Rafe M. Brown

University of Kansas | KU · Department of Ecology and Evolutionary Biology

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...

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 con...

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...

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 squamate vi...

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...

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 and species delimitation inferences, the...

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...

Historical and contemporary processes shaping striking variation in terrestrial biodiversity along elevational gradients have received much attention from evolutionary biologists, often by way of comparisons to latitudinal environmental gradients. Here we synthetically review what is known of the diversity and origin of upland endemic geckos across...

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 monophyl...

Falcaustra samarensis n. sp. (Ascaridida, Kathlaniidae) from the intestines of Megophrys stejnegeri Taylor 1920 (Anura, Megophryidae) is described and illustrated. Falcaustra samarensis n. sp. represents the one hundred fourth species assigned to the genus and the thirty-seventh Oriental species. It is distinguished from other Oriental species by t...

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...

Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultra-conserved elements) is becoming important to alleviate these ph...

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobat...