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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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Karin BR, Arellano S, Wang L, Walzer K, Pomerantz A, Vasquez JM, Chatla K, Sudmant PH, Bach BH, Smith LL, McGuire JA. Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes. BMC Genomics 2023; 24:229. [PMID: 37131128 PMCID: PMC10155392 DOI: 10.1186/s12864-023-09277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/24/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods. RESULTS With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes. CONCLUSIONS This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.
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Affiliation(s)
- Benjamin R Karin
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA.
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
| | - Selene Arellano
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Laura Wang
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kayla Walzer
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Aaron Pomerantz
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Juan Manuel Vasquez
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Peter H Sudmant
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Lydia L Smith
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Jimmy A McGuire
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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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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Sata N, Nakano T. Insights into the phylogenetic position and phylogeography of the monospecific skink-parasite genus. INVERTEBR SYST 2022. [DOI: 10.1071/is21026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Neoentomelas asatoi Hasegawa, 1989 is a parasitic nematode that infests only the scincid lizard Ateuchosaurus pellopleurus (Hallowell, 1861) that inhabits the forest floor in the Northern and Central Ryukyu Archipelago, Japan. As a member of Rhabdiasidae, the reproductive mode of N. asatoi is characterised by the alternation of the protandrous hermaphroditic mode and gonochoristic mode throughout the life cycle. The intrafamily phylogenetic position and intraspecific diversity of this nematode species were inferred by molecular phylogenetic analyses. The results revealed the phylogenetic distinctiveness of Neoentomelas Hasegawa, 1989 in Rhabdiasidae that supports the unique generic status of Neoentomelas within the family. The intraspecific phylogenetic analyses of N. asatoi revealed a minor concordant phylogenetic pattern with the host and mosaic geographic arrangement of the major clades that was discordant with the host. The analyses and distribution pattern of subclades suggested that this geographic arrangement can be explained by at least three dispersal events and subsequent switching to indigenous host populations. Colonisation events might be promoted by the high establishment rate of new populations stemming from the parthenogenesis-like reproduction mode of N. asatoi. This study demonstrated that reproductive modes can affect the intraspecific genetic diversity of parasites.
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Mirza ZA, Bragin AM, Bhosale H, Gowande GG, Patel H, Poyarkov NA. A new ancient lineage of ablepharine skinks (Sauria: Scincidae) from eastern Himalayas with notes on origin and systematics of the group. PeerJ 2022; 10:e12800. [PMID: 35111410 PMCID: PMC8781319 DOI: 10.7717/peerj.12800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/24/2021] [Indexed: 01/10/2023] Open
Abstract
The Himalayas represent a renowned biodiversity hotspot and an important biogeographic realm that has influenced origin and diversification of multiple taxa. A recent herpetological investigation of the eastern Himalayas of the Indian state of Arunachal Pradesh led to the discovery of a unique lineage of ablepharine skink, which is herein described as a new genus along with a new species. The findings are based an integrated taxonomic approach incorporating data from external morphology, microCT scans of the skull and molecular data. The molecular phylogeny of ablepharine skinks is also presented that suggests taxonomic amendments. Discovery of this unique lineage of skinks further highlights the biogeographic importance of the eastern Himalayas as a source for origin of several relic biota.
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Affiliation(s)
- Zeeshan A Mirza
- National Centre for Biological Sciences, Bangalore, Karnataka, India
| | - Andrey M Bragin
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Gaurang G Gowande
- Abasaheb Garware College, Pune, Maharashtra, India.,Department of Biotechnology, Fergusson College, Pune, Maharasshtra, India
| | - Harshil Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India.,Voluntary Nature Conservancy, Vallabh Vidyanagar, Gujarat, India
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Nghia Do, Cau Giay, Vietnam
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6
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De novo Assembly, Annotation, and Analysis of Transcriptome Data of the Ladakh Ground Skink Provide Genetic Information on High-Altitude Adaptation. Genes (Basel) 2021; 12:genes12091423. [PMID: 34573405 PMCID: PMC8466045 DOI: 10.3390/genes12091423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
The Himalayan Arc is recognized as a global biodiversity hotspot. Among its numerous cryptic and undiscovered organisms, this composite high-mountain ecosystem harbors many taxa with adaptations to life in high elevations. However, evolutionary patterns and genomic features have been relatively rarely studied in Himalayan vertebrates. Here, we provide the first well-annotated transcriptome of a Greater Himalayan reptile species, the Ladakh Ground skink Asymblepharus ladacensis (Squamata: Scincidae). Based on tissues from the brain, an embryonic disc, and pooled organ material, using pair-end Illumina NextSeq 500 RNAseq, we assembled ~77,000 transcripts, which were annotated using seven functional databases. We tested ~1600 genes, known to be under positive selection in anurans and reptiles adapted to high elevations, and potentially detected positive selection for 114 of these genes in Asymblepharus. Even though the strength of these results is limited due to the single-animal approach, our transcriptome resource may be valuable data for further studies on squamate reptile evolution in the Himalayas as a hotspot of biodiversity.
