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Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super‐volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co‐distributed species of parachuting frogs (GenusRhacophorus) on Sumatra. We generate target‐capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction‐site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full‐likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid‐Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.

 

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences. 

This is the first release to serve as an archive of this project.

This work was made possible by funding provided to Jamie Oaks from the National Science Foundation (grant number DEB 1656004). 

An integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene ND2 recovered four new species of Hemiphyllodactylus Bleeker that are endemic to the Shan Plateau or Salween Basin in eastern Myanmar. Hemiphyllodactylus ngwelwini sp. nov. from the Shan Plateau is part of the earlier described “eastern Myanmar clade” renamed herein as the north lineage and H. kyaiktiyoensis sp. nov. and H. pinlaungensis sp. nov. of the Shan Plateau and H. zwegabinensis sp. nov. of the Salween Basin compose an entirely new Burmese clade herein referred to as the south lineage. Although the north and south lineages come within 46 km of one another on the Shan Plateau, they are not sister lineages but sequentially separated by two lineages from Yunnan, China and another from northwestern Thailand. Hemiphyllodactylus zwegabinensis sp. nov. is the first species of this genus to be recorded from the Salween Basin and is known only from a wind-blown cloud forest on the top of the insular, karstic mountain Zwegabin in Kayin State. All other Burmese species except for H. typus, are endemic to the various localities throughout the Shan Plateau. These four new species bring the total number of Hemiphyllodactylus in Myanmar to at least 10 which is certainly an extreme underestimate of the diversity of this genus given that we discover new species at every upland locality we survey. 

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis. 

An integrative taxonomic analysis of the 10 species of the Cyrtodactylus sinyineensis group based on squamation, color pattern, and the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNA regions, recovered the newly discovered populations from Datt Kyaik and Taung Wine Hills in Kayin State as the new species Cyrtodactylus dattkyaikensis sp. nov. and C. taungwineensis sp. nov. The Maximum Likelihood and Bayesian phylogenetic estimates supported C. dattkyaikensis sp. nov. as the sister species of C. bayinnyiensis and C. taungwineensis sp. nov. as the sister species of C. sinyineensis. Each new species is differentially diagnosable from all other C. sinyineensis group species based on their morphological placement in multivariate space and several statistically significant mean differences is meristic squamation and color pattern data. The C. sinyineensis group ranges across an archipelago of karstic habitat-islands in the Salween Basin of southern Myanmar. The discovery of these new species continues to underscore the unprecedented high degree of diversity and site-specific endemism in this relatively small region and the urgent need for the conservation of its karstic terranes. 

A survey of a limestone forest at Gunung Baling, Kedah, West Malaysia lead to the discovery of an undescribed species of Bent-toed Gecko from the Cyrtodactylus pulchellus complex. Cyrtodactylus evanquahi sp. nov. can be distinguished from all other species in the C. pulchellus complex by a suite of morphological and color pattern characteristics: prominent tuberculation, higher number of dark body bands, and a smaller maximum SVL. It is further differentiated from all other species as follows; no tubercles on the ventral surface of the forelimbs, gular region, or in the ventrolateral folds; 31–34 paravetebral dorsal tubercles; 18–23 longitudinal rows of tubercles; 29–33 ventral scales; 22–23 subdigital lamellae on the fourth toe; 32–36 femoroprecloacal pores; a shallow precloacal groove in males; body bands and nuchal loop edged with a thin white line bearing tubercles; no scattered white spots on the dorsum; six or seven dark body bands much thinner than interspaces; 9–11 dark caudal bands on original tail; bands on the original tail separated by immaculate white caudal bands. It is further differentiated by an uncorrected pairwise genetic divergence of 6.50–15.67% from all other congeners in the C. pulchellus complex. It is most closely related to C. pulchellus from Penang Island ∼76 km to the southwest. In addition to the new samples from Gunung Baling, we added four samples of C. bintangrendah from the new locality of Belukar Semang, Perak. The discovery of yet another new species of the C. pulchellus complex from a limestone habitat continues to underscore the high degree of endemism and the importance of these unique habitats for biodiversity, and the continued need for their conservation.