Chan Kin Onn

University of Kansas | KU · University of Kansas Biodiversity Institute and Natural History Museum

Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian T...

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 and species delimitation inferences, the...

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 boot-strapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topol...

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...

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distrib...

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgen...

A Cyan-Blue Bamboo Pit viper (Trimeresurus stejnegeri stejnegeri) in Taiwan. Color variation is common in many species of Trimeresurus, including T. purpureomaculatus (Chan et al. 2022) and T. insularis, in which blue individuals tend to be uniformly colored and lack green altogether (Jones et al. 2019). However, color variation in T. s. stejnegeri...

We have updated and added several new functions to the GroupStruct R package. Initially it mainly did allometric size correction using the allom() function. Now, we have added a wrapper function called morpho_struct() that takes raw morphological data as input, does allometric size correction, performs PCA, and ANOVA/Tukey analysis for every charac...

With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time‐consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command‐line. These impediments present significant economic and technol...

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urge...

Although the differentiation of clades at the species level is usually based on a justifiable and testable conceptual framework, the demarcation of supraspecific boundaries is less objective and often subject to differences of opinion. The increased availability of large-scale phylogenies has in part promulgated a practice of what we consider exces...

In a genomic study by Chan and colleagues, pit-vipers of the Trimeresurus erythrurus – purpureomaculatus complex from the Ayeyarwady and Yangon regions in Myanmar were demonstrated to be a distinct species based on robust population genetic and species delimitation analyses. Here, we provide morphological characterizations and a formal description...

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the Inter...

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the Inter...

Limestone karst and its surrounding areas in the tropics are home to unique fauna and flora. However, extensive studies on herpetofauna in limestone areas in Peninsu-lar Malaysia are still limited. Previous surveys of Batu Caves have focused on the cave fauna or on specific groups like bent-toed geckos Cyrtodactylus metropolis is endemic in Batu Ca...

Amphibians of Sekayu lowland forest have been studied more than a decade, with discoveries of new records of species showing no sign of abating between the years 2003 to 2020, indicating the remarkably rich diversity of anurans in this forest. Despite ceaseless anthropogenic activities in this area, this study successfully recorded 52 species of am...

The Oriental Dwarf Kingfisher species‐complex of South and Southeast Asia comprises two forms, the dark‐backed Ceyx erithaca of India and Indochina and the rufous‐backed Ceyx rufidorsa of Java and the Lesser Sunda Islands. Between these two extremes, the large area of Sundaland and the Philippines is occupied by individuals that have a rufous back,...

Citation: Chan KO, Grismer LL, Santana F, Pinto P, Loke FW, Conaboy N (2023) Scratching the surface: a new species of Bent-toed gecko (Squamata, Gekkonidae, Cyrtodactylus) from Timor-Leste of the darmandvillei group marks the potential for future discoveries. ZooKeys 1139: 107-126. https://doi. Abstract A new species of limestone-dwelling Bent-toed...

Maximum likelihood and Bayesian phylogenies for the brachyuran crab superfamily Xanthoidea were estimated based on three mitochondrial and four nuclear genes to infer phylogenetic relationships and inform taxonomy. Habitat data was then used in conjunction with several diversification rates analyses (BAMM, BiSSE, HiSSE, and FiSSE) to test evolution...

We present the first multilocus molecular phylogeny focused on mangrove pit vipers of the Trimeresurus erythrurus‐purpureomaculatus complex based on novel topotypic material and expanded geographic sampling. Previously inferred paraphyly of T. purpureomaculatus was resolved and our results demonstrate distinct phylogeographic patterns that are lati...

The genus Micryletta, also known as paddy frogs, ranges across much of south, east, and southeast Asia. Due to their relatively broad distribution and overall morphological similarities, many species have gone undetected until recently, largely owing to the use of molecular data. Consequently, the species diversity within this genus has quadrupled...

The efficacy of an allometric growth model to correct for ontogenetic body size variation has been known for decades, yet this method remains relatively obscure and rarely applied. We optimize the implementation of this method through a newly developed and easy-to-use R package GroupStruct and further extend its application from intraspecific to in...

Background The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from comple...

We review the status, patterns, and progress of Malaysia's amphibian research in the 21 st century (2000-2021) with the main goal of identifying areas for improvement that can help focus and prioritise future research initiatives. Between the period of January 2000-September 2021, we found 280 publications that can be broadly grouped into five cate...

This study re-analyzes morphometric and meristic data among island night lizards, Xantusia riversiana, from the California Channel Islands of San Clemente, Santa Barbara, and San Nicolas in order to ascertain whether the implementation of different statistical methods can recover different results that could potentially alter biological interpretat...

Herein we provide new information on Cnemaspis assamensis, the only species of Cnemaspis known from north-eastern India. Based on five new samples, morphological parameters are described. The species was found to have pre-cloacal and femoral pores, not accounted for in the original description. Genetic assessment of the species was made using a 914...

This study provides a review of reptile research in Malaysia from the years 2000-2020 to reveal trends and biases that can be leveraged to improve future research and conservation initiatives. Overall, the number of papers published shows an upward trend with an average of 10.1 papers published per year. The clear majority of papers published throu...

Although body size correction and inferential statistics have been used in morphological studies for many decades, their applications are far from being ubiquitous. We performed a meta-analysis to quantify the extent of taxonomic papers that performed body size correction and implemented a statistical hypothesis testing framework during the analysi...

Zootaxa is a mega-journal that since its inception, 20 years ago, has contributed to the documentation of the planet’s biodiversity. Its role concerning terrestrial vertebrates has been crucial especially for amphibians, which are the most threatened class of vertebrates. As current editors of the Amphibia section, we reviewed the state of knowledg...

We review the status, patterns, and progress of Peninsular Malaysia’s amphibian research in the 21st century with the main goal of identifying areas for improvement that can help focus and prioritize future research initiatives. Between 2000–2020 we found 130 publications that can be broadly categorized into four groups: 1) checklists and biodivers...

Using an allometric growth model to correct for body size variation has been known for many decades to be superior to several other widely used methods such as ratios, analysis of covariance, principal components analysis, and residual analysis. However, this technique remains relatively obscure and rarely applied. We optimize the implementation of...

Malaysia is recognized as a megadiverse country and biodiversity hotspot which necessitates sufficient levels of habitat protection and effective conservation management. However, conservation planning in Malaysia has hitherto relied largely on species distribution data without taking into account the rich evolutionary history of taxa. This represe...

Malaysia is recognized as a megadiverse country and biodiversity hotspot, which necessitates sufficient levels of habitat protection and effective conservation management. However, conservation planning in Malaysia has hitherto relied largely on species distribution data without taking into account the rich evolutionary history of taxa. This repres...

The appreciation of cryptic biological diversity, and the pace at which it is recognized, has greatly increased with the use of molecular systematic techniques. The gekkonid genus Cyrtodactylus Gray, 1827 is one example of a group that has undergone a particularly rapid increase in recognized diversity due to molecular systematic studies. Many of t...

Focusing on the phylogenetic relationships of puddle frog populations spanning the biogeographic interface between Sundaland (Borneo) and the Philippines, we demonstrate, for the first time, a widespread geographic pattern involving the existence of multiple divergent and co-distributed (sympatric) evolutionary lineages, most of which are not each...

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on...

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on...

The firefly genus Luciola sensu McDermott contains 282 species that are distributed across major parts of Asia, Europe, Africa, Australia, and the Pacific islands. Due to phenotypic similari‐ ties, species identification using external morphological characters can be unreliable for this group. Consequently, decades of piecemeal taxonomic treatments...

Despite a considerable amount of research, the systematics of the ranid genus Huia have remained unresolved, mostly owing to insufficient sampling and morphological similarities. As currently circumscribed, Huia consists of five species, but multiple studies have consistently demonstrated that it is not a monophyletic genus. However, no study has a...

A genomic study by Chan and colleagues demonstrated that Pulchrana picturata from Peninsular Malaysia and Sumatra (and southern Thailand by implication) are distinct from the name-bearing lineage from Borneo. In this study, we present additional morphological and bioacoustic data to support the recognition of the new species, which we describe here...

In a recent article, Chandramouli et al. (2020) re-assessed the systematic position of the hylaranine frog Indosylvirana nicobariensis and proposed a new monotypic genus, Bijurana, for this species. The authors re-examined the type series of specimens and attempted to justify the recognition of a new genus using morphological and phylogenetic data....

Pulchrana rawa is a peat swamp specialist that was described from eastern Sumatra in 2012 based on a single specimen. Since then, no confirmed records have been forthcoming; thus, virtually nothing is known about this species. Recent fieldwork at peat swamp forests in southwestern Peninsular Malaysia led to the discovery of a frog that morphologica...

An integrative taxonomic analysis based on mitochondrial and morphological data recovered the population of Cyrtodactylus on Koh Rong Island, Preah Sihanouk Province, Cambodiaa as an endemic insular species belonging to the Cyrtodactylus intermedius group. This brings the number of species in the C. intermedius group to at least 10 and the number o...

The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs...

Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet fundamental knowledge about their biodiversity is lacking. Recent studies have revealed notable population-level phylogeographical structure within the Pteroptyx tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Addit...

Using FrogCap, a recently-developed sequence-capture protocol, we obtained more than 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...

A reappraisal of the taxonomic status of the Dark-necked Slug Snake (Asthenodipsas malaccana Peters, 1864) across its range revealed that populations from Borneo are not conspecific with true A. malaccana from the Thai-Malay Peninsula and Sumatra, and is therefore described herein as new. Asthenodipsas borneensis sp. nov. can be distinguished from...

Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet fundamental knowledge about their biodiversity is lacking. Recent studies have revealed notable population-level phylogeographical structure within the Pteroptyx tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Addit...

We present a systematic revision of the Rentapia hosii complex based on morphological and bioacoustic data. In conjunction with genetic data from a previous study, our results show that populations from Peninsular Malaysia are distinct from the name-bearing population of R. hosii from Sarawak in terms of morphometrics, colour-pattern, and to a less...

The fi rst herpetological survey of Dalai Mountain in Phnom Samkos Wildlife Sanctuary revealed 24 species (nine amphibians and 15 reptiles), 18 of which are presently known only from the Cardamom Mountains. Of these, four represent fi rst records for Phnom Samkos Wildlife Sanctuary (Megophrys auralensis, Theloderma asperum, Philautus parvulus and D...

Amphibian communities were assessed in streams of primary and secondary forests in Taman Rimba Kenong, Pahang, between 16 and 22nd August 2004. The objective of this study was to record the species richness and diversity of amphibians. The aim of this study was to build a database to assist in the management of the park, especially for the Forestry...

This study represents the first report on the amphibians and reptiles of Mount Korbu, the highest peak in the Titiwan-gsa Range (2182 m a.s.l.) and the second highest peak in Peninsular Malaysia. The Titiwangsa Range is the longest and most contiguous mountain range in Peninsular Malaysia, but only three upland localities have been extensively samp...

Background Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index (gdi) was shown to be a viable alternative, especially for delimiting allopatric...

As molecular methods continue to elucidate genetic structure at increasingly finer resolutions, delimiting species in the grey zone of the speciation continuum is becoming more relevant in biodiversity research, especially in under-studied biodiversity hotspots such as Southeast Asia where new species are being described at an unprecedented rate. O...

The manuscript titled “Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )” has been withdrawn from BioRxiv temporarily. The manuscript has been withdrawn because it utilizes a new protocol for data collection, which has yet not been published. Once the paper describing the new method...

Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet, knowledge on its biodiversity and evolutionary history remains lacking. Recent studies have revealed notable population-level phylogeographic structure within the P. tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist....