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Burroughs RW, Parham JF, Stuart BL, Smits PD, Angielczyk KD. Morphological Species Delimitation in The Western Pond Turtle ( Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification? Integr Org Biol 2024; 6:obae010. [PMID: 38689939 PMCID: PMC11058871 DOI: 10.1093/iob/obae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.
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Affiliation(s)
- R W Burroughs
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Center for Inclusive Education, Stony Brook University, Stony Brook, NY 11794, USA
| | - J F Parham
- Department of Geological Sciences, California State University, Fullerton, CA 92834, USA
| | - B L Stuart
- Section of Research and Collections, NC Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - P D Smits
- 952 NW 60th St., Seattle, Washington, WA 98107, USA
| | - K D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
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2
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Li SZ, Chen JJ, Su HJ, Liu J, Tang XJ, Wang B. A new odorous frog species of Odorrana (Amphibia, Anura, Ranidae) from Guizhou Province, China. Zookeys 2024; 1192:57-82. [PMID: 38419744 PMCID: PMC10897836 DOI: 10.3897/zookeys.1192.114315] [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: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
The frog genus Odorrana is distributed across east and southeastern Asia. Based on morphological differences and molecular phylogenetics, a new species of the genus occurring from Leigong Mountain in Guizhou Province, China is described. Phylogenetic analyses based on DNA sequences of the mitochondrial 12S rRNA, 16S rRNA, and ND2 genes supported the new species as an independent lineage. The uncorrected genetic distances between the 12S rRNA, 16S rRNA, and ND2 genes between the new species and its closest congener were 5.0%, 4.9%, and 16.3%, respectively. The new species is distinguished from its congeners by a combination of the following characters: body size moderate (SVL 39.1-49.4 mm in males, 49.7 mm in female); head width larger than head length; tympanum distinctly visible; small rounded granules scattered all over dorsal body and limbs; dorsolateral folds absent; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level between eye to nostril when leg stretched forward; vocal sacs absent in male and nuptial pads present on the base of finger I.
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Affiliation(s)
- Shi-Ze Li
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
| | - Ji-Jun Chen
- Leigongshan National Nature Reserve Administration, Leishan 557100, China Leigongshan National Nature Reserve Administration Leishan China
| | - Hai-Jun Su
- College of Forestry, Guizhou University, Guiyang 550025, China Guizhou University Guiyang China
| | - Jing Liu
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu China
- College of Forestry, Guizhou University, Guiyang 550025, China Guizhou University Guiyang China
| | - Xiu-Jun Tang
- Leigongshan National Nature Reserve Administration, Leishan 557100, China Leigongshan National Nature Reserve Administration Leishan China
| | - Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
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3
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Edwards AW, Harrison XA, Smith MA, Chavarría Díaz MM, Sasa M, Janzen DH, Hallwachs W, Chaves G, Fernández R, Palmer C, Wilson C, North A, Puschendorf R. Amphibian diversity across three adjacent ecosystems in Área de Conservación Guanacaste, Costa Rica. PeerJ 2023; 11:e16185. [PMID: 38034867 PMCID: PMC10688307 DOI: 10.7717/peerj.16185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/05/2023] [Indexed: 12/02/2023] Open
Abstract
Amphibians are the most threatened species-rich vertebrate group, with species extinctions and population declines occurring globally, even in protected and seemingly pristine habitats. These 'enigmatic declines' are generated by climate change and infectious diseases. However, the consequences of these declines are undocumented as no baseline ecological data exists for most affected areas. Like other neotropical countries, Costa Rica, including Área de Conservación Guanacaste (ACG) in north-western Costa Rica, experienced rapid amphibian population declines and apparent extinctions during the past three decades. To delineate amphibian diversity patterns within ACG, a large-scale comparison of multiple sites and habitats was conducted. Distance and time constrained visual encounter surveys characterised species richness at five sites-Murciélago (dry forest), Santa Rosa (dry forest), Maritza (mid-elevation dry-rain forest intersect), San Gerardo (rainforest) and Cacao (cloud forest). Furthermore, species-richness patterns for Cacao were compared with historic data from 1987-8, before amphibians declined in the area. Rainforests had the highest species richness, with triple the species of their dry forest counterparts. A decline of 45% (20 to 11 species) in amphibian species richness was encountered when comparing historic and contemporary data for Cacao. Conservation efforts sometimes focus on increasing the resilience of protected areas, by increasing their range of ecosystems. In this sense ACG is unique containing many tropical ecosystems compressed in a small geographic space, all protected and recognised as a UNESCO world heritage site. It thus provides an extraordinary platform to understand changes, past and present, and the resilience of tropical ecosystems and assemblages, or lack thereof, to climate change.
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Affiliation(s)
- Alex W. Edwards
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Xavier A. Harrison
- Centre for Ecology & Conservation, University of Exeter, Penryn, Cornwall, UK
| | - M. Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Mahmood Sasa
- School of Biology, Universidad de Costa Rica, San Pedro, San Jose, Costa Rica
| | - Daniel H. Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Gerardo Chaves
- School of Biology, Universidad de Costa Rica, San Pedro, San Jose, Costa Rica
| | - Roberto Fernández
- Guanacaste Dry Forest Conservation Fund, Philadelphia, United States of America
| | - Caroline Palmer
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Chloe Wilson
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Alexandra North
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, UK
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4
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Suwannapoom C, Osathanunkul M. Distinguishing fanged frogs (Limnonectes) species (Amphibia: Anura: Dicroglossidae), from Thailand using high resolution melting analysis. Sci Rep 2023; 13:18615. [PMID: 37903792 PMCID: PMC10616069 DOI: 10.1038/s41598-023-43637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Morphologically, species of fanged frogs (Limnonectes) are exceedingly similar, making it difficult to distinguish them within the complex. In Thailand, it has been difficult to distinguish between the sympatric species L. bannaensis and L. taylori, particularly among tadpoles, adolescents, and adult females. A precise identification contributes to a greater understanding of biodiversity, particularly for assessing distributions and population dynamics. Therefore, a novel approach is required. The objective of this study was to develop a high resolution melting analysis (HRM) for the rapid and accurate identification of six species of Limnonectes of the L. kuhlii complex found in Thailand, particularly the two sympatric fanged frogs. Here, HRM assays using 16S rRNA mitochondrial primers were designed and developed. There was as much as a 25.3% variation in the nucleotide sequence of the fragment amplified by HRM16S primers among the six species of Limnonectes. Prior to conducting an in vitro HRM, the DNA sequences were used in a simulation HRM, uMELT Quartz, to predict the melting curve for each species of Limnonectes. There were discrepancies between the predicted melting curves of each species generated by the programme. Consequently, in vitro HRM tests were conducted. The obtained melting curve and Tm values were consistent with those predicted, albeit with a slightly different Tm value and a more distinct melting curve. All evaluated species of Limnonectes could be easily distinguished from one another by comparing the melting curve shapes. The HRM assay was then used to confirm the species of 18 Limnonectes samples in comparison to the reference samples (confidence interval > 90%). In addition, the results of HRM were consistent with those of experts who used morphological analysis to identify species. The HRM was found to be useful, and therefore the method would also contribute to future ecological and systematic studies on the target species.
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Affiliation(s)
- Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Muang District, Phayao, Thailand
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Muang District, Chiang Mai, 50200, Thailand.
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5
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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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6
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Thongproh P, Chunskul J, Makchai S, Cota M, Safoowong M, Duengkae P, Duangjai S, Thitichayaporn S, Chuaynkern Y, Chuaynkern C. The identity of Nanorana yunnanensis (Anderson, 1879) from Thailand, with a description of its tadpole (Anura, Dicroglossidae). Zootaxa 2023; 5263:365-388. [PMID: 37044981 DOI: 10.11646/zootaxa.5263.3.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Nanorana yunnanensis has been reported in Thailand for many years; however, no specimens have been verifiably described. To verify the identity of this species in Thailand, we observed Thai specimens formerly assigned to the species N. bourreti and N. yunnanensis. The 12S rRNA, 16S rRNA, and ND2 mitochondrial genes were used to clarify the taxonomic statuses of the Thai specimens. The results showed that our specimens formed a clade with N. yunnanensis, containing specimens from southern Yunnan and Vietnam. The respective mean sequence divergences of the 12S and 16S rRNA genes between populations from Thailand versus China were 0.59% and 1.09%, for populations from Thailand versus Vietnam were 0.57% and 0.61%, and for populations from China versus Vietnam were 0.59% and 1.09%. We provide descriptions of the tadpole and adult specimens of N. yunnanensis from Thailand.
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Affiliation(s)
- Prapaiporn Thongproh
- Department of Biology; Faculty of Science; Khon Kaen University; Mueang Khon Kaen; Khon Kaen; 40002 Thailand.
| | - Jidapa Chunskul
- Thailand Natural History Museum; National Science Museum; Technopolis; Khlong 5; Khlong Luang; Pathum Thani; 12120 Thailand.
| | - Sunchai Makchai
- Doi Chiang Dao Wildlife Research Station; Chiang Dao; Chiang Dao; Chiang Mai; 50170 Thailand.
| | - Michael Cota
- Department of Forest Biology; Faculty of Forestry; Kasetsart University; Chatuchak; Bangkok; 10900 Thailand.
| | - Mongkol Safoowong
- Doi Pha Hom Pok National Park; Pong Nam Ron; Fang; Chiang Mai; 50110 Thailand.
| | | | | | | | - Yodchaiy Chuaynkern
- Department of Biology; Faculty of Science; Khon Kaen University; Mueang Khon Kaen; Khon Kaen; 40002 Thailand.
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7
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Molecular phylogeny reveals distinct evolutionary lineages of the banded krait, Bungarus fasciatus (Squamata, Elapidae) in Asia. Sci Rep 2023; 13:2061. [PMID: 36739450 PMCID: PMC9899266 DOI: 10.1038/s41598-023-28241-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
The banded krait, Bungarus fasciatus is a widespread elapid snake, likely to comprise several distinct species in different geographic regions of Asia. Therefore, based on molecular phylogenetics and comparative morphology data, we present an overview of the systematic composition of the species to delimit potential biogeographic boundaries. Our phylogenetic analyses, based on four mitochondrial genes, reveal the existence of at least three evolutionary lineages within B. fasciatus, corresponding to Indo-Myanmar, Sundaic and eastern Asian lineages. We are convinced that there are at least three taxonomic entities within the nomen B. fasciatus and restrict the distribution of B. fasciatus sensu stricto to the Indo-Myanmar region. We also provide additional natural history data of the taxon from eastern India. Finally, we advocate further studies to establish the degree of reproductive isolation among these diverging evolutionary lineages and to reassess the systematic status of this species complex especially the Sundaic and eastern Asian lineages.
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8
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Skorinov DV, Bozkurt E, Olgun K, Litvinchuk SN. Ventral and lateral spot patterns differentiation between three smooth newt species (Amphibia: Salamandridae: Lissotriton). ACTA ZOOL ACAD SCI H 2022. [DOI: 10.17109/azh.68.3.261.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The location, shape and area of dark spots on the belly, throat and sides of the body of three closely related species of smooth newts (Lissotriton kosswigi, L. schmidtleri and L. vulgaris) were analysed. Differences were found between species and sexes in the location and shape of dark spots on the belly, throat and lateral surfaces of the body. Discriminant analysis of these spot characteristics allows to identificate of males of all three species with a high degree of confidence (85–91%). In females, only L. vulgaris was correctly distinguished from the other two species (accuracy 81–94%). Anatolian and Thracian populations of L. schmidtleri have very similar patterns of dark spots, which confirm their conspecificity. The differences in the location and size of dark spots make possible successful identification of the species during field research and study of museum specimens. The developed method could be useful for comparative studies of other animal species which have spotted camouflage or aposematic colouration.
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9
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Arifin U, Smart U, Husemann M, Hertwig ST, Smith EN, Iskandar DT, Haas A. Phylogeographic inference of Sumatran ranids bearing gastromyzophorous tadpoles with regard to the Pleistocene drainage systems of Sundaland. Sci Rep 2022; 12:12013. [PMID: 35853951 PMCID: PMC9296532 DOI: 10.1038/s41598-022-14722-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs (Sumaterana and Wijayarana) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north–south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island.
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Affiliation(s)
- Umilaela Arifin
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany. .,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany.
| | - Utpal Smart
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.,Amphibian & Reptile Diversity Research Center Department of Biology, University of Texas at Arlington, Arlington, TX, 76019-0498, USA
| | - Martin Husemann
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Eric N Smith
- Amphibian & Reptile Diversity Research Center Department of Biology, University of Texas at Arlington, Arlington, TX, 76019-0498, USA
| | - Djoko T Iskandar
- Basic Science Committee, Indonesian Academy of Sciences, Jalan Medan Merdeka Selatan 11, Jakarta, 10110, Indonesia
| | - Alexander Haas
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany
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10
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Cruz DD, Arellano E. Molecular data confirm Triatoma pallidipennis Stål, 1872 (Hemiptera: Reduviidae: Triatominae) as a novel cryptic species complex. Acta Trop 2022; 229:106382. [PMID: 35189124 DOI: 10.1016/j.actatropica.2022.106382] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 12/11/2022]
Abstract
Triatoma pallidipennis constitues one of the most important Chagas disease vector in Mexico. Previous studies based on molecular data suggest T. pallidipennis as a complex of cryptic species. For that reason, we analyzed the phylogenetic relationships of T. pallidipennis using DNA sequences from the mitochondrial ND4 gene and the ITS-2 gene. In addition, the divergence times were estimated, and possible new taxa were delimited with three species delimitation methods. Finally, genetic distances and possible connectivity routes based on shared haplotypes were obtained among the T. pallidipennis populations. Five haplogroups (possible cryptic species) were found, based on delimitation methods and genetic distances. Haplogroup divergence began about 3 Ma, in the Pleistocene. Moreover, none of the haplogroups showed potential connectivity routes between them, evidencing lack of gene flow. Our results suggest the existence of a new cryptic species complex within what is currently recognized as a T. pallidipennis.
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Affiliation(s)
- Daryl D Cruz
- Centro de Investigación en Biodiversidad y Conservación (CIByC), UAEM, Cuernavaca, Morelos, Mexico
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y Conservación (CIByC), UAEM, Cuernavaca, Morelos, Mexico.
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11
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Malleret MM, Freire MD, Lemes P, Brum FT, Camargo A, Verrastro L. Phylogeography and species delimitation of the Neotropical frog complex (Hylidae:
Scinax granulatus
). ZOOL SCR 2022. [DOI: 10.1111/zsc.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matías M. Malleret
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Marcelo D. Freire
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
| | - Priscila Lemes
- Laboratório de Ecologia e Conservação Departamento de Botânica e Ecologia, Insituto de Biociências, Universidade Federal do Mato Grosso Cuiabá Mato Grosso Brazil
| | - Fernanda T. Brum
- Programa de Pós‐graduação em Ecologia e Conservação Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Arley Camargo
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Laura Verrastro
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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12
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Chornelia A, Lu J, Hughes AC. How to Accurately Delineate Morphologically Conserved Taxa and Diagnose Their Phenotypic Disparities: Species Delimitation in Cryptic Rhinolophidae (Chiroptera). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.854509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.
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13
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Ozalp O, Kaya O, Soylak M. Cloud Point Microextraction of Sudan IV from Food and Cosmetics with Determination by Spectrophotometry. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2047998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Ozgur Ozalp
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
- Technology Research and Application Center (TAUM), Erciyes University, Kayseri, Turkey
| | - Ozlem Kaya
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
| | - Mustafa Soylak
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
- Technology Research and Application Center (TAUM), Erciyes University, Kayseri, Turkey
- Turkish Academy of Sciences (TUBA), Cankaya, Ankara, Turkey
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14
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Nogueira L, Rodrigues Filho LFDS, Solé M, Affonso PRADM, Siqueira S, Sampaio I. DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest. Genet Mol Biol 2022; 45:e20210177. [PMID: 35262169 PMCID: PMC8905458 DOI: 10.1590/1678-4685-gmb-2021-0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022] Open
Abstract
Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.