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Slavenko A, Tamar K, Tallowin OJS, Kraus F, Allison A, Carranza S, Meiri S. Revision of the montane New Guinean skink genus Lobulia (Squamata: Scincidae), with the description of four new genera and nine new species. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The skink genus Lobulia is endemic to New Guinea, the largest and highest tropical island in the world. Lobulia and its related genera represent an important component of the montane herpetofauna of New Guinea, but it remains understudied and poorly known. We here provide the first, large-scale, systematic revision of Lobulia, using molecular phylogenetic and morphological comparisons to assess the monophyly of the genus and the diversity of species within it. We find that Lobulia, as currently defined, is polyphyletic. The eight species currently assigned to it form three clades. Furthermore, many specimens from New Guinea of unknown specific affinity are genetically and morphologically distinct from each other. Based on these data, we re-diagnose Lobulia and two of its closely related genera, Prasinohaema and Papuascincus. We erect four new genera (Alpinoscincus gen. nov., Nubeoscincus gen. nov., Ornithuroscincus gen. nov. and Palaia gen. nov.) to address the problem of polyphyly and describe nine new species Lobulia fortis sp. nov., Lobulia huonensis sp. nov., Loublia marmorata sp. nov., Lobulia vogelkopensis sp. nov., Ornithuroscincus bengaun sp. nov., Ornithuroscincus inornatus sp. nov., Ornithuroscincus pterophilus sp. nov., Ornithuroscincus shearmani sp. nov. and Ornithuroscincus viridis sp. nov. We supplement this taxonomic revision by investigating the biogeographic history of Lobulia s.l. and find evidence for a large radiation in the accreted terranes of New Guinea, with multiple independent colonizations of montane habitats and subsequent recolonization of lowland habitats. Our study reinforces the uniqueness and richness of the montane herpetofauna of New Guinea and the importance of mountains to biodiversity in the Tropics.
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Affiliation(s)
- Alex Slavenko
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Karin Tamar
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Oliver J S Tallowin
- UN Environment Programme World Conservation Monitoring Centre, Cambridge, UK
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Michigan, USA
| | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Shai Meiri
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
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8
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Aguilar-López JL, Luría-Manzano R, Pineda E, Canseco-Márquez L. Selva Zoque, Mexico: an important Mesoamerican tropical region for reptile species diversity and conservation. Zookeys 2021; 1054:127-153. [PMID: 34393566 PMCID: PMC8355003 DOI: 10.3897/zookeys.1054.67916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/08/2021] [Indexed: 11/12/2022] Open
Abstract
The Selva Zoque region is characterized by a great variety of ecosystems for which there is little information about reptile species diversity and their conservation status. This study is the first assessment of the species richness, composition, and conservation status of reptiles of this region. Additionally, this information is compared with that of seven other tropical regions in northern Mesoamerica. In total, 141 native reptile species belonging to 81 genera and 29 families are recorded for the Selva Zoque region. Sixty species (42% of the total) recorded in Selva Zoque are in high-risk categories according to the Mexican Ministry of the Environment, the highest number for the Mexican regions of Mesoamerica. According to the IUCN, six species are in high-risk categories, seven species are in Data Deficient, and 23 (16%) have not been evaluated yet. According to the Environmental Vulnerability Scores approach, 28 species (20%) are in the high vulnerability category. The Selva Zoque species composition is most similar to Los Tuxtlas and Lacandona regions, and most dissimilar to Sian Ka´an Biosphere Reserve. The reptilian fauna of Selva Zoque has a distinctive composition, with the highest number (11 species) of endemic reptiles in the northern Mesoamerican, and species from two biogeographic provinces: the Gulf of Mexico and the Mexican Pacific Coast. These results indicate that the Selva Zoque is the most diverse region in native reptile species in northern Mesoamerica, highlighting it as extremely important for the conservation of the reptile fauna at local (southern Mexico) and regional levels (northern Mesoamerica).
