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Meneses CG, Pitogo KME, Supsup CE, Brown RM. Philippine herpetology (Amphibia, Reptilia), 20 years on: two decades of progress towards an increasingly collaborative, equitable, and inclusive approach to the study of the archipelago's amphibians and reptiles. Zookeys 2024; 1190:213-257. [PMID: 38327266 PMCID: PMC10848817 DOI: 10.3897/zookeys.1190.109586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024] Open
Abstract
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 re-assesses what Philippine herpetology has accomplished, both as a discipline and a community, during the last two decades (2002-2022). A total of 423 herpetological publications was collated, revealing a substantial increase in annual publications, rising from approximately four per year during 2002-2008 to around 28 per year in 2009-2022. Half of the published studies focused on squamate reptiles (lizards 30.5%, snakes 21%) and 28.4% on amphibians, 5.9% on turtles, and 2.6% on crocodiles. The remaining 11.6% of studies focused simultaneously on multiple taxa (i.e., faunal inventories). Diversity and distribution (35.2%) and ecological (26.5%) studies remained popular, while studies on taxonomy (14.9%), phylogenetics and biogeography (11.8%), and conservation (11.6%) all increased. However, geographical gaps persist urging immediate surveys in many understudied regions of the country. Finally, we found a balanced representation between Filipino and foreign first authors (1.0:1.1), yet a substantial gender gap exists between male and female first authors (7.1:1.0). Nonetheless, the steep increase in publications and the diversity of people engaged in Philippine herpetology is a remarkable positive finding compared to the 20 years preceding the last review (1980-2000). Our hope is that the next decades will bring increasingly equitable, internationally collaborative, and broadly inclusive engagement in the study of amphibians and reptiles in the Philippines.
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Affiliation(s)
- Camila G. Meneses
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Kier Mitchel E. Pitogo
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Christian E. Supsup
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
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Abstract
Phylogenetic models have long assumed that lineages diverge independently. Processes of diversification that are of interest in biogeography, epidemiology, and genome evolution violate this assumption by affecting multiple evolutionary lineages. To relax the assumption of independent divergences and infer patterns of divergences predicted by such processes, we introduce a way of conceptualizing, modeling, and inferring phylogenetic trees. We apply the approach to genomic data from geckos distributed across the Philippines and find support for patterns of shared divergences predicted by repeated fragmentation of the archipelago by interglacial rises in sea level. 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 difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.
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Abraham RK, Herr MW, Sterkhova VV, Otterholt R, Siler CD, Sanguila MB, Brown RM. Revisiting Linnaean and Wallacean Shortfalls in Mindanao Fanged Frogs: The Limnonectes magnus Complex Consists of Only Two Species. HERPETOLOGICAL MONOGRAPHS 2021. [DOI: 10.1655/herpmonographs-d-20-00010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Robin Kurian Abraham
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, KS 66045, USA
| | - Mark William Herr
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, KS 66045, USA
| | - Viktoria V. Sterkhova
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, KS 66045, USA
| | - Rayanna Otterholt
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, KS 66045, USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Marites Bonachita Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, San Francisco Street, Butuan City, 8600 Agusan del Norte, Philippines
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, KS 66045, USA
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Responte M, Chiu Y, Peng P, Brown RM, Dai C, Su Y. Northward geographic diversification of a kleptoparasitic spider Argyrodes lanyuensis (Araneae, Theridiidae) from the Philippine Archipelago to Orchid Island. Ecol Evol 2021; 11:11241-11266. [PMID: 34429915 PMCID: PMC8366866 DOI: 10.1002/ece3.7910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
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 especially among parasitic organisms. Here, we tested for biogeographical structure in novel populations of the "generalist" kleptoparasitic spider, Argyrodes lanyuensis Yoshida, Tso & Severinghaus, 1998 in the Philippines. Results showed that, in addition to Orchid/Lanyu Island, this species has a wide geographic distribution in the Philippine Archipelago. The estimated divergence time of this lineage using the mitochondrial cytochrome oxidase 1 (mt-CO1) suggests that this species diverged ca 3.12 MYA, during the Pliocene. Two reciprocal monophyletic clades were elucidated in A. lanyuensis, but with limited differentiation across Pleistocene Aggregate Island Complex (PAIC) boundaries and modern-day islands. However, in our analyses of morphological variation, we identified two phenotypically differentiated units in males (Orchid Island, Taiwan + Luzon, Philippine PAIC populations vs. Palawan + West Visayan + Mindanao PAIC populations). We infer that this species diverged in the southern portion of the Philippine Archipelago and only recently colonized Orchid Island. Our study provides new information on the extensive distribution of A. lanyuensis outside Orchid Island, Taiwan, but we documented a very limited geographically associated genetic variation. Our study points to behavioral phenomena such as foraging behavior as essential contributor to the evolutionary process of species diversification, in contrast to the traditionally invoked geographic drivers of divergence.
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Affiliation(s)
- Mae Responte
- Graduate Institute of MedicineCollege of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
- Department of Biological Sciences and Environmental StudiesCollege of Science and MathematicsUniversity of the Philippines MindanaoDavao CityPhilippines
| | - Yi‐Fan Chiu
- Department of Biomedical Science and Environmental BiologyCollege of Life ScienceKaohsiung Medical UniversityKaohsiungTaiwan
| | - Po Peng
- Department of Biomedical Science and Environmental BiologyCollege of Life ScienceKaohsiung Medical UniversityKaohsiungTaiwan
| | - Rafe M. Brown
- Biodiversity InstituteDepartment of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansasUSA
| | - Chia‐Yen Dai
- Department of MedicineCollege of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
| | - Yong‐Chao Su
- Department of Biomedical Science and Environmental BiologyCollege of Life ScienceKaohsiung Medical UniversityKaohsiungTaiwan
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Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, Scheidt U, Iskandar DT, Jankowski A, Hertwig ST. Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822). Mol Phylogenet Evol 2021; 163:107210. [PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
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.
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Affiliation(s)
- Jana M Flury
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
| | - Alexander Haas
- Centrum für Naturkunde, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Dyche Hall, Lawrence, KS 66045, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Yong Min Pui
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Kueh Boon-Hee
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Ulrich Scheidt
- Naturkundemuseum Erfurt, Große Arche 14, 99084 Erfurt, Germany
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesa 10, Bandung 40132, Indonesia
| | - André Jankowski
- Centrum für Naturkunde, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland; University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3006 Bern, Switzerland.
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Onn Chan K, Hutter CR, Wood PL, Su YC, Brown RM. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis). Syst Biol 2021; 71:40-57. [PMID: 33964168 DOI: 10.1093/sysbio/syab034] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022] Open
Abstract
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.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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Weinell JL, Paluh DJ, Siler CD, Brown RM. A New, Miniaturized Genus and Species of Snake (Cyclocoridae) from the Philippines. COPEIA 2020. [DOI: 10.1643/ch2020110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jeffrey L. Weinell
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045; (JLW) . Send reprint requests to JLW
| | - Daniel J. Paluh
- Department of Biology and Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, Oklahoma 73072-7029
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045; (JLW) . Send reprint requests to JLW
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Brown RM, Meneses CG, Wood PL, Fernandez JB, Cuesta MA, Clores MA, Tracy C, Buehler MD, Siler CD. Unexpected Discovery of Another New Species of Philippine False Gecko (Gekkonidae; Pseudogekko) from the Bicol Peninsula of Luzon Island. HERPETOLOGICA 2020. [DOI: 10.1655/herpetologica-d-19-00029.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - Camila G. Meneses
- Animal Biology Division, Graduate School, University of the Philippines at Los Baños, College, Laguna 4031, Philippines
| | - Perry L. Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - Jason B. Fernandez
- Phase 5, Block 3, Lot 14 Marycris Complex, Malagasang 2-G Imus Cavite, Philippines
| | - Michael A. Cuesta
- Graduate School, Ateneo de Naga University, Ateneo Avenue, Bagumbayan Sur, 4400 Naga City, Philippines
| | - Michael A. Clores
- Graduate School, Ateneo de Naga University, Ateneo Avenue, Bagumbayan Sur, 4400 Naga City, Philippines
| | - Claire Tracy
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - Matthew D. Buehler
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
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Supsup CE, Asis AA, Carestia Jr UV, Diesmos AC, Mallari NAD, Brown RM. Variation in species richness, composition and herpetological community structure across a tropical habitat gradient of Palawan Island, Philippines. HERPETOZOA 2020. [DOI: 10.3897/herpetozoa.33.e47293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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 communities across primary habitat types of the Victoria-Anepahan Mountain Range on Palawan Island along the western edge of the archipelago. A total of 41 amphibian and reptile species were recorded throughout our sampling sites (n = 27 species) or in targeted habitat searches (14 species). A species richness estimator predicted that 35 species may be present in our sampling sites, suggesting that a significant proportion of secretive species may continue to be unrecorded, especially for reptiles. Higher species richness was found in secondary growth than in mixed-use agricultural areas or even pristine forest. The low species richness recorded from pristine forest types may be due to these forests now being restricted to higher elevations where species diversity has been documented to decrease. Our results also show that complex community structures (species assemblages) are to be equally expected in both secondary growth and pristine forests. Together, our results show how species richness and community assemblages may vary across habitats, highlighting that old growth forest does not always support higher species richness, particularly in high elevations.
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Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns. Mol Phylogenet Evol 2020; 147:106785. [PMID: 32135306 DOI: 10.1016/j.ympev.2020.106785] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/03/2020] [Accepted: 02/27/2020] [Indexed: 11/24/2022]
Abstract
The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of cryptic diversity and revealed numerous taxonomic complications, especially within the C. consobrinus, C. malayanus, and C. pubisulcus groups. Comparisons of pairwise genetic distances and a preliminary species delimitation analysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-ranging species on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricted distributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneo into the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derived from multiple separate invasions into the geopolitical areas comprising the Philippines. Although our investigation of Bornean Cyrtodactylus is the most comprehensive to-date, it highlights the need for expanded taxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeography of Bornean Cyrtodactylus is far from complete.
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11
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Wood PL, Guo X, Travers SL, Su YC, Olson KV, Bauer AM, Grismer LL, Siler CD, Moyle RG, Andersen MJ, Brown RM. Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements. Mol Phylogenet Evol 2020; 146:106731. [PMID: 31904508 DOI: 10.1016/j.ympev.2020.106731] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/31/2019] [Accepted: 01/02/2020] [Indexed: 11/18/2022]
Abstract
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 monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately "derived" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements (UCEs) to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyze multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme addresses four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic, and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesi's L. iskandari as the sister taxon to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high-elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister taxon relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not grouped with Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our resolved and strongly supported phylogeny, we present a new classification emphasizing the most inclusive, original generic name (Gekko) for these ~60 taxa, arranged into seven subgenera.
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Affiliation(s)
- Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Xianguang Guo
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Yong-Chao Su
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City 80708, Taiwan.
| | - Karen V Olson
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship , 800 Lancaster Avenue, Villanova University, Villanova, PA 19085, USA.
| | - L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Cameron D Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA.
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
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12
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Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species. PLoS One 2018; 13:e0194877. [PMID: 29718922 PMCID: PMC5931476 DOI: 10.1371/journal.pone.0194877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/11/2018] [Indexed: 11/19/2022] Open
Abstract
The Philippine island of Palawan is highly biodiverse. During fieldwork there in 2011 & 2014 we found five unknown species in the large genus Begonia. The species are similar in their rhizomatous stems, four-tepaled flowers, inferior two- or three-locular ovaries with bilamellate placentas, and are assignable to Begonia sect. Baryandra. Our observations support the recognition of these as five new species endemic to Palawan: B. elnidoensis, B. gironellae, B. quinquealata, B. tabonensis and B. tenuibracteata which are described here. The five new species were added to phylogenies based Bayesian analysis of nrDNA (ITS) and chloroplast DNA (ndhA, ndhF-rpl32, rpl32-trnL, trnC-trnD), along with 45 other allied ingroup species. A majority of the species show incongruent positions in the two phylogenies, with evidence of prevalent chloroplast capture. Models show chloroplast capture is more likely in plant populations with high levels of inbreeding following a reduction in selfing rate after hybridisation; we suggest that this is a possible explanation for the massive amount of chloroplast exchange seen in our phylogeny, as Begonia species often exist as small isolated populations and may be prone to inbreeding depression. Our data also indicate a level of nuclear genetic exchange between species. The high prevalence of hybrid events in Begonia is potentially an important factor in driving genomic change and species evolution in this mega-diverse genus.
