Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses

Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China

There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.

Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan

BACKGROUND

The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins.

RESULTS

In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan.

CONCLUSIONS

All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.

Population structure of Aphyocypris normalis: phylogeography and systematics

Aphyocyprisnormalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A.normalis using sequences of the mitochondrial DNA control region and cytochrome b gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of A.normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices N_ST (0.532) and G_ST (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus Aphyocypris were estimated.

Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis

Opsariichthine (sensu Oceanologi Et Limnologia Sinica, 1982, 13, 293-298) is a cyprinid group consisting of five genera and endemic to East Asia. Previous studies suggested that there may be many possible cryptic species in this group, but this has not been confirmed. In this study, using mitochondrial cyt b sequences on 1,388 samples and 739 haplotypes, we showed very high species diversity within this group. The results showed that phylogenetic relationships of the opsariichthine group were as ([Nipponocypris-Parazacco-Candidia] + [Zacco + Opsariichthys]), and there were multiple deep lineages within several species, flagging putative cryptic species. When a 3% genetic distance was used as a threshold for species delimitation, 35 haplogroups were found, nine haplogroups in Candidia-Parazacco-Nipponocypris group, six haplogroups in the Zacco group, and 20 haplogroups in the Opsariichthys group. We consider all of them to be putative until determination of distinct species based on the tree topology, geographic distributions, or a combination of both. In addition, two kinds of species delimitation tools, ABGD and PTP, were applied to construct molecular operational taxonomic units (MOTUs). The ABGD method revealed nine MOTUs in Candidia-Parazacco-Nipponocypris group, two MOTUs in the Zacco group, and 17 MOTUs in the Opsariichthys group. And the PTP method revealed 10 MOTUs in Candidia-Parazacco-Nipponocypris group, 10 MOTUs in the Zacco group, and 29 MOTUs in the Opsariichthys group. Therefore, there should be more species in the opsariichthine group than presently described. Based on the molecular data and morphological characteristics, we proposed Opsariichthys macrolepis as a valid species and described its morphological diagnostic characters.

Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

A new phylogeographic pattern of endemic Bufo bankorensis in Taiwan Island is attributed to the genetic variation of populations

Aim

To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China.

Methodology/Principal Findings

Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades.

Conclusions

The multiple origins (different clades) of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B. bankorensis, implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups.

Diversification, biogeographic pattern, and demographic history of Taiwanese Scutellaria species inferred from nuclear and chloroplast DNA

The ragged topography created by orogenesis generates diversified habitats for plants in Taiwan. In addition to colonization from nearby mainland China, high species diversity and endemism of plants is also present in Taiwan. Five of the seven Scutellaria species (Lamiaceae) in Taiwan, for example, are endemic to the island. Hypotheses of multiple sources or in situ radiation have arisen to explain the high endemism of Taiwanese species. In this study, phylogenetic analyses using both nuclear and chloroplast markers revealed the multiple sources of Taiwanese Scutellaria species and confirmed the rapid and recent speciation of endemic species, especially those of the "indica group" composed of S. indica, S. austrotaiwanensis, S. tashiroi, and S. playfairii. The common ancestors of the indica group colonized first in northern Taiwan and dispersed regionally southward and eastward. Climate changes during glacial/interglacial cycles led to gradual colonization and variance events in the ancestors of these species, resulting in the present distribution and genetic differentiation of extant populations. Population decline was also detected in S. indica, which might reflect a bottleneck effect from the glacials. In contrast, the recently speciated endemic members of the indica group have not had enough time to accumulate much genetic variation and are thus genetically insensitive to demographic fluctuations, but the extant lineages were spatially expanded in the coalescent process. This study integrated phylogenetic and population genetic analyses to illustrate the evolutionary history of Taiwanese Scutellaria of high endemism and may be indicative of the diversification mechanism of plants on continental islands.