101
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Jardim de Queiroz L, Cardoso Y, Jacot-des-Combes C, Bahechar IA, Lucena CA, Rapp Py-Daniel L, Sarmento Soares LM, Nylinder S, Oliveira C, Parente TE, Torrente-Vilara G, Covain R, Buckup P, Montoya-Burgos JI. Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus. Mol Phylogenet Evol 2019; 145:106711. [PMID: 31857199 DOI: 10.1016/j.ympev.2019.106711] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/20/2019] [Accepted: 12/14/2019] [Indexed: 10/25/2022]
Abstract
With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.
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Affiliation(s)
- Luiz Jardim de Queiroz
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Yamila Cardoso
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque S/N, B1900FWA, La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - Cécile Jacot-des-Combes
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Ilham Anne Bahechar
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Carlos Alberto Lucena
- Museu de Ciências e Tecnologia, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil
| | - Lucia Rapp Py-Daniel
- Coordenação de Biodiversidade, Programa de Coleções Científicas e Biológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, 69060-001 Manaus, AM, Brazil
| | - Luisa Maria Sarmento Soares
- Museu de Biologia Professor Mello Leitão, Instituto Nacional da Mata Atlântica, Av. José Ruschi 4, 29650-000 Santa Teresa, ES, Brazil
| | - Stephan Nylinder
- Department of Psychology, University of Gothenburg. Haraldsgatan 1, 413 14 Gothenburg, Sweden
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual de São Paulo, Rua Professor Doutor Antonio Celso Wagner Zanin 250, 18618-689 Botucatu, SP, Brazil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Laboratório de Genética Molecular de Microrganismos, Fundação Oswaldo Cruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Gislene Torrente-Vilara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Av. Doutor Carvalho de Mendonça 144, 11070-100 Santos, SP, Brazil
| | - Raphaël Covain
- Department of Herpertology and Ichthyology, Museum of Natural History of Geneva, Route de Malagnou 1, 1211 Geneva, Switzerland
| | - Paulo Buckup
- Departamento de Vertebrados, Vista Museu Nacional do Rio de Janeiro/Universidade Federal do Rio de Janeiro, Quinta da Boa, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.
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102
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Taming the Red Bastards: Hybridisation and species delimitation in the Rhodanthemum arundanum-group (Compositae, Anthemideae). Mol Phylogenet Evol 2019; 144:106702. [PMID: 31812569 DOI: 10.1016/j.ympev.2019.106702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 01/13/2023]
Abstract
Delineating species boundaries in a group of recently diverged lineages is challenging due to minor morphological differences, low genetic differentiation and the occurrence of gene flow among taxa. Here, we employ traditional Sanger sequencing and restriction-site associated DNA (RAD) sequencing, to investigate species delimitation in the close-knit Moroccan daisy group around Rhodanthemum arundanum B.H.Wilcox & al. that diverged recently during the Quaternary. After evaluation of genotyping errors and parameter optimisation in the course of de-novo assembly of RADseq reads in Ipyrad, we assess hybridisation patterns in the study group based on different data assemblies and methods (Neighbor-Net networks, FastStructure and ABBA-BABA tests). RADseq data and Sanger sequences are subsequently used for delimitation of species, using both, multi-species coalescent methods (Stacey and Snapp) and a novel approach based on consensus k-means clustering. In addition to the unveiling of two novel subspecies in the R. arundanum-group, our study provides insights into the performance of different species delimitation methods in the presence of hybridisation and varying quantities of data.
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103
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Zhao Z, Heideman N, Grobler P, Jordaan A, Bester P, Hofmeyr MD. Unraveling the diversification and systematic puzzle of the highly polymorphic Psammobates tentorius(Bell, 1828) complex (Reptilia: Testudinidae) through phylogenetic analyses and species delimitation approaches. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Neil Heideman
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Paul Grobler
- Department of Genetics University of the Free State Bloemfontein South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Phillip Bester
- Department of Virology University of the Free State and National Health Laboratory Service (NHLS) Bloemfontein South Africa
| | - Margaretha D. Hofmeyr
- Chelonian Biodiversity and Conservation Department of Biodiversity and Conservation Biology University of the Western Cape Bellville South Africa
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104
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Shazib SUA, Vďačný P, Slovák M, Gentekaki E, Shin MK. Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea). Sci Rep 2019; 9:16360. [PMID: 31704993 PMCID: PMC6841689 DOI: 10.1038/s41598-019-52722-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
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Affiliation(s)
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, 845 23, Bratislava, Slovakia.,Department of Botany, Charles University, 128 01, Prague, Czech Republic
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Mann Kyoon Shin
- Department of Biological Science, University of Ulsan, Ulsan, 44610, South Korea.
