Recent genomic studies have suggested that ancient introgression may facilitate rapid diversification. The cave-dwelling group (TCG) of Triplophysa sensu lato, cave fishes endemic to the karst regions of southwestern China, exhibits high diversity and rapid evolution, representing a compelling potential example of rapid speciation during the evolution of karst landscapes. Here, we investigated the complex evolutionary history of the TCG by sampling 24 species and analysing whole-genome resequencing data. We reconstructed the phylogeny using different methods and quantified introgression to infer speciation and dispersal processes, which collectively confirm extensive historical gene flow both between TCG and Claea, as well as among TCG species. Our study demonstrated that, against the backdrop of widespread phylogenetic discordance within the TCG, interspecific introgression has played a more significant role than incomplete lineage sorting. Genomic regions with the highest levels of introgression (top 1% of fdM values) are enriched for Gene Ontology terms related to circadian behaviour, phenotypic plasticity, lipid metabolism, oxygen transport and reproduction. Demographic simulations further suggest that geoclimatic factors, together with the unique genetic attributes of the group, likely promoted founder effects, inbreeding, and subsequent declines in effective population size, resulting in two distinct demographic trajectories. Additionally, our results indicate that the origin and speciation of the TCG were closely synchronised with the rapid uplift of the Qinghai-Tibet Plateau and associated climatic transitions. We further identify three distinct stages of lineage diversification, characterised by alternating accelerations and declines driven by tectonic-climate interactions that were synchronised with major Asian orogenic events and monsoon cycles.

Inference of interspecific gene flow using genomic data is important to reliable reconstruction of species phylogenies and to our understanding of the speciation process. Gene flow is harder to detect if it involves sister lineages than nonsisters; for example, most heuristic methods based on data summaries are unable to infer gene flow between sisters. Likelihood-based methods can identify introgression between sisters but the test exhibits several nonstandard features, including boundary problems, indeterminate parameters, and multiple routes from the alternative to the null hypotheses. In the Bayesian test, those irregularities pose challenges to the use of the Savage-Dickey (S-D) density ratio to calculate the Bayes factor. Here we develop a theory for applying the S-D approach under nonstandard conditions. We show that the Bayesian test of introgression between sister lineages has low false-positive rates and high power. We discuss issues surrounding the estimation of the rate of gene flow between sister lineages, especially at very low or very high rates, and suggest that evidence for gene flow between sisters be assessed via a Bayesian test. We find that the species split time has a major impact on the information content in the data, with more information at deeper divergence. We use a genomic dataset from Sceloporus lizards to illustrate the test of gene flow between sister lineages.

Allochrony can be a cause or consequence of speciation, either creating temporal reproductive isolation that reduces gene flow between diverging populations or reinforcing divergence that has already occurred through geographic isolation. The former appears to apply to band-rumped storm-petrels (Hydrobates castro) at some breeding sites, where there are genetically differentiated hot and cool season breeding populations. It is unclear, however, whether seasonally segregated but genetically similar populations retain the same habitat preferences or whether divergence in foraging behaviour is associated with the process of allochronic speciation. We quantified the foraging distribution of band-rumped storm-petrels at St Helena, the largest known breeding colony in the South Atlantic at which hot and cool season breeders do not appear to be genetically differentiated. Fifty-four GPS tags were deployed on experienced breeders across two hot and two cool breeding seasons. We compared foraging trip parameters, foraging effort and examined whether environmental (oceanographic and atmospheric) conditions and habitat selection varied between seasonal populations. Long foraging trips lasted up to 9 days and involved travel distances of up to 3,285 km. The trip durations and distances were similar between the two seasonal populations, but directions differed markedly, resulting in pronounced differences in at-sea distributions. Adults breeding in the cool season foraged across ~ 619,000 km2 southeast of St Helena selecting warmer waters (~ 23.1 ± 0.7 °C). In the hot season, adults used a similarly sized area (~ 600,000 km2) to the southwest, but selected cooler waters (~ 21.2 ± 0.4 °C) even though overall conditions at unused but available locations were warmer (~ 23.7 ± 0.7 °C) than in the cool season (~ 20.6 ± 0.5 °C). Seasonal differences in oceanographic conditions likely force hot season breeders to select cool nutrient-rich waters, whereas cool season breeders may select wind or temperature conditions that minimise travel or thermoregulatory costs. This clear segregation in foraging range and habitat selection suggests that the divergence in at-sea distributions between two genetically similar seasonal breeding populations may contribute to allochrony and ultimately to sympatric speciation in the band-rumped storm-petrel at St Helena and elsewhere.

