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Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.

The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.

Sex chromosomes are classically predicted to stop recombining in the heterogametic sex, thereby enforcing linkage between sex-determining (SD) and sex-antagonistic (SA) genes. With the same rationale, a pre-existing sex asymmetry in recombination is expected to affect the evolution of heterogamety, for example, a low rate of male recombination might favor transitions to XY systems, by generating immediate linkage between SD and SA genes. Furthermore, the accumulation of deleterious mutations on nonrecombining Y chromosomes should favor XY-to-XY transitions (which discard the decayed Y), but disfavor XY-to-ZW transitions (which fix the decayed Y as an autosome). Like many anuran amphibians, Hyla tree frogs have been shown to display drastic heterochiasmy (males only recombine at chromosome tips) and are typically XY, which seems to fit the above expectations. Instead, here we demonstrate that two species, H. sarda and H. savignyi, share a common ZW system since at least 11 Ma. Surprisingly, the typical pattern of restricted male recombination has been maintained since then, despite female heterogamety. Hence, sex chromosomes recombine freely in ZW females, not in ZZ males. This suggests that heterochiasmy does not constrain heterogamety (and vice versa), and that the role of SA genes in the evolution of sex chromosomes might have been overemphasized.

The rich genetic and phenotypic diversity of species complexes is best recognized through formal taxonomic naming, but one must first assess the evolutionary history of phylogeographic lineages to identify and delimit candidate taxa. Using genomic markers, mitochondrial DNA barcoding, and morphometric analyses, we examined lineage diversity and distribution in the Iberian endemic frog Rana parvipalmata. We confirmed two deep phylogeographic lineages, one relatively homogenous genetically, found in Asturias and adjacent areas (T2), and one more fragmented and locally genetically impoverished, restricted to Galicia (T1). Analyses of their hybrid zone suggested a shallow transition characterized by far-ranging admixture, which was modelled by a wide geographic cline (~60 km for the genome average) and no obvious barrier loci (i.e. loci showing disproportionally restricted introgression). The relatively young T1 and T2 have thus remained reproductively compatible, which argues against their distinction as biological species, and we accordingly describe T2 as a new subspecies, Rana parvipalmata asturiensis ssp. nov. Remarkably, we highlight striking discordances between mitochondrial and nuclear distributions across their hybrid zones, as well as between their genetic and morphological differentiation. Our study illustrates how genomic-based phylogeographic frameworks can help decipher the high genetic and phenotypic variation of species complexes and substantiate the taxonomic assessment of candidate lineages. [ABSTRACT FROM AUTHOR]

An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population‐level lineages, the rise of integrative approaches to delimit such lineages, and the advent of high‐throughput sequencing have considerably renewed the discipline of taxonomy. Using genome‐scale molecular datasets, the extent of admixture across hybrid zones can now be effectively assessed and the evolutionary independence of lineages inferred, leading to more reliable and comparable species delimitation criteria. Substantially divergent but admixing phylogeographical lineages can conveniently be named as subspecies, thus avoiding taxonomic oversplitting and taxonomic inflation. At the same time, comprehensive DNA barcoding and DNA metabarcoding efforts are uncovering an enormous proportion of undiscovered biotic diversity, and we encourage the development of bioinformatic pipelines that combine high‐throughput species discovery and delimitation with diagnosis and scientific naming, to approach a biotic inventory of the globe without abandoning the established Linnaean system. [ABSTRACT FROM AUTHOR]

The canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent sex-chromosome turnovers, yet we know little about which forces drive them. Here, we describe an extremely fast rate of turnover among 28 species of Ranidae. Transitions are not random, but converge on several chromosomes, potentially due to genes they harbour. Transitions also preserve the ancestral pattern of male heterogamety, in line with the hot-potato model of sex-chromosome transitions, suggesting a key role for mutation-load accumulation in non-recombining genomic regions. The importance of mutation-load selection in frogs might result from the extreme heterochiasmy they exhibit, making frog sex chromosomes differentiate immediately from emergence and across their entire length.