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Affiliation(s)
- Lídia Nogueira
- Instituto Federal de Educação, Ciência e Tecnologia, Jequié, BA, Brazil
| | | | - Mirco Solé
- Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | | | - Sergio Siqueira
- Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brazil
| | - Iracilda Sampaio
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Bragança, PA, Brazil
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15
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Stephens K, Alexander GJ, Makhubo BG, Telford NS, Tolley KA. Mistaken identity: challenges with specimen identification for morphologically conservative skinks (Trachylepis) leads to taxonomic error. AFR J HERPETOL 2022. [DOI: 10.1080/21564574.2021.2019838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kirstin Stephens
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Graham J Alexander
- Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Buyisile G Makhubo
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas S Telford
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
- Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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16
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Akram A, Rais M, Lopez‐Hervas K, Tarvin RD, Saeed M, Bolnick DI, Cannatella DC. An insight into molecular taxonomy of bufonids, microhylids, and dicroglossid frogs: First genetic records from Pakistan. Ecol Evol 2021; 11:14175-14216. [PMID: 34707849 PMCID: PMC8525160 DOI: 10.1002/ece3.8134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
The current study was focused on documentation of amphibian assemblage in North Punjab and Islamabad Capital Territory, Pakistan, by using mitochondrial gene sequences of 16S rRNA. Our study entailed 37% of the known amphibian species of the country. We provided a phylogenetic analysis based on 74 newly generated mitochondrial 16S rRNAs from nine species of genus Microlyla, Duttaphrynus, Allopaa, Nanorana, Sphaerotheca, Minervarya, Hoplobatrachus, and Euphlyctis. We employed the maximum-likelihood inference and Bayesian analysis to assess the taxonomic status of the samples obtained from Pakistan, with respect to other congeneric species from surrounding regions. Our findings confirmed the taxonomic status of South Asian anuran species Duttaphrynus stomaticus, Duttaphrynus melanostictus, Microhyla nilphamariensis, Allopaa hazarensis, Nanorana vicina, Sphaerotheca maskeyi (synonym: S. pashchima), Minervarya pierrei, Hoplobatrachus tigerinus, and Euphlyctis kalasgramensis in Pakistan. We have reported new country records of genus Minervarya ( M. pierrei). Minervarya pierrei was previously misidentified as Fejervarya limnocharis, due to dearth of genetic information. We provided the first genetic records of our endemic species N. vicina. The results revealed the taxonomic placement of N. vicina with respect to its congeners and validated the taxonomic status of N. vicina from its type locality (Murree) for the first time. The findings of the present study also indicated the paraphyletic relationship of A.- hazarensis with Nanorana species. So, based on our phylogenetic inferences, morphological characters, and habitat preferences, validity of generic status of A. hazarensis is undecided. As our data were not enough to resolve this issue, we suggest sequencing of additional mitochondrial and nuclear genes in the future studies to get a better resolution. We recommend carrying out extensive surveys throughout the country for proper scientific documentation of amphibians of Pakistan. Many new species, some of them might be endemic to Pakistan, are expected to be discovered, and taxonomic status of other species would be resolved.
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Affiliation(s)
- Ayesha Akram
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Muhammad Rais
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Karem Lopez‐Hervas
- Department of Wetland EcologyDoñana Biological StationConsejo Superior de Investigaciones CientíficasSevilleSpain
| | - Rebecca D. Tarvin
- Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Museum of Vertebrate Zoology and Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Muhammad Saeed
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - David C. Cannatella
- Department of Integrative Biology and Biodiversity CenterUniversity of TexasAustinTexasUSA
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17
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Gowri Shankar P, Swamy P, Williams RC, Ganesh SR, Moss M, Höglund J, Das I, Sahoo G, Vijayakumar SP, Shanker K, Wüster W, Dutta SK. King or royal family? Testing for species boundaries in the King Cobra, Ophiophagus hannah (Cantor, 1836), using morphology and multilocus DNA analyses. Mol Phylogenet Evol 2021; 165:107300. [PMID: 34474153 DOI: 10.1016/j.ympev.2021.107300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 01/15/2023]
Abstract
In widespread species, the diverse ecological conditions in which the populations occur, and the presence of many potential geographical barriers through their range are expected to have created ample opportunities for the evolution of distinct, often cryptic lineages. In this work, we tested for species boundaries in one such widespread species, the king cobra, Ophiophagus hannah (Cantor, 1836), a largely tropical elapid snake distributed across the Oriental realm. Based on extensive geographical sampling across most of the range of the species, we initially tested for candidate species (CS) using Maximum-Likelihood analysis of mitochondrial genes. We then tested the resulting CS using both morphological data and sequences of three single-copy nuclear genes. We used snapclust to determine the optimal number of clusters in the nuclear dataset, and Bayesian Phylogenetics and Phylogeography (BPP) to test for likely species status. We used non-metric multidimensional scaling (nMDS) analysis for discerning morphological separation. We recovered four independently evolving, geographically separated lineages that we consider Confirmed Candidate Species: (1) Western Ghats lineage; (2) Indo-Chinese lineage (3) Indo-Malayan lineage; (4) Luzon Island lineage, in the Philippine Archipelago. We discuss patterns of lineage divergence, particularly in the context of low morphological divergence, and the conservation implications of recognizing several endemic king cobra lineages.
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Affiliation(s)
- P Gowri Shankar
- Maharaja Shrirama Chandra Bhanja Deo University, Baripada, Takatpur, Odisha, India; CES, Indian Institute of Science, Bangalore, India; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden; Kālinga Foundation, Agumbe, Karnataka, India.
| | | | - Rhiannon C Williams
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - S R Ganesh
- Chennai Snake Park, Raj Bhavan Post, Chennai, India
| | - Matt Moss
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Malaysia
| | | | | | | | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Sushil K Dutta
- Maharaja Shrirama Chandra Bhanja Deo University, Baripada, Takatpur, Odisha, India; Department of Zoology, Assam Don Bosco University, Tapesia, Assam, India
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18
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Patel NG, Garg S, Das A, Stuart BL, Biju S. Phylogenetic position of the poorly known montane cascade frog Amolops monticola (Ranidae) and description of a new closely related species from Northeast India. J NAT HIST 2021. [DOI: 10.1080/00222933.2021.1946185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Naitik G. Patel
- Department of Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
| | - Abhijit Das
- Department of Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Bryan L. Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - S.D. Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
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19
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A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida). Mol Phylogenet Evol 2021; 163:107240. [PMID: 34197900 DOI: 10.1016/j.ympev.2021.107240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 12/28/2022]
Abstract
There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.
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20
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Wikramanayake SA, Wikramanayake ED, Pallewatta N, Leaché AD. Integration of genetic structure into conservation of an endangered, endemic lizard,
Ceratophora aspera
: A case study from Sri Lanka. Biotropica 2021. [DOI: 10.1111/btp.12970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Shanelle A. Wikramanayake
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Washington, Seattle WA USA
| | | | - Nirmalie Pallewatta
- Department of Zoology and Environment Science Faculty of Science University of Colombo Colombo Sri Lanka
| | - Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Washington, Seattle WA USA
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21
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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: 2] [Impact Index Per Article: 0.7] [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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22
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Binks RM, Steane DA, Byrne M. Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris. Ecol Evol 2021; 11:5096-5110. [PMID: 34025994 PMCID: PMC8131811 DOI: 10.1002/ece3.7403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non-contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.
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Affiliation(s)
- Rachel M. Binks
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
| | - Dorothy A. Steane
- School of Natural Sciences and ARC Training Centre for Forest ValueUniversity of TasmaniaHobartTasmaniaAustralia
- CSIRO Land and WaterSandy BayTasmaniaAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
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23
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Davis HR, Das I, Leaché AD, Karin BR, Brennan IG, Jackman TR, Nashriq I, Onn Chan K, Bauer AM. Genetically diverse yet morphologically conserved: Hidden diversity revealed among Bornean geckos (Gekkonidae:
Cyrtodactylus
). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hayden R. Davis
- Department of Biology Burke Museum of Natural History and Culture University of Washington Seattle WA USA
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova PA USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan Malaysia
| | - Adam D. Leaché
- Department of Biology Burke Museum of Natural History and Culture University of Washington Seattle WA USA
| | - Benjamin R. Karin
- Department of Integrative Biology Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Ian G. Brennan
- Division of Ecology and Evolution Research School of Biology The Australian National University Canberra ACT Australia
| | - Todd R. Jackman
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova PA USA
| | - Izneil Nashriq
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan Malaysia
| | - Kin Onn Chan
- Lee Kong Chian Natural History Museum National University of Singapore Singapore
| | - Aaron M. Bauer
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova PA USA
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24
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Raposo MA, Kirwan GM, Lourenço ACC, Sobral G, Bockmann FA, Stopiglia R. On the notions of taxonomic ‘impediment’, ‘gap’, ‘inflation’ and ‘anarchy’, and their effects on the field of conservation. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1829157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marcos A. Raposo
- Setor de Ornitologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, Rio de Janeiro, 20940–040, RJ, Brazil
- UMR 8590, IHPST–Institut d'Histoire et de Philosophie des Sciences et des Techniques, UMR 8590, Université Paris 1, Panthéon-Sorbonne & CNRS, 13 rue du Four, Paris, 75006, France
| | - Guy M. Kirwan
- Setor de Ornitologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, Rio de Janeiro, 20940–040, RJ, Brazil
| | - Ana Carolina Calijorne Lourenço
- Departamento de Ciências Biológicas, Universidade do Estado de Minas Gerais, Campus Ubá, Av. Olegário Maciel, 1427, Ubá, 36502-000, MG, Brazil
| | - Gisela Sobral
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo, 05508-270, SP, Brazil
| | - Flávio Alicino Bockmann
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, 14040–901, SP, Brazil
- Programa de Pós-Graduação em Biologia Comparada, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, Paris, 14040-901, SP, Brazil
| | - Renata Stopiglia
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, 14040–901, SP, Brazil
- Institut de Systématique, Évolution, Biodiversité, ISYEB, UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP 30, Paris, F-75005, France
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25
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Salvi D, Mariottini P. Revision shock in Pacific oysters taxonomy: the genus Magallana (formerly Crassostrea in part) is well-founded and necessary. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The description of the genus Magallana provoked taxonomic ‘revision shock’ among Bayne and colleagues, who criticised: (1) the supporting evidence for this taxonomic change, (2) the procedure used and (3) its impact on the nomenclatural stability of oysters. Here, we demonstrate that the description of the genus Magallana fulfils the norms of taxonomic and indexing revisions, and is well-founded on a scientific basis. The clade named Magallana is supported by a robust phylogeny based on comprehensive taxon sampling, independent datasets and varied analytical methods. A new maximum likelihood phylogenetic analysis of oysters, based on mitochondrial gene order data (representing molecular phenotypes above the sequence level), has provided additional support for this classification. These results are fully consistent with all previously published phylogenetic studies, thus providing an unambiguous indication of the stability of the clade that meets all the currently accepted criteria for naming clades as taxa. We show that, while the criterion of ‘morphological diagnosability’ is not applicable at any level of oyster classification, several striking molecular phenotypes are diagnostic of Magallana, both at the nuclear and the mitochondrial genome level. The classification with three genera Magallana, Crassostrea and Talonostrea reflects the evolutionary diversity of Crassostreinae and is consistent with taxonomic ranking criteria adopted for other oyster subfamilies.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L’Aquila, Coppito, L’Aquila, Italy
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26
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Loureiro LO, Engstrom MD, Lim BK. Does evolution of echolocation calls and morphology in Molossus result from convergence or stasis? PLoS One 2020; 15:e0238261. [PMID: 32970683 PMCID: PMC7514107 DOI: 10.1371/journal.pone.0238261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022] Open
Abstract
Although many processes of diversification have been described to explain variation of morphological traits within clades that have obvious differentiation among taxa, not much is known about these patterns in complexes of cryptic species. Molossus is a genus of bats that is mainly Neotropical, occurring from the southeastern United States to southern Argentina, including the Caribbean islands. Molossus comprises some groups of species that are morphologically similar but phylogenetically divergent, and other groups of species that are genetically similar but morphologically distinct. This contrast allows investigation of unequal trait diversification and the evolution of morphological and behavioural characters. In this study, we assessed the role of phylogenetic history in a genus of bat with three cryptic species complexes, and evaluated if morphology and behavior are evolving concertedly. The Genotype by Sequence genomic approach was used to build a species-level phylogenetic tree for Molossus and to estimate the ancestral states of morphological and echolocation call characters. We measured the correlation of phylogenetic distances to morphological and echolocation distances, and tested the relationship between morphology and behavior when the effect of phylogeny is removed. Morphology evolved via a mosaic of convergence and stasis, whereas call design was influenced exclusively through local adaptation and convergent evolution. Furthermore, the frequency of echolocation calls is negatively correlated with the size of the bat, but other characters do not seem to be evolving in concert. We hypothesize that slight variation in both morphology and behaviour among species of the genus might result from niche specialization, and that traits evolve to avoid competition for resources in similar environments.
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Affiliation(s)
- Livia O. Loureiro
- Hospital for Sick Children SickKids Learning Institute, The Centre for Applied Genomics, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Mark D. Engstrom
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Burton K. Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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27
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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28
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Ramesh V, Vijayakumar SP, Gopalakrishna T, Jayarajan A, Shanker K. Determining levels of cryptic diversity within the endemic frog genera, Indirana and Walkerana, of the Western Ghats, India. PLoS One 2020; 15:e0237431. [PMID: 32877402 PMCID: PMC7467320 DOI: 10.1371/journal.pone.0237431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 07/28/2020] [Indexed: 01/24/2023] Open
Abstract
A large number of species in the tropics are awaiting discovery, many due to their cryptic morphology ie. lack of discernable morphological difference. We explored the presence of cryptic lineages within the frog genera, Indirana and Walkerana, which are endemic to the Western Ghats of Peninsular India. By reconstructing a phylogeny using 5 genes and robust geographic sampling, we delimited 19 lineages along a population—species continuum, using multiple criteria including haplotype clusters, genetic distance, morphological distinctness, and geographical separation. Of these 19 lineages, 14 belonged to the genus Indirana and 5 to the genus Walkerana. Divergence dating analyses revealed that the clade comprising Indirana and Walkerana began diversifying around 71 mya and the most recent common ancestor of Indirana and Walkerana split around 43 mya. We tested for the presence of cryptic lineages by examining the relationship between genetic and morphological divergence among related pairs within a pool of 15 lineages. The pairs showed strong morphological conservatism across varying levels of genetic divergence. Our results highlight the prevalence of morphologically cryptic lineages in these ancient endemic clades of the Western Ghats. This emphasizes the significance of other axes, such as geography, in species delimitation. With increasing threats to amphibian habitats, it is imperative that cryptic lineages are identified so that appropriate conservation measures can be implemented.
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Affiliation(s)
- Vijay Ramesh
- Department of Ecology, Evolution & Environmental Biology, Columbia University, New York, NY, United States of America
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail:
| | - S. P. Vijayakumar
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Trisha Gopalakrishna
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Aditi Jayarajan
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
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29
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Lima LR, Bruschi DP, Do Nascimento FAC, Scherrer De Araújo PV, Costa LP, Thomé MTC, Garda AA, Zattera ML, Mott T. Below the waterline: cryptic diversity of aquatic pipid frogs (Pipa carvalhoi) unveiled through an integrative taxonomy approach. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1795742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Luana Rodrigues Lima
- Programa de Pós-Graduação em Diversidade Biológica e Conservação nos Trópicos, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
| | - Daniel Pacheco Bruschi
- Programa de Pós-graduaçäo em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Filipe Augusto Cavalcanti Do Nascimento
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
- Setor de Herpetologia, Museu de História Natural, Universidade Federal de Alagoas, Maceió, 57010-020, Alagoas, Brasil
| | - Paulo Victor Scherrer De Araújo
- Programa de Pós-Graduação em Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo, Vitória, 29075-910, Espírito Santo, Brasil
| | - Leonora Pires Costa
- Programa de Pós-Graduação em Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo, Vitória, 29075-910, Espírito Santo, Brasil
| | - Maria Tereza Chiarioni Thomé
- Programa de Pós-Graduação em Diversidade Biológica e Conservação nos Trópicos, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, 59072-970, Rio Grande do Norte, Brasil
| | - Michelle Louise Zattera
- Programa de Pós-graduaçäo em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Tamí Mott
- Programa de Pós-Graduação em Diversidade Biológica e Conservação nos Trópicos, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, 57072-900, Alagoas, Brasil
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Othman SN, Chen YH, Chuang MF, Andersen D, Jang Y, Borzée A. Impact of the Mid-Pleistocene Revolution and Anthropogenic Factors on the Dispersion of Asian Black-Spined Toads ( Duttaphrynus melanostictus). Animals (Basel) 2020; 10:E1157. [PMID: 32650538 PMCID: PMC7401666 DOI: 10.3390/ani10071157] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 11/28/2022] Open
Abstract
Divergence-time estimation critically improves the understanding of biogeography processes underlying the distribution of species, especially when fossil data is not available. We hypothesise that the Asian black-spined toad, Duttaphrynus melanostictus, expanded into the Eastern Indomalaya following the Quaternary glaciations with the subsequent colonisation of new landscapes during the Last Glacial Maximum. Divergence dating inferred from 364 sequences of mitochondrial tRNAGly ND3 supported the emergence of a common ancestor to the three D. melanostictus clades around 1.85 (±0.77) Ma, matching with the Lower to Mid-Pleistocene transition. Duttaphrynus melanostictus then dispersed into Southeast Asia from the central Indo-Pacific and became isolated in the Southern Sundaic and Wallacea regions 1.43 (±0.10) Ma through vicariance as a result of sea level oscillations. The clade on the Southeast Asian mainland then colonised the peninsula from Myanmar to Vietnam and expanded towards Southeastern China at the end of the Mid-Pleistocene Revolution 0.84 (±0.32) Ma. Population dynamics further highlight an expansion of the Southeast Asian mainland population towards Taiwan, the Northeastern edge of the species' range after the last interglacial, and during the emergence of the Holocene human settlements around 7000 BP. Thus, the current divergence of D. melanostictus into three segregated clades was mostly shaped by Quaternary glaciations, followed by natural dispersion events over land bridges and accelerated by anthropogenic activities.
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Affiliation(s)
- Siti N. Othman
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yi-Huey Chen
- Department of Life Science, Chinese Culture University, Taipei 11114, Taiwan;
| | - Ming-Feng Chuang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Desiree Andersen
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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31
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Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T. Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. Zookeys 2020; 935:121-164. [PMID: 32508505 PMCID: PMC7256073 DOI: 10.3897/zookeys.935.37138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/28/2020] [Indexed: 11/12/2022] Open
Abstract
The Tylototritonasperrimus complex from northern Vietnam is reviewed based on morphological comparisons and analysis of the mitochondrial marker NADH dehydrogenase subunit 2 (ND2). Based on molecular divergences, which were revealed to be higher than in other congeners, in concert with morphological differences, two new species and one subspecies are described herein: Tylototritonpasmansisp. nov. differs from T.asperrimussensu stricto by 3.2 to 3.6 % genetic divergence and a combination of distinct morphological characters, such as head slightly longer than wide, distinct mid-dorsal ridge, relatively wide distance between the eyes, tips of fingers reaching the eye when foreleg is laid forward, labial and gular folds present, central belly skin with tubercles shaped like transverse wrinkles and distinct, pointy to round rib nodules. The population of T.pasmansisp. nov. consists of two subclades, the nominotypic one occurring on the eastern side of the Da River (or Black River, including Hoa Binh and Phu Tho provinces), and another occurring on the western side (including Son La and Thanh Hoa provinces). These two subclades differ by 2.5 to 3.1 % genetic divergence and distinct morphological characters. The western subclade is herein described as Tylototritonpasmansiobstissp. nov., which differs from the nominotypic form by a wider head, longer and narrower snout, shorter femur length, and an overall less granulose skin, without an increased concentration of warts on the body sides. A second new species, Tylototritonsparreboomisp. nov. is described from Lai Chau Province. It differs from T.asperrimussensu stricto by 4.1 to 4.2 % and from Tylototritonpasmansisp. nov. by 3.6 to 4.5 % genetic divergences as well as by a combination of distinct morphological characters, such as head longer than wide, tips of fingers reaching nostril when foreleg adpressed along head, rib nodules distinct, round and relatively enlarged, and wide distance between the eyes.
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Affiliation(s)
- Marta Bernardes
- Cologne Zoo, Riehler Str. 173, 50735 Cologne, Germany Cologne Zoo Cologne Germany.,Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany University of Cologne Cologne Germany
| | - Minh Duc Le
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Road, Hanoi, Vietnam University of Science Hanoi Vietnam.,Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hanoi, Vietnam Vietnam National University Hanoi Vietnam.,Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA American Museum of Natural History New York United States of America
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam Graduate University of Science and Technology Hanoi Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Cuong The Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam Graduate University of Science and Technology Hanoi Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Anh Van Pham
- Faculty of Natural Science and Technology, Tay Bac University, Quyet Tam Ward, Son La City, Son La Province, Vietnam Tay Bac University Son La City Vietnam
| | - Tao Thien Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam Vietnam Academy of Science and Technology Hanoi Vietnam.,Vietnam National Museum of Nature, 18 Hoang Quoc Viet St., Hanoi, Vietnam Vietnam National Museum of Nature Hanoi Vietnam
| | - Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany Zoologisches Forschungsmuseum Alexander Koenig Bonn Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany University of Cologne Cologne Germany
| | - Thomas Ziegler
- Cologne Zoo, Riehler Str. 173, 50735 Cologne, Germany Cologne Zoo Cologne Germany.,Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany University of Cologne Cologne Germany
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Barley AJ, Diesmos AC, Siler CD, Martinez CM, Brown RM. Taxonomic Revision of Philippine Sun Skinks (Reptilia: Squamata: Scincidae: Eutropis), and Descriptions of Eight New Species. HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/herpmonographs-d-19-00009.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Biology, University of Hawai‘i, Honolulu, HI 96822, USA
| | | | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA
| | | | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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de Oliveira EA, da Silva LA, Silva EAP, Guimarães KLA, Penhacek M, Martínez JG, Rodrigues LRR, Santana DJ, Hernández-Ruz EJ. Four new species of Pristimantis Jiménez de la Espada, 1870 (Anura: Craugastoridae) in the eastern Amazon. PLoS One 2020; 15:e0229971. [PMID: 32187206 PMCID: PMC7080247 DOI: 10.1371/journal.pone.0229971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/16/2020] [Indexed: 12/02/2022] Open
Abstract
The Pristimantis genus (Anura: Craugastoridae) is the most diverse among all vertebrates with 531 described species. The highest diversity occurs in Ecuador (215 species), followed by Colombia (202), Peru (139), Venezuela (60), Brazil (30), Bolivia (17), Guyana (6) Suriname and French Guiana (5). The genus is divided into 11 species groups. Of these, the P. conspicillatus group (containing 34 species), distributed in extreme southeastern Costa Rica, Isla Taboga (Panama), northern South America (from Colombia to eastern Guyana), south Bolivia, and is the best represented in Brazil (16 species). The main characteristics of this group are the tympanic membrane and tympanic annulus distinct (except in P. johannesdei); dorsum smooth or shagreen; dorsal lateral fold present or absent; usually smooth belly, but may be weakly granular in some species; toe V slightly larger than the toe III. Most of the taxonomic inconsistencies in species of Pristimantis could be due to its much conserved morphology and the lack of comprehensive taxonomic evaluations. Thus, an ongoing challenge for taxonomists dealing with the Pristimantis genus is the ubiquitous abundance of cryptic species. In this context, accurate species delimitation should integrate evidences of morphological, molecular, bioacoustics and ecological data, among others. Based on an integrative taxonomy perspective, we utilize morphological, molecular (mtDNA) and bioacoustic evidence to describe four new species of the Pristimantis conspicillatus group from the eastern Amazon basin. Pristimantis giorgiisp. nov. is known from the Xingu/Tocantins interfluve and can be distinguished from the other Pristimantis species of the region by presenting discoidal fold, dorsolateral fold absent, vocalization composed of three to four notes and genetic distance of 7.7% (16S) and 14.8% (COI) from P. latro, the sister and sympatric species with respect P. giorgiisp. nov.. Pristimantis pictussp. nov. is known to the northern Mato Grosso state, Brazil, and can be distinguished from the other species of Pristimantis by presenting the posterior surface of the thigh with light yellow patches on a brown background, also extending to the inguinal region, vocalization consisting of four to five notes and a genetic distance of 11.6% (16S) and 19.7% (COI) from P. pluviansp. nov., which occurs in sympatry. Pristimantis pluviansp. nov. is known to the northern Mato Grosso state, Brazil, and may be distinguished from the other Pristimantis species by having a posterior surface of the thigh reddish and vocalization composed of two notes. Pristimantis moasp. nov. is known to the northern Tocantins state and southwestern Maranhão state. This species can be distinguished from the other Pristimantis species by possessing slightly perceptible canthal stripe, external thigh surface with dark yellow spots on brown background, vocalization consisting of three to five notes and genetic distance of 2.3–11.7 (16S) and 10.5–23.1 (COI) for the new Pristimantis species of this study.
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Affiliation(s)
- Elciomar Araújo de Oliveira
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal do Amazonas, Manaus, Brazil
- * E-mail:
| | - Leandro Alves da Silva
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Elvis Almeida Pereira Silva
- Laboratório de Herpetologia, Departamento de Biologia Animal, Programa de Pós-Graduação em Biologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
- Mapinguari—Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Mato Grosso do Sul, Brazil
- Technische Universität Braunschweig, Zoological Institute, Braunschweig, Alemanha
| | - Karen Larissa Auzier Guimarães
- Programa de Pós-graduação em Recursos Naturais da Amazônia, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
- Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
| | - Marcos Penhacek
- Instituto de Ciências Naturais, Humanas e Sociais e Acervo Biológico da Amazônia Meridional–ABAM, Universidade Federal de Mato Grosso, Sinop, Mato Grosso, Brazil
| | - José Gregório Martínez
- Grupo de Investigación Biociencias, Facultad de Ciencias de la Salud, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia
| | - Luís Reginaldo Ribeiro Rodrigues
- Programa de Pós-graduação em Recursos Naturais da Amazônia, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
- Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
| | - Diego José Santana
- Mapinguari—Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Mato Grosso do Sul, Brazil
| | - Emil José Hernández-Ruz
- Laboratório de Zoologia Adriano Giorgi, Programa de Pós-Graduação em Biodiversidade e Conservação, Campus Universitário de Altamira, Universidade Federal do Pará, Altamira, Pará, Brazil
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34
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Wang D, Gao L, Tian H, Dong W, Duan X, Liu S, Chen D. Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA. Ecol Evol 2020; 10:50-58. [PMID: 31993113 PMCID: PMC6972953 DOI: 10.1002/ece3.5746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/02/2022] Open
Abstract
The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.
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Affiliation(s)
- Dengqiang Wang
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Lei Gao
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Huiwu Tian
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Weiwei Dong
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
- School of Life ScienceSouthwest UniversityChongqingChina
| | - Xinbin Duan
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Shaoping Liu
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Daqing Chen
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
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Patton A, Apodaca JJ, Corser JD, Wilson CR, Williams LA, Cameron AD, Wake DB. A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species. COPEIA 2019. [DOI: 10.1643/ch-18-052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Austin Patton
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Joseph J. Apodaca
- Amphibian and Reptile Conservancy and Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806; . Send reprint requests to this address
| | - Jeffrey D. Corser
- New York Natural Heritage Program, SUNY College of Environmental Science and Forestry, 625 Broadway, 5th Floor, Albany, New York 12233
| | | | - Lori A. Williams
- North Carolina Wildlife Resources Commission, 177 Mountain Laurel Lane, Fletcher, North Carolina 28732
| | - Alan D. Cameron
- North Carolina Wildlife Resources Commission, 177 Mountain Laurel Lane, Fletcher, North Carolina 28732
| | - David B. Wake
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160
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Yodthong S, Stuart BL, Aowphol A. Species delimitation of crab-eating frogs ( Fejervarya cancrivora complex) clarifies taxonomy and geographic distributions in mainland Southeast Asia. Zookeys 2019; 883:119-153. [PMID: 31719776 PMCID: PMC6828825 DOI: 10.3897/zookeys.883.37544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/21/2019] [Indexed: 12/02/2022] Open
Abstract
The taxonomy and geographic distributions of species of crab-eating frogs (Fejervaryacancrivora complex) in mainland Southeast Asia have been highly uncertain. Three taxonomic names are used in recent literature (F.cancrivora, F.raja, and F.moodiei) but the applications of these names to localities has been inconsistent, especially owing to the lack of available molecular data for F.raja. Morphometric and mitochondrial DNA variation was examined in these frogs, including name-bearing types and topotypes of all three species. Findings corroborate evidence for the existence of two species in coastal mainland Southeast Asia, with F.moodiei having a wide geographic distribution and F.cancrivora sensu stricto occurring only in extreme southern Thailand and peninsular Malaysia. Fejervaryaraja is shown to be only a large-bodied population of F.cancrivora sensu stricto and is synonymized with that species. Revised descriptions of F.moodiei and F.cancrivora sensu stricto are provided.
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Affiliation(s)
- Siriporn Yodthong
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand Kasetsart University Bangkok Thailand
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA North Carolina Museum of Natural Sciences Raleigh United States of America
| | - Anchalee Aowphol
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand Kasetsart University Bangkok Thailand
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von Oheimb KCM, von Oheimb PV, Hirano T, Do TV, Ablett J, Luong HV, Pham SV, Naggs F. Cryptic diversity of limestone karst inhabiting land snails (Cyclophorus spp.) in northern Vietnam, their evolutionary history and the description of four new species. PLoS One 2019; 14:e0222163. [PMID: 31644567 PMCID: PMC6808330 DOI: 10.1371/journal.pone.0222163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Limestone karsts can form terrestrial habitat islands for calcium-dependent organisms. In Vietnam, many karst habitats are threatened, while their rich biodiversity is still far from being thoroughly explored. Given that conservation of karst biota strongly relies on correct species identification, the presence of undetected cryptic species can pose severe problems. The present study focuses on cryptic diversity among karst-inhabiting land snails of the genus Cyclophorus in northern Vietnam, where specimens with a similar shell morphology have been reported from various regions. In order to examine the diversity and evolutionary history of this “widespread morphotype”, we generated a Bayesian phylogeny based on DNA sequence data. Automatic Barcode Gap Discovery (ABGD) and the Bayesian implementation of the Poisson tree processes model (bPTP) contributed to species delimitation and analyses of shell shape and size aided the morphological characterisation of individual species. We found that the examined specimens of the widespread morphotype did not form a single monophyletic group in the phylogeny but clustered into several different clades. We delimited nine different species that develop the widespread morphotype and described four of them as new. Processes of convergent evolution were probably involved in the origin of the delimited species, while their generally allopatric distribution could result from interspecific competition. Our findings indicate ongoing processes of speciation and a potential case of morphological character displacement. The high degree of morphological overlap found among the species underlines the importance of DNA sequence data for species delimitation and description in the genus Cyclophorus. Given the findings of the present study and the high potential that as yet undiscovered cryptic taxa have also evolved in other groups of karst-inhabiting organisms, we argue for a systematic and efficient detection and description of Vietnam’s karst biodiversity to provide a solid basis for future conservation planning.
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Affiliation(s)
- Katharina C. M. von Oheimb
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- * E-mail:
| | - Parm Viktor von Oheimb
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Takahiro Hirano
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tu Van Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Jonathan Ablett
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
| | - Hao Van Luong
- Centre for Rescue and Conservation of Organisms, Hoang Lien National Park, Sa Pa, Vietnam
| | - Sang Van Pham
- Department of Specimen Preparation and Exhibitive Design, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Fred Naggs
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
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Zozaya SM, Higgie M, Moritz C, Hoskin CJ. Are Pheromones Key to Unlocking Cryptic Lizard Diversity? Am Nat 2019; 194:168-182. [DOI: 10.1086/704059] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Cryer J, Wynne F, Price SJ, Puschendorf R. Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae). Zookeys 2019; 838:49-69. [PMID: 31048968 PMCID: PMC6477815 DOI: 10.3897/zookeys.838.29635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.
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Affiliation(s)
- James Cryer
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UK University of Plymouth Plymouth United Kingdom
| | - Felicity Wynne
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UK University of Plymouth Plymouth United Kingdom
| | - Stephen J Price
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK UCL Genetics Institute London United Kingdom.,Institute of Zoology, ZSL, Regents Park, London NW1 4RY, UK Institute of Zoology, ZSL London United Kingdom
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UK University of Plymouth Plymouth United Kingdom
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Chan KO, Grismer LL. To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae). BMC Evol Biol 2019; 19:95. [PMID: 31023232 PMCID: PMC6485082 DOI: 10.1186/s12862-019-1422-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
Background Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index (gdi) was shown to be a viable alternative, especially for delimiting allopatric populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes. Results Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (< 3%) and consistent with intraspecific divergences of other closely related taxa. The BPP analysis produced variable results depending on prior settings and priors estimated from empirical data produced the best results that were also congruent with the gdi analysis. Conclusions This study showed that the evolutionary history of Southeast Asian toads is difficult to resolve and numerous relationships remain ambiguous. Although some results from the species delimitation analyses were inconclusive, they were nevertheless efficacious at identifying potential new species and taxonomic incompatibilities for future in-depth investigation. We also demonstrated the sensitivity of BPP to different priors and that careful selection priors based on empirical data can greatly improve the analysis. Finally, the gdi can be a robust tool to complement other species delimitation methods. Electronic supplementary material The online version of this article (10.1186/s12862-019-1422-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore, 117377, Singapore.
| | - L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA, 92515, USA
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Gao YD, Gao XF, Harris A. Species Boundaries and Parapatric Speciation in the Complex of Alpine Shrubs, Rosa sericea (Rosaceae), Based on Population Genetics and Ecological Tolerances. FRONTIERS IN PLANT SCIENCE 2019; 10:321. [PMID: 30936888 PMCID: PMC6432857 DOI: 10.3389/fpls.2019.00321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 02/27/2019] [Indexed: 06/01/2023]
Abstract
Discerning species boundaries among closely related taxa is fundamental to studying evolution and biodiversity. However, species boundaries can be difficult to access in plants because ongoing divergence and speciation may leave an evolutionary footprint similar to introgression, which occurs frequently among species and genera. In this study, we sought to determine species boundaries between two closely related alpine shrubs, Rosa sericea and Rosa omeiensis, using population genetics, environmental data and ecological niche modeling, and morphological traits. We analyzed populations of R. sericea and R. omeiensis using genetic markers comprising a fragment of the single-copy nuclear gene, LEAFY, micro-satellites (EST-SSR), and plastid DNA sequences. The DNA sequence data suggested clusters of populations consistent with geography but not with previously proposed species boundaries based on morphology. Nevertheless, we found that the ecological niches of the previously proposed species only partially overlap. Thus, we suspect that these species are in the process of parapatric speciation; that is, differentiating along an ecological gradient, so that they exhibit differing morphology. Morphology has previously been the basis of recognizing the species R. sericea and R. omeiensis, which are the most widely distributed species within a broader R. sericea complex that includes several other narrow endemics. Here, we recognize R. sericea and R. omeiensis as independent species based on morphological and ecological data under the unified species concept, which emphasizes that these data types are of equal value to DNA for determining species boundaries and refining taxonomic treatments. While the DNA data did not delimit species within the R. sericea complex, we expect to develop and utilize new, robust DNA tools for understanding speciation within this group in future studies.
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Affiliation(s)
- Yun-Dong Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Aj Harris
- Oberlin College and Conservatory, Department of Biology, Oberlin, OH, United States
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Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches. Mol Phylogenet Evol 2019; 132:105-116. [DOI: 10.1016/j.ympev.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022]
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Ward CM, Baxter SW. Assessing Genomic Admixture between Cryptic Plutella Moth Species following Secondary Contact. Genome Biol Evol 2018; 10:2973-2985. [PMID: 30321345 PMCID: PMC6250210 DOI: 10.1093/gbe/evy224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2018] [Indexed: 12/30/2022] Open
Abstract
Cryptic species are genetically distinct taxa without obvious variation in morphology and are occasionally discovered using molecular or sequence data sets of populations previously thought to be a single species. The world-wide Brassica pest, Plutella xylostella (diamondback moth), has been a problematic insect in Australia since 1882, yet a morphologically cryptic species with apparent endemism (P. australiana) was only recognized in 2013. Plutella xylostella and P. australiana are able to hybridize under laboratory conditions, and it was unknown whether introgression of adaptive traits could occur in the field to improve fitness and potentially increase pressure on agriculture. Phylogenetic reconstruction of 29 nuclear genomes confirmed P. xylostella and P. australiana are divergent, and molecular dating with 13 mitochondrial genes estimated a common Plutella ancestor 1.96 ± 0.175 Ma. Sympatric Australian populations and allopatric Hawaiian P. xylostella populations were used to test whether neutral or adaptive introgression had occurred between the two Australian species. We used three approaches to test for genomic admixture in empirical and simulated data sets including 1) the f3 statistic at the level of the population, 2) pairwise comparisons of Nei's absolute genetic divergence (dXY) between populations, and 3) changes in phylogenetic branch lengths between individuals across 50-kb genomic windows. These complementary approaches all supported reproductive isolation of the Plutella species in Australia, despite their ability to hybridize. Finally, we highlight the most divergent genomic regions between the two cryptic Plutella species and find they contain genes involved with processes including digestion, detoxification, and DNA binding.
