1
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Sherlock MB, Streicher JW, Gower DJ, Maddock ST, Nussbaum RA, Oommen OV, Serra Silva A, Day JJ, Wilkinson M. Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles. Mol Phylogenet Evol 2024; 198:108130. [PMID: 38889862 DOI: 10.1016/j.ympev.2024.108130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/20/2024]
Abstract
Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.
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Affiliation(s)
- Miranda B Sherlock
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | | | - David J Gower
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
| | - Simon T Maddock
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles; School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Ronald A Nussbaum
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Oommen V Oommen
- Department of Zoology, University of Kerala, Kariavattom 695 581, Thiruvananthapuram, Kerala, India
| | - Ana Serra Silva
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; School of Earth Sciences, University of Bristol, Queens Road, Bristol BS8 1RL, UK
| | - Julia J Day
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Mark Wilkinson
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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2
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Taylor RS, Manseau M, Keobouasone S, Liu P, Mastromonaco G, Solmundson K, Kelly A, Larter NC, Gamberg M, Schwantje H, Thacker C, Polfus J, Andrew L, Hervieux D, Simmons D, Wilson PJ. High genetic load without purging in caribou, a diverse species at risk. Curr Biol 2024; 34:1234-1246.e7. [PMID: 38417444 DOI: 10.1016/j.cub.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/17/2023] [Accepted: 02/01/2024] [Indexed: 03/01/2024]
Abstract
High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.
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Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Micheline Manseau
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Sonesinh Keobouasone
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Peng Liu
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | | | - Kirsten Solmundson
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, ON K9L 1Z8, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Mary Gamberg
- Gamberg Consulting, Jarvis Street, Whitehorse, YK Y1A 2J2, Canada
| | - Helen Schwantje
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Caeley Thacker
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Jean Polfus
- Canadian Wildlife Service - Pacific Region, Environment and Climate Change Canada, 1238 Discovery Avenue, Kelowna, BC V1V 1V9, Canada
| | - Leon Andrew
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Dave Hervieux
- Alberta Ministry of Environment and Protected Areas, Government of Alberta, 10320-99 Street, Grande Prairie, AB T8V 6J4, Canada
| | - Deborah Simmons
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Paul J Wilson
- Biology Department, Trent University, East Bank Drive, Peterborough, ON K9L 1Z8, Canada
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3
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Souza LHB, Pierson TW, Tenório RO, Ferro JM, Gatto KP, Silva BC, de Andrade GV, Suárez P, Haddad CFB, Lourenço LB. Multiple contact zones and karyotypic evolution in a neotropical frog species complex. Sci Rep 2024; 14:1119. [PMID: 38212602 PMCID: PMC10784582 DOI: 10.1038/s41598-024-51421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Previous studies of DNA sequence and karyotypic data have revealed high genetic diversity in the Physalaemus cuvieri - Physalaemus ephippifer species complex-a group of small leptodactylid frogs in South America. To date, seven major genetic lineages have been recognized in this group, with species delimitation tests supporting four to seven of them as valid species. Among these, only P. ephippifer shows heteromorphic sex chromosomes, but the implications of cytogenetic divergence for the evolution of this group are unknown. We analyzed karyotypic, mitochondrial DNA, and 3RAD genomic data to characterize a putative contact zone between P. ephippifer and P. cuvieri Lineage 1, finding evidence for admixture and karyotypic evolution. We also describe preliminary evidence for admixture between two other members of this species complex-Lineage 1 and Lineage 3 of P. cuvieri. Our study sheds new light on evolutionary relationships in the P. cuvieri - P. ephippifer species complex, suggesting an important role of karyotypic divergence in its evolutionary history and underscoring the importance of hybridization as a mechanism of sex chromosome evolution in amphibians.
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Affiliation(s)
- Lucas H B Souza
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil.
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Renata O Tenório
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Juan M Ferro
- Laboratorio de Genética Evolutiva "Dr. Claudio J. Bidau", Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Kaleb P Gatto
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Bruno C Silva
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Gilda V de Andrade
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão (UFMA), Campus do Bacanga, São Luís, MA, 65080-040, Brazil
| | - Pablo Suárez
- Instituto de Biología Subtropical (CONICET-UNaM), Puerto Iguazú, Argentina
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Luciana B Lourenço
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
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4
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Di Santo LN, Quilodrán CS, Currat M. Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses. Mol Biol Evol 2023; 40:msad252. [PMID: 37992125 PMCID: PMC10715198 DOI: 10.1093/molbev/msad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.
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Affiliation(s)
- Lionel N Di Santo
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
| | | | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva CH-1205
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5
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Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
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Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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6
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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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7
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Alujević K, Streicher JW, Garcia RA, Riesgo A, Taboada S, Logan ML, Clusella-Trullas S. Mismatches between phenotype and environment shape fitness at hyperlocal scales. Proc Biol Sci 2023; 290:20230865. [PMID: 37312553 PMCID: PMC10265021 DOI: 10.1098/rspb.2023.0865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023] Open
Abstract
In the era of human-driven climate change, understanding whether behavioural buffering of temperature change is linked with organismal fitness is essential. According to the 'cost-benefit' model of thermoregulation, animals that live in environments with high frequencies of favourable thermal microclimates should incur lower thermoregulatory costs, thermoregulate more efficiently and shunt the associated savings in time and energy towards other vital tasks such as feeding, territory defence and mate acquisition, increasing fitness. Here, we explore how thermal landscapes at the scale of individual territories, physiological performance and behaviour interact and shape fitness in the southern rock agama lizard (Agama atra). We integrated laboratory assays of whole organism performance with behavioural observations in the field, fine-scale estimates of environmental temperature, and paternity assignment of offspring to test whether fitness is predicted by territory thermal quality (i.e. the number of hours that operative temperatures in a territory fall within an individual's performance breadth). Male lizards that occupied territories of low thermal quality spent more time behaviourally compensating for sub-optimal temperatures and displayed less. Further, display rate was positively associated with lizard fitness, suggesting that there is an opportunity cost to engaging in thermoregulatory behaviour that will change as climate change progresses.
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Affiliation(s)
- Karla Alujević
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch 7600, South Africa
- Department of Biology and Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, USA
| | | | - Raquel A. Garcia
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Sergio Taboada
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Facultad de Ciencias, 28049 Madrid, Spain
- Departamento de Ciencias de la Vida, EU-US Marine Biodiversity Group, Universidad de Alcalá, 28871 Alcalá de Henares, Spain
| | - Michael L. Logan
- Department of Biology and Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, USA
| | - Susana Clusella-Trullas
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch 7600, South Africa
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8
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Buckingham E, Streicher JW, Fisher‐Reid MC, Jezkova T, Wiens JJ. Population genomic analyses support sympatric origins of parapatric morphs in a salamander. Ecol Evol 2022; 12:e9537. [PMCID: PMC9702563 DOI: 10.1002/ece3.9537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Emily Buckingham
- Department of Life Sciences The Natural History Museum London UK
- Department of Life Sciences Imperial College London (South Kensington) London UK
| | - Jeffrey W. Streicher
- Department of Life Sciences The Natural History Museum London UK
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona USA
| | - M. Caitlin Fisher‐Reid
- Department of Biological Sciences Bridgewater State University Bridgewater Massachusetts USA
| | | | - John J. Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona USA
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9
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Tominaga A, Yoshikawa N, Matsui M, Nagata N, Sato Y. The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and are the key to understanding their true evolutionary processes. The genetic differentiation of the northern and Southern-Izu lineages of the Japanese newt, Cynops pyrrhogaster, was investigated through their single nucleotide polymorphism variations obtained via multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto and S-Kanto), that were not detected by mtDNA variations, in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The genetic groups are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history using the approximate Bayesian computation (ABC) approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split, and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of climatic oscillation in the Pleistocene. We conclude that the mitochondrial genome of S-Kanto was captured in Tohoku and that the original mitochondrial genome of Tohoku was entirely removed through hybridization.
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Affiliation(s)
- Atsushi Tominaga
- Faculty of Education, University of the Ryukyus , Senbaru 1, Nishihara, Okinawa 903-0213 , Japan
| | - Natsuhiko Yoshikawa
- National Museum of Nature and Science , 4-1-1 Amakubo, Tsukuba, Ibaraki 305 - 0005 , Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University , Yoshida Nihonmatsu-cho, Sakyo, Kyoto 606 - 8501 , Japan
| | - Nobuaki Nagata
- National Museum of Nature and Science , 4-1-1 Amakubo, Tsukuba, Ibaraki 305 - 0005 , Japan
| | - Yukuto Sato
- Faculty of Medicine, University of the Ryukyus , Uehara 207, Nishihara, Okinawa 903 - 0215 , Japan
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10
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Xia M, Cai M, Comes HP, Zheng L, Ohi-Toma T, Lee J, Qi Z, Konowalik K, Li P, Cameron KM, Fu C. An overlooked dispersal route of Cardueae (Asteraceae) from the Mediterranean to East Asia revealed by phylogenomic and biogeographical analyses of Atractylodes. ANNALS OF BOTANY 2022; 130:53-64. [PMID: 35533344 PMCID: PMC9295924 DOI: 10.1093/aob/mcac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/06/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS The East Asian-Tethyan disjunction pattern and its mechanisms of formation have long been of interest to researchers. Here, we studied the biogeographical history of Asteraceae tribe Cardueae, with a particular focus on the temperate East Asian genus Atractylodes DC., to understand the role of tectonic and climatic events in driving the diversification and disjunctions of the genus. METHODS A total of 76 samples of Atractylodes from 36 locations were collected for RAD-sequencing. Three single nucleotide polymorphism (SNP) datasets based on different filtering strategies were used for phylogenetic analyses. Molecular dating and ancestral distribution reconstruction were performed using both chloroplast DNA sequences (127 Cardueae samples) and SNP (36 Atractylodes samples) datasets. KEY RESULTS Six species of Atractylodes were well resolved as individually monophyletic, although some introgression was identified among accessions of A. chinensis, A. lancea and A. koreana. Dispersal of the subtribe Carlininae from the Mediterranean to East Asia occurred after divergence between Atractylodes and Carlina L. + Atractylis L. + Thevenotia DC. at ~31.57 Ma, resulting in an East Asian-Tethyan disjunction. Diversification of Atractylodes in East Asia mainly occurred from the Late Miocene to the Early Pleistocene. CONCLUSIONS Aridification of Asia and the closure of the Turgai Strait in the Late Oligocene promoted the dispersal of Cardueae from the Mediterranean to East China. Subsequent uplift of the Qinghai-Tibet Plateau as well as changes in Asian monsoon systems resulted in an East Asian-Tethyan disjunction between Atractylodes and Carlina + Atractylis + Thevenotia. In addition, Late Miocene to Quaternary climates and sea level fluctuations played major roles in the diversification of Atractylodes. Through this study of different taxonomic levels using genomic data, we have revealed an overlooked dispersal route between the Mediterranean and far East Asia (Japan/Korea) via Central Asia and East China.
