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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. 

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. 

Most new cryptic species are described using conventional tree‐ and distance‐based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence‐capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%–10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species—or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages—a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed “cryptic” groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.

 

Three new species of Rock GeckosCnemaspis lineogularissp. nov.,C. phangngaensissp. nov., andC. thachanaensissp. nov. of thechanthaburiensisandsiamensisgroups are described from the Thai portion of the Thai-Malay Peninsula. These new species are distinguished from all other species in their two respective groups based on a unique combination of morphological characteristics, which is further supported by mitochondrial DNA (mtDNA) from the NADH dehydrogenase subunit 2 gene (ND2).Cnemaspis lineogularissp. nov. is differentiated from all other species in thechanthaburiensisgroup by having a smaller maximum SVL 38 mm, 13 paravertebral tubercles, enlarged femoral scales, no caudal bands, and a 19.5–23.0% pairwise sequence divergence (ND2).Cnemaspis phangngaensissp. nov. is differentiated from all other species in the siamensis group by having the unique combination of 10 infralabial scales, four continuous pore-bearing precloacal scales, paravertebral tubercles linearly arranged, lacking tubercles on the lower flanks, having ventrolateral caudal tubercles anteriorly present, caudal tubercles restricted to a single paraveterbral row on each side, a single median row of keeled subcaudals, and a 8.8–25.2% pairwise sequence divergence (ND2).Cnemaspis thachanaensissp. nov. is distinguished from all other species in the siamensis group by having 10 or 11 supralabial scales 9–11 infralabial scales, paravertebral tubercles linearly arranged, ventrolateral caudal tubercles anteriorly, caudal tubercles restricted to a single paravertebral row on each side, a single median row of keeled subcaudal scales, lacking a single enlarged subcaudal scale row, lacking postcloaclal tubercles in males, the presence of an enlarged submetatarsal scale at the base if the 1st toe, and a 13.4–28.8% pairwise sequence divergence (ND2). The new phylogenetic analyses placeC. punctatonuchalisandC. vandeventeriin the siamensis group withC. punctatonuchalisas the sister species toC. huaseesomandC. vandeventerias the sister species toC. siamensis, corroborating previous hypotheses based on morphology. The discovery of three new karst-dwelling endemics brings the total number of nominal ThaiCnemaspisspecies to 15 and underscores the need for continued field research in poorly known areas of the Thai-Malay Peninsula, especially those that are threatened and often overlooked as biodiversity hot spots.