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Affiliation(s)
- José Luis Aguilar-López
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología A. C., Carretera antigua a Coatepec 351, El Haya, Xalapa, C.P. 91073, Veracruz, México
| | - Ricardo Luría-Manzano
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, Cidade Universitária, 05508-090, São Paulo, São Paulo, Brazil
| | - Eduardo Pineda
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología A. C., Carretera antigua a Coatepec 351, El Haya, Xalapa, C.P. 91073, Veracruz, México
| | - Luis Canseco-Márquez
- Departamento de Biología Evolutiva, Laboratorio de Herpetología, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-399, C.P. 04510, México City, México
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Diversity and distribution of amphibians and reptiles in the Caramoan Island Group, Maqueda Channel, Southern Luzon, Philippines. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2021. [DOI: 10.1016/j.japb.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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10
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Castiglia R, Flores-Villela OA, Bezerra AMR, Gornung E, Annesi F, Muñoz-Alonso LA, Solano E. Detection of cryptic diversity in lizards (Squamata) from two Biosphere Reserves in Mesoamerica. COMPARATIVE CYTOGENETICS 2020; 14:613-638. [PMID: 33384855 PMCID: PMC7772285 DOI: 10.3897/compcytogen.v14i4.57765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
A combined approach based on karyology and DNA taxonomy allowed us to characterize the taxonomic peculiarities in 10 Mesoamerican lizard species, belonging to six genera and five families, inhabiting two Biosphere Reserve in Chiapas, Mexico: La Sepultura Biosphere Reserve, and Montes Azules Biosphere. The karyotypes of four species, Phyllodactylus sp. 3 (P. tuberculosus species group) (2n = 38), Holcosus festivus (Lichtenstein et von Martens, 1856) (2n = 50), Anolis lemurinus Cope, 1861 (2n = 40), and A. uniformis Cope, 1885 (2n = 29-30) are described for the first time, the last one showing a particular X1X1X2X2/X1X2Y condition. In Aspidoscelis deppii (Wiegmann, 1834) (2n = 50) and Anolis capito Peters, 1863 (2n = 42), we found a different karyotype from the ones previously reported for these species. Moreover, in A. capito, the cytogenetic observation is concurrent with a considerable genetic divergence (9%) at the studied mtDNA marker (MT-ND2), which is indicative of a putative new cryptic species. The skink Scincella cherriei (Cope, 1893), showed high values of genetic divergence (5.2% at 16S gene) between the specimens from Montes Azules and those from Costa Rica and Nicaragua, comparable to the values typical of sister species in skinks. A lower level of genetic divergence, compatible with an intraspecific phylogeographic structure, has been identified in Lepidophyma flavimaculatum Duméril, 1851. These new data identify taxa that urgently require more in-depth taxonomic studies especially in these areas where habitat alteration is proceeding at an alarming rate.
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Affiliation(s)
- Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
| | - Oscar Alberto Flores-Villela
- Museo de Zoologia Fac. de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-399, Mexico D.F. 04510, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Alexandra M. R. Bezerra
- Mastozoologia/COZOO, Museu Paraense Emilio Goeldi, Campus de Pesquisa, Av. Perimetral 1901, CEP 66077-830, Belém, PA, BrazilMuseu Paraense Emilio GoeldiBelémBrazil
| | - Ekaterina Gornung
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
| | - Flavia Annesi
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
| | - Luis Antonio Muñoz-Alonso
- El Colegio de la Frontera Sur. Conservación de las Biodiversidad. Carretera Panamericana y Periférico Sur s/n. C.P. 29290, San Cristóbal de las Casas, Chiapas, MéxicoEl Colegio de la Frontera Sur. Conservación de las BiodiversidadSan Cristóbal de las CasasMexico
| | - Emanuela Solano
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
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Freitas ES, Miller AH, Reynolds RG, Siler CD. A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar. Mol Phylogenet Evol 2020; 146:106754. [PMID: 32028030 DOI: 10.1016/j.ympev.2020.106754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, species delimitation analyses, and morphological data, we examine lineage diversification in a cryptic radiation of Riopa skinks in Myanmar. Four species of Riopa skinks are currently recognized from Myanmar based on morphological traits, but the boundaries between three of these species, R. anguina, R. lineolata, and R. popae, are not well-defined. We find high levels of genetic diversity within these three species. Our analyses suggest that they may comprise as many as 12 independently evolving lineages, highlighting the extent to which species diversity in the region is underestimated. However, quantitative trait data suggest that these lineages have not differentiated morphologically, possibly indicating that this cryptic radiation represents non-adaptive evolution, although additional data is needed to corroborate this.