A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues affecting species delimitations, especially an over-reliance on mitochondrial DNA data, and reiterate best practices; (ii) reanalyse the data available for anacondas to establish the true current state of knowledge and to highlight lines of further research; and (iii) analyse the nomenclatural history and status of the genus. While our analysis reveals significant morphological variation in both green and yellow anacondas, denser sampling and an analysis of informative nuclear markers are required for meaningful species delimitation in Eunectes. Tracing the history of name-bearing types establishes Trinidad as the type locality for Boa murina Linnaeus, 1758 and allows identification of the extant lectotype for the species. Finally, we emphasize the responsibility of both journals and authors to ensure that published taxonomic work meets the burden of evidence required to substantiate new species descriptions and that species are named in compliance with the rules of zoological nomenclature. [ABSTRACT FROM AUTHOR]

Traditional methods of phylogenetic reconstruction and species delimitation may be impeded by frequent hybridization among lineages. In this study, we conducted phylogenetic and clustering analyses of ddRAD genomic data on the entire genus Salamandra, which includes six species and over 25 subspecies of terrestrial salamanders. We expanded previous datasets to include missing subspecies and incorporated new samples, with an emphasis on secondary contact zones. Results obtained from a full dataset of 392 individuals (356,874 bp; 24,192 SNPs) were compared with those obtained after excluding substantially admixed individuals (n = 95; 835,467 bp; 51,557 SNPs) to explore the consequences of introgression on phylogenetic inference and taxonomic arrangement of subspecies. We found conflicting phylogenetic placements for taxa represented by many admixed individuals (identified by clustering ancestries). In contrast, a time-calibrated tree constructed without hybrids largely agrees with previous phylogenetic hypotheses. Within S. atra, we found paraphyly of S. atra atra, suggesting an additional candidate subspecies. Within S. infraimmaculata, two lineages are assignable to known subspecies and we additionally identified a third, deeply diverged lineage sampled near the Turkish/Syrian border. In S. algira, we found limited admixture between the subspecies S. a. tingitana and S. a. splendens despite their geographic proximity. Finally, within S. salamandra, we detected significant levels of hybridization between subspecies, which blurred their phylogenetic relationships, although the removal of admixed samples in subset analyses clarified the situation in most cases. Monophyly was recovered for subspecies that were previously found paraphyletic, including S. s. salamandra, S. s. gallaica, and S. s. fastuosa. Salamandra s. "alfredschmidti" was confirmed to be a junior synonym of S. s. bernardezi. Previously disputed subspecies, like S. s. "molleri" and S. s. "hispanica", correspond to separated lineages but are affected by admixture with other lineages. Further newly identified candidate subspecies in S. salamandra included a southern lineage within S. s. wer-neri and a western lineage within S. s. bernardezi. Finally, we re-evaluate the status of recognized subspecies in Salamandra, based on evidence from multiple delimitation criteria. Given that the evolutionary history could not be resolved for all subspecies, we highlight taxa within Salamandra that warrant further molecular examination and taxonomic revision, notably within the S. s. gallaica/"molleri"/bejarae complex. This study illustrates the impact of hybridization in phylogenetic analyses and its downstream effects in the identification of conservation units and their naming in the Linnean classification. [ABSTRACT FROM AUTHOR]

Uncertainties on species taxonomy and distribution are major factors hampering efficient conservation planning in the current context of biodiversity erosion, even concerning widespread and abundant species in relatively well‐studied regions. Species delimitation have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification through this approach can be hampered by incomplete lineage sorting, introgression or isolation by distance. In that context, analyses of introgression patterns at secondary contact zones offer an interesting alternative by allowing a direct estimation of reproductive isolation, especially when using genome‐wide markers. Here, we investigated a contact zone between two genetic groups of the Spiny‐footed Lizard Acanthodactylus erythrurus (Schinz, 1833) in Morocco, whose status as separate lineages remained disputed in previous multilocus studies. Based on thousands of genome‐wide markers obtained through a RADseq approach, we confirmed that they represent distinct evolutionary lineages. Furthermore, the transition at their contact zone was very steep, with spatially restricted gene flow, highlighting levels of reproductive isolation consistent with species‐level lineages. Our study further illustrates the power of RADseq‐based studies of contact zones to understand cryptic diversity in non‐model organisms. [ABSTRACT FROM AUTHOR]