Two new karst-adapted species in the Cyrtodactyluspulchellus group (Reptilia, Gekkonidae) from southern Thailand.

The exploration of unsurveyed areas in southern Thailand discovered two new karst-adapted species, Cyrtodactylussungaiupesp. nov. and Cyrtodactyluswangkhramensissp. nov., from Thung Wa and La-ngu Districts, Satun Province, respectively. These new species are members of the C.pulchellus group that occur along the Thai-Malay Peninsula. The new species can be distinguished from all other congeners by their key morphological characters and genetic divergence. Morphologically, Cyrtodactylussungaiupesp. nov. and Cyrtodactyluswangkhramensissp. nov. can be diagnosed from other members by having a combination of differences in body size; degree of dorsal tuberculation; absence of tubercles on ventral surfaces; number of ventral scales, paravertebral tubercles and femoroprecloacal pores in males only; deep precloacal groove only in males; absence of a scattered pattern of white dorsal tubercles; number of dark body bands; and the extent of caudal tubercles on an original tail. Although the two species are sister taxa and have nearly identical morphologies, they are considered to be different species, based on a relatively high uncorrected pairwise genetic divergence of the mitochondrial ND2 gene (6.59-6.89%), statistically significant univariate and multivariate morphological differences (PERMANOVA and ANOVA) and diagnostic characteristics of caudal tuberculation on the original tail. Moreover, Cyrtodactylussungaiupesp. nov. and Cyrtodactyluswangkhramensissp. nov. are currently restricted to their karstic type localities which may serve as a geographic barrier to dispersal and gene flow.

Generalizing Bayesian phylogenetics to infer shared evolutionary events.

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.

The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae).

The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges-followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene-the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.

FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales.

Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait  kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.

Hidden diversity of rock geckos within the Cnemaspissiamensis species group (Gekkonidae, Squamata): genetic and morphological data from southern Thailand reveal two new insular species and verify the phylogenetic affinities of C.chanardi and C.kamolnorranathi.

Two new insular rock geckos in the genus Cnemaspis are described from Ko Samui in Surat Thani Province and Ko Similan in Phang-nga Province, southern Thailand, based on a combination of morphological and mitochondrial NADH dehydrogenase subunit 2 (ND2) data. Both new species represent divergent lineages within the Cnemaspissiamensis species group. Cnemaspissamui sp. nov. is distinguished from other species in the group by having eight or nine supralabial and infralabial scales; 5-8 pore-bearing precloacal scales in males, pores rounded; 25-27 paravertebral tubercles, arranged randomly; 22-25 subdigital lamellae under 4th toe; enlarged median subcaudal scale row present; gular region, abdomen, limbs and subcaudal region yellowish only in males, and uncorrected pairwise divergences of 8.86-26.83% from all other species in the C.siamensis species group. Cnemaspissimilan sp. nov. is distinguished from other species in the group by having eight or nine supralabial and seven or eight infralabial scales; one pore-bearing precloacal scale in males, pore rounded; 24 or 25 paravertebral tubercles, arranged randomly; 23 or 24 subdigital lamellae under 4th toe; no enlarged median subcaudal scale row; pale yellow reticulum on head, neck, flanks, belly and limbs in male only, and uncorrected pairwise divergences of 9.34-27.11% from all other species in the C.siamensis species group. Cnemaspissamui sp. nov. is found along granitic rocky stream outcrops of Hin Lad Waterfall, Ko Samui, Gulf of Thailand, while Cnemaspissimilan sp. nov. occurs in granitic rocky outcrops near Ao Nguang Chang Bay, Ko Similan, Andaman Sea. The phylogenetic analyses confirmed that C.chanardi and C.kamolnorranathi are also nested within the C.siamensis species group, as previously hypothesized from morphology and color pattern characters.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis).

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: 1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and 2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear $p$-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow. [Cryptic species; gene flow; introgression; isolation-by-distance; isolation-by-environment; phylogenetic network; species delimitation.].

Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus).

Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. Together, these data suggest that sex chromosome turnover may be common in this clade, setting them apart as exceptionally diverse in a group already known for diverse sex determination systems.

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.

A new species of Cyrtodactylus Gray (Squamata; Gekkonidae) from the Thai Highlands with a discussion on the evolution of habitat preference.

A new gekkonid lizard, Cyrtodactylus maelanoi sp. nov., from Mae Hong Son Province of the Thai Highlands is described using an integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNAs. Phylogenetic analyses place the new species within clade 1 of the C. sinyineensis group and as the sister species to C. inthanon with an uncorrected pairwise sequence divergence of 3.9%. Collection data gathered in the field indicate that C. maelanoi sp. nov. is a habitat generalist. Reconstruction of the ancestral habitat preference for the C. sinyineensis group by way of stochasitc character mapping (SCM) indicates that karstic environments were the ancestral condition out of which the general habitat preference of the ancestor of C. maelanoi sp. nov. and C. inthanon and that of C. amphipetreaus and C. doisuthep evolved three times independently. Additionally, SCM demonstrated that the evolution of a granitic habitat preference from a karst-adapted ancestor happened in C. aequalis. The discovery of a new upland species in the Thai Highlands brings into focus the understudied nature of the mountain systems of western Thailand and the need for their continued exploration and conservation.

A new species of Cnemaspis Strauch 1887 (Squamata: Gekkonidae) from the Langkawi Archipelago, Kedah, Peninsular Malaysia with an updated checklist of the herpetofauna of Tuba Island.

A new, diminutive species of Rock Gecko Cnemaspis tubaensis sp. nov. of the C. kumpoli group, is described from Tuba Island, Langkawi Archipelago, Kedah, Peninsular Malaysia and is differentiated from all other species in the kumpoli group by having a unique combination of morphological and color pattern characteristics, including a maximum SVL of 37.0 mm; 10 or 11 supralabials; eight or nine infralabials; 15-18 semi-linearly arranged paravertebral tubercles; lateral caudal furrow present; lateral caudal tubercles on the anterior portion of the tail; caudal tubercles not encircling tail; five or six precloacal pores; 28 or 29 subdigital lamellae on the fourth toe; smooth ventrals; smooth subcaudals with an enlarged median row of scales; subcaudal region light-grey and speckled with yellow; absence of light-colored ocelli on the shoulder; no yellow postscapular band; dorsum light-brown with sage-green blotches and black spots; flanks with scattered yellow spots; absence of black gular markings in both sexes; and 13.0-22.0% uncorrected pairwise sequence divergences in the NADH dehydrogenase subunit 2 gene (ND2). Cnemaspis tubaensis sp. nov. is the fourth species of Cnemaspis to be described from the Langkawi Archipelago and underscores the underestimated biodiversity of the islands which is in need of more thorough herpetological inventories.

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia.

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12.

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex.

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.

Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana).

Using FrogCap, a recently-developed sequence-capture protocol, we obtained >12,000 highly informative exons, introns, and ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation error, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS). We then estimated species trees using concatenated datasets and Maximum Likelihood (IQ-TREE) in addition to summary (ASTRAL-III), distance-based (ASTRID), and site-based (SVDQuartets) multispecies coalescent methods. Topological congruence and branch support were examined using traditional bootstrap, local posterior probabilities, gene concordance factors, quartet frequencies, and quartet scores. Our results did not yield a single concordant topology. Instead, introns, exons, and UCEs clearly possessed different phylogenetic signals, resulting in conflicting, yet strongly-supported phylogenetic estimates. However, a combined analysis comprising the most informative introns, exons, and UCEs converged on a similar topology across all analyses, with the exception of SVDQuartets. Bootstrap values were consistently high despite high levels of incongruence and high proportions of gene trees supporting conflicting topologies. Although low bootstrap values did indicate low heuristic support, high bootstrap support did not necessarily reflect congruence or support for the correct topology. This study reiterates findings of some previous studies, which demonstrated that traditional bootstrap values can produce positively misleading measures of support in large phylogenomic datasets. We also showed a remarkably strong positive relationship between branch length and topological congruence across all datasets, implying that very short internodes remain a challenge to resolve, even with orders of magnitude more data than ever before. Overall, our results demonstrate that more data from unfiltered or combined datasets produced superior results. Although data filtering reduced gene tree incongruence, decreased amounts of data also biased phylogenetic estimation. A point of diminishing returns was evident, at which higher congruence (from more stringent filtering) at the expense of amount of data led to topological error as assessed by comparison to more complete datasets across different genomic markers. Additionally, we showed that applying a parameter-rich model to a partitioned analysis of concatenated data produces better results compared to unpartitioned, or even partitioned analysis using model selection. Despite some lingering uncertainties, a combined analysis of our genomic data and sequences supplemented from GenBank (on the basis of a few gene regions) revealed highly supported novel systematic arrangements. Based on these new findings, we transfer Amnirana nicobariensis into the genus Indosylvirana; and I. milleti and Hylarana celebensis to the genus Papurana. We also provisionally place H. attigua in the genus Papurana pending verification from positively identified (voucher substantiated) samples.

Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex.

Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.

Two new species of Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from a karstic archipelago in the Salween Basin of southern Myanmar (Burma).

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.

Four new Burmese species of Hemiphyllodactylus Bleeker (Squamata: Gekkonidae) from distantly related parapatric clades from the Shan Plateau and Salween Basin.

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.

A new potentially endangered limestone-associated Bent-toed Gecko of the Cyrtodactylus pulchellus (Squamata: Gekkonidae) complex from northern Peninsular Malaysia.

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.

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements.

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread "generalist" clades. This is especially true in Australasia, where monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately "derived" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements (UCEs) to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyze multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme addresses four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic, and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesi's L. iskandari as the sister taxon to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high-elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister taxon relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not grouped with Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our resolved and strongly supported phylogeny, we present a new classification emphasizing the most inclusive, original generic name (Gekko) for these ~60 taxa, arranged into seven subgenera.

Evolution of habitat preference in 243 species of Bent-toed geckos (Genus Cyrtodactylus Gray, 1827) with a discussion of karst habitat conservation.

Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independently over time in different lineages. The gekkonid genus Cyrtodactylus is just such a lineage with approximately 300 species that range from South Asia to Melanesia and occupy a vast array of habitats. Ancestral state reconstructions using a stochastic character mapping analysis of nine different habitat preferences were employed across a phylogeny composed of 76% of the known species of Cyrtodactylus. This was done in order to ascertain which habitat preference is the ancestral condition and from that condition, the transition frequency to more derived habitat preferences. The results indicate that a general habitat preference is the ancestral condition for Cyrtodactylus and the frequency of transitioning from a general habitat preference to anything more specialized occurs approximately four times more often than the reverse. Species showing extreme morphological and/or ecological specializations generally do not give rise to species bearing other habitat preferences. The evolution of different habitat preferences is generally restricted to clades that tend to occur in specific geographic regions. The largest radiations in the genus occur in rocky habitats (granite and karst), indicating that the transition from a general habitat preference to a granite or karst-dwelling life style may be ecologically uncomplicated. Two large, unrelated clades of karst-associated species are centered in northern Indochina and the largest clade of granite-associated species occurs on the Thai-Malay Peninsula. Smaller, independent radiations of clades bearing other habitat preferences occur throughout the tree and across the broad distribution of the genus. With the exception of a general habitat preference, the data show that karst-associated species far out-number all others (29.6% vs. 0.4%-10.2%, respectively) and the common reference to karstic regions as "imperiled arcs of biodiversity" is not only misleading but potentially dangerous. Karstic regions are not simply refugia harboring the remnants of local biodiversity but are foci of speciation that continue to generate the most speciose, independent, radiations across the genus. Unfortunately, karstic landscapes are some of the most imperiled and least protected habitats on the planet and these data continue to underscore the urgent need for their conservation.