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Affiliation(s)
| | | | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, Austria
| | - Li Zheng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Jiaxing Second Hospital, Jiaxing, Zhejiang, China
| | - Tetsuo Ohi-Toma
- Nature Fieldwork Center, Okayama University of Science, Okayama, Japan
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, South Korea
| | - Zhechen Qi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Kamil Konowalik
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631, Wroclaw, Poland
| | - Pan Li
- For correspondence. E-email
| | | | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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11
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Cisneros-Bernal AY, Rodríguez-Gómez F, Flores-Villela O, Fujita MK, Velasco JA, Fernández JA. Phylogeography supports lineage divergence for an endemic rattlesnake ( Crotalus ravus) of the Neotropical montane forest in the Trans-Mexican Volcanic Belt. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The formation of the Trans-Mexican Volcanic Belt (TMVB) and Pleistocene climatic fluctuations have been shown to influence the diversification of lineages and species distributed throughout central Mexico. In some taxa, however, evidence of lineage diversification is not easily recognized, as often is the case in reptiles. Here we present a phylogeographic study on a Mexican endemic rattlesnake species (Crotalus ravus), with the aim of understanding how distinct lineages are distributed across the TMVB. Genetic (mtDNA) and genomic (ddRADseq) data were generated from samples across the species’ range to evaluate phylogeographic structure, estimate phylogenetic relationships and divergence times, and perform environmental niche modeling (ENM). Both datasets recover strong phylogeographic structuring of two distinct lineages on an east-west axis, with an estimated Pleistocene divergence (~1.47 Myr). The ENM suggest that the distribution of the two lineages experienced expansion and reduction events throughout recent evolutionary time. We attribute the diversification of C. ravus lineages to geological events associated with the formation of the TMVB, as well as Quaternary climate changes, both of which have been previously recognized in co-distributed taxa in the TMVB. This work emphasizes the existence of cryptic diversification processes in a morphologically conserved species distributed in a region of complex climatic and orogenic heterogeneity.
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Affiliation(s)
- Antonio Yolocalli Cisneros-Bernal
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México , Circuito de los Posgrados S/N, coyoacán, 04510, Mexico City , Mexico
- Departamento de Biología Evolutiva, Universidad Nacional Autónoma de México, Mexico City , Circuito exterior, Ciudad Universitaria, Coyoacán, 04510 Mexico
- Totlok, A.C., Cerro del Agua, Integración Latinoamericana , Coyoacán, 04350, Mexico City , Mexico
| | - Flor Rodríguez-Gómez
- Departamento de Ingeniería Traslacional, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara , Blvd. Marcelino García Barragán 44430, Gadalajara, Jalisco , Mexico
| | - Oscar Flores-Villela
- Departamento de Biología Evolutiva, Universidad Nacional Autónoma de México, Mexico City , Circuito exterior, Ciudad Universitaria, Coyoacán, 04510 Mexico
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington , 501 S. Nedderman Drive 337 Life Science, Arlington, TX 76010-0498 , USA
| | - Julián A Velasco
- Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Investigación Científica s/n, Ciudad Universitaria , Coyoacán, 04510 Mexico City , Mexico
| | - Jesús A Fernández
- Departamento de Recursos Naturales, Universidad Autónoma de Chihuahua , Periférico Francisco R. Almada km 1, Zootecnia 31415 Chihuahua , Mexico
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12
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Laczkó L, Jordán S, Sramkó G. The
RadOrgMiner
pipeline: Automated genotyping of organellar loci from
RADseq
data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Levente Laczkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
- Department of Metagenomics University of Debrecen Nagyerdei körút 98., Debrecen, H‐4032 Hungary
| | - Sándor Jordán
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- Juhász‐Nagy Pál Doctoral School University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
| | - Gábor Sramkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
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13
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Satler JD, Herre EA, Heath TA, Machado CA, Zúñiga AG, Nason JD. Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs. Mol Ecol 2022; 31:2106-2123. [PMID: 35090071 PMCID: PMC9545327 DOI: 10.1111/mec.16373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here, we study the 19 pollinator species (Pegoscapus spp.) associated with an entire community of 16 Panamanian strangler fig species (Ficus subgenus Urostigma, section Americanae) to determine whether the previously documented history of pollinator host switching and current host sharing predicts genetic admixture among the pollinator species, as has been observed in their host figs. Specifically, we use genome‐wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and introgression among the pollinator species. In all cases, we recover well‐delimited pollinator species that contain high interspecific divergence. Even among pairs of pollinator species that currently reproduce within syconia of shared host fig species, we found no evidence of hybridization or introgression. This is in contrast to their host figs, where hybridization and introgression have been detected within this community, and more generally, within figs worldwide. Consistent with general patterns recovered among other obligate pollination mutualisms (e.g. yucca moths and yuccas), our results suggest that while hybridization and introgression are processes operating within the host plants, these processes are relatively unimportant within their associated insect pollinators.