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Affiliation(s)
- Elyse S Freitas
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA.
| | - Aryeh H Miller
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - R Graham Reynolds
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - 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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12
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Slavenko A, Tamar K, Tallowin OJS, Allison A, Kraus F, Carranza S, Meiri S. Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae). Mol Phylogenet Evol 2020; 146:106749. [PMID: 32014575 DOI: 10.1016/j.ympev.2020.106749] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/12/2019] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
New Guinea, the world's largest and highest tropical island, has a rich but poorly known biota. Papuascincus is a genus of skinks endemic to New Guinea's mountain regions, comprising two wide-ranging species and two species known only from their type series. The phylogeny of the genus has never been examined and the relationships among its species - as well as between it and closely related taxa - are hitherto unknown. We performed the first large-scale molecular-phylogenetic study of Papuascincus, including sampling across the genus' range in Papua New Guinea. We sequenced three mitochondrial and two nuclear markers from 65 specimens of Papuascincus and reconstructed their phylogenetic relationships. We also performed species-delimitation analyses, estimated divergence times and ancestral biogeography, and examined body-size evolution within the genus. Papuascincus was strongly supported as monophyletic. It began radiating during the mid-Miocene in the area now comprising the Central Cordillera of New Guinea, then dispersed eastward colonising the Papuan Peninsula. We found evidence of extensive cryptic diversity within the genus, with between nine and 20 supported genetic lineages. These were estimated using three methods of species delimitation and predominantly occur in allopatry. Distribution and body-size divergence patterns indicated that character displacement in size took place during the evolutionary history of Papuascincus. We conclude that the genus requires comprehensive taxonomic revision and likely represents a species-rich lineage of montane skinks.
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Affiliation(s)
- Alex Slavenko
- School of Zoology, Tel Aviv University, 6997801 Tel Aviv, Israel.
| | - Karin Tamar
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | | | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, MI, USA
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Shai Meiri
- School of Zoology, Tel Aviv University, 6997801 Tel Aviv, Israel; The Steinhardt Museum of Natural History, Tel Aviv, Israel
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13
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Chen L, Lin Y, Lin Y, Hu Y, Xiao Q, Zhou X, Liu Y, Li H. Complete mitochondrial genome of Scincella modesta (Squamata: Scincidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:676-677. [PMID: 33366699 PMCID: PMC7748724 DOI: 10.1080/23802359.2020.1713919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The first complete mitochondrial genome sequence was determined for an oviparous lizard, Scincella modesta (Scincella, Scincidae). The total length of the complete mitochondrial genome was 17,511 bp, encodes 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and 2 non-coding regions. The overall base composition of S. modesta is A: 31.9%, T: 27.2%, G: 14.5%, and C: 26.5%. Most of the S. modesta mitochondrial genes are encoded on the H-strand except for the ND6 gene and eight tRNA genes, which are encoded on the L-strand. Mrbayes and ML tree based on 13 protein-coding genes indicated that S. vandenburghi is the sister group of the S. modesta within the genus Scincella. The complete mitogenome sequence of S. modesta provided fundamental data for resolving phylogenetic and genetic problems related to genus Scincella.
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Affiliation(s)
- Lian Chen
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Youfu Lin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ying Lin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yaping Hu
- Ministry of Ecology and Environment of China, Nanjing Institute of Environmental Science, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing, China
| | - Qi Xiao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xu Zhou
- Ministry of Ecology and Environment of China, Nanjing Institute of Environmental Science, Nanjing, China.,State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing, China
| | - Yan Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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14
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Sánchez-Martínez PM, Ramírez-Pinilla MP, Meneses-Pelayo E, Nunes PMS. Hemipenial morphology of nine South American species of Mabuya (Scincidae: Lygosominae) with comments on the morphology of the family. Anat Rec (Hoboken) 2019; 303:2917-2930. [PMID: 31815369 DOI: 10.1002/ar.24329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/09/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022]
Abstract
Species of the genus Mabuya are barely recognizable because of their highly conservative external morphology, resulting in unstable systematic and taxonomic status. Considering that hemipenial morphology has been extensively used as a source of systematic information for several groups of Squamata, we described the hemipenial morphology of nine species of Mabuya, searching for diagnostic features useful to taxonomic and systematic studies. To have comparative parameters within the family, we also presented the description of the hemipenes of two other Scincidae species (i.e., Trachylepis atlantica and Tiliqua rugosa). This information, together with the available literature, was analyzed in a comparative framework, allowing us to define some variation for the genus and family. The hemipenial morphology of the species of Mabuya studied is very conservative; features that show subtle variation were the shape of the protuberances present on the asulcate face of the hemipenial body and the presence and type of a lateral fold, on the body. Also, within the family, some variation was found in the shape and length of lobes, length of branches of the sulcus spermaticus, and in the kind of folds and protuberances in both faces of the lobes and hemipenial body. Although these features were not tested in a systematic context, this information suggested variations in hemipenial morphology that could contribute to taxonomic diagnostics and phylogenetic characters. The importance of obtaining proper preparations for gathering accurate information is emphasized, and the use of fresh-killed specimens that shows fewer difficulties for the procedures of preparation is highly recommended.
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Affiliation(s)
- Paola María Sánchez-Martínez
- Grupo de Morfología y Ecología Evolutiva, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Sede Bogotá, Colombia
| | | | - Elson Meneses-Pelayo
- Grupo de estudios en anfibios y reptiles de Santander (GEARS), Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Pedro M Sales Nunes
- Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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15
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Oaks JR, Siler CD, Brown RM. The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago. Evolution 2019; 73:1151-1167. [PMID: 31017301 PMCID: PMC6767427 DOI: 10.1111/evo.13754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/10/2019] [Indexed: 01/05/2023]
Abstract
A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the "species-pump" model, in which repeated bouts of cospeciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago.
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Affiliation(s)
- Jamie R. Oaks
- Department of Biological Sciences & Museum of Natural HistoryAuburn UniversityAuburnAlabama36849
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahoma73072
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas66045
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16
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Freitas ES, Datta-Roy A, Karanth P, Grismer LL, Siler CD. Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.
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Affiliation(s)
- Elyse S Freitas
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Aniruddha Datta-Roy
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, California, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
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17
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Zhao Z, Verdú‐Ricoy J, Mohlakoana S, Jordaan A, Conradie W, Heideman N. Unexpected phylogenetic relationships within the world's largest limbless skink species (
Acontias plumbeus
) highlight the need for a review of the taxonomic status of
Acontias poecilus. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Joaquín Verdú‐Ricoy
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Setjhaba Mohlakoana
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Adriaan Jordaan
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld) Port Elizabeth South Africa
- School of Natural Resource ManagementNelson Mandela University George South Africa
| | - Neil Heideman
- Department of Zoology & EntomologyUniversity of the Free State Bloemfontein South Africa
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18
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Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae). Mol Phylogenet Evol 2018; 129:242-257. [DOI: 10.1016/j.ympev.2018.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/01/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022]
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19
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New Supple Skink, GenusLygosoma(Reptilia: Squamata: Scincidae), from Indochina and Redescription ofLygosoma quadrupes(). J HERPETOL 2018. [DOI: 10.1670/16-064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Lemos-Espinal JA, Smith GR, Woolrich-Piña GA. Amphibians and reptiles of the state of San Luis Potosí, Mexico, with comparisons with adjoining states. Zookeys 2018; 753:83-106. [PMID: 29731682 PMCID: PMC5934353 DOI: 10.3897/zookeys.753.21094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/28/2018] [Indexed: 01/29/2023] Open
Abstract
A summary of the species of amphibians and reptiles of the state has been compiled, including their geographic distributions, habitats, and conservation statuses. The herpetofauna of San Luis Potosí consists of 41 species of amphibians and 141 species of reptiles. San Luis Potosí shares the highest number of species with Hidalgo and Tamaulipas, and the least number of species with Nuevo León. In San Luis Potosí, there are several taxa of particular conservation concern including salamanders, emydid and trionychid turtles, anguid and xenosaurid lizards, and natricid and colubrid snakes.
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Affiliation(s)
- Julio A. Lemos-Espinal
- Laboratorio de Ecología-UBIPRO, FES Iztacala UNAM, Avenida los Barrios 1, Los Reyes Iztacala, Tlalnepantla, edo. de México, México 54090
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21
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Grismer LL, Wood PL, Quah ESH, Anuar S, Ngadi EB, Izam NAM, Ahmad N. Systematics, ecomorphology, cryptic speciation and biogeography of the lizard genus Tytthoscincus Linkem, Diesmos & Brown (Squamata: Scincidae) from the sky-island archipelago of Peninsular Malaysia. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, California, USA
| | - Perry L Wood
- Department of Biology, Brigham Young University, East Bulldog Boulevard, Provo, Utah, USA
| | - Evan S H Quah
- School of Biological Sciences, Universiti Sains Malaysia, USM, Pulau Pinang, Penang, Malaysia
| | - Shahrul Anuar
- School of Biological Sciences, Universiti Sains Malaysia, USM, Pulau Pinang, Penang, Malaysia
- Center for Marine and Coastal Studies, Universiti Sains Malaysia, USM, Penang, Malaysia
| | - Ehwan B Ngadi
- School of Environmental and Natural Resources Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nur Amalina Mohd Izam
- School of Environmental and Natural Resources Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Norhayati Ahmad
- School of Environmental and Natural Resources Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Institute for Environment and Development, (LESTARI), Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan, Malaysia
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22
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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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23
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Higham TE, Gamble T, Russell AP. On the origin of frictional adhesion in geckos: small morphological changes lead to a major biomechanical transition in the genusGonatodes. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Timothy E. Higham
- Department of Biology; University of California; Riverside CA 92521 USA
| | - Tony Gamble
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
| | - Anthony P. Russell
- Department of Biological Sciences; University of Calgary; Calgary AB T2N 1N4 Canada
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24
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Linkem CW, Minin VN, Leaché AD. Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae). Syst Biol 2016; 65:465-77. [PMID: 26738927 PMCID: PMC6383586 DOI: 10.1093/sysbio/syw001] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/29/2015] [Indexed: 01/28/2023] Open
Abstract
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.
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Affiliation(s)
| | - Vladimir N Minin
- Department of Biology, University of Washington, Seattle WA; Department of Statistics, University of Washington, Seattle WA
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle WA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
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25
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Molecular phylogenetics and biogeography of the Neotropical skink genus Mabuya Fitzinger (Squamata: Scincidae) with emphasis on Colombian populations. Mol Phylogenet Evol 2015; 93:188-211. [DOI: 10.1016/j.ympev.2015.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/23/2015] [Accepted: 07/24/2015] [Indexed: 01/05/2023]
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26
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Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Mol Ecol 2015; 24:1696-712. [DOI: 10.1111/mec.13151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Robert C. Thomson
- Department of Biology; University of Hawai'i at Mānoa; Honolulu HI 96822 USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA 92515 USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
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27
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Brown RM, Siler CD, Richards SJ, Diesmos AC, Cannatella DC. Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12232] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Rafe M. Brown
- Biodiversity Institute; Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History; Department of Biology; University of Oklahoma; Norman OK 73072-7029 USA
| | - Stephen J. Richards
- Herpetology Department; South Australian Museum; North Terrace Adelaide SA 5000 Australia
| | - Arvin C. Diesmos
- National Museum of the Philippines; Rizal Park, Padre Burgos Avenue Ermita 1000 Manila Philippines
| | - David C. Cannatella
- Department of Integrative Biology; Texas Biodiversity Collections; University of Texas at Austin; 1 University Station, C0990 Austin TX 78712 USA
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28
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Koizumi Y, Ota H, Hikida T. Phylogeography of the Two Smooth Skinks, Scincella boettgeri and S. formosensis (Squamata: Scincidae) in the Southern Ryukyus and Taiwan, as Inferred from Variation in Mitochondrial Cytochrome b Sequences. Zoolog Sci 2014; 31:228-36. [DOI: 10.2108/zs130180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Yuki Koizumi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, Yayoigaoka 6, Sanada, Hyogo 669–1546, Japan
| | - Tsutomu Hikida
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, JAPAN
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29
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Sales Nunes PM, Curcio FF, Roscito JG, Rodrigues MT. Are Hemipenial Spines Related to Limb Reduction? A Spiny Discussion Focused on Gymnophthalmid Lizards (Squamata: Gymnophthalmidae). Anat Rec (Hoboken) 2014; 297:482-95. [DOI: 10.1002/ar.22876] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Pedro M. Sales Nunes
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11.461, CEP 05422-970 São Paulo SP Brazil
| | - Felipe F. Curcio
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11.461, CEP 05422-970 São Paulo SP Brazil
| | - Juliana G. Roscito
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11.461, CEP 05422-970 São Paulo SP Brazil
| | - Miguel T. Rodrigues
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11.461, CEP 05422-970 São Paulo SP Brazil
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30
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A new species of Eimeria Schneider, 1875 (Apicomplexa: Eimeriidae) from the Solomon ground skink, Sphenomorphus solomonis (Boulenger) (Sauria: Scincidae) from Papua New Guinea. Syst Parasitol 2014; 87:83-6. [PMID: 24395577 DOI: 10.1007/s11230-013-9455-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/24/2013] [Indexed: 10/25/2022]
Abstract
Between September 1990 and November 1991, 19 Sphenomorphus spp. skinks, including nine S. jobiense, three S. simus, and seven Solomon ground skinks, S. solomonis (Boulenger), were collected from Madang and Morobe Provinces, Papua New Guinea (PNG), and examined for coccidia. A single S. solomonis was found to be infected with a new species of Eimeria Schneider, 1875. Oöcysts of Eimeria perkinsae n. sp. are ellipsoidal with a smooth, colourless, bi-layered wall, measure 18.6 × 14.7 μm, and have a length/width (L/W) ratio of 1.3; both micropyle and oöcyst residuum are absent, but a fragmented polar granule is present. Sporocysts are ovoidal, 8.9 × 6.4 μm, L/W 1.4; neither Stieda, sub-Stieda or para-Stieda bodies are present; a sporocyst residuum consisted of a loose cluster of granules dispersed between sporozoites. Sporozoites are comma-shaped with spheroidal anterior and posterior refractile bodies. This represents the first report of coccidia from this skink genus.
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31
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Phylogeny and divergence times of Australian Sphenomorphus group skinks (Scincidae, Squamata). Mol Phylogenet Evol 2013; 69:906-18. [DOI: 10.1016/j.ympev.2013.06.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 02/11/2013] [Accepted: 06/19/2013] [Indexed: 11/22/2022]
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32
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Grismer LL, Wood PL, Anuar S, Muin MA, Quah ESH, McGuire JA, Brown RM, Van Tri N, Hong Thai P. Integrative taxonomy uncovers high levels of cryptic species diversity inHemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) and the description of a new species from Peninsular Malaysia. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12064] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA USA
- Institute for Environment and Development; (LESTARI); Universiti Kebangsaan Malaysia; 43600 Bangi Malaysia
| | - Perry L. Wood
- Department of Biology; Brigham Young University; 150 East Bulldog Boulevard Provo UT 84602 USA
| | - Shahrul Anuar
- School of Biological Sciences; Universiti Sains Malaysia; 11800 USM Pulau Pinang Malaysia
| | - Mohd Abdul Muin
- School of Biological Sciences; Universiti Sains Malaysia; 11800 USM Pulau Pinang Malaysia
| | - Evan S. H. Quah
- Centre for Drug Research; Universiti Sains Malaysia; 11800 Minden Pulau Pinang Malaysia
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology; University of California; Berkeley CA 94720-3160 USA
- Department of Integrative Biology; University of California; Berkeley CA 94720-3160 USA
| | - Rafe M. Brown
- Biodiversity Institute; University of Kansas; Lawrence KS 66045-7651 USA
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7651 USA
| | - Ngo Van Tri
- Department of Environmental Management and Technology; Institute of Tropical Biology; Vietnamese Academy of Sciences and Technology; Ho Chi Minh City Vietnam
| | - Pham Hong Thai
- Cam Le Department of Education and Training; Cam Le District Da Nang City Vietnam
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Brown RM, Siler CD, Oliveros CH, Esselstyn JA, Diesmos AC, Hosner PA, Linkem CW, Barley AJ, Oaks JR, Sanguila MB, Welton LJ, Blackburn DC, Moyle RG, Townsend Peterson A, Alcala AC. Evolutionary Processes of Diversification in a Model Island Archipelago. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110411-160323] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rafe M. Brown
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Cameron D. Siler
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, Oklahoma 73073-7029;
| | - Carl H. Oliveros
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803;
| | - Arvin C. Diesmos
- Herpetology Section, Zoology Division, National Museum of the Philippines, Manila, Philippines;
| | - Peter A. Hosner
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Charles W. Linkem
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
- Current address: Department of Biology, University of Washington, Seattle, Washington 98195;
| | - Anthony J. Barley
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Jamie R. Oaks
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | | | - Luke J. Welton
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
- Department of Biology, Brigham Young University, Provo, Utah 84602;
| | - David C. Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California 94118;
| | - Robert G. Moyle
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - A. Townsend Peterson
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Angel C. Alcala
- Silliman University-Angelo King Center for Research and Environmental Management (SUAKCREM), SU-Marine Laboratory, 6200 Dumaguete City, Philippines;
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Güçlü O, Candan K, Kankiliç T, Kumlutaş Y, Durmuş SH, Poulakakis N, Ilgaz C. Phylogeny of Trachylepis sp. (Reptilia) from Turkey inferred from mtDNA sequences. ACTA ACUST UNITED AC 2013; 25:456-63. [PMID: 24004307 DOI: 10.3109/19401736.2013.814108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The taxonomic status of the species included into the genus Trachylepis in Turkey are doubtful. So far, three morphological species have been attributed to this genus in Turkey; Trachylepis aurata. T. vittata, and T. septemtaeniata. Here, we investigated the taxonomy of the Turkish Trachylepis species by employing phylogenetic and phylogeographic approaches and using mitochondrial DNA (cytochrome b and 12 S rRNA). In total, 45 Trachylepis and 6 Mabuya specimens were used analyzed. Phylogenetic analyses were carried out using Maximum Likelihood (ML) and Bayesian Inference (BI) methods. The phylogenetic relationships and the genetic distances retrieved, revealed that the Turkish species, which currently recognized as Trachylepis, are highly diversified, forming a distinct clade that shows closer phylogenetic affinity with the species of the genus Mabuya rather than the other Trachylepis species. In this clade, the three Turkish species are monophyletic with T. vittata to branch off first in late Miocene (10.54 Mya). The other two species (T. septemtaeniata and T. aurata) seem to have sister group relationship that diverged at the end of Messinian Salinity Crisis (5.27 Mya). As a whole, the examination of mtDNA lineages in the Turkish lizards of the genus Trachylepis may contribute substantially to the refining of their taxonomic status, since the three species of Turkey, although monophyletic, represent a distinct radiation that would could probably recognized as a different genus in Mabuya sensu lato.
