Phylogenomic species delimitation of studfishes (Fundulidae: Fundulus): evidence for cryptic species in agreement with the central highlands vicariance hypothesis

The Central Highlands ecoregion of the eastern United States represents a hotspot of freshwater biodiversity, with replicated patterns of vicariant speciation east and west of the Mississippi River. Previous phylogeographic investigation of the studfishes (Fundulus subgenus Fundulus) revealed evidence for vicariant speciation in the Central Highlands, but data were limited to a small number of gene sequences generated with Sanger sequencing. We used double digest restriction-site associated DNA sequencing (ddRADseq) to improve resolution of phylogeographic patterns and better characterize population genetic variation. Our sample design included individuals from the Fundulus catenatus species group (F. catenatus, F. bifax, and F. stellifer) and two outgroup taxa (F. julisia and F. rathbuni). Phylogenetic analyses support a monophyletic F. catenatus complex and a sister relationship with Mobile Basin studfishes (F. bifax and F. stellifer). Population genomics and species delimitation tests provide evidence for three species-level subdivisions of F. catenatus. We describe F. catenatus as limited to the Tennessee River and its drainages, F. caddo sp. nov., in the Ouachita Highlands, and F. cryptocatenatus sp. nov., occupying the remainder of the range. Modally, F. catenatus was characterized by fewer left pectoral rays (16 vs. 17). Fundulus caddo sp. nov. had modally fewer anal rays (15 vs. 16) and lateral scale rows (13 vs. 14). Fundulus cryptocatenatus sp. nov. was characterized by modally higher dorsal rays (15 vs. 14) and fewer caudal rays (16 vs. 17). The geographic distribution is likely the result of multiple pre-Pleistocene vicariance events congruent with the Central Highlands Vicariance Hypothesis as well as separate, possibly subsequent, dispersal events. Overall, results of this study corroborate previous evidence for a complex biogeographic history of taxa endemic to rivers of the Central Highlands ecoregion. The improved resolution of genomic variation among studfish populations will guide future studies of morphological variation and will improve conservation plans for rare and endemic taxa in a freshwater biodiversity hotspot.

Integrative taxonomy, phylogenetics and historical biogeography of subgenus Aeschyntelus Stål, 1872 (Hemiptera: Heteroptera: Rhopalidae)

The subgenus Aeschyntelus includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of Rhopalus and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (COI, whole mitochondrial data) and nuclear genomic data (18S + 28S rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of Rhopalus and proposed the recognition of one new species known as Rhopalus qinlinganus sp. nov., which is classified within the subgenus Aeschyntelus. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising R. kerzhneri and R. latus, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of R. sapporensis into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of Aeschyntelus, thus indicating that it likely originated in East Asia during the middle Miocene. The development of Aeschyntelus biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China.

Establishing species boundaries in Bornean geckos

Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.

Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype

Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex)

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally 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 distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiates the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.

Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex

PREMISE

Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts.

METHODS

Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries.

RESULTS

None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries.

CONCLUSIONS

Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high-throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes.

Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation

Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].

Morphological variation and its correlation with bioclimatic factors in Odorrana graminea sensu stricto

The large green cascade frog (Odorrana graminea sensu stricto) shows significant genetic differentiation in China, forming western, southern, and eastern clades. However, the morphological differentiation among the three clades is unclear, and the influence of bioclimatic factors on morphological variation among clades is unknown. Based on 20 morphological traits of 309 specimens from 28 localities, the present study explored the morphological differentiation and variation among clades and their correlation with bioclimatic factors through the multivariate statistical analysis. The results of the present study showed that O. graminea sensu stricto was divided into western, southern, and eastern morphological groups, and the gene flow between neighboring populations had caused an individual misidentification. With the three-step terrain and population distribution latitude and humidity, the annual mean temperature (Bio1) was significantly different between the southern and eastern–western clades; the maximum temperature of the hottest month (Bio5) was significantly different between the southern and western clades, and the mean temperature of the wettest quarter (Bio8) and the precipitation seasonality (Bio15) were significantly different between the eastern and western–southern clades. The southern clade that was affected by a high temperature had a smaller body size and larger sensory organs, and the eastern clade distributed in highly humid areas had a larger body size and smaller sensory organs. Moreover, the annual mean temperature range (Bio7) was the dominant factor in the morphological variation of O. graminea sensu stricto, and it had significant negative correlations with seven traits of male frogs and four traits of female frogs. The effect of precipitation factors on the morphological differentiation of each clade remained unclear. The local adaptation caused by climatic differences was the main reason for the morphological differentiation among clades. These findings will help us to understand amphibians’ abilities to adapt to environmental variation.