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Affiliation(s)
- Jordan D Satler
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO AA 34002-9998, USA
| | - Tracy A Heath
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, Maryland, USA, 20742
| | | | - John D Nason
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
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14
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Cruz-Machuca TE, Palacios-Aguilar R. A new distributional record for the Martin del Campo’s Arboreal Alligator Lizard (Abronia martindelcampoi) with comments on the biogeography of arboreal Alligator-lizards in the Sierra Madre del Sur, Mexico. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.2000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Thalia E. Cruz-Machuca
- Laboratorio de Ecología, UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, México, México
| | - Ricardo Palacios-Aguilar
- Museo de Zoología “Alfonso L. Herrera”, Facultad de Ciencias, Universidad Nacional Autónoma de México, México, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er. Piso, Circuito de Posgrados, Ciudad Universitaria, Universidad Nacional Autónoma de México, Cuidad de México, México
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15
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Rivera D, Prates I, Firneno TJ, Rodrigues MT, Caldwell JP, Fujita MK. Phylogenomics, introgression, and demographic history of South American true toads (Rhinella). Mol Ecol 2021; 31:978-992. [PMID: 34784086 DOI: 10.1111/mec.16280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/24/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022]
Abstract
The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.
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Affiliation(s)
- Danielle Rivera
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Janalee P Caldwell
- Sam Noble Museum & Department of Biology, University of Oklahoma, Norman, Oklahoma, 73072-7029, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
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16
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Jin L, Liao WB, Merilä J. Genomic evidence for adaptive differentiation among
Microhyla fissipes
populations: Implications for conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme Faculty of Biological and Environmental Sciences FI‐00014 University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity School Biological Sciences The University of Hong KongHong Kong SAR
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17
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Jaynes KE, Myers EA, Gvoždík V, Blackburn DC, Portik DM, Greenbaum E, Jongsma GFM, Rödel MO, Badjedjea G, Bamba-Kaya A, Baptista NL, Akuboy JB, Ernst R, Kouete MT, Kusamba C, Masudi FM, McLaughlin PJ, Nneji LM, Onadeko AB, Penner J, Vaz Pinto P, Stuart BL, Tobi E, Zassi-Boulou AG, Leaché AD, Fujita MK, Bell RC. Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits. Mol Ecol 2021; 31:3979-3998. [PMID: 34516675 DOI: 10.1111/mec.16169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/18/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.
