Rafe M. Brown

• Ph.D.
• Professor (Associate) at University of Kansas

Hybridization plays a major role in the evolutionary history of many taxa and can generate confounding patterns affecting many downstream applications. In this study, we empirically demonstrate how hybridization obfuscates phylogenetic inference (via the artefactual branch effect), species boundaries, and taxonomy in an adaptive radiation of frogs....

The rise of DNA-based studies has revealed extensive cryptic species diversity across the Tree of Life, reshaping our understanding of biodiversity, yet virtually nothing is known about their evolutionary history. Moreover, most research rely on mitochondrial DNA and methods that focus on quantifying divergence, assuming species evolve in isolation...

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 gene...

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,...

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling...

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 bara...

Exploitation of different locomotor substrates in different ecological niches has driven the evolution of specialized morphological structures, and similar ecological demands, such as the structure of the microhabitat, often lead to convergent or parallel evolution. The evolution of adhesive toepads in geckos remains understudied because of the pau...

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling...

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...

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 coalescen...

We report a new island record for the genus Oligodon, and the purportedly Mindanao Island faunal region endemic species O. maculatus, both for the first time from Leyte Island. The genus Oligodon (Fitzinger, 1826) is a taxonomically and systematically challenging group, particularly in the Philippines, where the known species are rarely observed an...

Aim We assessed the population genetic structure of the kleptoparasitic spider Argyrodes bonadea across the Southwestern Pacific islands. Our aim is to evaluate the impact of overseas distances and, in particular, the Kerama gap, as potential drivers of genetic differentiation. If no relationship exists, then we assume dispersal following adaptive...

A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized the diverse topics studied and highlighted the development and achievements in research up to the year 2000. This study revisits and reassesses what Philippine herpetology has accomplished, both as a discipline and a...

Adaptive radiations garner considerable interest from evolutionary biologists. Lizard radiations diversifying along structural niche space often exhibit distinct changes in body and limb proportions. One prediction is that terrestrial species inhabiting open habitats will have relatively longer hindlimbs, associated with faster running speeds, whil...

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.

Aim We assessed the population genetic structure of the kleptoparasitic spider Argyrodes bonadea across the Southwestern Pacific islands. Our focus is on assessing the impact of overseas distances and, in particular, the Kerama gap, as potential drivers of genetic differentiation. We found that the spider kleptoparasite’s switch to a specific host...

Our knowledge of the biodiversity of Asia and Australasia continues to expand with more focused studies on systematics of various groups and their biogeography. Historically, fluctuating sea levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanism...

Chelonians (turtles, tortoises, and sea turtles) grow scute keratin in sequential layers over time. Once formed, scute keratin acts as an inert reservoir of environmental information. For chelonians inhabiting areas with legacy or modern nuclear activities, their scute has the potential to act as a time-stamped record of radionuclide contamination...

Chelonian scute samples examined as time stamps of radionuclide contamination for modern 20th century nuclear activity in surrounding environments.

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 coalescen...

The Solomon Islands host a diverse terrestrial vertebrate fauna which has played a formative role in the development of speciation theory. Yet, despite over a century of biological exploration in the region, there are many islands for which we have incomplete knowledge of the vertebrate fauna. In 2019, we spent 20 days on Tetepare Island in the Wes...

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 regional diversification, this has rarely been tested in the context of an explicit geological framework. Her...

Context Skinks comprise the dominant component of the terrestrial vertebrate fauna in Oceania, New Guinea, and Eastern Wallacea (ONGEW). However, knowledge of their diversity is incomplete, and their conservation needs are poorly understood. Aims To explore the diversity and threat status of the skinks of ONGEW and identify knowledge gaps and cons...

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary rel...

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 variati...

Aim Viviparity has evolved more times in squamates than in any other vertebrate group; therefore, squamates offer an excellent model system in which to study the patterns, drivers and implications of reproductive mode evolution. Based on current species distributions, we examined three selective forces hypothesized to drive the evolution of squamat...

