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Summary Biodiversity knowledge gaps and biases persist across low-income tropical regions. Genetic data are essential for addressing these issues, supporting biodiversity research and conservation planning. To assess progress in wildlife genetic sampling within the Philippines, I evaluated the scope, representativeness, and growth of publicly available genetic data and research on endemic vertebrates from the 1990s through 2024. Results showed that 82.3% of the Philippines’ 769 endemic vertebrates have genetic data, although major disparities remain. Reptiles had the least complete coverage but exhibited the highest growth, with birds, mammals, and amphibians following in that order. Species confined to smaller biogeographic subregions, with narrow geographic ranges, or classified as threatened or lacking threat assessments were disproportionately underrepresented. Research output on reptiles increased markedly, while amphibian research lagged behind. Although the number of non-unique authors in wildlife genetics studies involving Philippine specimens has grown steeply, Filipino involvement remains low. These results highlight the uneven and non-random distribution of wildlife genetic knowledge within this global biodiversity hotspot. Moreover, the limited participation of Global South researchers underscores broader inequities in wildlife genomics. Closing these gaps and addressing biases creates a more equitable and representative genetic knowledge base and supports its integration into national conservation efforts aligned with global biodiversity commitments. 

ABSTRACT Adaptive introgression involves the acquisition of advantageous genetic variants through hybridisation, which are subsequently favoured by natural selection due to their association with beneficial traits. Here, we analysed speciation patterns of the kleptoparasitic spider,Argyrodes lanyuensis, through genomic analyses and tested for possible genetic evidence of adaptive introgression at the Taiwan–Philippines transition zone. Our study used highly polymorphic SNPs to demonstrate that speciation occurred when the Hualien (on Taiwan Island + Green Island) and Orchid Island + Philippine lineages separated during the early to mid‐Pleistocene. The best colonisation model suggested by approximate Bayesian computation and random forests and biogeographical analyses supported an inference of a bottleneck during speciation, an interpretation reinforced by observation of lowerF_STvalues and reduced genetic diversity of the Orchid Island + Philippines lineage. We also found the highest support for the occurrence of introgression on the youngest island (Green Island) of the Taiwan–Philippines transition zone based on the ABBA‐BABA test. Our study highlights the inference of two noteworthy species (Hualien + Green Island and Orchid Island + Philippines) based on our species delimitation tests, with gene flow between Green Island and Orchid Island that indicates introgression. The potential adaptive alleles in Green Island population, which are under balancing selection, provide initial evidence of possible rare case of adaptive introgression. This could represent an evolutionary response to a newly formed niche (or novel geographical context) lying between the tropical climate of the Philippines and the subtropical climate of Hualien, Taiwan. 

Abstract Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae:Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis thatHypsiscopusdiversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggestHypsiscopusdiversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species ofHypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets. 

Abstract 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.] 

Abstract 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. 

Reptiles and amphibians are among the least appreciated of animals and are victims of many negative perceptions and erroneous ideas. In this ethnoherpetological research, we uncover the perceptions of the residents using 20 focus group discussions participated by a total of 339 residents and community surveys to a total of 1464 residents in 29 barangays in five municipalities along our Ridge-to-Reef Megatransect which commences from Mt. Isarog National Part to Caramoan National Park, Bicol Region, Philippines. Many residents do simply dislike reptiles and amphibians while others do not have any understanding of the life history and ecological roles these animals play in the environment. They created folklore narratives and tales, superstitions, and myths depicting these animals as demonic and evil. Their phobia-inducing aversion toward herpetofauna are reflected in their stories and interpretation of their experiences of encounter with these animals. They believe that although there are medicinal, cultural, and some economic values brought by these animals, the harm that they can cause outweighs their ecological importance. The findings are of potential conservation concern because these imply the need for more intensive and extensive measures to transmit and disseminate knowledge about the ecological functions of herpetofauna and correct the misconceptions about reptiles and amphibians. Furthermore, the success of future conservation plans in the area with the local community’s participation will be dependent not only on the species account but also on unraveling of community perceptions through ethnoherpetology. 

Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019–2023) for Philippine populations of bockadams (Homalopsidae:Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies reportCerberusinland. We report the frequency of encounters ofCerberus schneiderii, and the IUCN data-deficient, Philippine-endemicCerberus microlepisduring six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69C. schneideriiand6 C. microlepisfor coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats forCerberus. Our study is the most comprehensive assessment of PhilippineCerberuspopulations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes.