1
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Sitam FT, Salgado‐Lynn M, Denel A, Panjang E, McEwing R, Lightson A, Ogden R, Maruji NA, Yahya NK, Ngau C, Mohd Kulaimi NA, Ithnin H, Rovie‐Ryan J, Abu Bakar MS, Ewart KM. Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics. Ecol Evol 2023; 13:e10373. [PMID: 37593756 PMCID: PMC10427774 DOI: 10.1002/ece3.10373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023] Open
Abstract
The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the 'out of Borneo hypothesis', whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.
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Affiliation(s)
- Frankie T. Sitam
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Milena Salgado‐Lynn
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | - Azroie Denel
- Sarawak Forestry Corporation (SFC)KuchingMalaysia
| | - Elisa Panjang
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies and the Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Nur Alwanie Maruji
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Sabah Wildlife Department (SWD)Kota KinabaluMalaysia
| | - Nurhartini Kamalia Yahya
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
| | - Cosmas Ngau
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Noor Azleen Mohd Kulaimi
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Hartini Ithnin
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | | | | | - Kyle M. Ewart
- TRACE Wildlife Forensics NetworkEdinburghUK
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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2
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Balakirev AE, Abramov AV, Phuong BX, Rozhnov VV. Natural Diversity and Phylogeny of Asian Red-Cheeked Squirrels (Rodentia, Sciuridae, Dremomys) in Eastern Indochina. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Based on new molecular data for mitochondrial (Cyt b) and nuclear (IRBP, RAG1) genes, as well as an extensive analysis of morphological material, we accessed actual species taxonomy and relationships among Asian red-cheeked squirrels Dremomys distributed in eastern Indochina and southern China. Phylogenetic analyses demonstrated that Asian red-cheeked squirrels, which are currently attributed to D. rufigenis, are not homogenic but instead consisted of two independent species-level clades—northern and south-central. The latter clade was additionally subdivided into two highly divergent clades based on Cyt b gene phylogeny. In spite of multidimensional statistics approach applied (PCA) only minor cranial differences were found between populations of study what lay a basis to treat it as cryptic species. Based on our findings, red-cheeked squirrels inhabit northern Vietnam and southern China, which are usually attributed to D. rufigenis, should be treated as distinct genetic species D. ornatus Thomas, 1914. In ones turn, based on its peculiar external morphology we can attribute the specimens from southern and central Vietnam to D. rufigenis proper and treat them as D. rufigenisfuscus Bonhote, 1907 and D. r. laomache Bonhote, 1921, respectively.
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3
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Hinckley A, Camacho-Sanchez M, Ruedi M, Hawkins MTR, Mullon M, Cornellas A, Tuh Yit Yuh F, Leonard JA. Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Abstract
The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.
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Affiliation(s)
- Arlo Hinckley
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA) Centro Las Torres, Alcalá del Río, Spain
| | | | - Melissa T R Hawkins
- National Museum of Natural History, Department of Vertebrate Zoology, Smithsonian Institution, USA
| | | | - Anna Cornellas
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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4
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Jackson SM, Li Q, Wan T, Li XY, Yu FH, Gao G, He LK, Helgen KM, Jiang XL. Across the great divide: revision of the genus Eupetaurus (Sciuridae: Pteromyini), the woolly flying squirrels of the Himalayan region, with the description of two new species. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The woolly flying squirrel, Eupetaurus cinereus, is among the rarest and least studied mammals in the world. For much of the 20th century it was thought to be extinct, until it was rediscovered in 1994 in northern Pakistan. This study outlines the first taxonomic and biogeographical review of the genus Eupetaurus, which until now has contained only a single species. Careful review of museum specimens and published records of Eupetaurus demonstrates that the genus occurs in three widely disjunct areas situated on the western (northern Pakistan and north-western India), north-central (south-central Tibet, northern Sikkim and western Bhutan) and south-eastern margins (north-western Yunnan, China) of the Himalayas. Taxonomic differentiation between these apparently allopatric populations of Eupetaurus was assessed with an integrative approach involving both morphological examinations and molecular phylogenetic analyses. Phylogenetic reconstruction was implemented using sequences of three mitochondrial [cytochrome b (Cytb), mitochondrially encoded 12S and 16S ribosomal RNA (12S, 16S)] and one nuclear [interphotoreceptor retinoid-binding protein (IRBP)] gene fragment. Morphological assessments involved qualitative examinations of features preserved on museum skins and skulls, supplemented with principal components analysis of craniometric data. Based on genetic and morphological comparisons, we suggest that the three widely disjunct populations of Eupetaurus are each sufficiently differentiated genetically and morphologically to be recognized as distinct species, two of which are described here as new.
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Affiliation(s)
- Stephen M Jackson
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange Agricultural Institute, 1447 Forest Road,Orange, NSW 2800, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
| | - Quan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi 710119, China
| | - Xue-You Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Fa-Hong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Ge Gao
- Baoshan Management Bureau of Gaoligongshan National Nature Reserve, Baoshan, Yunnan 678000, China
| | - Li-Kun He
- Gongshan Management Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan 673500, China
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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5
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Camacho-Sanchez M, Leonard JA. Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland. J Hered 2021; 111:392-404. [PMID: 32485737 PMCID: PMC7423070 DOI: 10.1093/jhered/esaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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6
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Menéndez I, Gómez Cano AR, Cantalapiedra JL, Peláez‐Campomanes P, Álvarez‐Sierra MÁ, Hernández Fernández M. A multi‐layered approach to the diversification of squirrels. Mamm Rev 2020. [DOI: 10.1111/mam.12215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
| | | | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, GloCEE Global Change Ecology and Evolution Research Group Universidad de Alcalá Plaza de San Diego s/n, Alcalá de Henares Madrid28801 Spain
| | - Pablo Peláez‐Campomanes
- Departameto de Paleobiología Museo Nacional de Ciencias Naturales, MNCN‐CSIC C/ José Gutiérrez Abascal, 2 Madrid28006 Spain
| | - María Ángeles Álvarez‐Sierra
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
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7
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Hinckley A, Hawkins MTR, Achmadi AS, Maldonado JE, Leonard JA. Ancient Divergence Driven by Geographic Isolation and Ecological Adaptation in Forest Dependent Sundaland Tree Squirrels. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A surprising amount of hidden phylogenetic diversity exists in the small to medium size, drab colored squirrels of the genus Sundasciurus. This genus is endemic to Sundaland and the Philippines, where it is widespread. An earlier revision of this genus found that the high elevation ‘populations’ of the widespread, lowland slender squirrel (S. tenuis) were different species. Previous phylogenies based on mitochondrial cytochrome b sequences also suggested that the widespread, lowland Low’s squirrel (S. lowii) and the narrow endemic Fraternal squirrel (S. fraterculus) are not reciprocally monophyletic. Additionally, deep divergences have been identified between lineages within Low’s squirrel that date to the early Pliocene. Here we focus on evaluating the relationships and differences within and between populations of these two nominal species using whole mitochondrial genome sequences, nuclear intron sequences, and morphology. We reassess the taxonomy of this group, revalidate the species status of Robinson’s squirrel (Sundasciurus robinsoniBonhote, 1903) support the species level recognition of the Natuna squirrel (Sundasciurus natunensisThomas, 1895) and identify three other lineages that require further study. We estimate times of divergence and integrate geologic history to find that most of the divergences are pre-Pleistocene, and thus predate the Pleistocene flooding of Sundaland. Biogeographic, and ecological factors may have played a more important role than climatic factors in generating these patterns. While divergence in allopatry seems to be the main process driving speciation in lowland Sundaland squirrels (Sundasciurus), ecomorphological and behavioral adaptations in this clade suggest an important role of niche divergence.
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8
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Zelditch ML, Li J, Swiderski DL. Stasis of functionally versatile specialists. Evolution 2020; 74:1356-1377. [DOI: 10.1111/evo.13956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 01/02/2023]
Affiliation(s)
| | - Jingchun Li
- Ecology and Evolutionary Biology University of Colorado Boulder Colorado 80309
| | - Donald L. Swiderski
- Kresge Hearing Research Institute and Museum of Zoology University of Michigan Ann Arbor Michigan 48109
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9
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Mason VC, Helgen KM, Murphy WJ. Comparative Phylogeography of Forest-Dependent Mammals Reveals Paleo-Forest Corridors throughout Sundaland. J Hered 2020; 110:158-172. [PMID: 30247638 DOI: 10.1093/jhered/esy046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life-history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors and their influence on observed biogeographic patterns. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins, but not in greater mouse deer. This deep east-west split within Borneo has not been commonly described in mammals. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos, and suggests that forests present during the middle Pliocene within the Sunda Shelf were more evergreen and contiguous, while forests were more fragmented, transient, seasonal, or with lower density canopies in the Pleistocene.
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Affiliation(s)
- Victor C Mason
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX.,Victor C. Mason is now at Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, Länggassstrasse, Bern, Switzerland
| | - Kristofer M Helgen
- School of Biological Sciences, Environment Institute, and Centre for Applied Conservation Science, University of Adelaide, Adelaide, SA, Australia
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
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10
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Camacho-Sanchez M, Hawkins MTR, Tuh Yit Yu F, Maldonado JE, Leonard JA. Endemism and diversity of small mammals along two neighboring Bornean mountains. PeerJ 2019; 7:e7858. [PMID: 31608182 PMCID: PMC6788440 DOI: 10.7717/peerj.7858] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2019] [Indexed: 11/20/2022] Open
Abstract
Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Sevilla, Spain.,CiBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Melissa T R Hawkins
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.,Department of Biological Sciences, Humboldt State University, Arcata, CA, USA.,Division of Mammals, National Museum of Natural History, Washington, DC, USA
| | | | - Jesus E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Sevilla, Spain
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11
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Gutiérrez EE, Garbino GST. Species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy. Zool Res 2018; 39:301-308. [PMID: 29551763 PMCID: PMC6102684 DOI: 10.24272/j.issn.2095-8137.2018.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/12/2018] [Indexed: 11/30/2022] Open
Abstract
A recently proposed taxonomic classification of extant ungulates sparked a series of publications that criticize the Phylogenetic Species Concept (PSC) claiming it to be a particularly poor species concept. These opinions reiteratively stated that (1) the two fundamental elements of the "PSC", i.e., monophyly and diagnosability, do not offer objective criteria as to where the line between species should be drawn; and (2) that extirpation of populations can lead to artificial diagnosability and spurious recognitions of species. This sudden eruption of criticism against the PSC is misleading. Problems attributed to the PSC are common to most approaches and concepts that modern systematists employ to establish species boundaries. The controversial taxonomic propositions that sparked criticism against the PSC are indeed highly problematic, not because of the species concept upon which they are based, but because no evidence (whatsoever) has become public to support a substantial portion of the proposed classification. We herein discuss these topics using examples from mammals. Numerous areas of biological research rest upon taxonomic accuracy (including conservation biology and biomedical research); hence, it is necessary to clarify what are (and what are not) the real sources of taxonomic inaccuracy.