Abstract Species delimitation models are important quantitative tools for facilitating the discovery of cryptic species and clarifying the boundaries between focal taxa. However, distinct evolutionary processes may promote diversification at different points in a radiation, complicating efforts to identify speciation processes and diagnostic characters. Moreover, traits such as dispersal ability can have opposing effects on diversification rate versus population subdivision, which causes coalescent models to oversplit samples. We examined the effects of larval dispersal and host use on population structure and diversity in a Caribbean radiation of photosynthetic herbivores, sea slugs in the genus Elysia. Five methods of species delimitation broadly supported six described taxa and a previously unrecognized taxon, but species with less dispersive offspring were more likely to be oversplit using the multispecies coalescent. Surprisingly, species that shared a phylogeographic break were likely to be split into multiple taxa by coalescent models regardless of dispersal ability. Some host shifts may have contributed to divergence, but others pre-dated speciation, suggesting ecological specialization can promote reproductive isolation but often acted at deeper timescales; recent speciation was more often driven by sea level fluctuations and changes in reproductive anatomy, potentially reinforced by dispersal limitation.

ABSTRACT Speciation is frequently accompanied by gene flow, a phenomenon that is recognised as ubiquitous in nature. However, the role of gene flow in speciation remains unclear, particularly in tiny and sympatric arthropods that lack clear geographic isolations. This study aims to uncover how sympatry, parapatry and allopatry underlie the speciation process in two monophagous mites, Epitrimerus sabinae and Glossilus juniperensis , which belong to the E. sabinae complex and infest coniferous plant ( Juniperus chinensis ). We conducted whole‐genome resequencing of 298 mite individuals from 56 populations, spanning nearly 20 years of field surveys, to determine the drivers shaping species distribution patterns and to explore the role of gene flow in speciation. Population structure analyses revealed four genetic groups, corresponding to allopatric southern G. juniperensis and northern E. sabinae , and sympatric central G. juniperensis and central E. sabinae ; the sympatric E. sabinae and G. juniperensis populations were linked by sharing mixed ancestry. Our demographic history analyses showed that these two species derived from an ancestral lineage in southern China and diverged in the late Pleistocene, followed by a northward expansion along with varied degrees of gene flow. The genetic differentiation of both species was positively affected by geographic distance and environmental factors. Our results reveal a pattern of speciation in two mite species, initiated by genetic divergence with gene exchange between two species (sympatry) and followed by genetic isolation and habitat expansion (parapatry or allopatry). Our findings underscore a one‐way—northward—habitat expansion along with directional gene flow in two herbivores speciation.

Abstract The evolutionary dynamics of morphological traits can often blur the boundaries between interspecific divergence and intraspecific variability, complicating species recognition. This study investigates the variation in secondary sexual traits and the existence of potential speciation processes within what is now considered Berberomeloe insignis (Coleoptera: Meloidae), an endangered blister beetle taxon endemic to southeastern Spain. Despite previous evidence of substantial genetic and phenotypic differentiation, key characters as the morphological variation in secondary sexual traits, such as antennomeres, remain unexplored. Using geometric morphometrics, we analyzed the shape variation of male and female antennomeres VII–XI across all previously recognized lineages of B. insignis . Our results reveal significant morphological differentiation, particularly in antennomeres VII, IX, and XI, which correlate broadly with genetic lineages. Based on the study of newly recorded populations, we confirm that cephalic coloration patterns correspond with mitochondrial lineages, further supporting the existence of geographic lineage differentiation within what was previously considered B. insignis . Climatic niche modeling indicates low climatic niche overlap between the isolated western lineage and the remaining lineages, which also show relatively low to moderate overlap, suggesting that ecological factors could have contributed to the divergence among them. These findings underscore the intricate interplay of genetics and ecology, highlighting the importance of integrating multiple data sources for accurate species delimitation. Based on our results, we describe B. nazari sp. nov . and B. insignis trisanguinatus ssp. nov . reflecting the evolutionary history of this group.

Pterogyne (Fabaceae) is a monospecific genus of trees native to South America. Its sole species, P. nitens, was described by Tulasne in 1843, in reference to its winged fruit and shiny leaflets, with no subsequent taxonomic studies published since. The species is distributed across the Caatinga, semideciduous Atlantic Forest and Gran Chaco, where it favors drier climates and is commonly found in second-growth forests. These trees can reach over 35 m tall and are characterized by leaves ranging from paripinnate to imparipinnate, adaxially glossy leaflets, and axillary fascicles of racemes bearing numerous small, pentamerous, yellow flowers. The fruit is a brown samara with a single well-developed wing. Given the lack of taxonomic studies and the intense morphological plasticity of the genus varying in number, shape and size of leaflets, types of inflorescences, and fruit shapes and sizes, we refined the taxonomic circumscription and describe the phenotypical plasticity of Pterogyne, based on fieldwork in Brazil and analysis of 462 herbarium specimens. Our data, drawn from ecological, geographical, and morphological evidence, support the genus as monospecific and include a more complete description with newly documented morphological traits, as well as preliminary conservation assessment of Least Concern (LC). Notable findings include the andromonoecious inflorescences—a rare condition in Fabaceae—and a correlation between pubescence density and wetter climates, which may suggest an ongoing speciation process. We provided a detailed description of the genus, along with an illustration, photographs, distribution maps, and a nomenclatural treatment that includes a lectotypification, accompanied by a discussion of all new data gathered in this study.

The family Arthrodermataceae, the dermatophytes and allies, ancestrally began with Ascomycetous bifactorial sexual cycles built into an ecology that also featured considerable clonal propagation via conidia. When keratinolytic capabilities made ecological crossover to dermatopathogenicity possible, that conventional cycle, requiring moist, deposited keratinous material, could only be maintained by pathogens infecting animals burrowing or denning in habitats with soil. Lineages adapted to animals not nesting in soil became established clonally from representatives of single mating types. They became transformed in morphology and physiology, tending to develop reduced conidiation and more exogenous growth factor requirements in addition to retaining specific host adaptations. Viewing this speciation process through the lens of population biology tools designed for interbreeding populations can give a distorted picture, since the often ecologically neutral factors considered, like spacer regions, introns, restriction sites and single nucleotide polymorphisms, likely have a slower rate of change over time than the directly adaptive factors enabling these unifactorial radiate host switching events. The current state of species concepts in the dermatophytes and related, mostly nonpathogenic dermatophytoids is reviewed in light of this contrast of perspectives. Practical steps that can be taken in the clinical laboratory to make accurate identifications based on accurate species concepts are addressed. Some species concepts are supported in lineages that have previously reduced to lower rank, such as Trichophyton indotineae, T. interdigitale, and T. soudanense. The diversity of internal transcribed spacer barcodes in T. tonsurans suggests that research into clinical differences among genotypes is warranted.

Saccharina japonica is a commercially and ecologically important seaweed and shows rapid ecological speciation. This kelp represents an excellent model for understanding the process and genetic mechanism of diversification and speciation of brown seaweeds. Up to now, there was limited research about the ecological speciation of seaweeds from genomic perspective. In this study, we conducted genome resequencing of four varieties of S. japonica and two sister species (S. angustata and S. longissima) to investigate the genetic mechanism of ecological speciation. The demographic history suggests that the lineage of S. angustata and S. longissima is a sister lineage to that of S. japonica, rather than its direct ancestor, with the genetic lineage of S. japonica var. religiosa diverging earliest from the rest of the taxa. Even though there is lower genetic differentiation among these varieties, natural hybridization and gene flow are limited. We detected some heat resistance (e.g. heat shock protein 70), stress response (e.g. ubiquitin-like protein) and growth-related genes (e.g. immediate upright (imm) upregulated 3) were under positive selection during the ecological speciation. Low linkage disequilibrium decay rate and extensive signals of selective sweeps were detected in these varieties, suggesting that adaptive differentiation under natural selection was the driving force for ecological speciation. The main force driving speciation in this species does not appear to be ongoing hybridization but historical admixture and adaptive differentiation due to natural selection. An understanding of the evolutionary history and ecological speciation of S. japonica represents an important prerequisite for effective use of germplasm in breeding and for the conservation of natural resources.

Many evolutionary radiations involve diversification of exaggerated sexual displays, but little is known about how they are formed. It has been theorized that there can be multiple stable equilibria in the evolution of sexually selected traits, by which multiple species having distinct sexual displays and mate preferences can stably persist. However, these theories alone do not fully explain the speciation process because the stability of each equilibrium will impede the formation of a new species from an existing species that is already occupying one of the stable equilibria. To explain the evolutionary process that forms species with diverse sexual displays, we here propose that hybridization between phenotypically similar but genetically divergent lineages can catalyse speciation by sexual selection, via the creation of genotypic and phenotypic variation. Using evolutionary simulations, we show that hybridization giving rise to variation in mate preference and sexual displays can alter the sexual selection regime, thereby creating opportunities for evolutionary shifts towards previously unoccupied stable equilibria. Thus, hybridization can facilitate evolutionary exploration of the stable evolutionary equilibria that sexual selection generates, leading to speciation accompanied by the diversification of exaggerated sexual displays.

ABSTRACTThis study reports the first complete mitochondrial genome of Rhithrogena elasmaris and provides a comprehensive analysis of its structural features and codon usage patterns. Combined with published mitochondrial genomes of 29 Heptageniidae species, we further evaluated genetic diversity, phylogenomic relationships, and differentiation patterns within the family. The mitochondrial genome of R. elasmaris is 15,326 bp in length with a GC content of 36.12%, and comprises the 37 typical mitochondrial genes. It shows a strong AT bias and clear codon usage preferences, with neutrality and PR2 plots indicating natural selection as the dominant evolutionary force. Simple sequence repeats are widely distributed, and tRNA structures are generally conserved despite frequent base mismatches. Comparative analyses demonstrate that gene order in Heptageniidae is highly conserved, although one copy of trnM has been lost in some species. Nucleotide diversity is relatively high (Pi = 0.223), with nad6 being the most variable protein‐coding gene and cox1 the most conserved. Ka/Ks values < 1 across all 13 protein‐coding genes indicate strong purifying selection, with varying intensity reflecting functional constraints. Genetic structure and phylogenomic analyses support distinct subfamily level divergence within Heptageniidae. However, R. elasmaris and Paegniodes cupulatus exhibit mixed mitochondrial signals, suggesting possible incomplete lineage sorting or ancient mitochondrial introgression. The phylogeny supports the subfamily framework (Heptageniinae + [Ecdyonurinae + Rhithrogeninae]), with Rhithrogena forming a basal lineage within Rhithrogeninae. Divergence modeling indicates that Ecdyonurinae and Heptageniinae diverged first, followed by the split of Rhithrogeninae from Heptageniinae. This study enriches the molecular data resources for Heptageniidae and provides a refined framework for studying its systematics, evolutionary history, and ecological adaptation. Future work integrating nuclear genomic datasets will be necessary to further clarify speciation processes and adaptive evolution.