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Affiliation(s)
- Christopher M Ward
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Australia
| | - Simon W Baxter
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Australia
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Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae). Mol Phylogenet Evol 2018; 129:214-225. [PMID: 30189319 DOI: 10.1016/j.ympev.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022]
Abstract
Accurate representation of lineage diversity through complete taxon sampling is crucial to understanding the evolution of biodiversity, particularly when using molecular phylogenetics to estimate evolutionary relationships. In this interest, taxonomic diversity is often used as a proxy for lineage diversity even though the two concepts are not synonymous. We explore this within the snake tribe Lampropeltini which includes some of the most conspicuous and heavily studied snakes in North America. Both the taxonomy and hypothesized relationships within this tribe have been in flux. The number of species has increased from 23 to 51 over the last thirty years, predominately within three of the nine genera (Lampropeltis, Pantherophis, Pituophis). The remaining six depauperate genera (Arizona, Bogertophis, Cemophora, Pseudelaphe, Rhinocheilus, and Senticolis) have been poorly represented in phylogenetic studies. To estimate evolutionary relationships and determine if the dichotomy in depauperate and speciose genera within Lampropeltini is a function of taxon sampling or truly represents the lineage diversity, we estimated the phylogeny of this group using nuclear and mitochondrial loci in a concatenated and coalescent framework with the largest sampling of the six depauperate genera to date. In addition, we estimated the divergence dates among the genera to assess whether the instability of Lampropeltini phylogenetic relationships is due to an adaptive radiation. While some nodes still remain unresolved, the generic-level relationships we recovered agree with those of a recent next-generation study that used a much larger set of loci for fewer individuals. We also tested two putative species, Arizona pacata and Pseudelaphe phaescens, for the first time phylogenetically and find evidence that they are distinct lineages. Overall, we find that the taxonomic and genetic diversity are not correlated in Lampropeltini and that representing putative diversity in phylogenies will lead to a better estimate of evolutionary histories, especially in groups with complex radiations.
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Laska A, Majer A, Szydło W, Karpicka-Ignatowska K, Hornyák M, Labrzycka A, Skoracka A. Cryptic diversity within grass-associated Abacarus species complex (Acariformes: Eriophyidae), with the description of a new species, Abacarus plumiger n. sp. EXPERIMENTAL & APPLIED ACAROLOGY 2018; 76:1-28. [PMID: 30171478 DOI: 10.1007/s10493-018-0291-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 05/20/2023]
Abstract
Accurate estimation of species richness is often complex as genetic divergence is not always accompanied by appreciable morphological differentiation. In consequence, cryptic lineages or species evolve. Cryptic speciation is common especially in taxa characterized by small and simplified bodies, what makes their proper identification challenging. The cereal rust mite, Abacarus hystrix, was regarded for a long time as a species associated with a wide range of grass hosts, whereas wide host ranges are rather rare in eriophyoid mites. Therefore, the generalist status of A. hystrix was questioned. In this paper we demonstrate that the diversity within Abacarus species associated with grasses is more complex than it was previously thought. The 78 Abacarus mtDNA COI sequences used in this study formed 10 highly supported clades (bootstrap value 99%) and four more distinct genetic lineages were represented by unique sequences. The genetic distances between them ranged from 6.6 to 26.5%. Moreover, morphological study and genetic approach based on the combination of the Poisson Tree Processes model for species delimitation (PTP) and a Bayesian implementation of PTP (bPTP), and Neighbour Joining analyses led to delimitation of a new species within the Abacarus complex: Abacarus plumiger, specialized on smooth brome (Bromus inermis). Furthermore, our analyses demonstrated a pattern of host-associated differentiation within the complex. Overall, our study indicates that cryptic speciation occurs in the grass-associated Abacarus genus, and suggests the need for more extensive sampling using integrative methods.
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Affiliation(s)
- Alicja Laska
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland.
| | - Agnieszka Majer
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Wiktoria Szydło
- Department of Entomology, University of Nebraska-Lincoln, 103 Entomology Hall, Lincoln, NE, 68583-0816, USA
| | - Kamila Karpicka-Ignatowska
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Marta Hornyák
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland
| | - Anna Labrzycka
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
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Székely P, Eguiguren JS, Székely D, Ordóñez-Delgado L, Armijos-Ojeda D, Riofrío-Guamán ML, Cogălniceanu D. A new minute Pristimantis (Amphibia: Anura: Strabomantidae) from the Andes of southern Ecuador. PLoS One 2018; 13:e0202332. [PMID: 30157209 PMCID: PMC6114709 DOI: 10.1371/journal.pone.0202332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/31/2018] [Indexed: 11/18/2022] Open
Abstract
We describe a new rainfrog species (Pristimantis), from the wetland complex Oña, Nabón, Saraguro and Yacuambi, in the Andes of southern Ecuador, at altitudes ranging between 3000–3400 m a.s.l. Pristimantis tiktik sp. nov. is a small frog, displaying sexual dimorphism (the males with dorsum of various shades of gray, brown, orange or green and a whitish or pinkish yellow venter; females with brownish gray or gray dorsum and a reticulated white and black venter), with SVL ranging between 19.7–20.4 mm in females (n = 3) and 16.1–18.4 mm in males (n = 6). The skin on dorsum is tuberculated, that on venter is coarsely areolate, dorsolateral folds are absent, tympanic membrane is absent but the tympanic annulus is evident, cranial crests are absent, discs on fingers just slightly expanded, heel is lacking enlarged tubercles, inner edge of tarsus is bearing a long fold, Toe V is slightly longer than Toe III and the iris coloration is bronze with fine black reticulations. The males have a large subgular vocal sac that extends onto the chest and vocal slits but lack nuptial pads. The unique advertisement call consists of long duration series of periodically repeated clicks: “tik”. Molecular analyses place the new species in the recently resurrected P. orestes group, as the sister species of the assemblage that contains P. bambu, P. mazar, P. simonbolivari and an undescribed species.
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Affiliation(s)
- Paul Székely
- Universidad Técnica Particular de Loja, Departamento de Ciencias Biológicas, EcoSs Lab, San Cayetano Alto, calle Marcelino Champagnat s/n, Loja, Ecuador
- Association Chelonia Romania, Bucharest, Romania
| | - Juan Sebastián Eguiguren
- Universidad Técnica Particular de Loja, Departamento de Ciencias Biológicas, EcoSs Lab, San Cayetano Alto, calle Marcelino Champagnat s/n, Loja, Ecuador
| | - Diana Székely
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Group, Freshwater and OCeanic Science Unit of ReSearch (FOCUS), University of Liège, Liège, Belgium
- * E-mail:
| | - Leonardo Ordóñez-Delgado
- Universidad Técnica Particular de Loja, Departamento de Ciencias Biológicas, EcoSs Lab, San Cayetano Alto, calle Marcelino Champagnat s/n, Loja, Ecuador
| | - Diego Armijos-Ojeda
- Universidad Técnica Particular de Loja, Departamento de Ciencias Biológicas, EcoSs Lab, San Cayetano Alto, calle Marcelino Champagnat s/n, Loja, Ecuador
| | - María Lorena Riofrío-Guamán
- Universidad Técnica Particular de Loja, Departamento de Ciencias Biológicas, EcoSs Lab, San Cayetano Alto, calle Marcelino Champagnat s/n, Loja, Ecuador
| | - Dan Cogălniceanu
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania
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47
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Kizirian D, Truong NQ, Ngo HT, Le MD. Parahelicops, Pararhabdophis,Paraphyly: Phylogenetic Relationships among Certain Southeast Asian Natricine Snakes (Hebius). AMERICAN MUSEUM NOVITATES 2018. [DOI: 10.1206/3906.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- David Kizirian
- Division of Vertebrate Zoology, American Museum of Natural History
| | - Nguyen Quang Truong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology
| | - Hanh Thi Ngo
- Faculty of Biology, Hanoi University of Science, Vietnam National University
| | - Minh Duc Le
- Division of Vertebrate Zoology, American Museum of Natural History
- Faculty of Environmental Sciences, Hanoi University of Science, Vietnam National University
- Central Institute for Natural Resources and Environmental Studies, Hanoi National University
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48
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Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae). Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.02.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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49
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Rujirawan A, Stuart BL, Aowphol A. Expanded description of Odorrana livida (Blyth, 1856) with notes on its natural history in Thailand. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1481236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Attapol Rujirawan
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Bryan L. Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Anchalee Aowphol
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
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50
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Phylogenetic relationships and cryptic species diversity in the Brazilian egg-brooding tree frog, genus Fritziana Mello-Leitão 1937 (Anura: Hemiphractidae). Mol Phylogenet Evol 2018; 123:59-72. [DOI: 10.1016/j.ympev.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 02/11/2018] [Accepted: 02/11/2018] [Indexed: 11/23/2022]
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