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Affiliation(s)
- Ozgür Güçlü
- Aksaray University, Güzelyurt Vocational School, Department of Plant and Animal Production , Güzelyurt/Aksaray , Turkey
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Pyron RA, Burbrink FT, Wiens JJ. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol 2013; 13:93. [PMID: 23627680 PMCID: PMC3682911 DOI: 10.1186/1471-2148-13-93] [Citation(s) in RCA: 975] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. RESULTS The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. CONCLUSIONS We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA
| | - Frank T Burbrink
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 5th Ave., New York, NY 10016, USA
- Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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Brown RM, Siler CD, Oliveros CH, Welton LJ, Rock A, Swab J, Weerd MV, van Beijnen J, Jose E, Rodriguez D, Jose E, Diesmos AC. The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, northern Sierra Madre Mountain Range. Zookeys 2013; 266:1-120. [PMID: 23653519 PMCID: PMC3591760 DOI: 10.3897/zookeys.266.3982] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 01/09/2013] [Indexed: 11/25/2022] Open
Abstract
We provide the first report on the herpetological biodiversity (amphibians and reptiles) of the northern Sierra Madre Mountain Range (Cagayan and Isabela provinces), northeast Luzon Island, Philippines. New data from extensive previously unpublished surveys in the Municipalities of Gonzaga, Gattaran, Lasam, Santa Ana, and Baggao (Cagayan Province), as well as fieldwork in the Municipalities of Cabagan, San Mariano, and Palanan (Isabela Province), combined with all available historical museum records, suggest this region is quite diverse. Our new data indicate that at least 101 species are present (29 amphibians, 30 lizards, 35 snakes, two freshwater turtles, three marine turtles, and two crocodilians) and now represented with well-documented records and/or voucher specimens, confirmed in institutional biodiversity repositories. A high percentage of Philippine endemic species constitute the local fauna (approximately 70%). The results of this and other recent studies signify that the herpetological diversity of the northern Philippines is far more diverse than previously imagined. Thirty-eight percent of our recorded species are associated with unresolved taxonomic issues (suspected new species or species complexes in need of taxonomic partitioning). This suggests that despite past and present efforts to comprehensively characterize the fauna, the herpetological biodiversity of the northern Philippines is still substantially underestimated and warranting of further study.
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Affiliation(s)
- Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA
- Zoology Division, National Museum of the Philippines, Rizal Park, Padre Burgos Avenue, Ermita 1000, Manila, Philippines
| | - Cameron D. Siler
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA
- Zoology Division, National Museum of the Philippines, Rizal Park, Padre Burgos Avenue, Ermita 1000, Manila, Philippines
- Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA
| | - Carl. H Oliveros
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA
- Isla Biodiversity Conservation; 9 Bougainvillea Street, Manuela Subdivision, Las Piñas City 1741, Philippines
| | - Luke J. Welton
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA
| | - Ashley Rock
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA
| | - John Swab
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, USA
| | - Merlijn Van Weerd
- Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands
- Mabuwaya Foundation, Isabela State University Campus Garita, Cabagan, Isabela, Philippines
| | | | - Edgar Jose
- Herpetology Section, Zoology Division, Philippine National Museum, Rizal Park, Burgos St., Manila, Philippines
| | - Dominic Rodriguez
- Mabuwaya Foundation, Isabela State University Campus Garita, Cabagan, Isabela, Philippines
| | - Edmund Jose
- Mabuwaya Foundation, Isabela State University Campus Garita, Cabagan, Isabela, Philippines
| | - Arvin C. Diesmos
- Herpetology Section, Zoology Division, Philippine National Museum, Rizal Park, Burgos St., Manila, Philippines
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Oaks JR, Sukumaran J, Esselstyn JA, Linkem CW, Siler CD, Holder MT, Brown RM. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution 2012; 67:991-1010. [PMID: 23550751 DOI: 10.1111/j.1558-5646.2012.01840.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation-based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence-time parameters.
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Affiliation(s)
- Jamie R Oaks
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.
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Amphibians and Reptiles of Luzon Island, Philippines, VI: The Herpetofauna of the Subic Bay Area. ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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BRANDLEY MATTHEWC, OTA HIDETOSHI, HIKIDA TSUTOMU, NIETO MONTES DE OCA ADRIÁN, FERÍA-ORTÍZ MANUEL, GUO XIANGUANG, WANG YUEZHAO. The phylogenetic systematics of blue-tailed skinks (Plestiodon) and the family Scincidae. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2011.00801.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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