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105
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Schultz ED, Pérez-Emán J, Aleixo A, Miyaki CY, Brumfield RT, Cracraft J, Ribas CC. Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling. Mol Phylogenet Evol 2019; 140:106581. [DOI: 10.1016/j.ympev.2019.106581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 07/17/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023]
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106
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Loureiro LO, Engstrom M, Lim B, González CL, Juste J. Not All Molossus are Created Equal: Genetic Variation in the Mastiff Bat Reveals Diversity Masked by Conservative Morphology. ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2019.21.1.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Livia O. Loureiro
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2,Canada
| | - Mark Engstrom
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2,Canada
| | - Burton Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Celia López González
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR) Unidad Durango, Instituto Politécnico Nacional, Calle Sigma 119, Fraccionamiento 20 de Noviembre II, Durango, 34220 Mexico
| | - Javier Juste
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Cientifica (CSIC), 41092 Seville, Spain
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107
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Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Mol Phylogenet Evol 2019; 139:106549. [DOI: 10.1016/j.ympev.2019.106549] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
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108
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Hjalmarsson AE, Graf W, Vitecek S, Jähnig SC, Cai Q, Sharma S, Tong X, Li F, Shah DN, Shah RDT, Pauls SU. Molecular phylogeny of Himalopsyche(Trichoptera, Rhyacophilidae). SYSTEMATIC ENTOMOLOGY 2019; 44:973-984. [DOI: 10.1111/syen.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Anna E. Hjalmarsson
- Goethe University Frankfurt, Institute of Ecology, Evolution & Diversity Frankfurt am Main Germany
- Senckenberg Research Institute and Natural History Museum, Department of Terrestrial Zoology Frankfurt am Main Germany
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology ManagementUniversity of Natural Resources and Life Sciences Vienna Austria
| | - Simon Vitecek
- Senckenberg Research Institute and Natural History Museum, Department of Terrestrial Zoology Frankfurt am Main Germany
- Institute of Hydrobiology and Aquatic Ecology ManagementUniversity of Natural Resources and Life Sciences Vienna Austria
- WasserCluster Lunz – Biologische Station GmbH Lunz am See Austria
| | - Sonja C. Jähnig
- Department of Ecosystem ResearchLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - Qinghua Cai
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of Hydrobiology, Chinese Academy of Sciences Wuhan China
| | - Subodh Sharma
- Aquatic Ecology Centre (AEC), Department of Environmental Science and EngineeringKathmandu University Kathmandu Nepal
| | - Xiaoli Tong
- Department of Entomology, College of AgricultureSouth China Agricultural University Guangzhou China
| | - Fengqing Li
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of Hydrobiology, Chinese Academy of Sciences Wuhan China
- Department of River Ecology and ConservationSenckenberg Research Institute and Natural History Museum Gelnhausen Germany
| | - Deep Narayan Shah
- Department of River Ecology and ConservationSenckenberg Research Institute and Natural History Museum Gelnhausen Germany
- Central Department of Environmental ScienceTribhuvan University Kathmandu Nepal
| | - Ram Devi Tachamo Shah
- Senckenberg Research Institute and Natural History Museum, Department of Terrestrial Zoology Frankfurt am Main Germany
- Aquatic Ecology Centre (AEC), Department of Environmental Science and EngineeringKathmandu University Kathmandu Nepal
| | - Steffen U. Pauls
- Senckenberg Research Institute and Natural History Museum, Department of Terrestrial Zoology Frankfurt am Main Germany
- Department of Insect BiotechnologyJustus‐Liebig‐University Gießen Germany
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109
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Multigene phylogeny, phylogeography and population structure of Podarcis cretensis species group in south Balkans. Mol Phylogenet Evol 2019; 138:193-204. [DOI: 10.1016/j.ympev.2019.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 11/17/2022]
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110
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Wagner F, Ott T, Zimmer C, Reichhart V, Vogt R, Oberprieler C. 'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae). THE NEW PHYTOLOGIST 2019; 223:2039-2053. [PMID: 30851196 DOI: 10.1111/nph.15784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.
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Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Claudia Zimmer
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Verena Reichhart
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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111
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Bolotov IN, Konopleva ES, Vikhrev IV, Lopes-Lima M, Bogan AE, Lunn Z, Chan N, Win T, Aksenova OV, Gofarov MY, Tomilova AA, Kondakov AV. Eight new freshwater mussels (Unionidae) from tropical Asia. Sci Rep 2019; 9:12053. [PMID: 31427656 PMCID: PMC6700347 DOI: 10.1038/s41598-019-48528-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 08/07/2019] [Indexed: 11/25/2022] Open
Abstract
Freshwater mussels are sensitive to habitat and water quality, revealing the fastest rates of human-mediated global extinction among aquatic animals. These animals are especially diverse in tropical Asia, the faunas of which are characterized by high levels of endemism. Here we describe four new species and four new subspecies of freshwater mussels from Myanmar. Leoparreysia whittenisp. nov., the smallest representative of this genus, was discovered from the Ayeyarwady and Chindwin rivers. Radiatula myitthanensissp. nov. and R. chindwinensissp. nov. were recorded from the Chindwin Basin, and R. mouhoti haungthayawensisssp. nov. has been discovered from the Haungthayaw River. Indochinella pugio has been revised with a description of three subspecies: I. pugio viridissimassp. nov. from the Sittaung, Bilin and Bago rivers, I. pugio daweiensisssp. nov. from the Dawei River, and I. pugio paradoxassp. nov. from the Haungthayaw River. Yaukthwa elongatulasp. nov., a peculiar species, conchologically resembling representatives of the genus Solenaia (Gonideinae) with ultra-elongated shell was found in the Chindwin Basin. Our records highlight that tropical Asia harbors numerous, but still overlooked local endemic lineages of freshwater bivalves, which may be on the brink of extinction due to the high anthropogenic and climate change impacts.
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Affiliation(s)
- Ivan N Bolotov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation. .,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation.
| | - Ekaterina S Konopleva
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Ilya V Vikhrev
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal.,CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, CB2 3QZ, Cambridge, United Kingdom
| | - Arthur E Bogan
- North Carolina State Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, United States of America
| | - Zau Lunn
- Fauna & Flora International - Myanmar Program, Yangon, Myanmar
| | - Nyein Chan
- Fauna & Flora International - Myanmar Program, Yangon, Myanmar
| | - Than Win
- Department of Zoology, Hpa-An University, Hpa-An, Kayin State, Myanmar
| | - Olga V Aksenova
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Mikhail Yu Gofarov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Alena A Tomilova
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Alexander V Kondakov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
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112
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Pinto BJ, Titus-McQuillan J, Daza JD, Gamble T. Persistence of a Geographically-Stable Hybrid Zone in Puerto Rican Dwarf Geckos. J Hered 2019; 110:523-534. [PMID: 30859222 DOI: 10.1093/jhered/esz015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN.,Milwaukee Public Museum, Milwaukee, WI
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113
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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114
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Smith CH, Johnson NA, Inoue K, Doyle RD, Randklev CR. Integrative taxonomy reveals a new species of freshwater mussel, Potamilus streckersoni sp. nov. (Bivalvia: Unionidae): implications for conservation and management. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1607615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department, Baylor University, Waco, TX, 76798, USA
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Nathan A. Johnson
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Kentaro Inoue
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
| | | | - Charles R. Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
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115
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Ito Y, Tanaka N, Barfod AS, Bogner J, Li J, Yano O, Gale SW. Molecular phylogenetic species delimitation in the aquatic genus Ottelia (Hydrocharitaceae) reveals cryptic diversity within a widespread species. JOURNAL OF PLANT RESEARCH 2019; 132:335-344. [PMID: 30993554 DOI: 10.1007/s10265-019-01109-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/31/2019] [Indexed: 06/09/2023]
Abstract
Ottelia, a pantropical genus of aquatic plants belonging to the family Hydrocharitaceae, includes several narrowly distributed taxa in Asia. Although the Asian species have received comparatively more research attention than congeners in other areas, various key taxonomic questions remain unaddressed, especially with regards to apparent cryptic diversity within O. alismoides, a widespread species complex native to Asia, northern Australia and tropical Africa. Here we test taxonomic concepts and evaluate species boundaries using a phylogenetic framework. We sampled five of the seven species of Ottelia in Asia as well as each species endemic to Africa and Australia; multiple samples of O. alismoides were obtained from across Asia. Phylogenetic trees based on five plastid DNA markers and the nuclear ITS region shared almost identical topologies. A Bayesian coalescent method of species delimitation using the multi-locus data set discerned one species in Africa, one in Australia and four in Asia with the highest probability. The results lead us to infer that a population sampled in Thailand represents a hitherto unrecognised cryptic taxon within the widespread species complex, although the apparent lack of unambiguous diagnostic characters currently precludes formal description. Conversely, no molecular evidence for distinguishing O. cordata and O. emersa was obtained, and so the latter is synonymised under the former. Two accessions that exhibit inconsistent positions among our phylogenetic trees may represent cases of chloroplast capture, however incomplete lineage sorting or polyploidy are alternative hypotheses that ought to be tested using other molecular markers.
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Affiliation(s)
- Yu Ito
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, People's Republic of China.
- Faculty of Pharmaceutical Sciences, Setsunan University, Osaka, 573-0101, Japan.
| | - Norio Tanaka
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba, 305-0005, Japan
| | - Anders S Barfod
- Department of Bioscience, Aarhus University, Aarhus C, 8000, Denmark
| | - Josef Bogner
- , Augsburger Str. 43a, 86368, Gersthofen, Germany
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, People's Republic of China
| | - Okihito Yano
- Faculty of Biosphere-Geosphere Science, Okayama University of Science, Okayama, 700-0005, Japan
| | - Stephan W Gale
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, Hong Kong, People's Republic of China
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Bribiesca-Contreras G, Pineda-Enríquez T, Márquez-Borrás F, Solís-Marín FA, Verbruggen H, Hugall AF, O'Hara TD. Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star. Mol Phylogenet Evol 2019; 136:151-163. [PMID: 30981811 DOI: 10.1016/j.ympev.2019.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 11/28/2022]
Abstract
Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.
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Affiliation(s)
- Guadalupe Bribiesca-Contreras
- Museum Victoria, GPO Box 666, Melbourne 3001, Australia; School of Biosciences, University of Melbourne, Victoria 3010, Australia.
| | - Tania Pineda-Enríquez
- Department of Biology, Division of Invertebrate Zoology, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA; Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA 90007, USA
| | - Francisco Márquez-Borrás
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico; Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Francisco A Solís-Marín
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria 3010, Australia
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117
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Svantesson S, Larsson KH, Kõljalg U, W. May T, Patrik Cangren, Henrik Nilsson R, Larsson E. Solving the taxonomic identity of Pseudotomentellatristis s.l. (Thelephorales, Basidiomycota) - a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data. MycoKeys 2019; 50:1-77. [PMID: 31043855 PMCID: PMC6477855 DOI: 10.3897/mycokeys.50.32432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/08/2019] [Indexed: 01/01/2023] Open
Abstract
P.tristis is an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar to P.tristis, but no sequence data from type specimens have been available. With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution of P.tristis and its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material. We used gene trees generated in BEAST 2 and PhyML and species trees estimated in STACEY and ASTRAL to delimit species based on the ITS, LSU, Tef1α and mtSSU regions. We enriched our sampling with environmental ITS sequences from the UNITE database. We found the P.tristis group to contain 13 molecularly and morphologically distinct species. Three of these, P.tristis, P.umbrina and P.atrofusca, are already known to science, while ten species are here described as new: P.sciastra sp. nov., P.tristoides sp. nov., P.umbrinascens sp. nov., P.pinophila sp. nov., P.alnophila sp. nov., P.alobata sp. nov., P.pluriloba sp. nov., P.abundiloba sp. nov., P.rotundispora sp. nov. and P.media sp. nov. We discovered P.rhizopunctata and P.atrofusca to form a sister clade to all other species in P.tristis s.l. These two species, unlike all other species in the P.tristis complex, are dimitic. In this study, we designate epitypes for P.tristis, P.umbrina and Hypochnopsisfuscata and lectotypes for Auriculariaphylacteris and Thelephorabiennis. We show that the holotype of Hypochnussitnensis and the lectotype of Hypochnopsisfuscata are conspecific with P.tristis, but in the absence of molecular information we regard Pseudotomentellalongisterigmata and Hypochnusrhacodium as doubtful taxa due to their aberrant morphology. We confirm A.phylacteris, Tomentellabiennis and Septobasidiumarachnoideum as excluded taxa, since their morphology clearly show that they belong to other genera. A key to the species of the P.tristis group is provided. We found P.umbrina to be a common species with a wide, Holarctic distribution, forming ectomycorrhiza with a large number of host species in habitats ranging from tropical forests to the Arctic tundra. The other species in the P.tristis group were found to be less common and have narrower ecological niches.
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Affiliation(s)
- Sten Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia
| | - Karl-Henrik Larsson
- The Mycological Herbarium, Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
| | - Urmas Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
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118
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Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko. Mol Phylogenet Evol 2019; 133:54-66. [DOI: 10.1016/j.ympev.2018.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022]
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119
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Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2019; 15:e1006650. [PMID: 30958812 PMCID: PMC6472827 DOI: 10.1371/journal.pcbi.1006650] [Citation(s) in RCA: 1592] [Impact Index Per Article: 318.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/18/2019] [Accepted: 02/04/2019] [Indexed: 11/18/2022] Open
Abstract
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
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Affiliation(s)
- Remco Bouckaert
- Centre of Computational Evolution, University of Auckland, Auckland, New Zealand
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Timothy G. Vaughan
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joëlle Barido-Sottani
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mathieu Fourment
- ithree institute, University of Technology Sydney, Sydney, Australia
| | | | | | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridgeshire, UK
| | - Michael Matschiner
- Department of Environmental Sciences, University of Basel, 4051 Basel, Switzerland
| | - Fábio K. Mendes
- Centre of Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Nicola F. Müller
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Huw A. Ogilvie
- Department of Computer Science, Rice University, Houston, TX 77005-1892, USA
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Alex Popinga
- Centre of Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3FL UK
| | - David Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Igor Siveroni
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, W2 1PG, UK
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, OX1 3LB, UK
| | - Dong Xie
- Centre of Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Chi Zhang
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Tanja Stadler
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexei J. Drummond
- Centre of Computational Evolution, University of Auckland, Auckland, New Zealand
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120
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Aghová T, Palupčíková K, Šumbera R, Frynta D, Lavrenchenko LA, Meheretu Y, Sádlová J, Votýpka J, Mbau JS, Modrý D, Bryja J. Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny. BMC Evol Biol 2019; 19:69. [PMID: 30832573 PMCID: PMC6399835 DOI: 10.1186/s12862-019-1380-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
Background Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept. Results The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia. Conclusions The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa. Electronic supplementary material The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- T Aghová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65, Brno, Czech Republic. .,Department of Zoology, National Museum, 115 79, Prague, Czech Republic.
| | - K Palupčíková
- Department of Zoology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - R Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - D Frynta
- Department of Zoology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - L A Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution RAS, 119071, Moscow, Russia
| | - Y Meheretu
- Department of Biology and Institute of Mountain Research and Development, Mekelle University, P.O. Box 3102, Mekelle, Tigray, Ethiopia
| | - J Sádlová
- Department of Parasitology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - J Votýpka
- Department of Parasitology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - J S Mbau
- Department of Land Resource Management and Agricultural Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - D Modrý
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic.,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, 612 42, Brno, Czech Republic
| | - J Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, 602 00, Brno, Czech Republic
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121
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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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122
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Reydon TAC, Kunz W. Species as natural entities, instrumental units and ranked taxa: new perspectives on the grouping and ranking problems. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Thomas A C Reydon
- Institute of Philosophy, Leibniz University Hannover, Hannover, Germany
- Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, Hannover, Germany
| | - Werner Kunz
- Institute for Genetics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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123
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Zhang C, Ogilvie HA, Drummond AJ, Stadler T. Bayesian Inference of Species Networks from Multilocus Sequence Data. Mol Biol Evol 2019; 35:504-517. [PMID: 29220490 PMCID: PMC5850812 DOI: 10.1093/molbev/msx307] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network, and we assume a multispecies network coalescent prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. To quantify the power of our method, we reanalyze two large data sets of genes from spruces and yeasts. For the three closely related spruces, we verify the previously suggested homoploid hybridization event in this clade; for the yeast data, we find extensive hybridization events. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides an extensible framework for Bayesian inference of reticulate evolution.
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Affiliation(s)
- Chi Zhang
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Switzerland.,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Huw A Ogilvie
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia.,Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.,Department of Computer Science, University of Auckland, Auckland, New Zealand
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Switzerland
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124
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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125
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Naciri Y, Christe C, Bétrisey S, Song YG, Deng M, Garfì G, Kozlowski G. Species delimitation in the East Asian species of the relict tree genus Zelkova (Ulmaceae): A complex history of diversification and admixture among species. Mol Phylogenet Evol 2019; 134:172-185. [PMID: 30769098 DOI: 10.1016/j.ympev.2019.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/04/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneideriana and Z. sinica) have at least partly overlapping distributions. The phylogenetic and phylogeographic status of these East Asian species is still not well understood, mainly since all previous studies used almost exclusively plant material collected in botanical gardens and were based on very small numbers of individuals. Our study is the first based on 33 natural populations covering all important areas with Zelkova species in the Sino-Japanese Floristic Region. Chloroplast and microsatellite markers were used, and Bayesian analyses were run for both types of markers. East Asian Zelkova species cluster into two groups that partially overlap when comparing the two types of markers. For chloroplast markers, the two groups coincide with all Japanese, some Korean and northern Chinese Z. serrata in one group and all other individuals in the other group, regardless of whether they are attributed to Z. serrata, Z. sinica or Z. schneideriana from Korea, mainland China and Taiwan. At the nuclear level, however, the clustering clearly groups all the Z. serrata individuals together, regardless of whether they are from Japan, Korea or China, and the two other species in a second group. This complex genetic pattern in East Asian Zelkova species is most likely due to a combination of ancient diversification and speciation events and more recent hybridization during the last glacial/interglacial retractions and recolonizations. One of the surprising results of our study concerns the populations from Taiwan, which are genetically similar to Z. schneideriana. Thus, their assignation to a separate taxon (Z. tarokoensis) or to a variety of Z. serrata (Z. serrata var. tarokoensis), as currently reported in all local and national floras, might be in need of revision. Furthermore, our results indicate that the East Asian species are more closely related to Z. carpinifolia than to any other Western European species. Haplotypes of Z. sicula and Z. abelicea (Mediterranean region) as well as those of Z. sinica and Z. schneideriana (East Asia) seem to have diversified more recently. The most ancient haplotypes are found among the western Eurasian Z. carpinifolia and the East Asian Z. serrata. This result is in agreement with the carpinifolia and serrata-like morphotypes commonly found in the fossil record.
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Affiliation(s)
- Yamama Naciri
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland; Laboratoire de Systématique végétale et Biodiversité, University of Geneva, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland.
| | - Camille Christe
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Genève, Switzerland
| | - Sébastien Bétrisey
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Yi-Gang Song
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Giuseppe Garfì
- Institute of Biosciences and BioResources, National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy
| | - Gregor Kozlowski
- Natural History Museum Fribourg, Chemin du Musée 6, 1700 Fribourg, Switzerland; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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126
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Klimov PB, Skoracki M, Bochkov AV. Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes. Parasit Vectors 2019; 12:8. [PMID: 30611284 PMCID: PMC6321676 DOI: 10.1186/s13071-018-3242-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique. RESULTS We conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4-7.8%) while that of nuclear genes was low (0.06-0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting. CONCLUSIONS Our research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.
