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Telomere lengths and telomere dynamics can correlate with lifespan, behaviour and individual quality. Such relationships have spurred interest in understanding variation in telomere lengths and their dynamics within and between populations. Many studies have identified how environmental processes can influence telomere dynamics, but the role of genetic variation is much less well characterized. To provide a novel perspective on how telomeric variation relates to genetic variability, we longitudinally sampled individuals across a narrow hybrid zone (n = 127 samples), wherein two Manacus species characterized by contrasting genome‐wide heterozygosity interbreed. We measured individual (n = 66) and population (n = 3) differences in genome‐wide heterozygosity and, among hybrids, amount of genetic admixture using RADseq‐generated SNPs. We tested for population differences in telomere lengths and telomere dynamics. We then examined how telomere lengths and telomere dynamics covaried with genome‐wide heterozygosity within populations. Hybrid individuals exhibited longer telomeres, on average, than individuals sampled in the adjacent parental populations. No population differences in telomere dynamics were observed. Within the parental population characterized by relatively low heterozygosity, higher genome‐wide heterozygosity was associated with shorter telomeres and higher rates of telomere shortening—a pattern that was less apparent in the other populations. All of these relationships were independent of sex, despite the contrasting life histories of male and female manakins. Our study highlights how population comparisons can reveal interrelationships between genetic variation and telomeres, and how naturally occurring hybridization and genome‐wide heterozygosity can relate to telomere lengths and telomere dynamics. [ABSTRACT FROM AUTHOR]

Interspecific hybridization has been historically neglected in research and conservation practice, but it is a common phenomenon in nature, and several models have been developed to characterize it genetically. Even though Trichechus inunguis (Amazonian manatee) and T. manatus (West Indian manatee) exhibit large morphological, karyotypic, and molecular differences, a hybrid zone was identified on the northern coast of South America, from the Amazon River estuary toward the Guianas coastline. Two major populations or evolutionarily significant units (ESUs) within T. manatus, namely, the Caribbean and Atlantic, were separated and their differentiation was likely promoted or reinforced by the interspecific hybridization zone. We used nuclear and mtDNA sequences to reconstruct manatee speciation, population diversification through time and space, and secondary contact, which resulted in a hybrid zone. In this hybrid zone, the genetic contribution of each parental species was estimated, and different models for generating the current scenario were tested using statistical phylogeographic tools. All the results suggest a long hybridization history, during which a stable and structured hybrid swarm is generated. The coastline hybrid zone is composed of individuals with a lesser genomic contribution from T. inunguis; this zone works as a genetic sink that restricts gene flow between neighbouring Atlantic (Brazil) and Caribbean (all others) T. manatus populations, which further reinforces the isolation and differentiation of the Brazilian manatees. [ABSTRACT FROM AUTHOR]

Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross‐mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross‐ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross‐ploidy hybridisation has been confirmed with genetic data. These results show cross‐ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross‐ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross‐ploidy hybrid speciation shows the potential for important evolutionary outcomes. [ABSTRACT FROM AUTHOR]

Hybridisation is commonly observed in geographical zones of contact between distinct lineages. These contact zones have long been of interest for biogeographers because they provide insight into the evolutionary and ecological processes that influence the distribution of species as well as the process of speciation. Here we review research on hybrid zones and zones of past introgression, both terrestrial and marine, in Aotearoa New Zealand. Many of New Zealand's hybrid zones occur between lineages or species that diverged prior to the Last Glacial Maximum (LGM), with numerous divergences dating to the early Pleistocene or Pliocene. Few secondary contact zones have been detected in terrestrial plants and in marine taxa. This may reflect a lack of the intensive sampling required to detect hybrid zones in these groups but for plants may also indicate widespread Pleistocene survival across the country. Lastly, we suggest avenues for research into New Zealand hybrid zones that are likely to be fruitful. [ABSTRACT FROM AUTHOR]

Genetic introgression, allele exchange across species boundaries, is a commonly recognized feature of animal evolution. Under such a paradigm, contemporary contact zones provide first-hand insight into the geographic, phenotypic, and genetic details of introgression. Also, when mate choice phenotypes are conspicuous and variable in hybrids, contact zones provide potential insight into how sexual selection interacts with species boundary maintenance, particularly when postzygotic reproductive isolation is weak. The Habronattus americanus subgroup includes several recently evolved jumping spider species, with an estimated age of about 200,000 yr, and substantial evidence for hybridization and introgression. We explored a contact zone involving H. americanus (Keyserling, 1885) and H. kubai (Griswold, 1979) on Mount Shasta, CA, in alpine habitats that would have been unavailable (under ice) at the Last Glacial Maximum. We characterized morphological diversity within the contact zone, including the fine-scale geographic distribution of hybrid and parental individuals, and assessed genetic variation using ddRADseq data. Combined results indicate a lack of measured genomic differentiation between specimens with distinct morphologies, including individuals with phenotypes of the parental species. We identified a diverse array of hybrid morphologies, with phenotypic evidence for backcrossing, essentially forming a phenotypic bridge between parental taxa. The study area is characterized by more hybrid than parental individuals, with a significantly larger number of red-palped morphologies than white- and/or yellow-palped morphologies; the novel, white-palped phenotype is perhaps transgressive. Overall, these results contribute to a better understanding of the expected ebb and flow of lineage interactions during the early stages of speciation. [ABSTRACT FROM AUTHOR]

The research into the structure, population and genetic patterns of formation and long-term existence of natural hybrid zones is of paramount importance for modern biology and the theory of evolution. The article presents the research results on the 22-year monitoring (2002–2023) of a hybrid zone and hybrid colonies of russet (Spermophilus major Pallas, 1778) and yellow (Spermophilus fulvus Lichtenstein, 1823) ground squirrels. This hybrid zone arose as a result of active dispersal of S. major to the south in the Saratov Trans-Volga region in the early 2000s. Twelve rodent colonies attributed to different research periods were studied. A total of 405 individuals (including 103 individuals of S. major, 52 individuals of S. fulvus, and 250 genetically confirmed interspecific hybrids) were trapped and sampled. Based on evidence, the article examines the structure and factors for formation of the hybrid zone between russet and yellow ground squirrels. Hybrid colony features and the evolution of hybrid population are considered. Introgressive hybridization between russet and yellow ground squirrels clearly manifests itself towards actively dispersing S. major. The revealed structural and genetic features of the hybrid zone between S. major and S. fulvus have enabled it to be termed as a bimodal hybrid zone of an ecological type with introgressive hybridization and stable hybrid colonies. [ABSTRACT FROM AUTHOR]

A major goal of evolutionary biology is to understand how sexual traits arise and diversify among populations. One way to address this objective is by studying sexual traits in closely related species and their hybrids. Here, we used this approach to study the evolution of elaborate behavioural display characteristics used during courtship. We focus on bearded manakins (genus: Manacus), where males of this avian clade perform an acrobatic jump-snap display to court females. Hybridization is common among Manacus taxa, and thus, we studied courtship dance behaviour in a hybrid population between golden-collared manakins, Manacus vitellinus , and white-collared manakins, Manacus candei. We found that, despite being genetically more similar to white-collared manakins, hybrid males performed key dance manoeuvres like golden-collared manakins. Hybrids performed other dance manoeuvres intermediate to the two species, or more like their white-collared parents. Select components of the birds' dance routines may have therefore introgressed from the golden-collared population into the white-collared populations. We hypothesize that such modular evolution occurs in response to sexual selection, whereby specific components of the bird's dance routine shift to yield a broader change in its functional appearance. • We studied courtship display in a hybrid population of manakin birds. • Hybrids performed many display traits intermediately to their parental lineages. • Some hybrid traits, however, resembled their high-performing parental line. • Asymmetrical introgression may account for display evolution in hybrids. [ABSTRACT FROM AUTHOR]

Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts. [ABSTRACT FROM AUTHOR]