Gene drive in species complexes: defining target organisms

Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.

Cryptic lineages and standing genetic variation across independent cane toad introductions

Widespread introduced species can be leveraged to investigate the genetic, ecological and adaptive processes underlying rapid evolution and range expansion, particularly the contributions of genetic diversity to adaptation. Rhinella marina, the cane toad, has been a focus of invasion biology for decades in Australia. However, their introduction history in North America is less clear. Here, we investigated the roles of introduction history and genetic diversity in establishment success of cane toads across their introduced range. We used reduced representation sequencing (ddRAD) to obtain 34,000 SNPs from 247 toads in native (French Guiana, Guyana, Ecuador, Panama, Texas) and introduced (Bermuda, southern Florida, northern Florida, Hawai'i, Puerto Rico) populations. Unlike all other cane toad introductions, we found that Florida populations were more closely related to native Central American lineages (R. horribilis), than to native Southern American lineages (R. marina). Furthermore, we found high levels of diversity and population structure in the native range, corroborating suggestions that R. marina is a species complex. We also found that introduced populations exhibit only slightly lower genetic diversity than native populations. Together with demographic analyses, this indicates founding populations of toads in Florida were larger than previously reported. Lastly, within R. marina, only one of 245 putatively adaptive SNPs showed fixed differences between native and introduced ranges, suggesting that putative selection in these introduced populations is based upon existing genetic variation. Our findings highlight the importance of genetic sequencing in understanding biological introductions and hint at the role of standing genetic variation in range expansion.

Complex population history affects admixture analyses in nine-spined sticklebacks

Introgressive hybridization is an important process in evolution but challenging to identify, undermining the efforts to understand its role and significance. On the contrary, many analytical methods assume direct descent from a single common ancestor, and admixture among populations can violate their assumptions and lead to seriously biased results. A detailed analysis of 888 whole-genome sequences of nine-spined sticklebacks (Pungitius pungitius) revealed a complex pattern of population ancestry involving multiple waves of gene flow and introgression across northern Europe. The two recognized lineages were found to have drastically different histories, and their secondary contact zone was wider than anticipated, displaying a smooth gradient of foreign ancestry with some curious deviations from the expected pattern. Interestingly, the freshwater isolates provided peeks into the past and helped to understand the intermediate states of evolutionary processes. Our analyses and findings paint a detailed picture of the complex colonization history of northern Europe and provide backdrop against which introgression and its role in evolution can be investigated. However, they also expose the challenges in analyses of admixed populations and demonstrate how hidden admixture and colonization history misleads the estimation of admixture proportions and population split times.

The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation

With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and L. gentilis, we examined a ∼700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and L. elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa.

Delimiting 33 Carpinus (Betulaceae) species with a further phylogenetic inference

Carpinus (Betulaceae) has approximately 52 species distributed in the Northern Hemisphere, with many species of Carpinus found in China. However, the species boundaries and phylogenetic relationships remain poorly understood. This study reported ITS sequences for 225 individuals of 33 Carpinus species, mainly from China. We also included eight Ostrya species in our analyses, the closely related sister group of Carpinus. We aimed to delimit these species based on ITS sequences and clarify their phylogenetic relationships by constructing tree-like topology and networks at population level. We found that only 17 of 33 species could be delimited from the closely related ones based on species-specific mutations in ITS sequence variation, including all species of sect. Distegocarpus, and sect. Carpinus subsect. Carpinus. Carpinus subsect. Carpinus contained two endangered species, although one seemed to be a recently originated allopolyploid species with genetic additivity from two likely parents in the ITS sequence variation. Sixteen species of sect. Carpinus subsect. Polyneurae were classified into three species complexes, in each of which two or more could be not distinguished from each other. The closely related species of these complexes may still diverge at the early stage without genetic distinction in the nuclear ITS sequences because of too short of divergence time and frequent gene flow. Otherwise, some species may be established based on the intraspecific variations without genetic bases for an independently evolving unit.

Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (A. californica) and Woodhouse's Scrub-Jay (A. woodhouseii), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.

Phylogenetic and multivariate analyses of Gekko smithii Gray, 1842 recover a new species from Peninsular Malaysia and support the resurrection of G. albomaculatus (Giebel, 1861) from Sumatra

Abstract

An integrative taxonomic analysis of Sundaic populations of Gekko smithii from the Thai-Malaya Peninsula, Sumatra, and Borneo recovered four deeply divergent mitochondrial lineages that are separated by major geographic barriers (mountains and seaways). Furthermore, they bear a number of concordant statistically significant differences in meristic and morphometric features, morphospatial separation in multivariate space, and discrete differences in color pattern. Gekko smithiisensu stricto is restricted to southern Thailand south of the Isthmus of Kra and Peninsular Malaysia west of the Banjaran (mountain range) Titiwangsa, being that the type locality is on Penang Island, Penang. Gekko hulksp. nov. is a new species from extreme southern Thailand and Peninsular Malaysia east of the Banjaran Titiwangsa and five east coast islands—the type locality being Pulau (island) Tioman, Pahang. Gekko cf. albofasciolatus is tentatively used to include Bornean populations west of the Iran Mountains in Sabah and Sarawak which, in the absence of molecular data, cannot unequivocally be separated morphologically from G. albofasciolatus from the type locality at Banjarmasin, Kalimantan, Indonesia east of the Iran Mountains. In the absence of molecular data, G. albomaculatus is resurrected to include mainland Sumatran, Nias Island, and Banyak Islands populations which, based on their morphology, cannot be separated from descriptions of G. albomaculatus from the type locality of Bangka Island, 15 km off the southeast coast of mainland Sumatra. Further integrative analyses of all Sumatran and Bornean populations are currently underway as well as the enigmatic Wallacean populations from Sulawesi. Data are presented that strongly suggest all references to G. smithii from Java stem from a 151 year-old misidentification of a specimen of G. gecko of unknown provenance. Additionally, there are no vouchered records of G. smithii from Myanmar. The phylogeographic patterns of Sundaic populations of the G. smithii complex are concordant with those of a plethora of other Sundaic lineages.

Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species-level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early-diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation.

The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses

Fungi are rich in complexes of cryptic species that need a combination of different approaches to be delimited, including genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. In this study we present a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana s.lat. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and among three clades in B. bassiana, supporting their subdivision as distinct species. Morphological examination focusing on the width and the length of phialides and conidia showed no difference among the clades within B. bassiana while conidial length was significantly different among clades within B. asiatica. The secondary metabolite profiles obtained by liquid chromatography-mass spectrometry (LC-MS) allowed a distinction between B. asiatica and B. bassiana, but not between the clades therein. Based on these genomic, morphological, chemical data, we proposed a clade of B. asiatica as a new species, named B. thailandica, and two clades of B. bassiana to respectively represent B. namnaoensis and B. neobassiana spp. nov. Such closely related but divergent species with different host ranges have potential to elucidate the evolution of host specificity, with potential biocontrol application. Citation: Kobmoo N, Arnamnart N, Pootakham W, et al. 2021. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia 47: 136-150. https://doi.org/10.3767/persoonia.2021.47.04.

Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation

The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.

Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands

Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.

Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)

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-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

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 gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake

As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)

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 bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

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.

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae)

The genus Amolops ("torrent frogs") is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of Amolops remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate species-level diversity within the genus Amolops throughout southern China and Southeast Asia, and infer evolutionary relationships among the species using mtDNA data (16S, COI, and ND2). Molecular analyses indicate nine unnamed species, mostly distributed in the Himalayas. We then utilized anchored hybrid enrichment to generate a dataset representing the major mitochondrial lineages to resolve phylogenetic relationships, biogeography, and pattern of species diversification. Our resulting phylogeny strongly supports the monophyly of four previously identified species groups (the A. ricketti, A. daiyunensis, A. hainanensis, and A. monticola groups), but paraphyly for the A. mantzorum and A. marmoratus groups, as previously defined. We erect one new species group, the A. viridimaculatus group, and recognize Dubois' (1992) subgenus Amo as the A. larutensis species group. Biogeographic analysis suggests that Amolops originated on the Indo-Burma/Thai-Malay Peninsula at the Eocene/Oligocene boundary, and dispersed outward, exemplifying a common pattern observed for the origin of Asian biodiversity. The early divergence within Amolops coincides with the Himalayan uplift and the lateral extrusion of Indochina at the Oligocene/Miocene boundary. Our results show that paleoclimatic and geomorphological events have profoundly influenced the patterns of lineage diversification within Amolops.

Phylogenetic relationships of the Chinese torrent frogs (Ranidae: Amolops) revealed by phylogenomic analyses of AFLP-Capture data

The torrent frog genus Amolops contains nearly sixty species distributed in swift mountain streams throughout southeast Asia. The taxonomy of this genus has proven complicated due to unstable morphological diagnostic characters. The relationships of Amolops species and species groups were not readily resolved with a small number of molecular markers. Here, we applied the novel AFLP-Capture approach and acquired two large datasets (242 anonymous nuclear sequences and the mitochondrial genome) from 70 Chinese Amolops samples to study their relationships. The phylogenies inferred from the nuclear data and the mitochondrial data were both robust and revealed a primary phylogenetic split between eastern and western Chinese Amolops species. The relationships of the six species groups were clarified. While the three species groups in east China (the A. ricketti, A. daiyunensis and A. hainanensis groups) were monophyletic, the three species groups in the west (the A. mantzorum, A. monticola and A. marmoratus groups) were not monophyletic, suggesting a need for further investigation and revision. The robust phylogenies also provided new insights into species relationships, especially for the A. mantzorum group, which has been difficult to resolve due to multiple speciation events occurring approximately 7-8 million years ago. The divergence times estimated with the nuclear data indicated that the ancestor of the Chinese Amolops appeared in the late Eocene or early Oligocene, and that speciation events in the Chinese Amolops were often related to geological events (e.g. the uprising of mountains and the formation of islands). By including the mitochondrial sequences from GenBank, a more comprehensive Amolops phylogeny was constructed that reflected the origin of the Chinese Amolops. Based on all these results, a dispersal scenario of the torrent frogs was hypothesized. Our research serves as the first example of using AFLP-Capture to obtain a large amount of data for shallow-scale phylogenetic and taxonomic studies, which should be useful for other nonmodel organism groups.

Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

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. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis)

The identification and delimitation of species boundaries are essential for understanding speciation and adaptation processes and for the management of biodiversity as well as development for applications. Ophiocordyceps unilateralis sensu lato is a complex of fungal pathogens parasitizing Formicine ants, inducing zombie behaviors in their hosts. Previous taxonomic works with limited numbers of samples and markers led to the "one ant-one fungus" paradigm, resulting in the use of ant species as a proxy for fungal identification. Here, a population genomics study with sampling on three ant species across Thailand supported the existence of host-specific species in O. unilateralis s.l. with no footprints of long term introgression despite occasional host shifts and first-generation hybrids. We further detected genetic clusters within the previously delimited fungal species, with each little footprints of recombination, suggesting high levels of inbreeding. The clusters within each of O. camponoti-leonardi and O. camponoti-saundersi were supported by differentiation throughout the genome, suggesting they may constitute further cryptic species parasitizing the same host, challenging the one ant-one fungus paradigm. These genetic clusters had different geographical ranges, supporting different biogeographic influences between the north/center and the south of Thailand, reinforcing the scenario in which Thailand endured compartmentation during the latest Pleistocene glacial cycles.

To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

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 populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes.

RESULTS

Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (< 3%) and consistent with intraspecific divergences of other closely related taxa. The BPP analysis produced variable results depending on prior settings and priors estimated from empirical data produced the best results that were also congruent with the gdi analysis.

CONCLUSIONS

This study showed that the evolutionary history of Southeast Asian toads is difficult to resolve and numerous relationships remain ambiguous. Although some results from the species delimitation analyses were inconclusive, they were nevertheless efficacious at identifying potential new species and taxonomic incompatibilities for future in-depth investigation. We also demonstrated the sensitivity of BPP to different priors and that careful selection priors based on empirical data can greatly improve the analysis. Finally, the gdi can be a robust tool to complement other species delimitation methods.

Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis

We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994.

Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).