Diversification in a biodiversity hotspot – The evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae)

Tadpole of the Vietnamese jelly-nest tree frog, Feihyla palpebralis (Anura: Rhacophoridae): external morphology and chondrocranium

The genus Feihyla Frost, Grant, Faivovich, Bain, Haas, Haddad, de S, Channing, Wilkinson, Donnellan, Raxworthy, Campbell, Blotto, Moler, Drewes, Nussbaum, Lynch, Green & Wheeler was established relatively recently (Frost et al. 2006), but to date its composition has changed several times due to the extremely confusing and labile systematics of small rhacophorids (e.g., Grosjean et al. 2008; Hertwig et al. 2013; Biju et al. 2020). It embeds rather miniature, delicate tree frogs and currently comprises six species (Frost 2023). The type species, Feihyla palpebralis (Smith 1924), was described from Mount Langbian in the southern part of the Truong Son Range (Annamite Mountains) and was long considered endemic to Vietnam; recent reports that it is also distributed in China can be based on misidentification and need reliable confirmation (Biju et al. 2020).

Phylogenetic relationships of xenodermid snakes (Squamata: Serpentes: Xenodermidae), with the description of a new genus

Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mitochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermusgen. nov. We also present new morphological data for P. borneensis.

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)

Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Rhacophoridae are one of the most speciose and ecologically diverse families of amphibians. Resolution of their evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated phylogenetic hypothesis clarifies several long-disputed relationships and facilitates the testing of evolutionary hypotheses on spatiotemporal diversification and reproductive modes. The major extant lineages of Rhacophoridae appear to have radiated in mainland Asia, and the spatiotemporal process corresponds with several common accumulations of biodiversity in Asia. Analyses do not detect any case of "Out of Himalaya" in Rhacophoridae. All transitions of reproductive modes appear to have evolved in an ordered, gradual sequence associated with gaining independence of standing water for larval development. The different reproductive modes are phylogenetically conserved and the completion of their transitions appear to have occurred over a period of ~30 Ma, which does not fit a pattern of a rapid burst of diversification. Innovations in reproductive modes associate statistically with the uneven distribution of species-richness between clades, where higher diversification is linked to increased terrestrial modes of reproduction. These results strengthen the hypothesis that breeding innovations drive diversification by providing new opportunities for ecological release and dispersion.

Geological data indicate that the interpretation for the age-calibrated phylogeny for the Kurixalus-genus frogs of South, South-east and East Asia (Lv et al., 2018) needs to be rethought

Recently, Lv et al. (2018) published an age-calibrated phylogenetic tree for the Kurixalus frogs, members of which occur across parts of South, South-east and East Asia. A clade on Taiwan, represented by Kurixalus idiootocus and the Kurixalus eiffingeri species complex, is deemed to have been resident since the middle Cenozoic; its closest congeners are in southern Indochina (not in the adjacent parts of south-east China), and the split between the two is dated at 32.8 Ma. Furthermore, a sub-population of Kurixalus eiffingeri is believed to have colonized islands in the western Ryukyus c. 13.5 Ma. There is, however, a problem with this scenario: the landmass regarded as modern-day Taiwan has existed only for 4-5 million years (it results from a young and ongoing tectonic-plate collision). Assuming the Kurixalus phylogeny and the dating of its branchings are correct, then a palaeobiogeographical scenario involving an older, alternative land surface with later transfer to Taiwan, possibly involving over-water dispersal, would reconcile the biology, but testing this may be difficult/impossible. If the ages of the nodes in the proposed tree are found to be significantly overestimated, the geology and biology might more easily be accommodated.

A comprehensive phylogeny of the genus Kurixalus (Rhacophoridae, Anura) sheds light on the geographical range evolution of frilled swamp treefrogs

Currently, the genus Kurixalus comprises 14 species distributed in Southern, Southeast and East Asia. Because of their relatively low dispersal capability and intolerance of seawater, this group is ideal for the study of terrestrial range evolution, especially that portion of its range that extends into the island archipelagos of Southern Asia. We assembled a large dataset of mitochondrial and nuclear genes, and estimated phylogeny by maximum likelihood and Bayesian methods, and we explored the history of each species via divergence-time estimation based on fossil-calibrations. A variety of ancestral-area reconstruction strategies were employed to estimate past changes of the species' geographical range, and to evaluate the impact of different abiotic barriers on range evolution. We found that frilled swamp treefrogs probably originated in Taiwan or South Vietnam in the Oligocene. Alternatively, the lineage leading to Kurixalus appendiculatus strongly supports a hypothesis of terrestrial connection between the Indian and Asian continents in the Oligocene. The outcome of both our divergence-time estimates and ancestral-area reconstruction suggests that the divergence between species from Indochina and Taiwan can probably be attributed to the opening of the South China Sea, approximately 33 million years ago. We could not find evidence for dispersal between mainland China and Taiwan Island. Formation of both Mekong and Red River valleys did not have any impact on Kurixalus species diversification. However, coincidence in timing of climate change and availability of plausible dispersal routes from the Oligocene to the middle Miocene, plausibly implied that Kurixalus diversification in Asia resulted from contemporaneous, climate-induced environmental upheaval (Late Oligocene Warming at 29 Ma; Mi-1 glaciation since 24.4-21.5 Ma; Mid-Miocene Climatic Optimum at 14 Ma), which alternatively opened and closed dispersal routes.

Systematic revision of the Taiwanese genus Kurixalus members with a description of two new endemic species (Anura, Rhacophoridae)

Two new species of rhacophorid tree frog were identified in Taiwan. In both new taxa, derived reproductive characteristics of laying eggs in tree holes and oophagous tadpoles are shared with Kurixalus eiffingeri, but they are divergent from each other in molecular genetics, mating calls, and tadpole and adult morphology. The morphological characteristics and the molecular phylogenetic evidence support the hypothesis that the two new species, Kurixalus berylliniris sp. n. and Kurixalus wangi sp. n., are both monophyletic lineages.

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

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.