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Hybridization and introgression are complex evolutionary mechanisms that can increase species diversity and lead to speciation, but may also lead to species extinction. In this study, we tested the presence and genetic consequences of hybridization between the rare and Ecuadorian endemic O. loxensis van der Werff and the widespread O. infrafoveolata van der Werff (Lauraceae). Phenotypically, some trees are difficult to identify, and we expect that some might in fact be cryptic hybrids. Thus, we developed nuclear microsatellites to assess the existence of hybrids, as well as the patterns of genetic diversity and population structure in allopatric and sympatric populations. The results revealed high levels of genetic diversity, even in the rare O. loxensis, being usually significantly higher in sympatric than in allopatric populations. The Bayesian assignment of individuals into different genetic classes revealed a complex scenario with different hybrid generations occurring in all sympatric populations, but also in allopatric ones. The absence of some backcrossed hybrids suggests the existence of asymmetric gene flow, and that some hybrids might be more fitted than others might. The existence of current and past interspecific gene flow also explains the blurring of species boundaries in these species and could be linked to the high rates of species found in Ocotea. [ABSTRACT FROM AUTHOR]

Summary: The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation.Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification.Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species.Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non‐model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity. [ABSTRACT FROM AUTHOR]

SUMMARY: The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome‐scale haplotype‐resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor‐AA and Ancestor‐BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high‐quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics. Significance Statement: Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. [ABSTRACT FROM AUTHOR]

Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid dysfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridize. Here, we use controlled hybrid crosses and high‐resolution respirometry to provide the first experimental evidence in a bird that inter‐lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two mitodiscordant backcrosses (with mismatched mitonuclear combinations) differs from one another, although they do not differ significantly from the parental groups or mitoconcordant backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies, the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild. [ABSTRACT FROM AUTHOR]

The genetic dissection of reproductive barriers between diverging lineages provides enticing clues into the origin of species. One strategy uses linkage analysis in experimental crosses to identify genomic locations involved in phenotypes that mediate reproductive isolation. A second framework searches for genomic regions that show reduced rates of exchange across natural hybrid zones. It is often assumed that these approaches will point to the same loci, but this assumption is rarely tested. In this perspective, we discuss the factors that determine whether loci connected to postzygotic reproductive barriers in the laboratory are inferred to reduce gene flow in nature. We synthesize data on the genetics of postzygotic isolation in house mice, one of the most intensively studied systems in speciation genetics. In a rare empirical comparison, we measure the correspondence of loci tied to postzygotic barriers via genetic mapping in the laboratory and loci at which gene flow is inhibited across a natural hybrid zone. We find no evidence that the two sets of loci overlap beyond what is expected by chance. In light of these results, we recommend avenues for empirical and theoretical research to resolve the potential incongruence between the two predominant strategies for understanding the genetics of speciation. [ABSTRACT FROM AUTHOR]

Trophic polymorphism and temporal reproductive isolation are the drivers of sympatric differentiation in many fish taxa. We present a new case of ecologically based diversification of Arctic charr in a Transbaikalian mountain lake inhabited by reproductively isolated dwarf and normal forms. These forms differ in size, diets and morphology and breed, respectively, in April–May and in September–October representing a rare example of sympatric spring- and autumn-spawning charr pair. Microsatellite analysis reveals clear-cut genetic differences and low-level hybridization between them. Dwarf form charr are planktivorous and manifest uniform slow growth. Normal form charr, though genetically homogeneous, are highly heterogeneous in size-at-age. They are subdivided into omnivorous small-size and piscivorous large-size groups, which can be considered as incipient forms at an early divergence stage. As evidenced by back-calculated growth data, their size-at-age heterogeneity results from highly variable individual growth patterns, which include different combinations of slow and fast growth periods presumably associated with spawning and non-spawning years. Growth acceleration in late ontogeny may result in the transformation of some normal charr from the smaller into the larger group during their lifetime. [ABSTRACT FROM AUTHOR]

We represent a comparative analysis of GBSS1 gene fragment sequences for a number of species related to Elymus caninus: Elymus prokudinii, Elymus viridiglumis, Elymus goloskokovii, as well as a number of morphologically deviating biotypes, inhabiting Russia and Kazakhstan. Microevolutionary relationships between species were assessed from dendrograms derived from sequences of exons and introns. In all taxa, the St subgenome was represented by St2 variants, rather typical of the North American ancestral line of Pseudoroegneria spicata than of the Asian line descending from Pseudoroegneria strigosa. All putative relatives of E. caninus had H1 subgenome variants linked around the Asian diploid carrier of the H genome from Hordeum jubatum and were divided into two subclades. One of them (H1‐1) contained most of the closely related E. caninus clones, including Elymus uralensis. Another subclade (H1‐2) consisted of five variants phylogenetically related to Elymus mutabilis. We have also studied reproductive relationships between species E. goloskokovii, E. prokudinii, and E. viridiglumis and the degree of their integration into the E. caninus complex. Biotypes included in sexual hybridization formed a single recombination gene pool, within which slight differences in reproductive compatibility were observed. A comprehensive study of microevolutionary differentiation of taxa showed the expediency of taxonomic revision. The species mentioned should probably be relegated to the infraspecific rank within E. caninus s. l. [ABSTRACT FROM AUTHOR]

Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection. [ABSTRACT FROM AUTHOR]

Haldane’s rule occupies a special place in biology as one of the few ‘rules’ of speciation, with empirical support from hundreds of species. And yet, its classic purview is restricted taxonomically to the subset of organisms with heteromorphic sex chromosomes. I propose explicit acknowledgement of generalized hypotheses about Haldane’s rule that frame sex bias in hybrid dysfunction broadly and irrespective of the sexual system. The consensus view of classic Haldane’s rule holds that sex-biased hybrid dysfunction across taxa is a composite phenomenon that requires explanations from multiple causes. Testing of the multiple alternative hypotheses for Haldane’s rule is, in many cases, applicable to taxa with homomorphic sex chromosomes, environmental sex determination, haplodiploidy, and hermaphroditism. Integration of a variety of biological phenomena about hybrids across diverse sexual systems, beyond classic Haldane’s rule, will help to derive a more general understanding of the contributing forces and mechanisms that lead to predictable sex biases in evolutionary divergence and speciation.

A hybridological study of biotypes of species close to Elymus caninus: E. prokudinii, E. viridiglumis, E. goloskokovii, as well as a number of morphologically deviant biotypes in Russia and Kazakhstan, was carried out. The objectives were to study the levels of reproductive relationships and the degree of integration of the species E. goloskokovii, E. prokudinii, and E. viridiglumis into the E. caninus complex. Our estimates of the seed fertility of natural parental biotypes were within 60–90 %. Among the combinations of crossing in F1, the highest seed setting was found in the hybrids formed by parental pairs from close habitats, regardless of the taxonomic rank of biotypes. The highest fertility values (55.6 and 46.1 %) were found in combinations involving E. caninus, E. viridiglumis and E. goloskokovii. It has been concluded that the biotypes of these species included in sexual hybridization form a single recombination gene pool, within which slight differences in reproductive compatibility are observed. The nature of the inheritance of the diagnostic features of lemmas“presence of trichomes” and“length of awns”, according to the digenic and monogenic type, respectively, is shown. The high seed fertility of the created hybrids and the presence of intermediate forms in the F2 generation according to distinctive features indicate the possibility of interspecific introgression when species grow together in natural populations. Thus, the assessment of the inheritance of diagnostic characters makes it possible to classify E. goloskokovii, E. prokudinii, and E. viridiglumis as intraspecific taxa of E. caninus s. l. Data were obtained on the morphological and reproductive properties of interspecific hybrids with the participation of the species E. mutabilis as a possible donor in the speciation of taxa close to E. caninus. In cross combinations of E. caninus × E. mutabilis and E. mutabilis × E. caninus, lower values of seed fertility of hybrids in the F1 and F2 generations were noted compared to hybrids between the species E. caninus, E. goloskokovii, E. prokudinii and E. viridiglumis. Nevertheless, on the basis of chorological and morphological criteria, we concluded that E. caninus and E. mutabilis are independent species.

Key message: Pollen tubes from closely related species and mutants lacking pollen tube MYB transcription factors are able to initiate FER/LRE-dependent synergid cell calcium oscillations. Reproductive isolation leads to the evolution of new species; however, the molecular mechanisms that maintain reproductive barriers between sympatric species are not well defined. In flowering plants, sperm cells are immotile and are delivered to female gametes by the pollen grain. After landing on the stigmatic surface, the pollen grain germinates a polarized extension, the pollen tube, into floral tissue. After growing via polar extension to the female gametes and shuttling its cargo of sperm cells through its cytoplasm, the pollen tube signals its arrival and identity to synergid cells that flank the egg. If signaling is successful, the pollen tube and receptive synergid cell burst, and sperm cells are released for fusion with female gametes. To better understand cell–cell recognition during reproduction and how reproductive barriers are maintained between closely related species, pollen tube-initiated synergid cell calcium ion dynamics were examined during interspecific crosses. It was observed that interspecific pollen tubes successfully trigger synergid cell calcium oscillations—a hallmark of reproductive success—but signaling fails downstream of key signaling genes and sperm are not released. This work further defines pollen tube–synergid cell signaling as a critical block to interspecific hybridization and suggests that the FERONIA/LORELEI signaling mechanism plays multiple parallel roles during pollen tube reception. [ABSTRACT FROM AUTHOR]

Sex chromosome turnover is the transition between sex chromosomes and autosomes. Although many cases have been reported in poikilothermic vertebrates, their evolutionary causes and genetic mechanisms remain unclear. In this study, we report multiple transitions between the Y chromosome and autosome in the Japanese Tago's brown frog complex. Using chromosome banding and molecular analyses (sex-linked and autosomal single nucleotide polymorphisms, SNPs, from the nuclear genome), we investigated the frogs of geographic populations ranging from northern to southern Japan of two species, Rana tagoi and Rana sakuraii (2n = 26). Particularly, the Chiba populations of East Japan and Akita populations of North Japan in R. tagoi have been, for the first time, investigated here. As a result, we identified three different sex chromosomes, namely chromosomes 3, 7, and 13, in the populations of the two species. Furthermore, we found that the transition between the Y chromosome (chromosome 7) and autosome was repeated through hybridization between two or three different populations belonging to the two species, followed by restricted chromosome introgression. These dynamic sex chromosome turnovers represent the first such findings in vertebrates and imply that speciation associated with inter- or intraspecific hybridization plays an important role in sex chromosome turnover in frogs. [ABSTRACT FROM AUTHOR]

