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The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.]., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

Pygmy Chameleons of the genus Rhampholeon represent a moderately diverse, geographically circumscribed radiation, with most species (18 out of 19 extant taxa) limited to East Africa. The one exception is Rhampholeon spectrum, a species restricted to West-Central African rainforests. We set out to characterize the geographic basis of genetic variation in this disjunctly distributed Rhampholeon species using a combination of multilocus Sanger data and genomic sequences to explore population structure and range-wide phylogeographic patterns. We also employed demographic analyses and niche modeling to distinguish between alternate explanations to contextualize the impact of past geological and climatic events on the present-day distribution of intraspecific genetic variation. Phylogenetic analyses suggest that R. spectrum is a complex of five geographically delimited populations grouped into two major clades (montane vs. lowland). We found pronounced population structure suggesting that divergence and, potentially, speciation began between the late Miocene and the Pleistocene. Sea level changes during the Pleistocene climatic oscillations resulted in allopatric divergence associated with dispersal over an ocean channel barrier and colonization of Bioko Island. Demographic inferences and range stability mapping each support diversification models with secondary contact due to population contraction in lowland and montane refugia during the interglacial period. Allopatric divergence, congruent with isolation caused by geologic uplift of the East African rift system, the "descent into the Icehouse," and aridification of sub-Saharan Africa during the Eocene-Oligocene are identified as the key events explaining the population divergence between R. spectrum and its closely related sister clade from the Eastern Arc Mountains. Our results unveil cryptic genetic diversity in R. spectrum, suggesting the possibility of a species complex distributed across the Lower Guinean Forest and the Island of Bioko. We highlight the major element of species diversification that modelled today's diversity and distributions in most West-Central African vertebrates., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Tapondjou Nkonmeneck et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

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 gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of cryptic diversity and revealed numerous taxonomic complications, especially within the C. consobrinus, C. malayanus, and C. pubisulcus groups. Comparisons of pairwise genetic distances and a preliminary species delimitation analysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-ranging species on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricted distributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneo into the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derived from multiple separate invasions into the geopolitical areas comprising the Philippines. Although our investigation of Bornean Cyrtodactylus is the most comprehensive to-date, it highlights the need for expanded taxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeography of Bornean Cyrtodactylus is far from complete., (Copyright © 2020 Elsevier Inc. All rights reserved.)

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., (Copyright © 2020 Elsevier Inc. All rights reserved.)

An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivariate and univariate analyses of continuous and discrete morphological and color pattern characters statistically and discretely diagnose each lineage from one another and together, with maximum likelihood and Bayesian inference analyses, provide the foundation for the recognition of each lineage as a new species-hypotheses corroborated with a Generalized Mixed Yule Coalescent species delimitation analysis. Ptychozoon cicakterbang sp. nov. ranges throughout Peninsular Malaysia to Pulau Natuna Besar, Indonesia; P. kabkaebin sp. nov. is endemic to northern and central Laos; and P. tokehos sp. nov. ranges from southern Thailand south of the Isthmus of Kra northward to Chiang Mai, fringing the Chao Phraya Basin and ranging southward through Cambodia to southern Vietnam. Ptychozoon lionotum sensu stricto ranges from northwestern Laos through southern Myanmar to eastern India. The phylogeographic structure within each species varies considerably with P. lionotum s.s. showing no genetic divergence across its 1,100 km range compared to P. cicakterbang sp. nov. showing upwards of 8.2% sequence divergence between syntopic individuals. Significant phylogeographic structure exists within P. tokehos sp. nov. and increased sampling throughout Thailand may require additional taxonomic changes within this species.

A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the "species-pump" model, in which repeated bouts of cospeciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago., (© 2019 The Author(s). Evolution © 2019 The Society for the Study of Evolution.)

A molecular phylogenetic analysis of Parachute Geckos (Genus Ptychozoon Kuhl van Hasselt, 1822) based on the mitochondrial gene ND2 indicates that a newly discovered population from the Mt. Popa volcano-a habitat island in the northern portion of the Bago Yoma mountains, Myanmar-is a new species, P. popaense sp. nov. This species is part of a clade that contains P. bannanense Wang, Wang, Liu, 2016 and P. lionotum Annandale, 1905 of Indochina. Ptychozoon popaense sp. nov. is morphologically most similar to its sister species P. lionotum  which manifests considerable geographic substructuring of genetic variation but differs from the nominate taxon by an uncorrected pairwise sequence divergence of 16.0-17.1% and by discrete differences in morphology and color pattern. This discovery highlights the unique, insular nature of the Bago Yoma mountains of the Ayeyarwady Basin, which support other endemic gekkonids. It also underscores the growing diversity in this highly derived clade of cryptic, parachuting, geckos characterized by highly divergent genetic lineages, which may indicate the presence of additional, unrecognized species.

Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the world's most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallace's Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia., (© 2018 The Author(s).)

We describe a new species of lizard in the genus Pseudogekko from Sibuyan and Tablas islands in the Romblon Island Group of the central Philippines. The new species is diagnosed from other Philippine Pseudogekko by body size and shape, color pattern, and multiple differences in scale characteristics. Pseudogekko isapa sp. nov. has been collected only twice from leaves of shrubs in forested habitat on Sibuyan and Tablas islands. The distinctive new species of false gecko is undoubtedly endemic to this single, isolated island group. The fact that populations of such a distinctive new species of Pseudogekko has escaped notice of herpetologists on the reasonably well-studied and largely protected Sibuyan Island further emphasizes the secretive and forest-dependent habits of Philippine false geckos. These characteristics of their behavior and natural history render them difficult to study and challenge biologists' efforts to accurately assess their conservation status.

We describe a new digitless scincid lizard of the genus Brachymeles from northern Luzon and Camiguin Norte islands in the Philippines. This species belongs to the Brachymeles bonitae Complex, and both molecular and morphological data confirm that this species is distinct from all other congeners. Formerly considered to be a single widespread species, this group of species has been the focus of recent systematic reviews. Here we describe a new species in the B. bonitae Complex, recognized currently to constitute five species. Brachymeles ilocandia sp. nov. is the second digitless and the seventeenth non-pentadactyl species in genus. The description of this species brings the total number of species in the genus to 40, and provides new insight into unique distribution patterns of species of the northern Philippines.

A new species of slender skink is described from the Philippines. The species is endemic to Lubang Island, and is assigned to the Brachymeles bonitae Complex based on phenotypic and genetic data. Specimens were collected from Lubang Island between 1991 and 2012, and were examined based on morphological data (qualitative traits, meristic counts, and mensural measurements). Published genetic sequence data from phylogenetic studies of the genus reveal the new species to be highly divergent from congeners. Brachymeles ligtas sp. nov. is differentiated from other members of the genus based on a number of distinct morphological features, including small body size (SVL 60.7-79.6 mm), bidactyl fore-limbs, digitless hind limbs, high number of presacral vertebrae (50), and the absence of auricular openings. Additionally, the new species has diagnostic, distinct dorsal head scale patterns. This new species becomes the only member of the genus known to occur on the deep-ocean island of Lubang.

Studies of the diversity of Philippine amphibians and reptiles have resulted in the continued description of cryptic species. Species formerly thought to range across multiple recognized faunal regions are now considered to be assemblages of multiple unique species, each restricted to a single faunal region. This pattern continues to hold true when considering Philippine skinks of the genus Brachymeles. Recent studies have resulted in the description of numerous unique species with many exhibiting various degrees of digit loss or limb reduction, as well as suggesting that unique lineages are still present in the B. bonitae Complex. In this paper, we describe a new species of fossorial skink within this species complex from Tablas Island based on collections made nearly 50 years ago. Although no genetic data are available for the new species, examinations of morphological data (qualitative traits, meristic counts, and mensural measurements) support its distinction from all other members of the genus. Brachymeles dalawangdaliri sp. nov. is differentiated from other members of the genus based on a suite of unique phenotypic characteristics, including a small body size (SVL 66.0-80.9 mm), bidactyl fore-limbs, digitless, unidactyl, or bidactyl hind limbs, a high number of presacral vertebrae (49), the absence of auricular openings, and distinct dorsal head scale patterns. The description of the new species increases the diversity of endemic vertebrates recognized to occur in the Romblon Island Group in the central Philippines.

Background: The Indian Tectonic Plate split from Gondwanaland approximately 120 MYA and set the Indian subcontinent on a ~ 100 million year collision course with Eurasia. Many phylogenetic studies have demonstrated the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey, suggesting this isolated subcontinent served as a source of biodiversity subsequent to its collision with Eurasia. However, recent molecular studies suggest that Eurasia may have served as the faunal source for some of India's biodiversity, colonizing the subcontinent through land bridges between India and Eurasia during the early to middle Eocene (~35-40 MYA). In this study we investigate whether the Draconinae subfamily of the lizard family Agamidae is of Eurasian or Indian origin, using a multi locus Sanger dataset and a novel dataset of 4536 ultraconserved nuclear element loci., Results: Results from our phylogenetic and biogeographic analyses revealed support for two independent colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinent's hard collision with Eurasia., Conclusion: These results are consistent with other faunal groups and new geologic models that suggest ephemeral Eocene land bridges may have allowed for dispersal and exchange of floras and faunas between India and Eurasia during the Eocene.