Mating behavior can play a key role in speciation by inhibiting or facilitating gene flow between closely related taxa. Hybrid zones facilitate a direct examination of mating behavior and the traits involved in establishing species barriers. The long‐tailed finch (Poephila acuticauda) has two hybridizing subspecies that differ in bill color (red and yellow), and the yellow bill phenotype appears to have introgressed ~350 km eastward following secondary contact. To examine the role of mate choice on bill color introgression, we performed behavioral assays using natural and manipulated bill colors. We found an assortative female mating preference for males of their own subspecies when bill color was not manipulated. However, we did not find this assortative preference in trials based on artificially manipulated bill color. This could suggest that assortative preference is not fixed entirely on bill color and instead may be based on a different trait (e.g., song) or a combination of traits, or alternatively may be due to lower statistical power alongside the bill manipulations being unconvincing to the female choosers. Intriguingly, we find a bias in the inheritance of bill color in captive bred F1 hybrid females. Previous modeling suggests that assortative mate preference and this kind of partial dominance in the underlying genes may together contribute to introgression, making the genetic architecture of bill color in this system a priority for future research. [ABSTRACT FROM AUTHOR]

Semi‐permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre‐adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non‐trivial.We extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome‐scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals' hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along‐genome barrier strength heterogeneity allows for barrier regions to be identified. Furthermore, blocks of genetic material that have introgressed across a barrier are easily identified with high power.diem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demonstrations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier.diem is a genome analysis solution, which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier‐informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers. [ABSTRACT FROM AUTHOR]

Artificial structures, and particularly in urban settings, attract species showing similar ecological niches and provide nest‐sites for cavity‐breeding species. It is, however, unknown whether this proximity creates opportunities for hybridization and gene flow across related species. We investigated whether two colonial species, the Common Swift Apus apus and the Pallid Swift Apus pallidus, are experiencing gene flow by genotyping individuals that breed in sympatry in the town of Bastia (Corsica, France). We compared them with individuals sampled in colonies where a single species is breeding, in the Mediterranean region and in Switzerland. Our results provided evidence of gene flow between the two species and showed that introgression was not limited to sympatric urban colonies. Gene flow was asymmetrical, with more Pallid Swifts than Common Swifts showing evidence of mixed ancestry. Several individuals were assessed as late‐generation hybrids, suggesting that introgression between the two species was associated with their range expansion since the Last Glacial Maximum. However, we also identified individuals that exhibit the characteristics of recent‐generation hybrids, particularly in Bastia. This result suggests that hybridization between the two species is an ongoing and underestimated phenomenon, with a single observation of a mixed pair in the literature, and may be favoured by close proximity in urban colonies. [ABSTRACT FROM AUTHOR]

• Molecular data suggest that there are still populations of purebred Senecio hercynicus in the Bavarian and Bohemian Forest. • While western populations are strongly introgressed by S. ovatus genotypes, introgressive hybridisation is less pronounced towards the (north)east of the study area. • Regression analyses show that bio-climatological conditions do not shape hybridisation intensity patterns in the species pair. • The fate of Senecio hercynicus in a climate-change scenario is discussed. Genetic swamping by introgressive hybridisation threatens diversity, caused by climate warming particularly in mountainous regions worldwide. Recent studies resulted in a threatening perspective for Senecio hercynicus in the Bavarian Forest due to genetic swamping by introgressive hybridisation with its cogener S. ovatus. To examine the situation more closely, the distribution and hybridization of S. hercynicus and S. ovatus in high elevation regions of the Bavarian and Bohemian Forest was analyzed by restriction enzyme digestion of nrDNA ITS1 (PCR-RFLP; PCR restriction fragment length polymorphism). For a total of 706 samples from 94 different sample localities a hybrid index was inferred from the fragment band intensities after PCR-RFLP digestion. Boxplot diagrams of the hybrid indices show a tendency of western populations towards S. ovatus genotypes and for populations to the east towards S. hercynicus genotypes. When the hybrid index data was subjected to a regression analysis with nine factors (five habitat patterns inferred during sampling and four bioclimatic variables), only geographical longitude and latitude seemed to describe the observed distribution of S. hercynicus and S. ovatus significantly, arguing for the distribution and hybridisation patterns being shaped rather due to historical than to eco-climatological determinants. While a broad zone of hybridisation between the two species in the Bavarian and Bohemian Forest region was inferred, our study demonstrates that purebred S. hercynicus still exists and remnant stands of this species should be the target of species conservation measures. [ABSTRACT FROM AUTHOR]

Abstract Background Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson’s Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone. Results A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane’s Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection. Conclusions Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.

Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa in alpines, especially submerged macrophytes. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants across an altitudinal gradient. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to variation differences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands. [ABSTRACT FROM AUTHOR]

Abstract Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental‐like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits.

Abstract Background Invasion of organisms into new ecosystems is increasingly common, due to the global trade in commodities. One of the most complex post-invasion scenarios occurs when an invasive species is related to a native pest, and even more so when they can hybridize and produce fertile progeny. The global pest Helicoverpa armigera was first detected in Brazil in 2013 and generated a wave of speculations about the possibility of hybridization with the native sister taxon Helicoverpa zea. In the present study, we used genome-wide single nucleotide polymorphisms from field-collected individuals to estimate hybridization between H. armigera and H. zea in different Brazilian agricultural landscapes. Results The frequency of hybridization varied from 15 to 30% depending on the statistical analyses. These methods showed more congruence in estimating that hybrids contained approximately 10% mixed ancestry (i.e. introgression) from either species. Hybridization also varied considerably depending on the geographic locations where the sample was collected, forming a ‘mosaic’ hybrid zone where introgression may be facilitated by environmental and landscape variables. Both landscape composition and bioclimatic variables indicated that maize and soybean cropland are the main factors responsible for high levels of introgression in agricultural landscapes. The impact of multiple H. armigera incursions is reflected in the structured and inbred pattern of genetic diversity. Conclusions Our data showed that the landscape composition and bioclimatic variables influence the introgression rate between H. armigera and H. zea in agricultural areas. Continuous monitoring of the hybridization process in the field is necessary, since agricultural expansion, climatic fluctuations, changing composition of crop species and varieties, and dynamic planting seasons are some factors in South America that could cause a sudden alteration in the introgression rate between Helicoverpa species. Introgression between invasive and native pests can dramatically impact the evolution of host ranges and resistance management.

Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa in alpines, especially submerged macrophytes. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants across an altitudinal gradient. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to variation differences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.

Northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels are widespread species distributed across North America. Northern flying squirrels are common inhabitants of the boreal forest, also occurring in coniferous forest remnants farther south, whereas the southern flying squirrel range is centered in eastern temperate woodlands. These two flying squirrel species exhibit a hybrid zone across a latitudinal gradient in an area of recent secondary contact. Glaucomys hybrid offspring are viable and can successfully backcross with either parental species, however, the fitness implications of such events are currently unknown. Some populations of G. sabrinus are endangered, and thus, interspecific hybridization is a key conservation concern in flying squirrels. To provide a resource for future studies to evaluate hybridization and possible introgression, we sequenced and assembled a de novo long-read genome from a G. volans individual sampled in southern Ontario, Canada, while four short-read genomes (two G. sabrinus and two G. volans, all from Ontario) were resequenced on Illumina platforms. The final genome assembly consisted of approximately 2.40Gb with a scaffold N50 of 455.26Kb. Benchmarking Universal Single-Copy Orthologs reconstructed 3,742 (91.2%) complete mammalian genes and genome annotation using RNA-Seq identified the locations of 19,124 protein-coding genes. The four short-read individuals were aligned to our reference genome to investigate the demographic history of the two species. A principal component analysis clearly separated resequenced individuals, while inferring population size history using the Pairwise Sequentially Markovian Coalescent model noted an approximate species split 1 million years ago, and a single, possibly recently introgressed individual. [ABSTRACT FROM AUTHOR]