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Affiliation(s)
- Kyle E Jaynes
- Department of Biology, Adrian College, Michigan, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Integrative Biology, W.K. Kellogg Biological Station, Michigan State University, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, Michigan, USA
| | - Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Daniel M Portik
- Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Gregory F M Jongsma
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,Department of Biology, University of Florida, Florida, USA
| | - Mark-Oliver Rödel
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des Ressources Aquatiques, Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, République Démocratique du Congo
| | | | - Ninda L Baptista
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Faculdade de Ciências da, Universidade do Porto, Porto, Portugal.,Instituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento Rodrigues, Lubango, Angola
| | - Jeannot B Akuboy
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Marcel T Kouete
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,School of Natural Resources and Environment, University of Florida, Florida, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, République Démocratique du Congo, Lwiro
| | - Franck M Masudi
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Patrick J McLaughlin
- Bioko Biodiversity Protection Project, Drexel University, Philadelphia, Pennsylvania, USA.,Institute of Conservation Science and Learning, Bristol Zoological Society, Bristol, UK
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
| | - Abiodun B Onadeko
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Johannes Penner
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.,Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | - Pedro Vaz Pinto
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Fundação Kissama, Luanda, Angola
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, North Carolina, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | | | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
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18
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Hsiao YW, Tseng HY, Nguyen HN, Lin SM. Asymmetric acoustic signal recognition led to asymmetric gene flow between two parapatric frogs. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Correct discrimination between courtship signals could help to maintain genetic integrity between closely related species. However, asymmetric usage of signals might cause asymmetric gene flow across the contact zone. Buergeria choui and B. otai are sibling-species with a parapatric distribution pattern in Taiwan, having two narrow contact zones on the east and west sides of the island. Combining behavioural experiments with genome-wide RAD-seq analyses, we test whether the ability of signal recognition influences genetic introgression across their species boundary. The playback experiments show that all B. choui populations respond strongest to their own ‘cricket’ trills, while the western population of B. otai have evolved a strong level of reproductive character displacement by showing the inclusive usage of the unique ‘chicken’ signals. In contrast, the eastern B. otai population uses both ‘chicken’ and ‘cricket’ trills, and has a stronger preference for the latter. The weak reproductive character displacement in the eastern population has led to asymmetry genetic introgression from B. choui toward B. otai. Our results support the prediction that a more specialized signal-user, compared to its sibling, generalized signal-user, might have a higher probability of maintaining their genetic integrity in the secondary contact region.
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Affiliation(s)
- Yu-Wei Hsiao
- School of Life Science, National Taiwan Normal University, Taiwan
| | - Hui-Yun Tseng
- Department of Entomology, National Taiwan University, Taiwan
| | - Hung Ngoc Nguyen
- School of Life Science, National Taiwan Normal University, Taiwan
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Si-Min Lin
- School of Life Science, National Taiwan Normal University, Taiwan
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19
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Zhang Y, De Meyer M, Virgilio M, Feng S, Badji K, Li Z. Phylogenomic resolution of the Ceratitis FARQ complex (Diptera: Tephritidae). Mol Phylogenet Evol 2021; 161:107160. [PMID: 33794396 DOI: 10.1016/j.ympev.2021.107160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
The Ceratitis FARQ complex (formerly FAR complex) includes four frugivorous tephritids, Ceratitis fasciventris, C. anonae, C. rosa and C. quilicii, the latter two causing important agricultural losses in Africa. Although FARQ species can be identified on the basis of subtle morphological differences, they cannot be resolved as monophyletic when trying phylogenetic tree reconstructions based on mitochondrial or nuclear gene fragments except for microsatellites. In this study, we used mitogenome and genome-wide SNPs to investigate the phylogenetic relationship within the complex as well as between all four Ceratitis subgenera. The analysis of 13 species supported the monophyly of the Ceratitis subgenera Ceratitis, Ceratalaspis, Pardalaspis, and recovered Pterandrus as paraphyletic but could not properly resolve species within the FARQ complex. Conversely, gene and species tree reconstructions based on 785,484 genome-wide SNPs could consistently resolve the FARQ taxa and provide insights into their phylogenetic relationships. Gene flow was detected by TreeMix analysis from C. quilicii to C. fasciventris, suggesting the existence of introgression events in the FARQ complex. Our results suggest that genome-wide SNPs represent a suitable tool for the molecular diagnosis of FARQ species and could possibly be used to develop rapid diagnostic methods or to trace the origins of intercepted samples.
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Affiliation(s)
- Yue Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Marc De Meyer
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium.
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium.
| | - Shiqian Feng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Kemo Badji
- Crop Protection Directorate, Dakar, Senegal.
| | - Zhihong Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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20
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Firneno TJ, O'Neill JR, Portik DM, Emery AH, Townsend JH, Fujita MK. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Mol Ecol 2020; 29:3543-3559. [PMID: 32500624 DOI: 10.1111/mec.15496] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/18/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Justin R O'Neill
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Josiah H Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA.,Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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21
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Pulido‐Santacruz P, Aleixo A, Weir JT. Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*. Evolution 2020; 74:842-858. [DOI: 10.1111/evo.13902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Paola Pulido‐Santacruz
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
- Current address: Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Calle 28A No. 15 – 09 Bogotá Colombia
| | | | - Jason T. Weir
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Department of Biological SciencesUniversity of Toronto Scarborough Toronto Canada
- Department of OrnithologyRoyal Ontario Museum Toronto Canada
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22
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23
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The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes. Genes (Basel) 2019; 10:genes10121027. [PMID: 31835491 PMCID: PMC6947334 DOI: 10.3390/genes10121027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022] Open
Abstract
Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.