Recent investigations into the species diversity of false geckos (genus Pseudogekko Taylor) have revealed several cryptic species, highlighting the need for a more thorough understanding of diversity within this enigmatic genus of endemic Philippine geckos. Newly available genetic data reveal that two of the four currently recognized species are complexes of multiple deeply divergent evolutionary lineages. In this paper we evaluate species diversity in one of these complexes, P. brevipes Boettger, and describe one additional new species. For nearly a century, P. brevipes has been recognized as a single, "widespread" species with a geographic range spanning two major faunal regions and several island groups. Poor understanding of this species has persisted due to both limited sampling and its apparent rarity. We evaluate both morphological and genetic data to define species limits in P. brevipes, and find character-based evidence to justify the recognition of two unique evolutionary lineages, one of which we describe as a new species (P. atiorum sp. nov.). The species included in this study have allopatric distributions and differ from congeners by numerous diagnostic characters of external morphology, and therefore should be recognized as full species in accordance with lineage-based species concepts. This newly described species increases the total number of species of Pseudogekko to seven.

Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South-East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this system and find elevated genetic differentiation between populations from island archipelagos compared to those on the adjacent South-East Asian continent, which is consistent with expectations concerning landscape fragmentation in island archipelagos. We also identify a pattern of isolation by distance, but find no substantial effect of ecological/environmental variables on genetic differentiation. To assess whether morphological conservatism in skinks may result from stabilizing selection on morphological traits, we perform FST -PST comparisons, but observe that results are highly dependent on the method of comparison. Taken together, this work provides novel insights into the manner by which micro-evolutionary processes may impact macro-evolutionary scale biodiversity patterns across diverse landscapes, and provide genomewide confirmation of classic predictions from biogeographical and landscape ecological theory., (© 2015 John Wiley & Sons Ltd.)

We describe two new species of morphologically cryptic monitor lizards (genus Varanus) from the Philippine Archipelago:  Varanus dalubhasa sp. nov. and V. bangonorum sp. nov. These two distinct evolutionary lineages are members of the V. salvator species complex, and historically have been considered conspecific with the widespread, northern Philippine V. marmoratus. However, the new species each share closer phylogenetic affinities with V. nuchalis (and potentially V. palawanensis), than either does to one another or to V. marmoratus. Divergent from other recognized species within the V. salvator Complex of water monitors by as much as 3.5% pairwise genetic distance, these lineages are also distinguished by unique gular coloration, metrics of body size and scalation, their non-monophyly with "true" V. marmoratus, and insular allopatric distributions, suggesting biogeographically distinct and unique evolutionary histories. We compare the new species with the most geographically proximate and phenotypically relevant lineages.  Although we show that these new taxa are nearly indistinguishable morphologically from V. marmoratus, both species can be readily distinguished from their closest relatives (each's respective sister taxon, V. palawanensis and V. nuchalis) by traditional morphological characters.  Our findings underscore the high herpetological diversity and biogeographical complexity of vertebrates in the Philippines, and further emphasize the need for detailed study of species-level diversity, mechanisms of reproductive isolation, gene flow, and biologically relevant boundaries between taxa within the V. salvator Complex.

We review the recent discovery of multiple populations of the enigmatic, semi-aquatic Sphenomorphus Group skink, Parvoscincus leucospilos Peters, and investigate the morphological and genetic diversity of isolated, allopatric populations of this unique skink. Our investigations support the recognition of four unique evolutionary lineages distributed across Luzon Island in the Philippines, three of which are herein described as new species (P. tikbalangi sp. nov., P. manananggalae sp. nov., and P. duwendorum sp. nov.). All four recognized species are genetically divergent in both mitochondrial and nuclear DNA sequences, and morphologically distinct. The description of three new Luzon Island endemic species adds to the growing body of literature suggesting that mechanisms driving the accumulation of vertebrate diversity in the Philippines may vary regionally across the archipelago.

We utilize robust geographical genetic sampling, a multilocus dataset, a new synthesis of numerous fossil calibration points, a time-calibrated phylogeny, and the Dispersal-Extinction-Cladogenesis model to test the prediction that widespread Southeast Asian water monitor species initially diversified on the Asian mainland and subsequently invaded the island archipelagos of the Philippines, Sundaland, and Wallacea. Our results strongly contradict these expectations and instead infer an initial water monitor radiation of range-restricted but highly divergent evolutionary lineages (now recognized as endemic species) in one archipelago around 3.6 mya, followed by an out-of-the-Philippines reinvasion of the mainland (2.2 mya), resulting in a few, widespread species that now inhabit most the islands of the Sunda Shelf and the Southeast Asian mainland as far north as Myanmar, as well as an out-of-the-Philippines invasion of Sulawesi (2.1 mya). Our analyses both confirm the importance of island archipelagos as drivers of diversification for mainland biodiversity and emphasize the global evolutionary significance and conservation priority of the Philippines for understanding processes of diversification in island archipelagos., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Recent studies of forest lizards in Southeast Asia have highlighted spectacular morphological and cryptic genetic diversity in several poorly known clades. Unfortunately, many of the included species have microhabitat preferences for forested environments, and therefore they are threatened by extensive forest destruction throughout the region. This is particularly true in the Philippines, an archipelago with a strikingly high proportion (84%) of endemic geckos. Abundances inferred from historical museum collections suggests that we are in a critical period where apparent declines in population viability and species' abundance have taken place faster than the growth in our understanding of alpha diversity. This phenomenon is exemplified in the exceedingly rare Philippine slender forest geckos of the genus Pseudogekko. Most of the known species are rarely encountered by field biologists, and species boundaries are unclear; this poor state of knowledge impedes effective conservation measures. Using the first multilocus phylogeny for these taxa, and phylogenetic and population genetic approaches, we elucidate evolutionary lineages and delimit species-level conservation targets in this unique radiation of endemic Philippine geckos. The results support the presence of widespread cryptic diversity in the genus, providing a framework for the re-evaluation of conservation priorities aimed at protecting these rare, forest-obligate species., (Copyright © 2013 Elsevier Inc. All rights reserved.)

An accurate understanding of species diversity is essential to studies across a wide range of biological subdisciplines. However, delimiting species remains challenging in evolutionary radiations where morphological diversification is rapid and accompanied by little genetic differentiation or when genetic lineage divergence is not accompanied by morphological change. We investigate the utility of a variety of recently developed approaches to examine genetic and morphological diversity, and delimit species in a morphologically conserved group of Southeast Asian lizards. We find that species diversity is vastly underestimated in this unique evolutionary radiation, and find an extreme case where extensive genetic divergence among lineages has been accompanied by little to no differentiation in external morphology. Although we note that different conclusions can be drawn when species are delimited using molecular phylogenetics, coalescent-based methods, or morphological data, it is clear that the use of a pluralistic approach leads to a more comprehensive appraisal of biodiversity, and greater appreciation for processes of diversification in this biologically important geographic region. Similarly, our approach demonstrates how recently developed methodologies can be used to obtain robust estimates of species limits in "nonadaptive" or "cryptic" evolutionary radiations., (© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.)

Analysis of external morphological characters, color pattern, and DNA sequence data, plus consideration of biogeographical patterns, leads us to the hypothesis that the Parvoscincus decipiens complex of Philippine forest skinks consists of a minimum of eight highly divergent, phenotypically distinct, cohesive evolutionary lineages. We rectify this taxonomic underestimation of species diversity with formal descriptions of seven new species (P. abstrusus sp. nov., P. agtorum sp. nov., P. arvindiesmosi sp. nov., P aurorus sp. nov., P banahaoensis sp. nov., P. jimmymcguirei sp. nov., and P. palaliensis sp. nov.) and highlight geographical sampling deficiencies, which, if addressed with additional fieldwork, should lead to additional new species discoveries. Due to the difficulty of identifying non-overlapping differences in scalation on similarly sized, small-bodied skinks, species level diversity in diminutive Philippine forest skinks is undoubtedly substantially underestimated.

The closed-canopy forests of Southeast Asia are home to an impressive number of vertebrates that have independently evolved morphologies that enhance directed aerial descent (gliding, parachuting). These assemblages include numerous mammal, frog, snake, and lizard clades. Several genera of gekkonid lizards, in particular, have evolved specialized structures such as cutaneous expansions, flaps, and midbody patagia, that enhance lift generation in the context of unique gliding and parachuting locomotion. The genus Ptychozoon represents arguably the most morphologically extreme, highly specialized clade of gliding geckos. Despite their notoriety and celebrated locomotor ability, members of the genus Ptychozoon have never been the subject of a species-level molecular phylogenetic analysis. In this paper, we utilize molecular sequence data from mitochondrial and nuclear gene fragments to estimate the evolutionary relationships of this unique group of flying geckos. Capitalizing on the recent availability of genetic samples for even the rarest of known species, we include the majority of known taxa and use model-based phylogenetic methods to reconstruct their evolutionary history. Because one species, P. kuhli, exhibits an unusually wide distribution coupled with an impressive range of morphological variation, we additionally use intensive phylogeographic/population genetic sampling, phylogenetic network analyses, and Bayesian species delimitation procedures to evaluate this taxon for the possible presence of cryptic evolutionary lineages. Our results suggest that P. kuhli may consist of between five and nine unrecognized, distinct species. Although we do not elevate these lineages to species status here, our findings suggest that lineage diversity in Ptychozoon is likely dramatically underestimated., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Some of Southeast Asia's most poorly known vertebrates include forest lizards that are rarely seen by field biologists. Arguably the most enigmatic of forest lizards from the Indo Australian archipelago are the Flap-legged geckos and the Flying geckos of the genera Luperosaurus and Ptychozoon. As new species have accumulated, several have been noted for their bizarre combination of morphological characteristics, seemingly intermediate between these genera and the pan-Asian gecko genus Gekko. We used the first multilocus phylogeny for these taxa to estimate their relationships, with particular attention to the phylogenetic placement of the morphologically intermediate taxa Ptychozoon rhacophorus, Luperosaurus iskandari, and L. gulat. Surprisingly, our results demonstrate that Luperosaurus is more closely related to Lepidodactylus and Pseudogekko than it is to Gekko but that some species currently classified as Luperosaurus are nested within Gekko. The Flying Gecko genus Ptychozoon is also nested within Gekko, suggesting that higher-level taxonomic revision of the generic boundaries within Southeast Asian gekkonines will be a priority for the immediate future., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Evolutionary simplification, or loss of complex characters, is a major theme in studies of body-form evolution. The apparently infrequent evolutionary reacquisition of complex characters has led to the assertion (Dollo's Law) that once lost, complex characters may be impossible to re-evolve, at least via the exact same evolutionary process. Here, we provide one of the most comprehensive, fine-scale analyses of squamate body-form evolution to date, introducing a new model system of closely related, morphologically variable, lizards. Our phylogenetic results support independent instances of complete limb loss as well as multiple instances of digit and external ear opening loss and re-acquisition. Even more striking, we find strong statistical support for the re-acquisition of a pentadactyl body form from a digit-reduced ancestor. Our study reveals that species of the genus Brachymeles exemplify regions of morphospace (body plans) previously undocumented in squamates. Our findings have broad, general implications for body-form evolution in burrowing vertebrates: whatever constraints have shaped trends in morphological evolution among other squamate groups (excluding Bipes) have been lost in this one exemplary clade. The results of our study join a nascent body of literature showing strong statistical support for character loss, followed by evolutionary re-acquisition of complex structures associated with a generalized pentadactyl body form., (© 2011 The Author(s).)

The spectacular, virtually endemic radiation of Philippine semi-fossorial skinks of the genus Brachymeles represent one of the few radiations of scincid lizards to possess both fully limbed and limbless species. And yet, nothing is known of the phylogenetic relationships of this exceptional group. Morphologically similar body plans have made it difficult to assess species-level diversity, and the genus has long been recognized as one of the more modest radiations of southeast Asian lizards. However, recent large-scale survey efforts have resulted in the discovery of numerous new species, and taxonomic studies indicate that the diversity within the genus Brachymeles is grossly underestimated. In this study we provide the first robust estimate of phylogenetic relationships within the genus Brachymeles using a multi-locus dataset and nearly complete taxonomic sampling. We provide statistical tests of monophyly for all polytypic species and two widespread limb-reduced species and our results indicate wholesale deviations from past summaries and taxonomic evaluations of the genus. With few exceptions, we are able to reject the monophyly of all polytypic and widespread species, thereby validating the need for large-scale taxonomic revisions. Our results reveal that the limbless, monotypic, genus Davewakeum is nested within Brachymeles. Mapping of body form on our preferred phylogenetic tree suggests that limb-reduction and digit loss has occurred on multiple occasions in the history of the genus. A Bayesian reconstruction of ancestral areas indicates strong statistical support for a minimum of five major dispersal events that have given rise to a major component of the observed species diversity on separate Pleistocene aggregate island platforms of the archipelago., (Copyright © 2011 Elsevier Inc. All rights reserved.)

As humans continue to explore the last uncharted regions of the planet, discoveries of previously unknown species of large vertebrates have become infrequent. Here, we report on the discovery of a spectacular new species of giant, secretive, frugivorous, forest monitor lizard (Genus: Varanus) from the forests of the northern Philippines. Using data from morphology and mitochondrial and nuclear DNA sequences, we demonstrate the taxonomic distinctiveness of this new 2 m long species and provide insight into its historical biogeography and systematic affinities. Our molecular phylogenetic analyses indicate that the new species is closely related to Varanus olivaceus (from southern Luzon and nearby islands), but it differs from this and other varanids with respect to characteristics of scalation, colour pattern, body size, anatomy of the reproductive organs and genetic divergence. The new species appears to be restricted to forests of the central and northern Sierra Madre mountain range; it is separated from the range of V. olivaceus by a more than 150 km stretch that includes at least three low-elevation river valley barriers to dispersal. This discovery identifies a seldom-perceived biogeographic boundary and emphasizes the need for continued biodiversity research in the megadiverse conservation hotspot of the Philippines. It is anticipated that the new species will serve as an important flagship species for conservation efforts aimed at preserving the remaining forests of northern Luzon.

In the megadiverse conservation hotspot of the Philippines, biodiversity is not uniformly distributed throughout the archipelago, but hierarchically partitioned into islands and island groups that were conjoined during the mid- to late-Pleistocene. Few species groups are widely distributed throughout the archipelago, but some exceptions exist, such as the common scincid lizards of the Sphenomorphus jagori complex (including S. jagori, S. coxi, and S. abdictus). Using mtDNA haplotype data we test biogeographic and taxonomic predictions in these abundant, large-bodied, forest floor lizards and arrive at conclusions that differ significantly from both past, and current, appraisals of species diversity. In contrast to expectations based on existing taxonomy (three species, each with two subspecies), we find evidence of at least eleven highly divergent species lineages diagnosed by haplotypic variation. Each lineage corresponds to a biogeographically circumscribed distribution (i.e., isolated islands or geological components of islands), suggesting lineage cohesion and allopatric differentiation. Parametric bootstrapping tests reject taxonomic and biogeographic hypotheses and suggest a complex pattern of unpredicted relationships. Only one of the former species (S. jagori) appears as a monophyletic entity (including four allopatric, highly divergent lineages that we suspect may represent evolutionary species), and the remaining species are paraphyletic, necessitating a comprehensive future taxonomic revision. The pattern of biogeographic provincialism and hidden cryptic species diversity detected here leads us to suspect that even the most common, presumably well-studied, and widespread species complexes in the Philippines are in need of thorough analysis with modern genetic and phylogenetic techniques. Such studies of speciation genetics in these common, widely distributed groups may lead to a better understanding of the genetic underpinnings of biodiversity, allow for an enhanced appreciation of the evolutionary history of this model island archipelago, and enable more informed conservation planning in a global biodiversity hotspot., (Copyright 2010 Elsevier Inc. All rights reserved.)

In the Philippines, Pleistocene sea level oscillations repeatedly connected and isolated neighboring islands. Hence, an understanding of the island platforms adjoined during periods of low sea level has led biologists to a suite of expectations that, taken together, represent a paradigm for the process of recent diversification in southeast Asia. We employ statistical tests of phylogenetic topology and population genetic analyses of widespread species of bent-toed geckos (Cyrtodactylus) to ascertain whether patterns of inter- and intra-specific diversity can be explained by a Pleistocene aggregate island model of diversification. Contrary to many classic studies of Philippine vertebrates, we find complex patterns that are only partially explained by past island connectivity. In particular, we determine that some populations inhabiting previously united island groups show substantial genetic divergence and are inferred to be polyphyletic. Additionally, greater genetic diversity is found within islands, than between them. Among the topological patterns inconsistent with the Pleistocene model, we note some similarities with other lineages, but no obviously shared causal mechanisms are apparent. Finally, we infer well-supported discordance between the gene trees inferred from mitochondrial and nuclear DNA sequences of two species, which we suspect is the result of incomplete lineage sorting. This study contributes to a nascent body of literature suggesting that the current paradigm for Philippine biogeography is an oversimplification requiring revision., (Published by Elsevier Inc.)