Abstract Background The hybridizing field crickets, Gryllus firmus and Gryllus pennsylvanicus have several barriers that prevent gene flow between species. The behavioral pre-zygotic mating barrier, where males court conspecifics more intensely than heterospecifics, is important because by acting earlier in the life cycle it has the potential to prevent a larger fraction of hybridization. The mechanism behind such male mate preference is unknown. Here we investigate if the female cuticular hydrocarbon (CHC) profile could be the signal behind male courtship. Results While males of the two species display nearly identical CHC profiles, females have different, albeit overlapping profiles and some females (between 15 and 45%) of both species display a male-like profile distinct from profiles of typical females. We classified CHC females profile into three categories: G. firmus-like (F; including mainly G. firmus females), G. pennsylvanicus-like (P; including mainly G. pennsylvanicus females), and male-like (ML; including females of both species). Gryllus firmus males courted ML and F females more often and faster than they courted P females (p

Studying species interactions at hybrid zones allows biologists to understand the forces that promote speciation. Hybridization among Sphyrapicus nuchalis, S. varius and S. ruber has long been acknowledged, and hybrid zones between S. nuchalis/S. ruber and S. varius/S. ruber have been characterized with both genetic and genomic data. Using a combination of next‐generation restriction site‐associated DNA sequencing (RAD‐Seq) and traditional genetic methods, we examined patterns of introgression in the poorly characterized S. nuchalis/S. varius contact zone; the two most similar species in the complex, though they are not each other's closest relatives. We found high introgression rates, with several early and many advanced generation hybrids along a 275 km stretch of Rocky Mountain foothill, pointing to a well‐established hybrid zone with hybrid individuals backcrossing with individuals from the parental species and each other. Plumage colouration in the hybrid zone was a relatively poor indicator of parental or hybrid status, which could be attributed to the possible involvement of few large effect genes. [ABSTRACT FROM AUTHOR]

Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts. [ABSTRACT FROM AUTHOR]

Aim: The amount of gene flow between parapatric species can be greatly variable depending on how species boundaries are maintained in respect to numerous genetic and ecological factors that affect the strength of reproductive isolation. We quantified this variability to understand its effect on the genetic integrity of a well‐studied pair of hybridizing amphibians. Location: Central and Eastern Europe. Taxa: The fire‐ and yellow‐bellied toads Bombina bombina and B. variegata. Methods: We first complemented the mitochondrial phylogeography of European Bombina by barcoding additional populations and built MaxEnt species distribution models to identify the routes of post‐glacial colonization that led to hybrid zone formation. Second, we targeted the areas of parapatry in Poland and Ukraine to assess nuclear admixture by population genetics (PCA, Bayesian clustering) of allozyme and genomic markers (RAD‐seq). Third, we harvested the rich Bombina literature to thoroughly compare the extent of geographical introgression across 11 transitions altogether, using cline analyses when possible. Results: We found sharp (2–11 km wide) but leaky transitions (geographically extensive traces of introgression) in all parapatric areas, either measured from a few allozymes or thousands of species‐diagnostic SNPs, and irrespective of the intraspecific lineages involved or the relative ages since first contact. Main conclusion: Bombina species are permeable to gene flow despite selection against hybrids that retards but cannot ultimately prevent putatively neutral introgression into the parental gene pools. Although local hybrid swarms face genetic assimilation, the species' integrities remain intact due to their large geographical ranges and ecological differentiation that enforces tight boundaries regardless of the biogeographical attributes of the contacts. Opposing the great variability of introgression patterns found between cryptic species, these results support that gene flow should not be viewed as a force of despeciation when reproductive isolation involves multiple intrinsic and extrinsic barriers. [ABSTRACT FROM AUTHOR]

Background: Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson's Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone. Results: A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane's Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection. Conclusions: Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent. [ABSTRACT FROM AUTHOR]

Non‐native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post‐introduction differentiation from native‐range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic‐derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein‐coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome‐wide trends and also diverged in parallel in both Atlantic‐derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre‐introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners. [ABSTRACT FROM AUTHOR]

Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental‐like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits. [ABSTRACT FROM AUTHOR]

Hybrid zones provide insights into the evolution of reproductive isolation. Sexual selection can contribute to the evolution of reproductive barriers, but it remains poorly understood how sexual traits impact gene flow in secondary contact. Here, we show that a recently evolved suite of sexual traits that function in male‐male competition mediates gene flow between two lineages of wall lizards (Podarcis muralis). Gene flow was relatively low and asymmetric in the presence of exaggerated male morphology and coloration compared to when the lineages share the ancestral phenotype. Putative barrier loci were enriched in genomic regions that were highly differentiated between the two lineages and showed low concordance between the transects. The exception was a consistently low genetic exchange around ATXN1, a gene that modulates social behavior. We suggest that this gene may contribute to the male mate preferences that are known to cause lineage‐assortative mating in this species. Although female choice modulates the degree of reproductive isolation in a variety of taxa, wall lizards demonstrate that both male‐male competition and male mate choice can contribute to the extent of gene flow between lineages. [ABSTRACT FROM AUTHOR]

We clarify the contribution of gene introgression in the recovery of the sable Martes zibellina, which has undergone significant population declines by the end of the nineteenth century. To verify the contribution of interspecific gene introgression, variation among the sable and the pine marten Martes martes was investigated utilizing restriction fragment analysis of the mitochondrial cytochrome b gene as a genetic markers. Evidence of symmetric introgression of mitochondrial genes between the species was detected. Frequency of marten haplotypes in the sable was 8.3%, while sable haplotype was found in 10% of the martens. The low frequency of mitochondrial DNA haplotype A indicates a comparatively low portion of the Eastern lines in the current sable populations in Western Siberia, despite the introduction of a large number of Eastern sable subspecies. These findings are of great importance for the conservation genetics of the sable. Overhunting of the sable as a more fur valuable species than the pine marten may lead to violation of the dynamic equilibrium between genetic systems of these related species. Mitochondrial markers can be used to identify genetic lines of other species or subspecies in hybrid zones. [ABSTRACT FROM AUTHOR]

Background: Invasion of organisms into new ecosystems is increasingly common, due to the global trade in commodities. One of the most complex post-invasion scenarios occurs when an invasive species is related to a native pest, and even more so when they can hybridize and produce fertile progeny. The global pest Helicoverpa armigera was first detected in Brazil in 2013 and generated a wave of speculations about the possibility of hybridization with the native sister taxon Helicoverpa zea. In the present study, we used genome-wide single nucleotide polymorphisms from field-collected individuals to estimate hybridization between H. armigera and H. zea in different Brazilian agricultural landscapes. Results: The frequency of hybridization varied from 15 to 30% depending on the statistical analyses. These methods showed more congruence in estimating that hybrids contained approximately 10% mixed ancestry (i.e. introgression) from either species. Hybridization also varied considerably depending on the geographic locations where the sample was collected, forming a 'mosaic' hybrid zone where introgression may be facilitated by environmental and landscape variables. Both landscape composition and bioclimatic variables indicated that maize and soybean cropland are the main factors responsible for high levels of introgression in agricultural landscapes. The impact of multiple H. armigera incursions is reflected in the structured and inbred pattern of genetic diversity. Conclusions: Our data showed that the landscape composition and bioclimatic variables influence the introgression rate between H. armigera and H. zea in agricultural areas. Continuous monitoring of the hybridization process in the field is necessary, since agricultural expansion, climatic fluctuations, changing composition of crop species and varieties, and dynamic planting seasons are some factors in South America that could cause a sudden alteration in the introgression rate between Helicoverpa species. Introgression between invasive and native pests can dramatically impact the evolution of host ranges and resistance management. [ABSTRACT FROM AUTHOR]

Background: The hybridizing field crickets, Gryllus firmus and Gryllus pennsylvanicus have several barriers that prevent gene flow between species. The behavioral pre-zygotic mating barrier, where males court conspecifics more intensely than heterospecifics, is important because by acting earlier in the life cycle it has the potential to prevent a larger fraction of hybridization. The mechanism behind such male mate preference is unknown. Here we investigate if the female cuticular hydrocarbon (CHC) profile could be the signal behind male courtship. Results: While males of the two species display nearly identical CHC profiles, females have different, albeit overlapping profiles and some females (between 15 and 45%) of both species display a male-like profile distinct from profiles of typical females. We classified CHC females profile into three categories: G. firmus-like (F; including mainly G. firmus females), G. pennsylvanicus-like (P; including mainly G. pennsylvanicus females), and male-like (ML; including females of both species). Gryllus firmus males courted ML and F females more often and faster than they courted P females (p < 0.05). Gryllus pennsylvanicus males were slower to court than G. firmus males, but courted ML females more often (p < 0.05) than their own conspecific P females (no difference between P and F). Both males courted heterospecific ML females more often than other heterospecific females (p < 0.05, significant only for G. firmus males). Conclusions: Our results suggest that male mate preference is at least partially informed by female CHC profile and that ML females elicit high courtship behavior in both species. Since ML females exist in both species and are preferred over other heterospecific females, it is likely that this female type is responsible for most hybrid offspring production. [ABSTRACT FROM AUTHOR]

Secondary contact zones are natural systems which can be efficiently used to measure genetic differentiation and gene flow and thus provide a good opportunity to assess the level of reproductive isolation between divergent evolutionary lineages. In this study, we used ten Z-linked and nine autosomal loci from seven chromosomes and twenty males to evaluate gene flow across a secondary contact zone between two mitochondrial lineages of the Eurasian Green Woodpecker (Picus viridis), that diverged around 1 million years ago. One lineage (Picus viridissharpei) is distributed throughout the Iberian Peninsula whereas the other one (Picus viridisviridis) is widespread across the Western Palearctic. These two lineages form a secondary contact zone in southern France. Formerly treated as two subspecies of Picus viridis, several authors have recently proposed assigning a specific rank to P. viridis sharpei and P. viridis viridis. Our results indicate no introgression of nuclear loci in allopatric populations located on both sides of the contact zone, which thus acts as an efficient barrier to gene flow. All males sampled within the contact zone and one male sampled near its eastern border were slightly admixed revealing that reproductive isolation between P. viridissharpei and P viridis viridis has not been completely achieved. In accordance with the geographical range of each lineage, the two admixed males sampled near the western border of the contact zone harboured a large proportion of P. viridissharpei alleles whereas admixed males sampled eastwardly near the Rhone Valley had a high proportion of P. viridis viridis alleles. Overall our results further support considering P. viridissharpei and P. viridisviridis as two biological species. [ABSTRACT FROM AUTHOR]

In hybrid zones in which two divergent taxa come into secondary contact and interbreed, selection can maintain phenotypic diversity despite widespread genetic introgression. Red‐breasted (Sphyrapicus ruber) and red‐naped (S. nuchalis) sapsuckers meet and hybridize along a narrow contact zone that stretches from northern California to southern British Columbia. We found strong evidence for changes in the structure of this hybrid zone across time, with significant temporal shifts in allele frequencies and in the proportions of parental phenotypes across the landscape. In addition to these shifts, we found that differences in plumage predict genetic differences (R2 = 0.80), suggesting that plumage is a useful proxy for assessing ancestry. We also found a significant bimodal distribution of hybrids across the contact zone, suggesting that premating barriers may be driving reproductive isolation, perhaps as a result of assortative mating based on plumage differences. However, despite evidence of selection and strong patterns of population structure between parental samples, we found only weak patterns of genetic divergence. Using museum specimens and genomic data, this study of sapsuckers provides insight into the ways in which phenotypic and genetic structure have changed over a 40‐year period, as well as insight into the mechanisms that may contribute to the maintenance of the hybrid zone over time. [ABSTRACT FROM AUTHOR]

Murine cytomegalovirus (MCMV) has been reported from house mice ( Mus musculus ) worldwide, but only recently from Eastern house mice ( M. m. musculus ), of particular interest because they form a semi-permeable species barrier in Europe with Western house mice, M. m. domesticus . Here we report genome sequences of EastMCMV (from Eastern mice), and set these in the context of MCMV genomes from genus Mus hosts. We show EastMCMV and WestMCMV are genetically distinct. Phylogeny splitting analyses show a genome wide (94%) pattern consistent with no West-East introgression, the major exception (3.8%) being a genome-terminal region of duplicated genes involved in host immune system evasion. As expected from its function, this is a region of maintenance of ancestral polymorphism: The lack of clear splitting signal cannot be interpreted as evidence of introgression. The EastMCMV genome sequences reported here can therefore serve as a well-described resource for exploration of murid MCMV diversity. [ABSTRACT FROM AUTHOR]

Abstract: Interactions between extrinsic factors, such as disruptive selection and intrinsic factors, such as genetic incompatibilities among loci, often contribute to the maintenance of species boundaries. The relative roles of these factors in the establishment of reproductive isolation can be examined using species pairs characterized by gene flow throughout their divergence history. We investigated the process of speciation and the maintenance of species boundaries between Pinus strobiformis and Pinus flexilis. Utilizing ecological niche modelling, demographic modelling and genomic cline analyses, we illustrated a divergence history with continuous gene flow. Our results supported an abundance of advanced generation hybrids and a lack of loci exhibiting steep transition in allele frequency across the hybrid zone. Additionally, we found evidence for climate‐associated variation in the hybrid index and niche divergence between parental species and the hybrid zone. These results are consistent with extrinsic factors, such as climate, being an important isolating mechanism. A build‐up of intrinsic incompatibilities and of coadapted gene complexes is also apparent, although these appear to be in the earliest stages of development. This supports previous work in coniferous species demonstrating the importance of extrinsic factors in facilitating speciation. Overall, our findings lend support to the hypothesis that varying strength and direction of selection pressures across the long lifespans of conifers, in combination with their other life history traits, delays the evolution of strong intrinsic incompatibilities. [ABSTRACT FROM AUTHOR]

Populations are often exposed to multiple sources of gene flow, but accounts are lacking of the population genetic dynamics that result from these interactions or their effects on local evolution. Using a genomic clines framework applied to 1,195 single nucleotide polymorphisms, we documented genomewide, locus-specific patterns of introgression between Choristoneura occidentalis biennis spruce budworms and two ecologically divergent relatives, C. o. occidentalis and Choristoneura fumiferana, that it interacts with at alternate boundaries of its range. We observe contrasting hybrid indexes between the two hybrid zones, no overlap in 'gene-flow outliers' (clines showing relatively extreme extents or rates of locus-specific introgression) and variable linkage disequilibrium among those outliers. At the same time, correlated genomewide rates of introgression between zones suggest the presence of processes common to both boundaries. These findings highlight the contrasting population genetic dynamics that can occur at separate frontiers of a single population, while also suggesting that shared patterns may frequently accompany cases of divergence-with-gene-flow that involve a lineage in common. Our results point to potentially complex evolutionary outcomes for populations experiencing multiple sources of gene flow. [ABSTRACT FROM AUTHOR]

Molecular approaches have proven efficient to identify cryptic lineages within single taxonomic entities. Sometimes these cryptic lineages maybe previously unreported or unknown invasive taxa. The genetic structure of the marine gastropod Stramonita haemastoma has been examined in the Western Mediterranean and North-Eastern Atlantic populations with mt DNA COI sequences and three newly developed microsatellite markers. We identified two cryptic lineages, differentially fixed for alternative mt DNA COI haplogroups and significantly differentiated at microsatellite loci. The mosaic distribution of the two lineages is unusual for a warm-temperate marine invertebrate with a teleplanic larval stage. The Atlantic lineage was unexpectedly observed as a patch enclosed in the north of the Western Mediterranean Sea between eastern Spain and the French Riviera, and the Mediterranean lineage was found in Macronesian Islands. Although cyto-nuclear disequilibrium is globally maintained, asymmetric introgression occurs in the Spanish region where the two lineages co-occur in a hybrid zone. A first interpretation of our results is mito-nuclear discordance in a stable postglacial hybrid zone. Under this hypothesis, though, the location of genetic discontinuities would be unusual among planktonic dispersers. An alternative interpretation is that the Atlantic lineage, also found in Senegal and Venezuela, has been introduced by human activities in the Mediterranean area and is introgressing Mediterranean genes during its propagation, as theoretically expected. This second hypothesis would add an additional example to the growing list of cryptic marine invasions revealed by molecular studies. [ABSTRACT FROM AUTHOR]