Taxonomic studies over the past decade of the endemic Night Frog genus Nyctibatrachus (originally described in 1882) from Peninsular India have more than tripled, from 11 at the turn of this century to 36 by 2017. Despite these revisionary contributions, it is still challenging for field biologists to identify night frog species reliably, due to a...

Despite multiple recent field studies, herpetological species diversity of the Romblon Island Group in the central Philippines—particularly Sibuyan Island—has remained underestimated. Recently, we investigated the diversity of the herpetofauna of Mount Guiting-Guiting Natural Park, based on an elevational transect (10–1557 m a.s.l.). Our surveys re...

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as “fieldwork.” Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of t...

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 difficu...

Cryptic ecologies, the Wallacean Shortfall of undocumented species' geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be undere...

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as “fieldwork.” Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of t...

We report on the first molecular estimates of phylogenetic relationships of Brachymeles dalawangdaliri (Scincidae) and Pseudogekko isapa (Gekkonidae), and present new data on phenotypic variation in these two poorly known taxa, endemic to the Romblon Island Group of the central Philippines. Because both species were recently described on the basis...

The Philippine coral snakes of the genus Hemibungarus consist of three poorly known endemic species, constituting some of the most enigmatic elapid snakes in the world. Because of their secretive, subterranean, and heretofore undocumented microhabitat preferences, very little is known of these lineages. We present a synthetic description of aposema...

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...

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...

The Philippine-endemic elapid genus Hemibungarus consists of three described species that are widely distributed across northern and central portions of the archipelago. Hemibungarus calligaster, H. mcclungi, and H. gemianulis were originally diagnosed, and remain recognized today, primarily based on differences in color pattern. Previous studies a...

Recent higher level phylogenetic analyses of gekkonid lizards of the genus Lepidodactylus uncovered an array of unrecognized species diversity, particularly within the Philippine archipelago. Novel phylogenetic analyses of multilocus data sets suggest that as many as five, previously undescribed, species-level lineages of Scaly-toed Geckos occur in...

We revisit the question of species diversity among Mindanao Fanged Frogs of the Limnonectes magnus complex consisting of L. magnus, L. diuatus, L. ferneri, and a previously hypothesized putative new species, inferred in the first molecular phylogenetic studies of the genus almost 2 decades ago. Using a multilocus molecular deoxyribonucleic acid seq...

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 publ...

We report on the second known specimen of the recently described banded coral snake, Calliophis salitan, identified among the Museo Nacional de Ciencias Naturales collections of Dr. Hipólito Fernández (1886), and originating in Mindanao Island, southern Philippines, as part of the “Comisión Central de Manila,” the Spanish Crown’s effort to catalogu...

Oceanic islands are unique geographic systems that promote local adaptations and allopatric speciation in many of their highly endemic taxa. This is a common case in the Philippine Archipelago, where numerous unrelated taxa on islands have been inferred to have diversified in isolation. However, few cases have been reported in invertebrates especia...

The unusually high floral and faunal similarity between the different regions of the Afromontane archipelago has been noted by biogeographers since the late 1800s. A possible explanation for this similarity is the spread of montane habitat into the intervening lowlands during the glacial periods of the Pleistocene, allowing biotic exchange between...

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we...

One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-c...

The genus Toxicodryas, historically included with the renowned Australasian cat-eyed snakes of the colubrid genus Boiga, currently includes two widespread species (T. blandingii and T. pulverulenta) in western, central, and eastern Africa. We leverage findings from a recent phylogenomic and historical demographic analysis of this genus (based on 28...

Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world's ~1714 described species) of the conservation 1 Joint senior authors...

We describe a new species of lizard in the genus Eutropis Fitzinger 1843 from the southwestern tip of the Zamboanga Peninsula on the western part of Mindanao Island, Philippines. The new species is related to Eutropis rugifera, which is a secretive, forest-adapted skink that ranges widely outside the Philippines from the western extent of its distr...

Tropical watershed ecosystems support heterogeneous habitats and diverse non-human species assemblages, together providing ecosystem services to humans. Amphibians and reptiles are recognized as sensitive indicators of ecosystem "health," related to beneficial services (provisional, regulating, cultural, structural, functional) human societies rece...