In song-learning birds, vocalizations are species recognition signals and may act as premating reproductive barriers; for allopatric taxa, testing how the signals can influence the speciation processes is quite challenging. This study aims to understand genomic divergence and species recognition via songs in 2 allopatric taxa, eastern and western Nashville warblers (Leiothlypis ruficapilla ruficapilla vs. Leiothlypis ruficapilla ridgwayi). We performed playback experiments to assess their reciprocal behavioral responses, which suggests an asymmetric barrier: the eastern L. r. ruficapilla discriminates between the 2 songs, but the western L. r. ridgwayi does not. Using whole-genome sequencing, we also examined the extent of the taxa's genomic divergence and estimated their demographic history. We identified dozens of highly differentiated genomic regions, as well as fluctuations in historical effective population sizes that indicate independent demographic trajectories during the Pleistocene. To contextualize the magnitude of divergence between L. ruficapilla subspecies, we applied the same genomic analyses to 2 additional eastern-western pairs of parulid warblers, Setophaga virens vs. Setophaga townsendi and Setophaga coronata coronata vs. Setophaga coronata auduboni, which have existing behavior studies but are not in strict allopatry. Our findings provide insights into the role of vocalizations in defining within-pair relationship and the important legacy of isolation during the Pleistocene.

The allopatric model of speciation has dominated our understanding of speciation biology and biogeography since the Modern Synthesis. It is uncontroversial because reproductive isolation may readily emerge as a by-product of evolutionary divergence during allopatry unopposed by gene flow. Recent genomic studies have found that gene flow between species is common, but whether allopatric speciation is common has rarely been systematically tested across a continuum of closely related species. Here, we fit a range of demographic models of evolutionary divergence to whole-genome sequence data from 93 pairs of Drosophila species to infer speciation histories and levels of post-divergence gene flow. We find that speciation with gene flow is common, even between currently allopatric pairs of species. Estimates of historical gene flow are not predicted by current range overlap. Whilst evidence for secondary contact is generally limited, a few sympatric pairs showed strong support for a secondary contact model. Our analyses suggest that most speciation processes involve some long-term gene flow, perhaps due to repeated cycles of allopatry and contact, without requiring an extensive allopatric phase.

The reference genome of Erebia palarica (Chapman’s ringlet; Lepidoptera: Nymphalidae, Satyrinae) provides valuable insights into evolutionary and conservation genomics. On one hand, it paves the way to unravel the speciation processes, reproductive barriers, and potential hybridisation between E. palarica and its closely related sister species, Erebia meolans . On the other hand, this genomic resource will be key for the genetic monitoring of this narrowly endemic species, restricted to the Cantabrian Mountains (NW Spain), facilitating the use of genomic data to estimate population genetic parameters. The genome of a female individual was assembled into 13 phased contiguous autosomes, two sex chromosomes (W and Z), and one mitochondrial genome. This chromosome-level assembly encompasses 0.51 Gb and has no gaps, making this a telomere-to-telomere (T2T) genome assembly. The assembly is composed of 15 contigs with an N50 value of 36.4 Mb.

