Vicariance and marine migration in continental island populations of a frog endemic to the Atlantic Coastal forest

Mitonuclear and phenotypic discordance in an Atlantic Forest frog hybrid zone

Discordance between mitochondrial and nuclear DNA is common among animals and can be the result of a number of evolutionary processes, including incomplete lineage sorting and introgression. Particularly relevant in contact zones, mitonuclear discordance is expected because the mitochondrial genome is haploid and primarily uniparentally inherited, whereas nuclear loci are evolving at slower rates. In addition, when closely related taxa come together in hybrid zones, the distribution of diagnostic phenotypic characters and their concordance with the mitochondrial or nuclear lineages can also inform on historical and ongoing dynamics within hybrid zones. Overall, genetic and phenotypic discordances provide evidence for evolutionary divergence and processes that maintain boundaries among sister species or lineages. In this study, we characterized patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We examined genomic-scale nuclear diversification across 19 populations, encompassing the two parental forms and a contact zone between them. We compared the distribution of genomic DNA variability with that of a mitochondrial locus (16S) and two morphological traits (dorsal tubercles and body size). Our results reveal multiple divergent lineages with ongoing admixture. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females, may be one mechanism leading to patterns of introgression observed between the species.

Genetic Differentiation and Relationship among Castanopsis chinensis, C. qiongbeiensis, and C. glabrifolia (Fagaceae) as Revealed by Nuclear SSR Markers

Castanopsis chinensis (Spreng.) Hance is widespread in the subtropical forests of China. Castanopsis qiongbeiensis G.A. Fu and Castanopsis glabrifolia J. Q. Li & Li Chen are limited to the coastal beaches of Wenchang county in the northeast of Hainan Island, and have similar morphological characteristics to C. chinensis. It is supposed that C. qiongbeiensis and C. glabrifolia are closely related to C. chinensis. In the present study, the genetic differentiation, gene flow, and genetic relationship of C. chinensis, C. qiongbeiensis, and C. glabrifolia were investigated by using 15 nuclear microsatellite markers; a total of 308 individuals from 17 populations were sampled in the three species. The allelic variation of nuclear microsatellites revealed moderate but significant genetic differentiation (FCT = 0.076) among C. chinensis, C. qiongbeiensis, and C. glabrifolia, and genetic differentiation between C. chinensis and C. glabrifolia was larger than that between C. chinensis and C. qiongbeiensis. Demographic simulations revealed unidirectional gene flow from C. chinensis to C. glabrifolia and C. qiongbeiensis, which highlight dispersal from mainland to island. The isolation effect of Qiongzhou Strait increased the genetic differentiation of species on both sides of the strait; however, the differentiation was diminished by gene flow that occurred during the historical period when Hainan Island was connected to mainland China. Our results supported the argument that C. glabrifolia should be considered an independent species and argued that C. qiongbeiensis should be regarded as an incipient species and independent conservation unit.

Contrasting genetic diversity between Planchonella obovata sensu lato (Sapotaceae) on old continental and young oceanic island populations in Japan

Genetic diversity of plant populations on islands is likely to be influenced by characteristics such as island origin (oceanic or continental) and their age, size, and distance to continental landmasses. In Japan, Planchonella obovata sensu lato which is found on both continental and oceanic islands of varying age, size, and distance to East Asian continental areas-is an ideal system in which to investigate the factors influencing genetic diversity of island plant species. In this study, we examined the genetic diversity of P. obovata s.l. populations, in the context of the species population genetic structure, demography, and between island migration, from 668 individuals, 28 populations and 14 islands including both continental (the Yaeyama Islands) and oceanic islands (the Daito, Bonin, and Volcano Islands) using 11 microsatellite markers. The Yaeyama and Volcano Islands respectively had the highest and lowest genetic diversity, and island origin and age significantly affected genetic diversity. Clustering analysis revealed that populations were grouped into Bonin, Volcano, and Yaeyama + Daito groups. However, Bonin and Volcano groups were distinct despite the relatively short geographical distance between them. Approximate Bayesian Computation analysis suggested that the population size was stable in Bonin and Yaeyama + Daito groups, whereas population reduction occurred in Volcano group, and migration between groups were very limited. Younger oceanic islands showed lower genetic diversity, probably due to limited gene flow and a lack of time to accumulate unique alleles. Genetic structure was generally consistent with the geographic pattern of the islands, but in Volcano, a limited number of founders and limited gene flow among islands are likely to have caused the large genetic divergence observed.

Geography, Host Genetics, and Cross-Domain Microbial Networks Structure the Skin Microbiota of Fragmented Brazilian Atlantic Forest Frog Populations

The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti-Bd bacteria were not broadly negatively co-associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial.

Biogeography of land snail genus Acusta (Gastropoda: Camaenidae): Diversification on East Asian islands

East Asia has highly diverse and endemic biota due to its complex geological and climatic history and its diversified topography. The continental and insular distributions of land snail genus Acusta in East Asia provide a good opportunity to compare the evolutionary processes in this group under different biogeographical conditions. In this study, we inferred the evolutionary history of the land snail genus Acusta by a molecular phylogeny and investigated how the palaeogeographic events shaped species diversity and the distribution of the Acusta genus within the island arc. A concatenated dataset generated from sequences of one nuclear (ITS2) and two mitochondrial (16S, COI) gene fragments, include most of nominal taxa of the genus, four related species and one outgroup. We constructed the phylogeny and the evolutionary history of the genus through maximum-likelihood and Bayesian inference methods, using a Bayesian molecular clock and ancestral range estimation. Our results suggested that currently recognized species in Acusta are polyphyletic. The traditionally accepted concept of the affinity of Acusta and Bradybaena is not supported. The hypothesis of colonization via land bridges during the Pleistocene glaciations for the biota of East Asian islands is not supported. Instead, the origin and diversification of the genus Acusta was dated to the late Miocene-Pliocene from an area around North and Northeast China to South China and East Asian islands Three major evolutionary lineages were identified. Two of the major lineages demonstrate distinct evolutionary histories, as sympatric speciation is the major speciation process for the continental clade, while the insular clade originated from founder events. Taiwan functioned as an important source of diversification for species on the East Asian islands possibly through passive dispersal of different mechanisms. The sea level fluctuations caused by the Pleistocene glacial cycles play a role in the subsequent dispersion and diversification of species of the continental clade, such as the more recent range expansion of A. redfieldi from South China to Taiwan and Japan.

Comparative phylogeography of two hemipteran species (Geisha distinctissima and Megacopta cribraria) in the Zhoushan Archipelago of China reveals contrasting genetic structures despite concordant historical demographies

Continental islands are useful models to explore the roles of shared historical factors in the evolution of sympatric species. However, China's largest continental group of islands, the Zhoushan Archipelago, was neglected by most studies focusing on biodiversity hotspots. Here we investigated the phylogeographic patterns and the historical demography of two sympatric hemipteran insects (Geisha distinctissima and Megacopta cribraria), which shared historical factors in the Zhoushan Archipelago. The results based on mtDNA (COX1, COX2-COX3, and CYTB) and nDNA (28S and ITS2) showed that G. distinctissima diverged into three genetic lineages (L1-L3) ~8.9-13.7 thousand years ago (kya), which coincided with the period of island isolation. However, the three lineages exhibit no clear phylogeographic patterns for frequent asymmetrical gene flow (starting around 5 kya) from the mainland and adjacent islands to other distant islands due to subsequent human activities. In contrast, only one genetic lineage exists for M. cribraria, without any phylogeographic structures. The ancestral range in the mainland as well as in neighboring islands, together with the frequent asymmetrical gene flow of M. cribraria (from the mainland and neighboring islands to more distant islands) within the last 5000 years suggests that human activities may have lead to the colonization of this species in the Zhoushan Archipelago. The contrasting genetic structures indicate shared historical factors but independent evolutionary histories for the two sympatric species in the Zhoushan Archipelago. Our demographic analysis clearly showed that both species underwent population expansion before 5 kya during the post-LGM (Last Glacial Maximum), which indicates that the two species shared concordant historical demographies. This result suggests that the population size of the two species was affected similarly by the climatic oscillations of post-LGM in Eastern China. Together, our findings reveal that the two insect species in the Zhoushan Archipelago exhibit contrasting genetic structures despite concordant historical demographies, which provides an important framework for the exploration of the evolution patterns of sympatric species in the continental island.

ORIGINS AND GENETIC DIVERSITY OF INTRODUCED POPULATIONS OF THE PUERTO RICAN RED-EYED COQUÍ, ELEUTHERODACTYLUS ANTILLENSIS, IN SAINT CROIX (U.S. VIRGIN ISLANDS) AND PANAMÁ

The Red-eyed Coquí, Eleutherodactylus antillensis, is a terrestrial frog endemic to the Puerto Rican Bank (Puerto Rico and numerous islands and cays off its eastern coast), in the eastern Caribbean Sea. The species was likely introduced in Saint Croix, an island c. 100 km southeast of Puerto Rico, in the late 1930s, and in Panamá City, Panamá, in the late 1950s or early 1960s, but the source(s) of these introductions are unknown. We analyzed sequence data from one mtDNA locus and four nuDNA introns to infer the origin(s) of the Saint Croix and Panamá City populations and quantify their genetic diversity. Saint Croix and Panamanian populations do not share any haplotypes, and they cluster with different native populations, suggesting that they are derived from separate sources in the Puerto Rican Bank. Patterns of population structure trace the probable sources of E. antillensis in Saint Croix to islands off Puerto Rico's eastern coast, which include Vieques, Culebra, Saint Thomas, Saint John, Tortola, and Virgin Gorda, and possibly to eastern Puerto Rico as well. In contrast, Panamá City E. antillensis probably originated from either western or eastern Puerto Rico. Genetic diversity in the introduced populations is similar to or lower than in populations in the species' native range, indicating that genetic diversity has not increased in the alien frogs. Our findings may facilitate the development of preventive measures to minimize introductions of non-native amphibians in the Caribbean and Central America.

Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world's most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.