We describe a new species of fanged frog (genus Limnonectes) from Mindoro and Semirara Islands, of the Mindoro Pleistocene Aggregate Island Complex, of the central Philippines. Although morphologically indistinguishable from its closest relative, Limnonectes acanthi, of the Palawan faunal region, the two species can be readily diagnosed on the basi...

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...

Dendrelaphis marenae capturing a typically sized adult female Sanguirana luzonensis on Luzon Island, Philippines.

and the University of Kansas conducted four collaborative expeditions between 2010 and 2014, resulting in accounts for all species of lacertid and agamid, except Phrynocephalus kulagini. These expeditions resulted in a range extension for Eremias arguta and the collection of specimens and tissues across 134 unique localities. In this paper we summa...

We describe a new species of reed snake of the genus Calamaria Boie 1827, from Mindoro Island, Philippines. The new species differs from all other species of Calamaria by having the following combination of characters: a high number of subcaudal scale pairs (> 40 in males, > 30 females) and ventrals + subcaudals (> 205 in males, > 210 in females);...

Mud snakes (Serpentes: Homalopsidae) are a family of 54 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuc...

One significant challenge to biodiversity assessment and conservation is persistent gaps in species diversity knowledge in Earth’s most biodiverse areas. Monitoring devices that utilize species-specific advertisement calls show promise in overcoming challenges associated with lagging frog species discovery rates. However, these devices generate dat...

The Philippine archipelago is an exceptionally biodiverse region that includes at least 112 species of land snakes from 41 genera and 12 families. Recently, Cyclocoridae (formerly Lamprophiidae: Cyclocorinae) was proposed as a distinct, Philippine-endemic family, containing four genera: Cyclocorus, Hologerrhum, Myersophis, and Oxyrhabdium. Here, we...

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...

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...

We report for the first time the herpetological biodiversity (amphibians and reptiles) of the Caramoan Island Group (CIG), Maqueda Channel, southern Luzon Island, the Philippines. Herpetofaunal biodiversity assessment, using the standard field-based methodology for survey work, was conducted at nine sites in the CIG, off the northeast coast of the...

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....

Philippine False Geckos (genus Pseudogekko) are secretive, delicate, slender-bodied, arboreal members of an obligate forest specialist clade that is substantially more species diverse than previously assumed. Over the last century, few species were added to this Philippine endemic genus. During the last decade, however, revisionary studies have res...

The diversity of Philippine amphibians and reptiles has increased over the last few decades, in part due to re-evaluation of species formerly believed to be widespread. Many of these investigations of widespread species have uncovered multiple closely related cryptic lineages comprising species complexes, each restricted to individual Pleistocene A...

Philippine False Geckos (genus Pseudogekko) are secretive, delicate, slender-bodied, arboreal members of an obligate forest specialist clade that is substantially more species diverse than previously assumed. Over the last century, few species were added to this Philippine endemic genus. During the last decade, however, revisionary studies have res...

We describe a new species of frog of the genus Platymantis Günther (subgenus Tirahanulap), from the east-central regions of the Philippines. It belongs to the the previously-defined P. hazelae Group) based on morphological and bioacoustic datasets. The new species is phenotypically and ecologically most similar to members of Tirahanulap, an assembl...

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...

The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in SouthEast Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian exti...

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 i...

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...

Information on species richness and community structure is invaluable for guiding conservation and management of biodiversity, but is rarely available in the megadiverse biodiversity conservation hotspot of Philippines-particularly for amphibians and reptiles. This study provides the first report and characterisation of amphibians and reptile commu...

Species descriptions of reptiles historically have relied exclusively on the use of morphological data; however, these external, phenotypic data do not always co-vary with lineage divergence. Consequently, it has become increasingly clear that species diversity has been underestimated in many evolutionary radiations. With the use of an integrative...

Colleagues: thank you for your interest in this work. A preprint for this paper was generated by accident and it requires major revisions before it will be published. Of course I will update the project when the paper is in press, but until then I will be declining requests for this preprint. Thank you for your understanding.

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 morpholo...