Parallel adaptations to nectarivory in parrots, key innovations and the diversification of the Loriinae

Specialization to nectarivory is associated with radiations within different bird groups, including parrots. One of them, the Australasian lories, were shown to be unexpectedly species rich. Their shift to nectarivory may have created an ecological opportunity promoting species proliferation. Several morphological specializations of the feeding tract to nectarivory have been described for parrots. However, they have never been assessed in a quantitative framework considering phylogenetic nonindependence. Using a phylogenetic comparative approach with broad taxon sampling and 15 continuous characters of the digestive tract, we demonstrate that nectarivorous parrots differ in several traits from the remaining parrots. These trait-changes indicate phenotype–environment correlations and parallel evolution, and may reflect adaptations to feed effectively on nectar. Moreover, the diet shift was associated with significant trait shifts at the base of the radiation of the lories, as shown by an alternative statistical approach. Their diet shift might be considered as an evolutionary key innovation which promoted significant non-adaptive lineage diversification through allopatric partitioning of the same new niche. The lack of increased rates of cladogenesis in other nectarivorous parrots indicates that evolutionary innovations need not be associated one-to-one with diversification events

Phylogeographic inference of Sumatran ranids bearing gastromyzophorous tadpoles with regard to the Pleistocene drainage systems of Sundaland.

Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs (Sumaterana and Wijayarana) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north-south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island

Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians.

BACKGROUND The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths. RESULTS Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content. CONCLUSIONS Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost

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

The tree-frog family Rhacophoridae is a major group contributing to the high pecies richness and reproductive diversity among vertebrates of Sundaland. Nonetheless, rhacophorid evolution, specially on Borneo, has not been studied within a phylogenetic context. In this study, we examine the phylogenetic relationships of 38 (out of 41) Bornean species of Rhacophoridae, in combination with data from previous phylogenetic studies. In the final super matrix of 91 species, we analyse sequence data from two mitochondrial and three nuclear genes. The resulting trees show the genus Rhacophorus as a paraphyletic assemblage. As a consequence, we transfer Rhacophorus appendiculatus and R. kajau to two other genera and propose the new phylogeny-based combinations- Kurixalus appendiculatus and Feihyla kajau, respectively. Furthermore, we use our phylogenetic hypotheses to reconstruct the evolution of reproductive modes in rhacophorid tree frogs. Direct development to the exclusion of a free larval stage evolved twice independently, once in an ancestor of the Pseudophilautus + Raorchestes clade in India and Sri Lanka, and once within Philautus in Southeast Asia. The deposition of egg clutches covered by a layer of jelly in Feihyla is also present in F. kajau and thus confirms our generic reassignment. The remarkably high diversity of rhacophorid tree frogs on Borneo is the outcome of a complex pattern of repeated vicariance and dispersal events caused by past changes in the climatic and geological history of the Sunda shelf. We identified geographic clades of closely related endemic species within Rhacophorus and Philautus, which result from local island radiations on Borne

Larval morphologies of three species of stream toads, genus Ansonia (Amphibia: Bufonidae) from East Malaysia (Borneo), with a key to known Bornean Ansonia tadpoles

We describe the external morphology of tadpoles of Ansonia longidigita Inger, 1960, A. minuta Inger, 1960, and A. platysoma Inger, 1960 from East Malaysia, Borneo. Specimens were collected from small to medium-sized streams with swift current in Sarawak State. Tadpole identities were confirmed by matching tadpole genetic sequences (16S mtRNA) to sequences from adult toads from the same collection sites. Among the three species, A. minuta appears to prefer the strongest current and was collected from fast-flowing waters in association with boulders. Ansonia longidigita larvae inhabit more moderate currents than sympatric A. platysoma. Species microhabitat choices are reflected in their body shape, with A. minuta and A. platysoma being more streamlined than A. longidigita. Colour photos of live specimens and a key to the known Bornean Ansonia tadpoles are provided to facilitate field identification

Larval morphologies of three species of stream toads, genus Ansonia (Amphibia: Bufonidae) from East Malaysia (Borneo), with a key to known Bornean Ansonia tadpoles

We describe the external morphology of tadpoles of Ansonia longidigita Inger, 1960, A. minuta Inger, 1960, and A. platysoma Inger, 1960 from East Malaysia, Borneo. Specimens were collected from small to medium-sized streams with swift current in Sarawak State. Tadpole identities were confirmed by matching tadpole genetic sequences (16S mtRNA) to sequences from adult toads from the same collection sites. Among the three species, A. minuta appears to prefer the strongest current and was collected from fast-flowing waters in association with boulders. Ansonia longidigita larvae inhabit more moderate currents than sympatric A. platysoma. Species microhabitat choices are reflected in their body shape, with A. minuta and A. platysoma being more streamlined than A. longidigita. Colour photos of live specimens and a key to the known Bornean Ansonia tadpoles are provided to facilitate field identification

A Guide to the Tadpoles of Borneo

The monograph describes 99 species of amphibian larvae from the island of Borneo