Jia-Tang Li

Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene

The accretion of the Indian subcontinent to Eurasia triggered a massive faunal and floral exchange, with Gondwanan taxa entering into Asia and vice versa. The traditional view on the Indian–Asian collision assumes contact of the continental plates during the Early Eocene. Many biogeographic studies rely on this assumption. However, the exact mode and timing of this geological event is still under debate. Here we address, based on an extensive phylogenetic analysis of rhacophorid tree frogs, if there was already a Paleogene biogeographic link between Southeast Asia and India; in which direction faunal exchange occurred between India and Eurasia within the Rhacophoridae; and if the timing of the faunal exchange correlates with one of the recently suggested geological models. Rhacophorid tree frogs showed an early dispersal from India to Asia between 46 and 57 Ma, as reconstructed from the fossil record. During the Middle Eocene, however, faunal exchange ceased, followed by increase of rhacophorid dispersal events between Asia and the Indian subcontinent during the Oligocene that continued until the Middle Miocene. This corroborates recent geological models that argue for a much later final collision between the continental plates. We predict that the Oligocene faunal exchange between the Indian subcontinent and Asia, as shown here for rhacophorid frogs, also applies for other nonvolant organisms with an Indian–Asian distribution, and suggest that previous studies that deal with this faunal interchange should be carefully reinvestigated.

Amphibians crossing the Bering Land Bridge: evidence from holarctic treefrogs (Hyla, Hylidae, Anura).

Based on an updated, time-calibrated phylogeny and applying biogeographical model testing and diversification analysis, we re-examined systematics and biogeography of the Holarctic treefrog genus Hyla with a focus on the East Asian species. We analyzed four mitochondrial genes (12S and 16S rRNA, tRNA(Leu), ND1) and one nuclear gene (POMC) for 192 samples representing 30 species of Hyla. Based on our results we suggest that H. ussuriensis is a synonym of H. japonica. Specimens from Sakhalin and Kunashir Islands might represent a cryptic species within H. japonica. We confirm earlier hypotheses that the genus Hyla originated during the Eocene to Early Oligocene and that Eurasian species originated from two independent dispersal events from North America via the Bering Land Bridge. Middle Eocene to Oligocene dispersal gave rise to the most recent common ancestor of the West Palearctic H. arborea-group and the East Palearctic, newly defined, H. chinensis-group. The Northeast Asian H. japonica-group resulted from a second wave of colonization from the Nearctic. A trans-Atlantic dispersal route could be excluded. Dispersal of the H. arborea-group to the western Palearctic coincides with the closure of the Turgai Strait at the end of the Oligocene. Diversification of Hyla decreased at the end of the Middle Miocene, possibly coinciding with the end of the Mid Miocene Climatic Optimum and the advent of cooler and drier climates in the Northern Hemisphere.

Biotic interchange between the Indian subcontinent and mainland Asia through time.

Biotic interchange after the connection of previously independently evolving floras and faunas is thought to be one of the key factors that shaped global biodiversity as we see it today. However, it was not known how biotic interchange develops over longer time periods of several million years following the secondary contact of different biotas. Here we present a novel method to investigate the temporal dynamics of biotic interchange based on a phylogeographical meta-analysis by calculating the maximal number of observed dispersal events per million years given the temporal uncertainty of the underlying time-calibrated phylogenies. We show that biotic influx from mainland Asia onto the Indian subcontinent after Eocene continental collision was not a uniform process, but was subject to periods of acceleration, stagnancy and decrease. We discuss potential palaeoenvironmental causes for this fluctuation.

Diversification and Demography of the Oriental Garden Lizard ( Calotes versicolor ) on Hainan Island and the Adjacent Mainland

The Oriental garden lizard (Calotes versicolor) is one of the few non-gekkonid lizards that are geographically widespread in the tropics. We investigated its population dynamics on Hainan Island and the adjacent mainland of China and Vietnam, focusing on the impact of cyclic upheaval and submergence of land bridges during the Pleistocene. Our Bayesian phylogenetic analysis reveals two mitochondrial lineages, A and B, which are estimated to have coalesced about 0.26 million years ago (95% credibility interval: 0.05–0.61 million years ago). Lineage A contains individuals mainly from central and southern Wuzhi Mountain on Hainan Island, whereas lineage B mainly comprises individuals from other sites on the island plus the adjacent mainland. The estimated coalescence times within lineages A (0.05 million years ago) and B (0.13 million years ago) fall within a period of cyclical land-bridge formation and disappearance in the Pleistocene. A spatial analysis of molecular variance identified two distinct population groupings: I, primarily containing lineage A, and II, mainly consisting of lineage B. However, haplotypes from lineages A and B occur sympatrically, suggesting that gene flow is ongoing. Neither Wuzhi Mountain nor Qiongzhou Strait and Gulf of Tonkin act as barriers to gene flow among C. versicolor populations. Analyses of the data using mismatch distributions and extended Bayesian skyline plots provide evidence of a relatively stable population size through time for Group I, and moderate population expansions and contractions during the end of the Pleistocene for Group II. We conclude that the phylogeographical patterns of C. versicolor are the combined product of Pleistocene sea-level oscillations and nonphysical barriers to gene flow.

Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia)

Li, J.T., Li, Y., Murphy, R.W., Rao, D.‐Q. & Zhang, Y.‐P. (2012). Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia). —Zoologica Scripta, 41, 557–570.

Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China.

The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.

Phylogeography reveals an ancient cryptic radiation in East-Asian tree frogs ( Hyla japonica group) and complex relationships between continental and island lineages

BackgroundIn contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H. japonica.ResultsWe document several cryptic lineages within the currently recognized H. japonica populations, including two main clades of Late Miocene divergence (~5 Mya). One occurs on the northeastern Japanese Archipelago (Honshu and Hokkaido) and the Russian Far-East islands (Kunashir and Sakhalin), and the second one inhabits the remaining range, comprising southwestern Japan, the Korean Peninsula, Transiberian China, Russia and Mongolia. Each clade further features strong allopatric Plio-Pleistocene subdivisions (~2-3 Mya), especially among continental and southwestern Japanese tree frog populations. Combined with paleo-climate-based distribution models, the molecular data allowed the identification of Pleistocene glacial refugia and continental routes of postglacial recolonization. Phylogenetic reconstructions further supported genetic homogeneity between the Korean H. suweonensis and Chinese H. immaculata, suggesting the former to be a relic population of the latter that arose when the Yellow Sea formed, at the end of the last glaciation.ConclusionsPatterns of divergence and diversity were likely triggered by Miocene tectonic activities and Quaternary climatic fluctuations (including glaciations), causing the formation and disappearance of land-bridges between the Japanese islands and the continent. Overall, this resulted in a ring-like diversification of H. japonica around the Sea of Japan. Our findings urge for important taxonomic revisions in East-Asian tree frogs. First, they support the synonymy of H. suweonensis (Kuramoto, 1980) and H. immaculata (Boettger, 1888). Second, the nominal H. japonica (Günther, 1859) represents at least two species: an eastern (new taxon A) on the northern Japanese and Russian Far East islands, and a southwestern species (n. t. B) on southern Japanese islands and possibly also forming continental populations. Third, these continental tree frogs may also represent an additional entity, previously described as H. stepheni Boulenger, 1888 (senior synonym of H. ussuriensis Nikolskii, 1918). A complete revision of this group requires further taxonomic and nomenclatural analyses, especially since it remains unclear to which taxon the species-epitheton japonica corresponds to.

Predicting the impacts of climate change on the potential distribution of major native non-food bioenergy plants in China.

Planting non-food bioenergy crops on marginal lands is an alternative bioenergy development solution in China. Native non-food bioenergy plants are also considered to be a wise choice to reduce the threat of invasive plants. In this study, the impacts of climate change (a consensus of IPCC scenarios A2a for 2080) on the potential distribution of nine non-food bioenergy plants native to China (viz., Pistacia chinensis, Cornus wilsoniana, Xanthoceras sorbifolia, Vernicia fordii, Sapium sebiferum, Miscanthus sinensis, M. floridulus, M. sacchariflorus and Arundo donax) were analyzed using a MaxEnt species distribution model. The suitable habitats of the nine non-food plants were distributed in the regions east of the Mongolian Plateau and the Tibetan Plateau, where the arable land is primarily used for food production. Thus, the large-scale cultivation of those plants for energy production will have to rely on the marginal lands. The variables of “precipitation of the warmest quarter” and “annual mean temperature” were the most important bioclimatic variables for most of the nine plants according to the MaxEnt modeling results. Global warming in coming decades may result in a decrease in the extent of suitable habitat in the tropics but will have little effect on the total distribution area of each plant. The results indicated that it will be possible to grow these plants on marginal lands within these areas in the future. This work should be beneficial for the domestication and cultivation of those bioenergy plants and should facilitate land-use planning for bioenergy crops in China.

Phylogeny and systematic revision of the genus Typhlomys (Rodentia, Platacanthomyidae), with description of a new species

The “blind mouse” genus, Typhlomys, is an ancient taxon in the family Platacanthomyidae, comprising 2 living species and 4 living subspecies. We sequenced 3 mitochondrial (CytB, COI, and ND2) and 2 nuclear (GHR and IRBP) gene segments to estimate the phylogenetic relationships of the species and subspecies, and to delimit species boundaries. We also evaluated patterns of morphological and morphometric variation of the skull. The molecular results suggest at least 5 species are present, corresponding to the 2 recognized species (Typhlomys cinereus and T. chapensis), 1 species previously considered a subspecies (T. ci. daloushanensis), 1 new species (Typhlomys nanus sp. nov.), and 1 putative new species, for which we lack adequate morphological specimens. We also determined that the subspecies Typhlomys cinereus jingdongensis is conspecific with T. chapensis. Diversification of the genus occurred in the late Miocene and Pliocene. The new species, T. nanus, is distributed in eastern and northeastern Yunnan at middle to high elevations (2,000 m to > 3,000 m above sea level). Interestingly, we detected a frameshift mutation within the IRBP gene, which is the 1st molecular evidence for the degradation of vision.

DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae)

Abstract The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.