over the Balkan Peninsula, but subsequent range-wide genomic analyses (>1000 SNPs) located this transition in Turkey, a thousand kilometers eastwards. In order to clarify the diversity and taxonomy of the circum-Aegean populations, we reconciled these conflicting findings by integrating previous data with pure sitibundus individuals. Our results confirmed that the viridis/sitibundus hybrid zone extends in Western Anatolia, but that southeastern European populations feature cytonuclear discordances and a high and structured microsatellite diversity. This remarkable situation may stem from a massive geographic displacement of the hybrid zone during the last glacial fluctuations, an underappreciated yet seemingly common feature among the herpetofauna of the region. Our study thus contributes to the rising view that mitochondrial DNA can be a poor predictor of current phylogeographic structure, hence the need for genomic data, especially for narrowly distributed taxa. Finally, the analyses unambiguously support the distinction of a micro-endemic clade of green toads unique to some Cyclades islands, for which we provide a formal taxonomic description.

Siberian stone pine (Pinus sibirica) and Siberian dwarf pine (P. pumila) are widespread in northern Asiafive-needle pines from subgenus Strobus. The natural hybridization occurs in many regions where the species growtogether. Traditional hybrid zone model was considered in the paper and, based on the accumulated data, it is determinedwhich one corresponds to the hybrid zone of Siberian stone pine and Siberian dwarf pine. The paper presents argumentsin favor of the mosaic model.

Mating behaviour and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. We test how social networks within a hybrid population of California Callipepla californica and Gambel's quail Callipepla gambelii change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. To achieve these aims, we combine RFID association data, phenotypic data and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based on genetic ancestry, suggesting weak behavioural reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predicts patterns of parentage. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analysing links between social context and gene flow within wild populations.

Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps and geological faults. The morphological (colour pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within river systems and, consequently, the dynamics of gene flow between freshwater lineages/species.

Describing the structure and dynamics of hybrid zones has important consequences for our understanding of lineage diversification. Herbarium collections constitute an extensive, though often underutilized, morphological resource that can potentially be leveraged to identify and describe hybrid zones. We demonstrate the use of herbarium collections to describe the structure of a hybrid zone between two North American columbines, Aquilegia flavescens S. Watson and A. formosa Fisch. ex DC. Hybrid indices were calculated from floral morphology measurements and mapped using geolocation data, revealing an extensive and consistent pattern of floral intermediacy in several contact zones. Population phenotype samples from contact zones corroborate these findings and strongly suggest introgression. At one locality with a confirmed hybrid population, floral phenotypes show clinal variation in parental-type morphology along an elevational gradient, in the direction predicted by the divergent elevational distributions of these taxa. We argue that these patterns together reflect a habitat-associated mosaic hybrid zone, consistent with divergent ecological selection maintaining the structure of the hybrid zone.

Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and are stabilized is the tension zone model. This model predicts that hybrid zones widths are determined by a a balance between random dispersal into hybrid zones and selection against hybrids, and it does not formally account for local ecological gradients. Given the model’s simplicity, it provides a useful starting point for examining variation in hybrid zone widths across animals. Here we examine whether random dispersal and a proxy for selection against hybrids (mtDNA distance) can explain variation in hybrid zone widths across 135 hybridizing taxon pairs. We show that dispersal explains >30% of hybrid zone width variation across animal diversity and that mtDNA distance explains little variation. Clade-specific analyses revealed idiosyncratic patterns. Dispersal and mtDNA distance predict hybrid zone widths especially well in reptiles, while hybrid zone width scaled positively with mtDNA distance in birds, opposite predictions. Lastly, the data suggest that lower bounds on hybrid zone widths may be set by dispersal and the extent of molecular divergence, suggesting that hybrid zones are unlikely to form in restricted geographic spaces in highly dispersive and/or recently diverged taxa. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation, and more generally in the ecology of range boundaries.

While estimates of genetic divergence are increasingly used in molecular taxonomy, hybrid zone analyses can provide decisive evidence for evaluating candidate species. Applying a population genomic approach (RAD-sequencing) to a fine-scale transect sampling, we analyzed the transition between two Iberian subspecies of the common midwife toad (Alytes obstetricans almogavarii and A. o. pertinax) in Catalonia (northeastern Spain), which putatively diverged since the Plio-Pleistocene. Their hybrid zone was remarkably narrow, with extensive admixture restricted to a single locality (close to Tarragona), and congruent allele frequency clines for the mitochondrial (13 km wide) and the average nuclear genomes (16 km wide). We also fitted clines independently for 89 taxon-diagnostic SNPs: Most of them behave like the nuclear background, but a subset (13%) is completely impermeable to gene flow and might be linked to barrier loci involved in hybrid incompatibilities. Assuming that midwife toads are able to disperse in the area of contact, we conclude that these taxa experience partial reproductive isolation and represent incipient species, i.e. Alytes almogavarii and Alytes obstetricans. Interestingly, their evolutionary age and mitochondrial divergence fall below the thresholds proposed in molecular systematics studies, emphasizing the difficulty of predicting the outcome of secondary contacts between young lineages entering the grey zone of speciation., This study was funded by the Swiss National Science Foundation (fellowship P2LAP3_171818 to CD, and grant 31003A_166323 to N. Perrin).

The widespread and locally massive introgression of Y chromosomes of the eastern house mouse (Mus musculus musculus) into the range of the western subspecies (M. m. domesticus) in Central Europe calls for an explanation of its underlying mechanisms. Given the paternal inheritance pattern, obvious candidates for traits mediating the introgression are characters associated with sperm quantity and quality. We can also expect traits such as size, aggression or the length of generation cycles to facilitate the spread. We have created two consomic strains carrying the non-recombining region of the Y chromosome of the opposite subspecies, allowing us to study introgression in both directions, something impossible in nature due to the unidirectionality of introgression. We analyzed several traits potentially related to male fitness. Transmission of the domesticus Y onto the musculus background had negative effects on all studied traits. Likewise, domesticus males possessing the musculus Y had, on average, smaller body and testes and lower sperm count than the parental strain. However, the same consomic males tended to produce less- dissociated sperm heads, to win more dyadic encounters, and to have shorter generation cycles than pure domesticus males. These data suggest that the domesticus Y is disadvantageous on the musculus background, while introgression in the opposite direction can confer a recognizable, though not always significant, selective advantage. Our results are thus congruent with the unidirectional musculus → domesticus Y chromosome introgression in Central Europe. In addition to some previous studies, they show this to be a multifaceted phenomenon demanding a multidisciplinary approach.

AimsIn a contact zone between related taxa, phenotypic variation can result from genetic and/or environmental gradients. This study aimed to clarify the cause of phenotypic variation in leaf morphology of two Quercus crispula varieties—crispula (QCC) and mongolicoides (QCM)—in their contact zone along an altitudinal gradient.MethodsWe measured 6 morphological traits of leaves and recorded genotypes of 13 nuclear microsatellite loci for 48 individuals in the contact zone and 24 individuals in each of the reference populations of QCC and QCM. We constructed a model explaining the phenotypic variation (leaf morphology) in relation to environmental (altitude) and genetic (ancestry from the reference population) gradients.Important FindingsBoth morphological and genetic markers distinguished the two varieties in the reference populations well. We were able to confirm the power of both morphological and genetic markers. Individuals within the contact zone population had intermediate ancestry that was slightly biased to QCM ancestry, and the distribution of their morphologies overlapped with those of the two varieties in the reference populations. The effect of altitude on leaf morphological traits was significant, while that of ancestry was not. Distributions of ancestry and interclass heterozygosity in the contact zone population resembled those in F2 or later generation hybrids. These results indicate that in the contact zone between QCC and QCM, there is no ongoing hybridization, but environmental pressure has created an altitudinal gradient in morphological traits through phenotypic plasticity and/or variation in functional genes.