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Affiliation(s)
- Pavel B. Klimov
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 3600 Varsity Drive, Ann Arbor, Michigan 48108 USA
- Tyumen State University, 10 Semakova Str, 625003 Tyumen, Russia
| | - Maciej Skoracki
- Department of Animal Morphology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 60-614 Poznan, Poland
| | - Andre V. Bochkov
- Tyumen State University, 10 Semakova Str, 625003 Tyumen, Russia
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, 199034 St Petersburg, Russia
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127
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Krásová J, Mikula O, Mazoch V, Bryja J, Říčan O, Šumbera R. Evolution of the Grey-bellied pygmy mouse group: Highly structured molecular diversity with predictable geographic ranges but morphological crypsis. Mol Phylogenet Evol 2019; 130:143-155. [DOI: 10.1016/j.ympev.2018.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023]
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128
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Andermann T, Fernandes AM, Olsson U, Töpel M, Pfeil B, Oxelman B, Aleixo A, Faircloth BC, Antonelli A. Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements. Syst Biol 2018; 68:32-46. [PMID: 29771371 PMCID: PMC6292485 DOI: 10.1093/sysbio/syy039] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/10/2018] [Indexed: 01/06/2023] Open
Abstract
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for nonmodel organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies. Instead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the multispecies coalescent model. Our empirical analyses of ultraconserved element locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last 3 myr. The phylogenetic results support the recognition of two species and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | | | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Mats Töpel
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden.,Department of Marine Sciences, University of Gothenburg, SE-413 19 Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi, Collection of Birds, Belém, Brazil
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden.,Gothenburg Botanical Garden, SE-413 19 Göteborg, Sweden.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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129
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Jones GR. Divergence Estimation in the Presence of Incomplete Lineage Sorting and Migration. Syst Biol 2018; 68:19-31. [PMID: 29800341 DOI: 10.1093/sysbio/syy041] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/16/2018] [Indexed: 11/14/2022] Open
Abstract
This article focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. I develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary processes which allows both the population size parameters and the migration rates between pairs of species tree branches to be integrated out. I then describe a BEAST2 package DENIM (Divergence estimation notwithstanding ILS and migration) which is based on this model and which uses an approximation to sample from the posterior. The approximation is based on the assumption that migrations are rare, and it only samples from certain regions of the posterior which seem likely given this assumption. The method breaks down if there is a lot of migration. Using simulations, Leaché et al. (2014) showed that using the standard multispecies coalescent model to infer a species tree can result in poor accuracy if migration is present. I reanalyze this simulated data to explore DENIM's performance and demonstrate substantial improvements in accuracy over *BEAST. I also reanalyze an empirical data set.
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Affiliation(s)
- Graham R Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden
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130
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Caro A, Gómez-Moliner BJ, Madeira MJ. Integrating multilocus DNA data and 3D geometric morphometrics to elucidate species boundaries in the case of Pyrenaearia (Pulmonata: Hygromiidae). Mol Phylogenet Evol 2018; 132:194-206. [PMID: 30550961 DOI: 10.1016/j.ympev.2018.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 07/03/2018] [Accepted: 12/06/2018] [Indexed: 01/21/2023]
Abstract
To accurately delimit species the use of multiple character types is essential as all speciation processes are not equally reflected in different data (e.g. morphological, molecular or ecological characters). With the introduction of geometric morphometrics methods and advances in 3D technology, a comprehensive combination of molecular and morphological data has been enabled in groups where exhaustively quantifying and measuring morphological shape change was not possible before such as gastropod shells. In this study, we combined multilocus coalescent species delimitation methods with 3D geometric morphometrics of shell shape to delimit species within the land snail genus Pyrenaearia. A new taxonomic scheme was constructed for the genus identifying ten species. Two nominal species were synonymized and a hitherto unrecognized cryptic species was identified. Our findings support the importance of combining multiple lines of evidence as molecular and morphological data on their own do not yield the same information. Further, the integration of morphological and molecular data shows the importance of allometry in shell shape and suggests a combined effect of population history and selection in different environments on shells morphological variation. Our new taxonomy and phylogenetic reconstruction suggest that, besides the glacial cycles of the Pleistocene, passive dispersal and rock substrate complexity could also have been involved in the speciation of the genus.
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Affiliation(s)
- Amaia Caro
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country, EHU/UPV, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Araba, Spain; Biodiversity Research Group, CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Araba, Spain.
| | - Benjamín Juan Gómez-Moliner
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country, EHU/UPV, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Araba, Spain; Biodiversity Research Group, CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Araba, Spain.
| | - María José Madeira
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country, EHU/UPV, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Araba, Spain; Biodiversity Research Group, CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Araba, Spain.
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131
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Hubka V, Barrs V, Dudová Z, Sklenář F, Kubátová A, Matsuzawa T, Yaguchi T, Horie Y, Nováková A, Frisvad J, Talbot J, Kolařík M. Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization. PERSOONIA 2018; 41:142-174. [PMID: 30728603 PMCID: PMC6344812 DOI: 10.3767/persoonia.2018.41.08] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/14/2018] [Indexed: 12/13/2022]
Abstract
Although Aspergillus fumigatus is the major agent of invasive aspergillosis, an increasing number of infections are caused by its cryptic species, especially A. lentulus and the A. viridinutans species complex (AVSC). Their identification is clinically relevant because of antifungal drug resistance and refractory infections. Species boundaries in the AVSC are unresolved since most species have uniform morphology and produce interspecific hybrids in vitro. Clinical and environmental strains from six continents (n = 110) were characterized by DNA sequencing of four to six loci. Biological compatibilities were tested within and between major phylogenetic clades, and ascospore morphology was characterised. Species delimitation methods based on the multispecies coalescent model (MSC) supported recognition of ten species including one new species. Four species are confirmed opportunistic pathogens; A. udagawae followed by A. felis and A. pseudoviridinutans are known from opportunistic human infections, while A. felis followed by A. udagawae and A. wyomingensis are agents of feline sino-orbital aspergillosis. Recently described human-pathogenic species A. parafelis and A. pseudofelis are synonymized with A. felis and an epitype is designated for A. udagawae. Intraspecific mating assay showed that only a few of the heterothallic species can readily generate sexual morphs in vitro. Interspecific mating assays revealed that five different species combinations were biologically compatible. Hybrid ascospores had atypical surface ornamentation and significantly different dimensions compared to parental species. This suggests that species limits in the AVSC are maintained by both pre- and post-zygotic barriers and these species display a great potential for rapid adaptation and modulation of virulence. This study highlights that a sufficient number of strains representing genetic diversity within a species is essential for meaningful species boundaries delimitation in cryptic species complexes. MSC-based delimitation methods are robust and suitable tools for evaluation of boundaries between these species.
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Affiliation(s)
- V. Hubka
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - V. Barrs
- Sydney School of Veterinary Science, Faculty of Science, and Marie Bashir Institute of Infectious Diseases & Biosecurity, University of Sydney, Camperdown, NSW, Australia
| | - Z. Dudová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - A. Kubátová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
| | - T. Matsuzawa
- University of Nagasaki, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Y. Horie
- Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - A. Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - J.J. Talbot
- Sydney School of Veterinary Science, Faculty of Science, and Marie Bashir Institute of Infectious Diseases & Biosecurity, University of Sydney, Camperdown, NSW, Australia
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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132
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Differentiation underground: Range-wide multilocus genetic structure of the silvery mole-rat does not support current taxonomy based on mitochondrial sequences. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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133
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Johnson NA, Smith CH, Pfeiffer JM, Randklev CR, Williams JD, Austin JD. Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act. Sci Rep 2018; 8:15892. [PMID: 30367102 PMCID: PMC6203750 DOI: 10.1038/s41598-018-33806-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/07/2018] [Indexed: 11/30/2022] Open
Abstract
Objectively delimiting species boundaries remains an important challenge in systematics and becomes urgent when unresolved taxonomy complicates conservation and recovery efforts. We examined species boundaries in the imperiled freshwater mussel genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across multiple lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex. The only genetically and morphologically diagnosable species in the C. pustulosa species complex were C. pustulosa and C. succissa and we consider C. aurea, C. houstonensis, C. mortoni, and C. refulgens to be synonyms of C. pustulosa. In contrast, all three species in the C. nodulata complex (C. necki, C. nodulata, and C. petrina) were genetically, geographically, and morphologically diagnosable. Our findings have important conservation and management implications, as three nominal species (C. aurea, C. houstonensis, and C. petrina) are being considered for protection under the Endangered Species Act.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA.
| | - Chase H Smith
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA.,Baylor University, Biology Department, Waco, TX, 76798, USA
| | - John M Pfeiffer
- University of Florida, Florida Museum, Gainesville, FL, 32611, USA
| | - Charles R Randklev
- Texas A&M Natural Resources Institute and AgriLife Research Center, Dallas, TX, 75252, USA
| | - James D Williams
- University of Florida, Florida Museum, Gainesville, FL, 32611, USA
| | - James D Austin
- Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32601, USA
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134
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Eberle J, Bazzato E, Fabrizi S, Rossini M, Colomba M, Cillo D, Uliana M, Sparacio I, Sabatinelli G, Warnock RCM, Carpaneto G, Ahrens D. Sex-Biased Dispersal Obscures Species Boundaries in Integrative Species Delimitation Approaches. Syst Biol 2018; 68:441-459. [DOI: 10.1093/sysbio/syy072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Jonas Eberle
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
| | - Erika Bazzato
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
- Department of Life and Environmental Sciences, Botany Division, University of Cagliari, viale Sant’Ignazio da Laconi 13, 09123, Cagliari (CA), Italy
| | - Silvia Fabrizi
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
| | - Michele Rossini
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
- Strada dei Guazzi, 1/3, 61122 Pesaro (PU), Italy
| | - Mariastella Colomba
- Università di Urbino, Dipartimento di Scienze Biomolecolari (DiSB), Via maggetti 22, 61029 Urbino (PU), Italy
| | | | - Marco Uliana
- Museo di Storia Naturale, Santa Croce 1730, 30135 Venezia, Italy
| | | | - Guido Sabatinelli
- Muséum d’Histoire Naturelle, Route de Malagnou 1, 1208 Geneva, Switzerland
| | | | - Giuseppe Carpaneto
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy
| | - Dirk Ahrens
- Zoological Research Museum Alexander Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113 Bonn, Germany
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135
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Tomasello S. How many names for a beloved genus? – Coalescent-based species delimitation in Xanthium L. (Ambrosiinae, Asteraceae). Mol Phylogenet Evol 2018; 127:135-145. [DOI: 10.1016/j.ympev.2018.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 11/13/2022]
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136
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Copilaș‐Ciocianu D, Zimța A, Petrusek A. Integrative taxonomy reveals a newGammarusspecies (Crustacea, Amphipoda) surviving in a previously unknown southeast European glacial refugium. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Denis Copilaș‐Ciocianu
- Department of Ecology Faculty of Science Charles University Prague Czechia
- Laboratory of Evolutionary Ecology of Hydrobionts Nature Research Centre Vilnius Lithuania
| | - Alina‐Andreea Zimța
- Department of Ecology Faculty of Science Charles University Prague Czechia
- Department of Biology–Chemistry Faculty of Chemistry, Biology, Geography West University of Timişoara Timişoara Romania
| | - Adam Petrusek
- Department of Ecology Faculty of Science Charles University Prague Czechia
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137
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Slos D, Couvreur M, Bert W. Hidden diversity in mushrooms explored: A new nematode species, Neodiplogaster unguispiculata sp. n. (Rhabditida, Diplogastridae), with a key to the species of Neodiplogaster. ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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138
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Demos TC, Webala PW, Bartonjo M, Patterson BD. Hidden Diversity of African Yellow House Bats (Vespertilionidae, Scotophilus): Insights From Multilocus Phylogenetics and Lineage Delimitation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00086] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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139
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Hjalmarsson AE, Graf W, Jähnig SC, Vitecek S, Pauls SU. Molecular association and morphological characterisation of Himalopsyche larval types (Trichoptera, Rhyacophilidae). Zookeys 2018; 773:79-108. [PMID: 30026662 PMCID: PMC6048183 DOI: 10.3897/zookeys.773.24319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/23/2018] [Indexed: 12/22/2022] Open
Abstract
Himalopsyche Banks, 1940 (Trichoptera, Rhyacophilidae) is a genus of caddisflies inhabiting mountain and alpine environments in Central and East Asia and the Nearctic. Of 53 known species, only five species have been described previously in the aquatic larval stage. We perform life stage association using three strategies (GMYC, PTP, and reciprocal monophyly) based on fragments of two molecular markers: the nuclear CAD, and the mitochondrial COI gene. A total of 525 individuals from across the range of Himalopsyche (Himalayas, Hengduan Shan, Tian Shan, South East Asia, Japan, and western North America) was analysed and 32 operational taxonomic units (OTUs) in our dataset delimited. Four distinct larval types of Himalopsyche are uncovered, and these are defined as the phryganea type, japonica type, tibetana type, and gigantea type and a comparative morphological characterisation of the larval types is presented. The larval types differ in a number of traits, most prominently in their gill configuration, as well as in other features such as setal configuration of the pronotum and presence/absence of accessory hooks of the anal prolegs.
