Genetic evidence of contemporary hybridization in one of North America's rarest anurans, the Florida bog frog

Hybridization despite elaborate courtship behavior and female choice in Neotropical tree frogs

The mechanisms of hybridization can be elucidated by analyzing genotypes as well as phenotypes that could act as premating barriers, as the reproductive interactions among heterospecifics can alter the evolutionary history of species. In frogs, hybrids typically occur among species that reproduce explosively (in dense aggregations) with few opportunities for mate selection but are rare in species with elaborate courtship behaviors that may prevent erroneous mating. Using 21 microsatellite markers, we examined hybridization in the prolonged-breeding tree frogs Bokermannohyla ibitiguara and B. sazimai sampled within a contact zone in the Brazilian savanna (72 tadpoles; 74 adults). We also compared acoustic and morphological data. We confirmed both parental species genetically; STRUCTURE results confirmed 14 hybrids, 11 of which were second-generation according to NEWHYBRIDS, all with intermediate values of genetic dissimilarities compared to the parentals. Morphological and acoustic analyses revealed that hybrids showed variable but not necessarily intermediate phenotypes. Moreover, 2 hybrids exhibited call types different from parentals. The reproduction of B. ibitiguara involves territorial and aggressive males, elaborate courtships with acoustic and tactile stimuli, choosy females, and opportunistic strategies. Our study uncovers a rare case of viable hybridization among closely related frogs with such a combination of complex courtship behaviors and mate choice. We discuss the likely directionality and mechanisms behind this phenomenon, and highlight the importance of investigating hybridization even in species that show elaborate reproduction and female choice to advance our understanding of animal diversification.

Hybridization of Two Species of Japanese Toads, Bufo torrenticola and Bufo japonicus formosus, in the Central Part of Japan

Interspecific hybridization between two species of Japanese toads, Bufo torrenticola (Bt) and Bufo japonicus formosus (Bjf), was not thought to have occurred due to the differences in their spawning habitats, although their hybridization was reported by previous research in a limited area. Such hybridization could have pivotal effects, such as genetic admixture, on Bt, which has a limited distribution and habitat. In this study, to clarify the details of hybridization, a total of 192 individuals were collected from multiple parapatric regions and an only Bjf allopatric region and analyzed based on morphology, mtDNA sequences, and nuclear DNA microsatellite loci. Each individual was identified based on morphological type and mtDNA lineage, and two mismatched combinations, Bt or an intermediate morphological type and the Bjf mtDNA lineage, were detected. In particular, the combination of Bt type and Bjf lineage was dominant in parapatric regions, and it was considered that asymmetric hybridization in which Bjf became a matriline had occurred. In addition, a Bayesian clustering method based on the microsatellite loci was conducted to detect a genetic admixture of the two toad species. Individuals representing a combination of the Bt type and Bjf lineage in the parapatric regions were largely assigned to the Bt cluster or equally to both clusters. These results indicate that backcross with Bt has been repeated, and therefore the traits of Bt might be maintained in this study.

Evolutionary principles guiding amphibian conservation

The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.

Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.

Conservation genetics and genomics of amphibians and reptiles

Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.

Comparative assessment of genetic and morphological variation at an extensive hybrid zone between two wild cats in southern Brazil

Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species.

Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.)

Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories, yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here, we analyse the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located within the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression, and hybridization) using nuDNA and mtDNA data analysed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (structure), bidirectional estimates of gene flow (migrate-n and IMa2) and phylogeny-based methods (*beast, bucky) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.

Development of SNP markers identifying European wildcats, domestic cats, and their admixed progeny

Introgression can be an important evolutionary force but it can also lead to species extinction and as such is a crucial issue for species conservation. However, introgression is difficult to detect, morphologically as well as genetically. Hybridization with domestic cats (Felis silvestris catus) is a major concern for the conservation of European wildcats (Felis s. silvestris). The available morphologic and genetic markers for the two Felis subspecies are not sufficient to reliably detect hybrids beyond first generation. Here we present a single nucleotide polymorphism (SNP) based approach that allows the identification of introgressed individuals. Using high-throughput sequencing of reduced representation libraries we developed a diagnostic marker set containing 48 SNPs (Fst > 0.8) which allows the identification of wildcats, domestic cats, their hybrids and backcrosses. This allows assessing introgression rate in natural wildcat populations and is key for a better understanding of hybridization processes.