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Weinell JL, Brown RM. Discovery of an old, archipelago-wide, endemic radiation of Philippine snakes. Mol Phylogenet Evol 2018; 119:144-150. [DOI: 10.1016/j.ympev.2017.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 11/26/2022]
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Brown RM, Prue A, Onn CK, Gaulke M, Sanguila MB, Siler CD. Taxonomic Reappraisal of the Northeast Mindanao Stream Frog, Sanguirana albotuberculata(Inger 1954), Validation ofRana mearnsi, Stejneger 1905, and Description of a New Species from the Central Philippines. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00009.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Allyson Prue
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
- Haskell Indian Nations University, Lawrence, KS 66045, USA
| | - Chan Kin Onn
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Maren Gaulke
- GeoBio Center LMU, Richard-Wagner-Strasse 10, 80333 München, Germany
| | - Marites B. Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, San Francisco Street, 8600, Butuan City, Philippines
| | - Cameron D. Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA
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Abstract
The interplay between range expansion and concomitant diversification is of fundamental interest to evolutionary biologists, particularly when linked to intercontinental dispersal and/or large scale extinctions. The evolutionary history of true frogs has been characterized by circumglobal range expansion. As a lineage that survived the Eocene-Oligocene extinction event (EOEE), the group provides an ideal system to test the prediction that range expansion triggers increased net diversification. We constructed the most densely sampled, time-calibrated phylogeny to date in order to: (i) characterize tempo and patterns of diversification; (ii) assess the impact of the EOEE; and (iii) test the hypothesis that range expansion was followed by increased net diversification. We show that late Eocene colonization of novel biogeographic regions was not affected by the EOEE and surprisingly, global expansion was not followed by increased net diversification. On the contrary, the diversification rate declined or did not shift following geographical expansion. Thus, the diversification history of true frogs contradicts the prevailing expectation that amphibian net diversification accelerated towards the present or increased following range expansion. Rather, our results demonstrate that despite their dynamic biogeographic history, true frogs diversified at a relatively constantly rate, even as they colonized the major land masses of Earth.
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Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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Siler CD, Davis DR, Watters JL, Freitas ES, Griffith OW, Binaday JWB, Lobos AHT, Amarga AKS, Brown RM. First Record of thePseudogekko brevipesComplex from the Northern Philippines, with Description of a New Species. HERPETOLOGICA 2017. [DOI: 10.1655/herpetologica-d-16-00074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
- Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Drew R. Davis
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Jessa L. Watters
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Elyse S. Freitas
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
- Department of Biology, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Oliver W. Griffith
- Department of Ecology and Evolutionary Biology, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | | | | | - Ace Kevin S. Amarga
- Crop Protection Cluster, College of Agriculture, University of the Philippines Los Banos, Laguna, Philippines
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
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Alexander AM, Su Y, Oliveros CH, Olson KV, Travers SL, Brown RM. Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs. Evolution 2016; 71:475-488. [DOI: 10.1111/evo.13133] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
Affiliation(s)
| | - Yong‐Chao Su
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
- Department of Biological Sciences National University of Singapore 117543 Singapore
| | - Carl H. Oliveros
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Karen V. Olson
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
| | - Scott L. Travers
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
| | - Rafe M. Brown
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
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Heitz BB, Diesmos AC, Freitas ES, Ellsworth ED, Grismer LL, Aowphol A, Brown RM, Siler CD. A New Supple Skink, GenusLygosoma(Reptilia: Squamata: Scincidae), from the Western Philippines. HERPETOLOGICA 2016. [DOI: 10.1655/herpetologica-d-16-00023.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sanguila MB, Cobb KA, Siler CD, Diesmos AC, Alcala AC, Brown RM. The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands. Zookeys 2016; 624:1-132. [PMID: 27833422 PMCID: PMC5096358 DOI: 10.3897/zookeys.624.9814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 08/31/2016] [Indexed: 11/12/2022] Open
Abstract
We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion.
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Affiliation(s)
- Marites B. Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, San Francisco St., 8600 Butuan City, Philippines
| | - Kerry A. Cobb
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA
| | - Arvin C. Diesmos
- Herpetology Section, Zoology Division, Philippine National Museum, Rizal Park, Burgos St., Ermita 1000, Manila, Philippines
| | - Angel C. Alcala
- Angelo King Center for Research and Environmental Management, Silliman University, Dumaguete City 6200, Philippines
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
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