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Affiliation(s)
- Anna E Hjalmarsson
- Goethe-University Frankfurt, 60323 Frankfurt am Main, Germany. Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 63025 Frankfurt am Main, Germany
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33/DG, 1180 Vienna, Austria
| | - Sonja C Jähnig
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Ecosystem Research, Justus-von-Liebig-Str. 7, 12489 Berlin, Germany
| | - Simon Vitecek
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 63025 Frankfurt am Main, Germany
| | - Steffen U Pauls
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 63025 Frankfurt am Main, Germany
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140
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A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic. PLoS One 2018; 13:e0198356. [PMID: 29924805 PMCID: PMC6010226 DOI: 10.1371/journal.pone.0198356] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/17/2018] [Indexed: 11/24/2022] Open
Abstract
We investigate mitochondrial (COI, 16S rDNA) and nuclear (ITS2, 28S rDNA) genetic structure of North East Atlantic lineages of Terebellides, a genus of sedentary annelids mainly inhabiting continental shelf and slope sediments. We demonstrate the presence of more than 25 species of which only seven are formally described. Species boundaries are determined with molecular data using a broad range of analytical methods. Many of the new species are common and wide spread, and the majority of the species are found in sympatry with several other species in the complex. Being one of the most regularly encountered annelid taxa in the North East Atlantic, it is more likely to find an undescribed species of Terebellides than a described one.
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141
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Almendra AL, González-Cózatl FX, Engstrom MD, Rogers DS. Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini). Mol Phylogenet Evol 2018; 128:12-25. [PMID: 29906608 DOI: 10.1016/j.ympev.2018.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 11/17/2022]
Abstract
Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. Unfortunately, the region continues to experience some of the highest deforestation rates in the world. For mammals, the evolutionary relationships of many endemic taxa are controversial, as it is the case for members of the genus Handleyomys. Estimation of a time-calibrated hypothesis for the evolution of these six genera (Euryoryzomys, Handleyomys, Hylaeamys, Nephelomys, Oecomys and Transandinomys) supported a monophyletic Handleyomys sensu lato. Based on their distinctive morphology and the amount of inter-generic genetic divergence, Handleyomys sensu stricto, H. alfaroi, the H. chapmani, and the H. melanotis species groups warrant recognition as separate genera. In addition, species delimitation documents the existence of cryptic species-level lineages within H. alfaroi and H. rostratus. Cryptic lineages within H. rostratus exhibited significant niche differentiation, but this was not the pattern among species-level clades within H. alfaroi. Similarly, age-range correlations revealed that niche evolution within Handleyomys is not correlated with evolutionary time, instead, ancestral climate tolerance reconstructions show niche disparities at specific diversification events within the chapmani and melanotis species groups, while the climatic niche of the rest of species of Handleyomys tended to be conservative.
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Affiliation(s)
- Ana Laura Almendra
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos C.P. 62209, Mexico.
| | - Francisco X González-Cózatl
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos C.P. 62209, Mexico
| | - Mark D Engstrom
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S 2C6, Canada
| | - Duke S Rogers
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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142
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Copilaş-Ciocianu D, Zimţa AA, Grabowski M, Petrusek A. Survival in northern microrefugia in an endemic Carpathian gammarid (Crustacea: Amphipoda). ZOOL SCR 2018. [DOI: 10.1111/zsc.12285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Denis Copilaş-Ciocianu
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
- Laboratory of Evolutionary Ecology of Hydrobionts; Nature Research Centre; Vilnius Lithuania
| | - Alina-Andreea Zimţa
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
- Department of Biology-Chemistry; Faculty of Chemistry, Biology, Geography; West University of Timişoara; Timişoara Romania
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology; Faculty of Biology and Environmental Protection; University of Lodz; Łódź Poland
| | - Adam Petrusek
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
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143
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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144
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Eilertsen MH, Georgieva MN, Kongsrud JA, Linse K, Wiklund H, Glover AG, Rapp HT. Genetic connectivity from the Arctic to the Antarctic: Sclerolinum contortum and Nicomache lokii (Annelida) are both widespread in reducing environments. Sci Rep 2018; 8:4810. [PMID: 29556042 PMCID: PMC5859262 DOI: 10.1038/s41598-018-23076-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/06/2018] [Indexed: 11/23/2022] Open
Abstract
The paradigm of large geographic ranges in the deep sea has been challenged by genetic studies, which often reveal putatively widespread species to be several taxa with more restricted ranges. Recently, a phylogeographic study revealed that the tubeworm Sclerolinum contortum (Siboglinidae) inhabits vents and seeps from the Arctic to the Antarctic. Here, we further test the conspecificity of the same populations of S. contortum with additional mitochondrial and nuclear markers. We also investigate the genetic connectivity of another species with putatively the same wide geographic range - Nicomache lokii (Maldanidae). Our results support the present range of S. contortum, and the range of N. lokii is extended from vents and seeps in the Nordic Seas to mud volcanoes in the Barbados Trench and Antarctic vents. Sclerolinum contortum shows more pronounced geographic structure than N. lokii, but whether this is due to different dispersal capacities or reflects the geographic isolation of the sampled localities is unclear. Two distinct mitochondrial lineages of N. lokii are present in the Antarctic, which may result from two independent colonization events. The environmental conditions inhabited by the two species and implications for their distinct habitat preference is discussed.