Epistatic interactions between loci that reduce fitness in interspecies hybrids, Dobzhansky–Muller incompatibilities (DMIs), contribute genetically to the inviability and infertility within hybrid populations. It remains a challenge, however, to identify the loci that contribute to DMIs as causes of reproductive isolation between species. Here, we assess through forward simulation the power of evolve‐and‐resequence (E&R) experimental evolution of hybrid populations to map DMI loci. We document conditions under which such a mapping strategy may be most feasible and demonstrate how mapping power is sensitive to biologically relevant parameters such as one‐way versus two‐way incompatibility type, selection strength, recombination rate, and dominance interactions. We also assess the influence of parameters under direct control of an experimenter, including duration of experimental evolution and number of replicate populations. We conclude that an E&R strategy for mapping DMI loci, and other cases of epistasis, can be a viable option under some circumstances for study systems with short generation times like Caenorhabditis nematodes. [ABSTRACT FROM AUTHOR]

Summary: Oceanic islands offer valuable natural laboratories for studying evolution. The Izu Islands, with their recent geological origin, provide an exceptional opportunity to explore the initial evolution on oceanic islands. Another noteworthy aspect is the absence of bumblebee species on most Izu Islands.We used ecological, morphological, and molecular data to investigate the impact of bumblebee absence on the evolution of two closely related orchid species, Goodyera henryi and Goodyera similis, focusing on Kozu Island, the Izu Islands.Our investigation revealed that while G. henryi exclusively relies on a bumblebee species for pollination on the mainland, G. similis is pollinated by scoliid wasps on both the mainland and the island. Intriguingly, all specimens initially categorized as G. henryi on Kozu Island are hybrids of G. henryi and G. similis, leading to the absence of pure G. henryi distribution on the island. These hybrids are pollinated by the scoliid wasp species that also pollinates G. similis on the island.The absence of bumblebees might result in sporadic and inefficient pollination of G. henryi by scoliid wasps, consequently promoting hybrid proliferation on the island. Our findings suggest that the absence of bumblebees can blur plant species boundaries. [ABSTRACT FROM AUTHOR]

Identifying mechanisms limiting hybridization is a central goal of speciation research. Here, we studied premating and postmating barriers to hybridization between two ant species, Formica selysi and Formica cinerea. These species hybridize in the Rhône valley in Switzerland, where they form a mosaic hybrid zone, with limited introgression from F. selysi into F. cinerea. There was no sign of temporal isolation between the two species in the production of queens and males. With choice experiments, we showed that queens and males strongly prefer to mate with conspecifics. Yet, we did not detect postmating barriers caused by genetic incompatibilities. Specifically, hybrids of all sexes and castes were found in the field and F1 hybrid workers did not show reduced viability compared to nonhybrid workers. To gain insights into the cues involved in species recognition, we analyzed the cuticular hydrocarbons (CHCs) of queens, males, and workers and staged dyadic encounters between workers. CHC profiles differed markedly between species, but were similar in F. cinerea and hybrids. Accordingly, workers also discriminated species, but they did not discriminate F. cinerea and hybrids. We discuss how the CHC-based recognition system of ants may facilitate the establishment of premating barriers to hybridization, independent of hybridization costs.

Hybridization and introgression are complex evolutionary mechanisms that can increase species diversity and lead to speciation, but may also lead to species extinction. In this study, we tested the presence and genetic consequences of hybridization between the rare and Ecuadorian endemic O. loxensis van der Werff and the widespread O. infrafoveolata van der Werff (Lauraceae). Phenotypically, some trees are difficult to identify, and we expect that some might in fact be cryptic hybrids. Thus, we developed nuclear microsatellites to assess the existence of hybrids, as well as the patterns of genetic diversity and population structure in allopatric and sympatric populations. The results revealed high levels of genetic diversity, even in the rare O. loxensis, being usually significantly higher in sympatric than in allopatric populations. The Bayesian assignment of individuals into different genetic classes revealed a complex scenario with different hybrid generations occurring in all sympatric populations, but also in allopatric ones. The absence of some backcrossed hybrids suggests the existence of asymmetric gene flow, and that some hybrids might be more fitted than others might. The existence of current and past interspecific gene flow also explains the blurring of species boundaries in these species and could be linked to the high rates of species found in Ocotea.

For agriculturally important plants, pollination and herbivory are two ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus x raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and anti-herbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by two opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.

Euschistus stink bugs are important pests on soybean crops, including the Neotropical representatives Euschistus heros , Euschistus crenator, and Euschistus taurulus. Despite their importance, little genomic and chromosomal information is available. Genomic and chromosomal differences can play an important role in establishing reproductive barriers between species and populations. Here we investigate the chromosomes, some repetitive DNAs, and genome sizes of three Euschistus species, including two E. heros strains (North strain-NS and South strain-SS), to address chromosomal evolution and genomic differentiation. Our data reveal conservative karyotypes and only one possible inversion among Euschistus species. Moreover, we observe Y chromosome reorganization through differential microsatellite accumulation. The nuclear genome sizes are slightly variable among species. We noticed a differential accumulation of satellite DNAs, mainly on the Y chromosome, in the two strains of E. heros. Although typical meiotic behaviour, demonstrating full compatibility, was observed in hybrids despite interference on chiasmata frequency. This data shows that chromosomal and repetitive DNAs do not prevent secondary contact between E. heros strains, contributing to genetic variability in hybrids. Therefore, we provide data about Euschistus pests and their chromosomal characteristics, representing the first step in understanding their genomic organization and evolution. [ABSTRACT FROM AUTHOR]

Premise: Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts. Methods: Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries. Results: None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries. Conclusions: Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high‐throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes. [ABSTRACT FROM AUTHOR]

Background: In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species. [ABSTRACT FROM AUTHOR]

Sexual reproduction is the primary mode of reproduction in eukaryotes, but some organisms have evolved deviations from classical sex and switched to asexuality. These asexual lineages have sometimes been viewed as evolutionary dead ends, but recent research has revealed their importance in many areas of general biology. Our review explores the understudied, yet important mechanisms by which sperm‐dependent asexuals that produce non‐recombined gametes but rely on their fertilization, can have a significant impact on the evolution of coexisting sexual species and ecosystems. These impacts are concentrated around three major fields. Firstly, sperm‐dependent asexuals can potentially impact the gene pool of coexisting sexual species by either restricting their population sizes or by providing bridges for interspecific gene flow whose type and consequences substantially differ from gene flow mechanisms expected under sexual reproduction. Secondly, they may impact on sexuals' diversification rates either directly, by serving as stepping‐stones in speciation, or indirectly, by promoting the formation of pre‐ and postzygotic reproduction barriers among nascent species. Thirdly, they can potentially impact on spatial distribution of species, via direct or indirect (apparent) types of competition and Allee effects. For each such mechanism, we provide empirical examples of how natural sperm‐dependent asexuals impact the evolution of their sexual counterparts. In particular, we highlight that these broad effects may last beyond the tenure of the individual asexual lineages causing them, which challenges the traditional perception that asexual lineages are short‐lived evolutionary dead ends and minor sideshows. Our review also proposes new research directions to incorporate the aforementioned impacts of sperm‐dependent asexuals. These research directions will ultimately enhance our understanding of the evolution of genomes and biological interactions in general. [ABSTRACT FROM AUTHOR]

Hybridization—the interbreeding of different species—plays an integral role in the evolution of numerous bird species. However, it remains unclear how widespread this phenomenon is within and across different bird groups. Estimating the incidence of hybridization in different bird lineages can inform comparative analyses to uncover the evolutionary and ecological forces that promote or prevent the formation of hybrids. Estimates on a species level have varied from about 10% to almost 20% of hybridizing bird species. The variation among the latest estimates largely depends on the choice of global species checklists with differing decisions on the taxonomic status of certain (sub)species. However, the hybrid records in these estimates have generally been taken at face value. Detailed assessments of these records revealed that some cases are unreliable or incorrect. Removing of these faulty records and discovery of novel hybrids will result in a fluctuating percentage of hybridizing species that can best be captured in a living document (e.g., a regularly updated website or checklist). Estimating hybridization on an individual level is more challenging. A first attempt, using citizen science data from the eBird project, reported 0.064% hybrid individuals in the United States. This percentage is probably an underestimate due to underreporting of hybrids by birdwatchers and remains to be finetuned by considering other confounding factors, such as spatial and temporal variation in hybridization dynamics. Future efforts in estimating avian hybridization will need to rely on a combination of data sources and techniques, such as genetics, museum specimens, and citizen science. [ABSTRACT FROM AUTHOR]

The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages. [ABSTRACT FROM AUTHOR]

Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats. [ABSTRACT FROM AUTHOR]

Abstract Epistatic interactions between loci that reduce fitness in interspecies hybrids, Dobzhansky–Muller incompatibilities (DMIs), contribute genetically to the inviability and infertility within hybrid populations. It remains a challenge, however, to identify the loci that contribute to DMIs as causes of reproductive isolation between species. Here, we assess through forward simulation the power of evolve‐and‐resequence (E&R) experimental evolution of hybrid populations to map DMI loci. We document conditions under which such a mapping strategy may be most feasible and demonstrate how mapping power is sensitive to biologically relevant parameters such as one‐way versus two‐way incompatibility type, selection strength, recombination rate, and dominance interactions. We also assess the influence of parameters under direct control of an experimenter, including duration of experimental evolution and number of replicate populations. We conclude that an E&R strategy for mapping DMI loci, and other cases of epistasis, can be a viable option under some circumstances for study systems with short generation times like Caenorhabditis nematodes.

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad phylogenetic spectrum, assessed by whole exome data. Gametogenic pathways generally followed a continuum from sexual reproduction in hybrids between closely related evolutionary lineages to sterile or inviable crosses between distant lineages. However, most crosses resulted in a combination of sterile males and asexually reproducing females. Their gametes usually experienced problems in chromosome pairing, but females also produced a certain proportion of oocytes with premeiotically duplicated genomes, enabling their development into clonal eggs. Interspecific hybridization may thus commonly affect cell cycles in a specific way, allowing the formation of unreduced oocytes. The emergence of asexual gametogenesis appears tightly linked to hybrid sterility and constitutes an inherent part of the extended speciation continuum.

SUMMARY: Despite the importance of hybridization in evolution, the evolutionary consequence of homoploid hybridizations in plants remains poorly understood. Specially, homoploid hybridization events have been rarely documented due to a lack of genomic resources and methodological limitations. Actinidia zhejiangensis was suspected to have arisen from hybridization of Actinidia eriantha and Actinidia hemsleyana or Actinidia rufa. However, this species was very rare in nature and exhibited sympatric distribution with its potential parent species, which implied it might be a spontaneous hybrid of ongoing homoploid hybridization. Here, we illustrate the dead‐end homoploid hybridization and genomic basis of isolating barriers between A. eriantha and A. hemsleyana through whole genome sequencing and population genomic analyses. Chromosome‐scale genome assemblies of A. zhejiangensis and A. hemsleyana were generated. The chromosomes of A. zhejiangensis are confidently assigned to the two haplomes, and one of them originates from A. eriantha and the other originates from A. hemsleyana. Whole genome resequencing data reveal that A. zhejiangensis are mainly F1 hybrids of A. hemsleyana and A. eriantha and gene flow initiated about 0.98 million years ago, implying both strong genetic barriers and ongoing hybridization between these two deeply divergent kiwifruit species. Five inversions containing genes involved in pollen germination and pollen tube growth might account for the fertility breakdown of hybrids between A. hemsleyana and A. eriantha. Despite its distinct morphological traits and long recurrent hybrid origination, A. zhejiangensis does not initiate speciation. Collectively, our study provides new insights into homoploid hybridization in plants and provides genomic resources for evolutionary and functional genomic studies of kiwifruit. Significance Statement: This work demonstrates dead‐end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation, providing new insight into Actinidia speciation and generating valuable genomic resources for future evolutionary and functional genomics studies of kiwifruit. [ABSTRACT FROM AUTHOR]

The impact of post‐divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide‐ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post‐divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding‐window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D‐statistics and f‐branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools. [ABSTRACT FROM AUTHOR]

Ecological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution. [ABSTRACT FROM AUTHOR]

Abstract Sexual reproduction is the primary mode of reproduction in eukaryotes, but some organisms have evolved deviations from classical sex and switched to asexuality. These asexual lineages have sometimes been viewed as evolutionary dead ends, but recent research has revealed their importance in many areas of general biology. Our review explores the understudied, yet important mechanisms by which sperm‐dependent asexuals that produce non‐recombined gametes but rely on their fertilization, can have a significant impact on the evolution of coexisting sexual species and ecosystems. These impacts are concentrated around three major fields. Firstly, sperm‐dependent asexuals can potentially impact the gene pool of coexisting sexual species by either restricting their population sizes or by providing bridges for interspecific gene flow whose type and consequences substantially differ from gene flow mechanisms expected under sexual reproduction. Secondly, they may impact on sexuals' diversification rates either directly, by serving as stepping‐stones in speciation, or indirectly, by promoting the formation of pre‐ and postzygotic reproduction barriers among nascent species. Thirdly, they can potentially impact on spatial distribution of species, via direct or indirect (apparent) types of competition and Allee effects. For each such mechanism, we provide empirical examples of how natural sperm‐dependent asexuals impact the evolution of their sexual counterparts. In particular, we highlight that these broad effects may last beyond the tenure of the individual asexual lineages causing them, which challenges the traditional perception that asexual lineages are short‐lived evolutionary dead ends and minor sideshows. Our review also proposes new research directions to incorporate the aforementioned impacts of sperm‐dependent asexuals. These research directions will ultimately enhance our understanding of the evolution of genomes and biological interactions in general.

Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst‐case” scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that “taxonomic disaster zones” like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization. [ABSTRACT FROM AUTHOR]

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.

Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within-species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfing Ipomoea lacunosa into mixed-mating Ipomoea cordatotriloba in regions where they co-occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected in I. cordatotriloba than I. lacunosa. We also predicted that changes to reproductive barriers in sympatric I. cordatotriloba populations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species' ranges. Consistent with our first prediction, we found that sympatric and allopatric I. lacunosa produce the same number of seeds in crosses with I. cordatotriloba, whereas crosses between sympatric I. cordatotriloba and I. lacunosa are more successful than crosses between allopatric I. cordatotriloba and I. lacunosa. This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatric I. cordatotriloba, which could be caused by I. lacunosa alleles that have introgressed into I. cordatotriloba. We further demonstrated that changes to sympatric I. cordatotriloba have decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between-species isolation but can also contribute to isolation within a species.

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.

Sex chromosome turnover is the transition between sex chromosomes and autosomes. Although many cases have been reported in poikilothermic vertebrates, their evolutionary causes and genetic mechanisms remain unclear. In this study, we report multiple transitions between the Y chromosome and autosome in the Japanese Tago’s brown frog complex. Using chromosome banding and molecular analyses (sex-linked and autosomal single nucleotide polymorphisms, SNPs, from the nuclear genome), we investigated the frogs of geographic populations ranging from northern to southern Japan of two species, Rana tagoi and Rana sakuraii (2n = 26). Particularly, the Chiba populations of East Japan and Akita populations of North Japan in R. tagoi have been, for the first time, investigated here. As a result, we identified three different sex chromosomes, namely chromosomes 3, 7, and 13, in the populations of the two species. Furthermore, we found that the transition between the Y chromosome (chromosome 7) and autosome was repeated through hybridization between two or three different populations belonging to the two species, followed by restricted chromosome introgression. These dynamic sex chromosome turnovers represent the first such findings in vertebrates and imply that speciation associated with inter- or intraspecific hybridization plays an important role in sex chromosome turnover in frogs.