Societal Impact Statement Biodiversity is threatened by human activities, with extinction debt accumulating rapidly. Many of these activities change the connectivity of populations, fragmenting existing population systems or bringing previously isolated populations or species into contact. Speciation research offers insights into both the short‐ and long‐term outcomes of changes in isolation and connectivity and thus provides fundamental knowledge that can inform biodiversity management. Here, we review what is known about the role of gene flow in speciation, highlighting that gene flow does not appear to be a major impediment to speciation in plants and instead often contributes to diversification. Summary The likelihood of speciation with gene flow represents one of the longest running debates in evolutionary biology. Gene flow can hamper speciation by disrupting associations between loci under divergent natural selection and those causing assortative mating. Conversely, variation introduced by gene flow can facilitate speciation, and some modes of speciation require interspecific gene flow. Here, we first describe the history of this debate. Next, we review theoretical models of speciation with gene flow, along with empirical evidence, emphasizing studies of plants. Our review includes both primary divergence with gene flow, as well as gene flow following secondary contact, including different forms of hybrid speciation. We find that plants have several characteristics that can promote the formation of associations between ecological and assortative mating traits, including magic traits (divergently selected traits that also cause assortative mating) and abundant recombination suppressors, such as inversions. Biogeographic studies of several plant groups show patterns of greater range overlap and range asymmetry in sister species compared with more distantly related species. This pattern suggests that geographic isolation is not required for speciation in plants and also that speciation by budding may be important. Genomic data further indicate that gene flow is frequent, but often intermittent, during the speciation process in plants and that speciation triggered by secondary gene flow (introgression) is common. We conclude that Darwin's skepticism about the necessity of geographic isolation in speciation is warranted, especially in the plant kingdom.

Phylogenetic reconstruction of African weakly electric fish (Campylomormyrus spp.) is suggestive of ancient introgression events.

Genome-wide SNP and mtDNA phylogeny of blind mole rats (Spalacinae Gray, 1821) reflects a complex history of relictualism, expansion, and speciation

Abstract Historical climatic oscillations and geographic barriers have profoundly shaped genetic diversity and speciation across Europe, particularly within glacial refugia. The widespread butterfly Cyaniris semiargus (Mazarine Blue) is a striking example of such divergence, especially in its southernmost populations, which are fragmented across montane and coastal habitats. Using genome‐wide ddRADseq data and environmental analyses, we investigated the genetic structure, gene flow and ecological differentiation of C. semiargus across the western Palearctic, with a focus on its isolated southern populations. Our results reveal four deeply diverged genetic lineages within the Iberian Peninsula and one in North Africa. These lineages exhibit strong genetic structure, ecological specialization and minimal gene flow, consistent with allopatric divergence strengthened by local adaptation. Coastal populations show host plant specialization and adaptation to milder and more stable climates, while montane lineages persist in climatically extreme refugia. Interestingly, another lineage in the Peloponnese is following similar high‐altitude climatic selective pressures. Together, these findings point to parallel processes of ecological speciation across both montane and coastal environments. Adopting a conservative taxonomic approach, albeit reflecting their evolutionary and conservation significance, we recognize these lineages as subspecies. Our study highlights the role of glacial refugia, habitat specialization and ecological divergence in shaping patterns of biodiversity, and underscores the urgent need for lineage‐specific conservation measures.

Transport of small ferrihydrite particles and Fe3+ ions in volcanic soil and natural zeolite: Potential for environmental dispersion.

Abstract Assessing the true dimension of biodiversity is a major challenge. Many species hide within them a diversity that is now being uncovered using molecular data. However, population genetic studies tend to be resource‐consuming and more difficult to apply to a broader range of taxa, limiting scalability. Moreover, the growing shortage of trained taxonomists makes it difficult to rely on comparative morphological studies to assess divergence and speciation processes for the vast majority of species‐rich taxonomic groups. Here, we explore the usefulness of ‘ecological speciation’ concept and explore how these hidden lineages tend to occupy a distinct environmental niche that can be used to identify natural groups in the geographical space. From a total of 298 species complexes, we assess the accuracy of five clustering methods and random forest models for correctly classifying the occurrences of the different subspecies based only on environmental data. For the best‐performing clustering method (Gaussian mixture models), we obtained that species can be predicted above random classification with a median Adjusted Rand Index of 0.37 only by their environmental profile. Random forest, on the other hand, showed high accuracy for most of the species (&gt;0.75). We believe accuracy could be further improved by using species‐specific climatic variables, although this study focuses on a widely applicable method. Our goal is to demonstrate that clustering methods can be used on a large scale to reveal the true diversity hidden within taxonomic complexes, thereby reducing the time and budget required for exploratory analysis. We also aim to demonstrate the extent to which different taxa are determined and delimited by the environment.