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24
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Peek RA, Bedwell M, O'Rourke SM, Goldberg C, Wengert GM, Miller MR. Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA. Mol Ecol 2019; 28:4636-4647. [DOI: 10.1111/mec.15236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
| | - Mallory Bedwell
- School of the Environment Washington State University Pullman WA USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis CA USA
| | - Caren Goldberg
- School of the Environment Washington State University Pullman WA USA
| | | | - Michael R. Miller
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
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25
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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26
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O'Connell KA, Santo VD, Maldonado J, Molina E, Fujita MK. A Tale of Two Skates: Comparative Phylogeography of North American Skate Species with Implications for Conservation. COPEIA 2019. [DOI: 10.1643/cg-18-114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kyle A. O'Connell
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Valentina Di Santo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138
| | - Jose Maldonado
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Erika Molina
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Matthew K. Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
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27
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Wiens JJ, Camacho A, Goldberg A, Jezkova T, Kaplan ME, Lambert SM, Miller EC, Streicher JW, Walls RL. Climate change, extinction, and Sky Island biogeography in a montane lizard. Mol Ecol 2019; 28:2610-2624. [PMID: 30843297 DOI: 10.1111/mec.15073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 02/16/2019] [Accepted: 02/26/2019] [Indexed: 12/24/2022]
Abstract
Around the world, many species are confined to "Sky Islands," with different populations in isolated patches of montane habitat. How does this pattern arise? One scenario is that montane species were widespread in lowlands when climates were cooler, and were isolated by local extinction caused by warming conditions. This scenario implies that many montane species may be highly susceptible to anthropogenic warming. Here, we test this scenario in a montane lizard (Sceloporus jarrovii) from the Madrean Sky Islands of southeastern Arizona. We combined data from field surveys, climate, population genomics, and physiology. Overall, our results support the hypothesis that this species' current distribution is explained by local extinction caused by past climate change. However, our results for this species differ from simple expectations in several ways: (a) their absence at lower elevations is related to warm winter temperatures, not hot summer temperatures; (b) they appear to exclude a low-elevation congener from higher elevations, not the converse; (c) they are apparently absent from many climatically suitable but low mountain ranges, seemingly "pushed off the top" by climates even warmer than those today; (d) despite the potential for dispersal among ranges during recent glacial periods (~18,000 years ago), populations in different ranges diverged ~4.5-0.5 million years ago and remained largely distinct; and (e) body temperatures are inversely related to climatic temperatures among sites. These results may have implications for many other Sky Island systems. More broadly, we suggest that Sky Island species may be relevant for predicting responses to future warming.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Agustín Camacho
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Aaron Goldberg
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona.,Department of Biology, Miami University, Oxford, Ohio
| | - Matthew E Kaplan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona.,Functional Genomics Core, Arizona Research Laboratories, Research, Discovery & Innovation, University of Arizona, Tucson, Arizona
| | - Shea M Lambert
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Jeffrey W Streicher
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona.,Department of Life Sciences, The Natural History Museum, London, UK
| | - Ramona L Walls
- CyVerse, Bio5 Institute, University of Arizona, Tucson, Arizona
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28
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Firneno TJ, Townsend JH. Evaluation of species boundaries in sympatric and parapatric populations of Mesoamerican toads. ZOOL SCR 2019. [DOI: 10.1111/zsc.12354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Thomas J. Firneno
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
| | - Josiah H. Townsend
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
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29
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Zarza E, Reynoso VH, Faria CMA, Emerson BC. Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation. PeerJ 2019; 7:e6744. [PMID: 31065455 PMCID: PMC6485205 DOI: 10.7717/peerj.6744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
Introgression, the transmission of genetic material of one taxon into another through hybridization, can have various evolutionary outcomes. Previous studies have detected signs of introgression between western populations of the Mexican endemic and threatened spiny-tailed iguana, Ctenosaura pectinata. However, the extent of this phenomenon along the geographic distribution of the species is unknown. Here, we use multilocus data together with detailed geographic sampling to (1) define genotypic clusters within C. pectinata; (2) evaluate geographic concordance between maternally and biparentally inherited markers; (3) examine levels of introgression between genotypic clusters, and (4) suggest taxonomic modifications in light of this information. Applying clustering methods to genotypes of 341 individuals from 49 localities of C. pectinata and the closely related C. acanthura, we inferred the existence of five genotypic clusters. Contact zones between genotypic clusters with signatures of interbreeding were detected, showing different levels of geographic discordance with mtDNA lineages. In northern localities, mtDNA and microsatellites exhibit concordant distributions, supporting the resurrection of C. brachylopha. Similar concordance is observed along the distribution of C. acanthura, confirming its unique taxonomic identity. Genetic and geographic concordance is also observed for populations within southwestern Mexico, where the recognition of a new species awaits in depth taxonomic revision. In contrast, in western localities a striking pattern of discordance was detected where up to six mtDNA lineages co-occur with only two genotypic clusters. Given that the type specimen originated from this area, we suggest that individuals from western Mexico keep the name C. pectinata. Our results have profound implications for conservation, management, and forensics of Mexican iguanas.