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Affiliation(s)
- Eliécer E Gutiérrez
- Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brazil; E-mail:
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Guilherme S T Garbino
- Pós-graduação, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
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12
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Camacho-Sanchez M, Leonard JA, Fitriana Y, Tilak MK, Fabre PH. The generic status of Rattus annandalei (Bonhote, 1903) (Rodentia, Murinae) and its evolutionary implications. J Mammal 2017. [DOI: 10.1093/jmammal/gyx081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Boonkhaw P, Prayoon U, Kanchanasaka B, Hayashi F, Tamura N. Colour polymorphism and genetic relationships among twelve subspecies of Callosciurus finlaysonii in Thailand. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Oshida T, Lin LK, Chang SW, Dang CN, Nguyen ST, Nguyen NX, Nguyen DX, Endo H, Kimura J, Sasaki M. Mitochondrial DNA Evidence Reveals Genetic Difference between Perny's Long-Nosed Squirrels in Taiwan and Asian Mainland. MAMMAL STUDY 2017. [DOI: 10.3106/041.042.0206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Tatsuo Oshida
- Laboratory of Wildlife Biology, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Liang-Kong Lin
- Laboratory of Wildlife Ecology, Department of Life Science, Tunghai University, Taichung 407, Taiwan, R.O.C
| | - Shih-Wei Chang
- Division of Zoology, Taiwan Endemic Species Research Institute, Chichi 552, Taiwan, R.O.C
| | - Can Ngoc Dang
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet Str., Caugiay Distr., Hanoi, Vietnam
| | - Son Truong Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet Str., Caugiay Distr., Hanoi, Vietnam
- Graduate University of Sciences and Technology, 18 Hoang Quoc Viet Str., Caugiay Distr., Hanoi, Vietnam
| | - Nghia Xuan Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet Str., Caugiay Distr., Hanoi, Vietnam
| | - Dang Xuan Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet Str., Caugiay Distr., Hanoi, Vietnam
| | - Hideki Endo
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junpei Kimura
- College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Motoki Sasaki
- Laboratory of Veterinary Anatomy, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
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Cong H, Kong L, Motokawa M, Harada M, Oshida T, Wu Y, Li Y. Complete mitochondrial genome of Perny's long-nosed squirrel Dremomys pernyi (Rodentia: Sciuridae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:744-745. [PMID: 33473611 PMCID: PMC7800828 DOI: 10.1080/23802359.2016.1197062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The complete mitochondrial genome of Perny's long-nosed squirrel (Dremomys pernyi) was firstly sequenced and characterized. The genome was 16,573 bp in length, and its composition and arrangement of genes were analogous to other rodents. The sequences of 13 protein-coding genes were used to construct phylogenetic tree for D. pernyi and other 13 sciurid species available on GenBank. To date, this is the first species whose complete mitochondrial genome sequence was sequenced in genus Dremomys. Our results will provide information for further molecular studies.
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Affiliation(s)
- Haiyan Cong
- Marine College, Shandong University, Weihai, China
| | | | | | - Masashi Harada
- Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Tatsuo Oshida
- Laboratory of Wildlife Biology, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Yi Wu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China
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Oshida T, Yasuda M, Sasaki M. Preliminary Study on Phylogeography ofCallosciurus prevostiiin Southeast Asia: Mitochondrial DNA Evidence Supports Riverine Barrier Hypothesis. MAMMAL STUDY 2016. [DOI: 10.3106/041.041.0305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Hawkins MTR, Leonard JA, Helgen KM, McDonough MM, Rockwood LL, Maldonado JE. Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens. BMC Evol Biol 2016; 16:80. [PMID: 27075887 PMCID: PMC4831120 DOI: 10.1186/s12862-016-0650-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 04/03/2016] [Indexed: 01/06/2023] Open
Abstract
Background The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0650-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melissa T R Hawkins
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA. .,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA. .,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, 22030, USA.
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana(EBD-CSIC), 41092, Sevilla, Spain
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Molly M McDonough
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Larry L Rockwood
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Jesus E Maldonado
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
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