Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes

Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5'-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.

Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad (Bufo japonicus)

Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.

Morphological diversification of Mediterranean anurans: the roles of evolutionary history and climate

Investigation of the ecological and evolutionary mechanisms governing the origin and diversification of species requires integrative approaches that often have to accommodate strong discordance among datasets. A common source of conflict is the combination of morphological and molecular characters with different evolutionary rates. Resolution of these discordances is crucial to assess the relative roles of different processes in generating and maintaining biodiversity. Anuran amphibians provide many examples of morphologically similar, genetically divergent lineages, posing questions about the relative roles of phylogeny and ecological factors in phenotypic evolution. We focused on three circum-Mediterranean anuran genera (Hyla, Alytes and Discoglossus), characterizing morphological and environmental disparity and comparing diversity patterns across biological levels of organization. Using a comparative phylogenetic framework, we tested how shared ancestry and climatic factors come together to shape phenotypic diversity. We found higher morphological differentiation within Hyla and Alytes than in Discoglossus. Body size and limb morphology contributed most to inter- and intraspecific morphological variation in Hyla and Alytes, but there was no strong phylogenetic signal, indicating that shared ancestry does not predict patterns of phenotypic divergence. In contrast, we uncovered a significant association between morphology and climatic descriptors, supporting the hypothesis that morphological disparity between species results from adaptive evolution.

Low neutral and immunogenetic diversity in northern fringe populations of the green toad Bufotes viridis: implications for conservation

Genetic variation is often lower at high latitudes, which may compromise the adaptability and hence survival of organisms. Here we show that genetic variability is negatively correlated with northern latitude in European green toads (Bufotes viridis). The result holds true for both putatively neutral microsatellite variation and supposedly adaptive MHC Class IIB variation. In particular, our findings have bearing on the conservation status of this species in Sweden, on the northern limit of its distribution where local populations are small and fragmented. These genetically impoverished populations are closely related to other populations found around the Baltic Sea basin. The low neutral and adaptive variation in these fringe populations compared to population at central ranges confirms a pattern shared across all other amphibians so far studied. In Sweden, the situation of green toads is of concern as the remaining populations may not have the evolutionary potential to cope with present and future environmental challenges.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'

We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

A reassessment of the diversity of green toads (Bufotes) in the circum-Aegean region

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

An odyssey out of Africa: an integrative review of past and present invasions by the Mediterranean tree frog (Hyla meridionalis)

An illustration of the human footprint on biodiversity are the faunal movements that have accompanied commercial and cultural exchanges between civilizations throughout history. In this article, we provide an integrative review of biogeographical and archaeological knowledge to understand these processes for the Mediterranean tree frog (Hyla meridionalis), an African species that has reached several regions of south-western Europe and associated islands. By re-analysing molecular (multilocus mitochondrial and genome-wide markers) and bioclimatic (ecological niche modelling) data, we give a comprehensive picture of the genetic diversity, structure and environmental suitability of H. meridionalis across its natural and exotic ranges, which in turn offer specific clues to the putative routes of colonization and associated events. Long-term monitoring efforts suggest northwards shifts of local range margins, potentially due to global warming, and we further demonstrate that this species is the most frequent amphibian to travel via the food supply chain in Western Europe. High dispersal ability, ecological tolerance and proximity to human settlements have made H. meridionalis a recurrent witness to the complexity and diversity of the civilizations that ruled the Western Mediterranean.