Simple Summary: The role of hybridization in biological evolution and cases of hybridogenic speciation is one of the most complicated but also interesting and actively studied topics. Russet ground squirrel Spermophilus major is known as a fine biological species according to a number of criteria—morphological, ecological, and behavioral, respectively. Nevertheless, a large body of evidence has accumulated on the hybridization of S. major with four neighboring Spermophilus species. Our goal was to identify their contribution to the nuclear and mitochondrial genome of S. major, and to propose a hypothesis describing the hybridization history in space and time. We found that 36% of S. major individuals had extraneous alleles, and every contacting species contributed to S. major's genetic variability. Our data suggested at least five independent hybridization events that were associated with shifts in the species ranges due to paleoclimate changes. Two of them were potentially accompanied by mitochondrial captures with replacement of the mitochondrial genome of one of the hybridizing species. We highlight the potential threat to the existence of S. major as a species under the current conditions of population decline along with the simultaneous influx of extraneous genes. It is also particularly important to emphasize the necessity of protecting this inhabitant of unique steppe communities. Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species. [ABSTRACT FROM AUTHOR]

According to the revisionist interpretation of Mendel's pea crosses, his primary aim was not to study the inheritance of traits. Instead, he was interested in the question raised by Linnaeus as to whether new species could arise from the hybridization of existing species. The genetic interpretation is therefore seen as ahistorical by the revisionists. This view goes back to the 1979 article "Mendel no Mendelian?" by the historian of science R.C. Olby. A closer analysis shows that Olby implicitly assumed Mendel adhered to the unusual strictest species definition for Pisum. However, we argue that Mendel only mentions the hypothetical application of this strict definition in his 1866 paper. Like most of his contemporaries, Mendel accepted variation within species where the differences between varieties and species were a matter of degree. After researching variable hybrids in peas (Pisum; 1854-1863), Mendel also studied constant hybrids in hawkweeds (Hieracium; 1866-1873), which he considered to be new species. There is no debate about the latter, but the matter becomes muddled because Olby lumps Pisum and Hieracium together, despite their having completely different reproduction systems. Based on newly discovered historical sources, we also dispute several other assumptions made by Olby. We do not consider Olby's claim that Mendel conducted the Pisum experiments to investigate species multiplication to be tenable. [ABSTRACT FROM AUTHOR]

Natural hybridization provides valuable insights into evolutionary processes, such as speciation and the forces driving or hindering it. Sulawesi tarsiers Tarsius dentatus and T. lariang hybridize within a limited area, suggesting selection against hybrids. Their species- and sex-specific duet songs might serve as a premating barrier in sympatry, especially if differences are strengthened by character displacement. Individuals of mixed origin might face disadvantages if they inherit intermediate song traits. To shed light on the processes shaping this hybrid zone, we analysed 55 duet songs from within and outside the zone. For females and males, we identified temporal and frequency-related parameters that differ between species. We inspected hybrid songs for intermediate characteristics and analysed purebred songs for character displacement in sympatry. Female hybrid songs (N = 2) were intermediate in four to five of six parameters; interpretation of male hybrid songs (N = 2) was inconclusive, because only two parameters were reliably quantifiable. There was no character displacement in female songs in sympatry (N = 11) compared with monospecific areas (N = 17). In male songs, interspecific differences in note rate were significantly larger within the hybrid zone (N = 8) compared with outside (N = 13). Intermediate song traits indicate inheritance and may disadvantage hybrids during mate choice. Character displacement in male songs is consistent with female mate choice, because females should opt for unmistakable signals to avoid costly hybridization. Our findings thus suggest that duet songs of T. lariang and T. dentatus play an important role in limiting this hybrid zone. [ABSTRACT FROM AUTHOR]

Background and Aims Grasses of the Festuca genus have complex phylogenetic relations due to morphological similarities among species and interspecific hybridization processes. Within Patagonian fescues, information concerning phylogenetic relationships is very scarce. In Festuca pallescens , a widely distributed species, the high phenotypic variability and the occurrence of interspecific hybridization preclude a clear identification of the populations. Given the relevance of natural rangelands for livestock production and their high degradation due to climate change, conservation actions are needed and knowledge about genetic variation is required. Methods To unravel the intraspecific phylogenetic relations and to detect genetic differences, we studied 21 populations of the species along its natural geographical distribution by coupling both molecular [internal transcribed spacer (ITS) and trn L-F markers] and morpho-anatomical analyses. Bayesian inference, maximum likelihood and maximum parsimony methods were applied to assemble a phylogenetic tree, including other native species. The morphological data set was analysed by discriminant and cluster analyses. Key Results The combined information of the Bayesian tree (ITS marker), the geographical distribution of haplotype variants (trn L-F marker) and the morpho-anatomical traits, distinguished populations located at the margins of the distribution. Some of the variants detected were shared with other sympatric species of fescues. Conclusions These results suggest the occurrence of hybridization processes between species of the genus at peripheral sites characterized by suboptimal conditions, which might be key to the survival of these populations. [ABSTRACT FROM AUTHOR]

Premise: Oceanic islands offer the opportunity to understand evolutionary processes underlying rapid diversification. Along with geographic isolation and ecological shifts, a growing body of genomic evidence has suggested that hybridization can play an important role in island evolution. Here we use genotyping‐by‐sequencing (GBS) to understand the roles of hybridization, ecology, and geographic isolation in the radiation of Canary Island Descurainia (Brassicaceae). Methods: We carried out GBS for multiple individuals of all Canary Island species and two outgroups. Phylogenetic analyses of the GBS data were performed using both supermatrix and gene tree approaches and hybridization events were examined using D‐statistics and Approximate Bayesian Computation. Climatic data were analyzed to examine the relationship between ecology and diversification. Results: Analysis of the supermatrix data set resulted in a fully resolved phylogeny. Species networks suggest a hybridization event has occurred for D. gilva, with these results being supported by Approximate Bayesian Computation analysis. Strong phylogenetic signals for temperature and precipitation indicate one major ecological shift within Canary Island Descurainia. Conclusions: Inter‐island dispersal played a significant role in the diversification of Descurainia, with evidence of only one major shift in climate preferences. Despite weak reproductive barriers and the occurrence of hybrids, hybridization appears to have played only a limited role in the diversification of the group with a single instance detected. The results highlight the need to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups prone to hybridization; patterns that might otherwise be obscured in species trees. [ABSTRACT FROM AUTHOR]

Understanding of the evolutionary history of two closely related canid sister taxa, the geographically restricted, arid-adapted Rüppell's fox (Vulpes rueppellii) and the widespread generalist red fox (Vulpes vulpes), has been hampered by limited sampling in the biogeographically complex region of North Africa and the Middle East. We sequenced mitochondrial DNA (mtDNA) cytochrome b and D-loop fragments from 116 samples for both species and combined these data with previously published sequences, resulting in 459 haplotypes. Obtained phylogenies showed high support for most branches, including for a newly described 'Palearctic clade' that includes North African and Asian individuals from both species. All V. rueppellii individuals fell within the Palearctic clade, forming two previously undescribed subclades that were intermingled with, but not shared with V. vulpes. Our robust placement of V. rueppellii within V. vulpes renders the latter paraphyletic. We propose three scenarios that could explain these observations: (1) rapid, recent speciation of V. rueppellii from V. vulpes , (2) incomplete lineage sorting, or (3) ancient divergence followed by introgression and secondary mtDNA similarity. The third scenario is in best agreement with evidence from the fossil record, and morphometric and ecological distinctiveness between the two taxa, and therefore seems most likely. [ABSTRACT FROM AUTHOR]

Introgressed DNA is often deleterious at many loci in the recipient species' genome, and is therefore purged by selection. Here, we use mathematical modeling and whole-genome simulations to study the influence of recombination on this process. We find that aggregate recombination controls the genome-wide rate of purging in the early generations after admixture, when purging is most rapid. Aggregate recombination is influenced by the number of chromosomes and heterogeneity in their size, and by the number of crossovers and their locations along chromosomes. A comparative prediction is that species with fewer chromosomes should purge introgressed ancestry more profoundly, and should therefore exhibit weaker genomic signals of historical introgression. Turning to within-genome patterns, we show that, in species with autosomal recombination in both sexes, more purging is expected on sex chromosomes than autosomes, all else equal. The opposite prediction holds for species without autosomal recombination in the heterogametic sex. Finally, positive correlations between recombination rate and introgressed ancestry have recently been observed within the genomes of several species. We show that these correlations are likely driven not by recombination's effect in unlinking neutral from deleterious introgressed alleles, but by recombination's effect on the rate of purging of deleterious introgressed alleles themselves. [ABSTRACT FROM AUTHOR]

Rapid adaptive radiation poses a distinct question apart from speciation and adaptation: what happens after one speciation event? That is, how are some lineages able to continue speciating through a rapid burst? This question connects global macroevolutionary patterns to microevolutionary processes. Here we review major features of rapid radiations in nature and their mismatch with theoretical models and what is currently known about speciation mechanisms. Rapid radiations occur on three major diversification axes - species richness, phenotypic disparity, and ecological diversity - with exceptional outliers on each axis. The paradox is that the hallmark early stage of adaptive radiation, a rapid burst of speciation and niche diversification, is contradicted by most existing speciation models which instead predict continuously decelerating speciation rates and niche subdivision through time. Furthermore, while speciation mechanisms such as magic traits, phenotype matching, and physical linkage of co-adapted alleles promote speciation, it is often not discussed how these mechanisms could promote multiple speciation events in rapid succession. Additional mechanisms beyond ecological opportunity are needed to understand how rapid radiations occur. We review the evidence for five emerging theories: 1) the 'transporter' hypothesis: introgression and the ancient origins of adaptive alleles, 2) the 'signal complexity' hypothesis: the dimensionality of sexual traits, 3) the connectivity of fitness landscapes, 4) 'diversity begets diversity', and 5) flexible stem/'plasticity first'. We propose new questions and predictions to guide future work on the mechanisms underlying the rare origins of rapid radiation.

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long‐read (Oxford nanopore) whole‐genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome‐wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry‐informative SVs exhibiting genomic clines that deviated from null expectations based on genome‐average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z‐linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation. [ABSTRACT FROM AUTHOR]

Understanding how reproductive isolation arises and accumulates between incipient species is an important goal of evolutionary biology. Patterns of interspecific hybridization in naturally occurring hybrid zones can provide an important insight into this process since they reflect the strength, symmetry and nature of reproductive barriers separating the species. Here we studied patterns of hybridization in two closely related passerine species, the common nightingale Luscinia megarhynchos and the thrush nightingale L. luscinia, that diverged ~1.8 Mya and co‐occur in a secondary contact zone spanning across Europe. Genome‐wide genotyping of more than three hundred individuals from the sympatric population and adjacent allopatric populations revealed that the vast majority of sympatric individuals were pure parental species. Only 6.5% of sympatric individuals were hybrids, from which 3.4% were F1 hybrids and 3.1% backcross hybrids from the first to the fifth backcross generation. Most F1 hybrids arose from the cross of a thrush nightingale female and a common nightingale male. F1 hybrids showed intermediate morphology and could be distinguished with high confidence from the parental species based on several diagnostic traits. However, backcrosses were morphologically difficult to distinguish from the parental species from which they inherited most of the genome. Our results suggest strong, yet incomplete, reproductive isolation between the two nightingale species both at a prezygotic and postzygotic level. Nightingales thus represent a useful model system for exploring the late stages of speciation with ongoing gene flow after secondary contact. [ABSTRACT FROM AUTHOR]

Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isolation among populations of the same species. Here, we investigated the population genetic outcomes of cascade reinforcement in North American chorus frogs (Hylidae: Pseudacris). Specifically, we estimated the frequency of hybridization among three taxa, assessed genetic structure within the focal species, P. feriarum, and ascertained the directionality of gene flow within P. feriarum across replicated contact zones via coalescent modeling. Through field observations and preliminary experimental crosses, we assessed whether hybridization is possible under natural and laboratory conditions. We found that hybridization occurs among P. feriarum and two conspecifics at a low rate in multiple contact zones, and that gene flow within the former species is unidirectional from allopatry into sympatry with these other species in three of four contact zones studied. We found evidence of substantial genetic structuring within P. feriarum including a divergent western allopatric cluster, a behaviorally‐distinct sympatric South Carolina cluster, and several genetically‐overlapping clusters from the remainder of the distribution. Furthermore, we found sub‐structuring between reinforced and nonreinforced populations in the two most intensely‐sampled contact zones. Our literature review indicated that P. feriarum hybridizes with at least five heterospecifics at the periphery of its range providing a mechanism for further intraspecific diversification. This work strengthens the evidence for cascade reinforcement in this clade, revealing the geographic and genetic landscape upon which this process can contribute to the proliferation of species. [ABSTRACT FROM AUTHOR]

Understanding how speciation occurs is central to biology. Gene flow between diverging taxa is correlated with geography and other aspects of speciation; therefore, the examination of gene flow during divergence is a potent approach to understanding the nature of speciation. Here, we inferred the speciation process of the sympatric rockfishes Sebastes steindachneri and Sebastes wakiyai in the north-western Pacific and its marginal seas based on genome-wide single nucleotide polymorphism and mitochondrial DNA data. Model-based demographic inference showed that gene flow between the two species was absent in the initial and late stages of divergence and present only in the middle stage. Population expansion occurred before or during the period of gene flow. The estimated timings of the initial divergence and population expansion fell within the Pleistocene, during which the seas currently inhabited by the two species were repeatedly isolated and reconnected. Contemporary isolation was supported by the absence of hybrids and the shared mitochondrial DNA haplotypes. Our results suggest that the two species initially diverged in allopatry, followed by secondary contact and introgression and by the completion of reproductive isolation. Given that complete isolation following secondary contact has rarely been tested or documented in marine organisms, we highlight the importance of careful consideration of alternative divergence scenarios to be tested, which should take into account the geological and environmental settings. [ABSTRACT FROM AUTHOR]

Northern Hemisphere forests changed drastically in the early Eocene, 50 million years ago, with the diversification of the oaks and their relatives. Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by the Fagaceae. Here I provide a chronicle to the results of a collaborative project (Zhou et al. 2022) that resolved major evolutionary events, including support for the origin of the oaks and evidence for ancient genome-wide signatures of hybridization across the family using analyses of nuclear and chloroplast genomes. Ecological correlations related to animal dispersal and mutualism with fungi are implicated in triggering waves of continental radiations beginning with the origin of major lineages just after the K-Pg (aka K-T) mass extinction event, 66 million years ago. Movement of genes between species was detected at multiple time scales suggesting that hybridization has long been part of the genetic legacy of Fagaceae. As the major oak lineages moved into their current ranges in the early Miocene, hybridization likely occurred between ancestral species of sections: Ilex and Cerris, Virentes and Quercus, Protobalanus and Quercus, and Ponticae and Quercus. Some of these historical hybridization events may have resulted in an adaptive advantage for the species involved. [ABSTRACT FROM AUTHOR]

Premise: Hybridization is increasingly being identified in the genomes of species across the tree of life, leading to a general recognition that hybridization plays an important role in the generation of species diversity. While hybridization may increase species diversity directly via the formation of new taxa through hybrid speciation, it may also act indirectly via the exchange of phenotypic and genetic variance between species, which may in turn stimulate future speciation events. Methods: Using high‐throughput sequence data, we resolved phylogenetic relationships and investigated the role of hybridization as a diversification mechanism in the shrubby beardtongues (Penstemon subgenus Dasanthera), a group of North American wildflowers that has undergone a recent and rapid adaptive radiation. Specifically, we tested four hypotheses of hybrid taxon formation resulting from hybridization between P. davidsonii and P. fruticosus. Results: Species tree inference supports the monophyly of subgenus Dasanthera and elucidates relationships between taxa distributed in the Cascades and Sierra Nevada Mountains. Results also provide evidence of gene flow between P. davidsonii and P. fruticosus and support at least one hybrid origin hypothesis (P. davidsonii var. menziesii) in a region of contemporary distributional overlap. Hybridization may have also been facilitated by historical overlap in geographic distribution caused by species' responses to climatic changes during the Pleistocene. Conclusions: Our results support a history of hybridization between focal taxa in a rapidly radiating clade of plants and more broadly contribute to our growing understanding of the role of hybridization as a diversification mechanism in plants. [ABSTRACT FROM AUTHOR]