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Affiliation(s)
- Mari H Eilertsen
- Department of Biological Sciences, University of Bergen, PO Box 7800, N-5020, Bergen, Norway. .,K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.
| | - Magdalena N Georgieva
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jon A Kongsrud
- Department of Natural History, University Museum of Bergen, PO Box 7800, N-5020, Bergen, Norway
| | - Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Adrian G Glover
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Hans T Rapp
- Department of Biological Sciences, University of Bergen, PO Box 7800, N-5020, Bergen, Norway.,K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.,Uni Research, Uni Environment, PO Box 7810, N-5020, Bergen, Norway
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145
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Barley AJ, Brown JM, Thomson RC. Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent. Syst Biol 2018; 67:269-284. [PMID: 28945903 DOI: 10.1093/sysbio/syx073] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent (MSC) to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the MSC model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across data sets. Posterior predictive tests find the poorest model performance in data sets that were hypothesized to be impacted by model violations. We also show that while the inferences assuming the MSC are robust to minor model violations, such inferences can be biased under some biologically plausible scenarios. Taken together, these results suggest that researchers can identify individual data sets in which species delimitation under the MSC is likely to be problematic, thereby highlighting the cases where additional lines of evidence to identify species boundaries are particularly important to collect. Our study supports a growing body of work highlighting the importance of model checking in phylogenetics, and the usefulness of tailoring tests of model fit to assess the reliability of particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].
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Affiliation(s)
- Anthony J Barley
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
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146
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Hubka V, Nováková A, Jurjević Ž, Sklenář F, Frisvad JC, Houbraken J, Arendrup MC, Jørgensen KM, Siqueira JPZ, Gené J, Kolařík M. Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov. Int J Syst Evol Microbiol 2018; 68:995-1011. [PMID: 29458472 DOI: 10.1099/ijsem.0.002583] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves and clinical material. The A. candidus sensu lato isolates were characterized by DNA sequencing of four genetic loci, and agreement between molecular species delimitation results, morphological characters and exometabolite spectra were studied. Classical phylogenetic methods (maximum likelihood, Bayesian inference) and species delimitation methods based on the multispecies coalescent model supported recognition of up to three species in A. candidus sensu lato. After evaluation of phenotypic data, a broader species concept was adopted, and only one new species, Aspergillus dobrogensis, was proposed. This species is represented by 22 strains originating from seven countries (ex-type strain CCF 4651T=NRRL 62821T=IBT 32697T=CBS 143370T) and its differentiation from A. candidus is relevant for bioprospecting studies because these species have different exometabolite profiles. Evaluation of the antifungal susceptibility of section Candidi members to six antifungals using the reference EUCAST method showed that all species have low minimum inhibitory concentrations for all tested antifungals. These results suggest applicability of a wide spectrum of antifungal agents for treatment of infections caused by species from section Candidi.
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Affiliation(s)
- Vit Hubka
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alena Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - František Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Maiken C Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - João P Z Siqueira
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain.,Laboratório de Microbiologia, Faculdade de Medicina de SãoJosé do Rio Preto, São José do Rio Preto, Brazil
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Miroslav Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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147
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Ogilvie HA, Bouckaert RR, Drummond AJ. StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates. Mol Biol Evol 2018; 34:2101-2114. [PMID: 28431121 PMCID: PMC5850801 DOI: 10.1093/molbev/msx126] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present. Another class of heuristics directly motivated by the MSC avoids many of the pitfalls of concatenation but cannot be used to estimate divergence times. To enable fuller use of available data and more accurate inference of species tree topologies, divergence times, and substitution rates, we have developed a new version of *BEAST called StarBEAST2. To improve convergence rates we add analytical integration of population sizes, novel MCMC operators and other optimizations. Computational performance improved by 13.5× and 13.8× respectively when analyzing two empirical data sets, and an average of 33.1× across 30 simulated data sets. To enable accurate estimates of per-species substitution rates, we introduce species tree relaxed clocks, and show that StarBEAST2 is a more powerful and robust estimator of rate variation than concatenation. StarBEAST2 is available through the BEAUTi package manager in BEAST 2.4 and above.
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Affiliation(s)
- Huw A Ogilvie
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia.,Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Remco R Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.,Department of Computer Science, University of Auckland, Auckland, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.,Department of Computer Science, University of Auckland, Auckland, New Zealand
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148
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Diversification dynamics and transoceanic Eurasian-Australian disjunction in the genus Picris (Compositae) induced by the interplay of shifts in intrinsic/extrinsic traits and paleoclimatic oscillations. Mol Phylogenet Evol 2018; 119:182-195. [DOI: 10.1016/j.ympev.2017.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 11/22/2022]
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149
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Gale SW, Duangjai S, Li J, Ito Y, Watthana S, Termwutthipreecha P, Cheuk ML, Suddee S. Integrative analyses of Nervilia (Orchidaceae) section Linervia reveal further undescribed cryptic diversity in Thailand. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2017.1415233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Stephan W. Gale
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Sutee Duangjai
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jihong Li
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Yu Ito
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Santi Watthana
- School of Biology, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima 30000, Thailand
| | - Phatsara Termwutthipreecha
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Mang Lung Cheuk
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Somran Suddee
- Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok 10900, Thailand
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150
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Bryja J, Kostin D, Meheretu Y, Šumbera R, Bryjová A, Kasso M, Mikula O, Lavrenchenko LA. Reticulate Pleistocene evolution of Ethiopian rodent genus along remarkable altitudinal gradient. Mol Phylogenet Evol 2018; 118:75-87. [DOI: 10.1016/j.ympev.2017.09.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/24/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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