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Affiliation(s)
- Eugenia Zarza
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Grupo Académico de Biotecnología Ambiental, El Colegio de la Frontera Sur, Unidad Tapachula, Tapachula, Chiapas, Mexico.,CONACYT, Ciudad de México, Mexico
| | - Víctor H Reynoso
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Christiana M A Faria
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Current Affiliation: Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, Fortaleza, Ceará, Brasil
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, Spain
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30
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Testo WL, Sessa E, Barrington DS. The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae). THE NEW PHYTOLOGIST 2019; 222:604-613. [PMID: 30326543 DOI: 10.1111/nph.15544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.
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Affiliation(s)
- Weston L Testo
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - David S Barrington
- Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington, VT, 05405, USA
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31
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Crotti M, Barratt CD, Loader SP, Gower DJ, Streicher JW. Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus
). ZOOL SCR 2019. [DOI: 10.1111/zsc.12335] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Marco Crotti
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; London UK
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
| | - Christopher D. Barratt
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Simon P. Loader
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | - David J. Gower
- Department of Life Sciences; The Natural History Museum; London UK
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32
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Stobie CS, Cunningham MJ, Oosthuizen CJ, Bloomer P. Finding stories in noise: Mitochondrial portraits from RAD data. Mol Ecol Resour 2018; 19:191-205. [DOI: 10.1111/1755-0998.12953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Cora Sabriel Stobie
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Michael J. Cunningham
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Carel J. Oosthuizen
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Hatfield, Pretoria South Africa
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33
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Schield DR, Adams RH, Card DC, Corbin AB, Jezkova T, Hales NR, Meik JM, Perry BW, Spencer CL, Smith LL, García GC, Bouzid NM, Strickland JL, Parkinson CL, Borja M, Castañeda-Gaytán G, Bryson RW, Flores-Villela OA, Mackessy SP, Castoe TA. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Mol Phylogenet Evol 2018; 127:669-681. [DOI: 10.1016/j.ympev.2018.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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34
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O'Connell KA, Smith EN. The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis). Mol Phylogenet Evol 2018; 127:356-366. [DOI: 10.1016/j.ympev.2018.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 01/10/2018] [Accepted: 03/14/2018] [Indexed: 11/30/2022]
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35
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Beckman EJ, Benham PM, Cheviron ZA, Witt C. Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins. Mol Ecol 2018; 27:4350-4367. [DOI: 10.1111/mec.14795] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Elizabeth J. Beckman
- Division of Biological Sciences University of Montana Missoula Montana
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
| | - Phred M. Benham
- Division of Biological Sciences University of Montana Missoula Montana
| | | | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
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36
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Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java. Mol Phylogenet Evol 2018; 123:101-112. [DOI: 10.1016/j.ympev.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/22/2022]
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37
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Lee KM, Kivelä SM, Ivanov V, Hausmann A, Kaila L, Wahlberg N, Mutanen M. Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus. Syst Biol 2018; 67:925-939. [DOI: 10.1093/sysbio/syy029] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
| | - Sami M Kivelä
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, EE-51014 Tartu, Estonia
| | - Vladislav Ivanov
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
| | - Axel Hausmann
- SNSB – Bavarian State Collection of Zoology, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, FI-00014 University of Helsinki, P. Rautatiekatu 13, P.O. Box 17, Helsinki, Finland
| | - Niklas Wahlberg
- Department of Biology, Sölvegatan 37, Lund University, SE-223 62 Lund, Sweden
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
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38
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Cox CL, Davis Rabosky AR, Holmes IA, Reyes-Velasco J, Roelke CE, Smith EN, Flores-Villela O, McGuire JA, Campbell JA. Synopsis and taxonomic revision of three genera in the snake tribe Sonorini. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1449912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Jacobo Reyes-Velasco
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
- Evolutionary Genomics Laboratory, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Corey E. Roelke
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Eric N. Smith
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | | | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jonathan A. Campbell
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
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Kallal RJ, Fernández R, Giribet G, Hormiga G. A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches. Mol Phylogenet Evol 2018; 126:129-140. [PMID: 29635025 DOI: 10.1016/j.ympev.2018.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/05/2018] [Accepted: 04/06/2018] [Indexed: 01/01/2023]
Abstract
The orb-weaving spider family Araneidae is extremely diverse (>3100 spp.) and its members can be charismatic terrestrial arthropods, many of them recognizable by their iconic orbicular snare web, such as the common garden spiders. Despite considerable effort to better understand their backbone relationships based on multiple sources of data (morphological, behavioral and molecular), pervasive low support remains in recent studies. In addition, no overarching phylogeny of araneids is available to date, hampering further comparative work. In this study, we analyze the transcriptomes of 33 taxa, including 19 araneids - 12 of them new to this study - representing most of the core family lineages, to examine the relationships within the family using genomic-scale datasets resulting from various methodological treatments, namely ortholog selection and gene occupancy as a measure of matrix completion. Six matrices were constructed to assess these effects by varying orthology inference method and gene occupancy threshold. Orthology methods used are the benchmarking tool BUSCO and the tree-based method UPhO; three gene occupancy thresholds (45%, 65%, 85%) were used to assess the effect of missing data. Gene tree and species tree-based methods (including multi-species coalescent and concatenation approaches, as well as maximum likelihood and Bayesian inference) were used totalling 17 analytical treatments. The monophyly of Araneidae and the placement of core araneid lineages were supported, together with some previously unsound backbone divergences; these include high support for Zygiellinae as the earliest diverging subfamily (followed by Nephilinae), the placement of Gasteracanthinae as sister group to Cyclosa and close relatives, and close relationships between the Araneus + Neoscona clade and Cyrtophorinae + Argiopinae clade. Incongruences were relegated to short branches in the clade comprising Cyclosa and its close relatives. We found congruence between most of the completed analyses, with minimal topological effects from occupancy/missing data and orthology assessment. The resulting number of genes by certain combinations of orthology and occupancy thresholds being analyzed had the greatest effect on the resulting trees, with anomalous outcomes recovered from analysis of lower numbers of genes.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA.
| | - Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA; Bioinformatics and Genomics Unit, Center for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA
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40
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Ortego J, Gugger PF, Sork VL. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). THE NEW PHYTOLOGIST 2018; 218:804-818. [PMID: 29274282 DOI: 10.1111/nph.14951] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 05/15/2023]
Abstract
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, Seville, E-41092, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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41
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Roelke CE, Maldonado JA, Pope BW, Firneno TJ, Laduc TJ, Hibbitts TJ, Ryberg WA, Rains ND, Fujita MK. Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1436726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Corey E. Roelke
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Jose A. Maldonado
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Blake W. Pope
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
| | - Thomas J. Firneno
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Travis J. Laduc
- Biodiversity Collections, Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Toby J. Hibbitts
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Wade A. Ryberg
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | | | - Matthew K. Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
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42
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Leduc-Robert G, Maddison WP. Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae). BMC Evol Biol 2018; 18:24. [PMID: 29471785 PMCID: PMC5824460 DOI: 10.1186/s12862-018-1137-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 02/15/2018] [Indexed: 01/12/2023] Open
Abstract
Background Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. Results To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson’s D statistics and DFOIL. We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups. Conclusions Our results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays. Electronic supplementary material The online version of this article (10.1186/s12862-018-1137-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Wayne P Maddison
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany and Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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43
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Meik JM, Schaack S, Flores-Villela O, Streicher JW. Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1429689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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44
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Ieda R, Hosoya S, Tajima S, Atsumi K, Kamiya T, Nozawa A, Aoki Y, Tasumi S, Koyama T, Nakamura O, Suzuki Y, Kikuchi K. Identification of the sex-determining locus in grass puffer (Takifugu niphobles) provides evidence for sex-chromosome turnover in a subset of Takifugu species. PLoS One 2018; 13:e0190635. [PMID: 29293639 PMCID: PMC5749833 DOI: 10.1371/journal.pone.0190635] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/18/2017] [Indexed: 12/23/2022] Open
Abstract
There is increasing evidence for frequent turnover in sex chromosomes in vertebrates. Yet experimental systems suitable for tracing the detailed process of turnover are rare. In theory, homologous turnover is possible if the new sex-determining locus is established on the existing sex-chromosome. However, there is no empirical evidence for such an event. The genus Takifugu includes fugu (Takifugu rubripes) and its two closely-related species whose sex is most likely determined by a SNP at the Amhr2 locus. In these species, males are heterozygous, with G and C alleles at the SNP site, while females are homozygous for the C allele. To determine if a shift in the sex-determining locus occurred in another member of this genus, we used genetic mapping to characterize the sex-chromosome systems of Takifugu niphobles. We found that the G allele of Amhr2 is absent in T. niphobles. Nevertheless, our initial mapping suggests a linkage between the phenotypic sex and the chromosome 19, which harbors the Amhr2 locus. Subsequent high-resolution analysis using a sex-reversed fish demonstrated that the sex-determining locus maps to the proximal end of chromosome 19, far from the Amhr2 locus. Thus, it is likely that homologous turnover involving these species has occurred. The data also showed that there is a male-specific reduction of recombination around the sex-determining locus. Nevertheless, no evidence for sex-chromosome differentiation was detected: the reduced recombination depended on phenotypic sex rather than genotypic sex; no X- or Y-specific maker was obtained; the YY individual was viable. Furthermore, fine-scale mapping narrowed down the new sex-determining locus to the interval corresponding to approximately 300-kb of sequence in the fugu genome. Thus, T. niphobles is determined to have a young and small sex-determining region that is suitable for studying an early phase of sex-chromosome evolution and the mechanisms underlying turnover of sex chromosome.
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Affiliation(s)
- Risa Ieda
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Sho Hosoya
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shota Tajima
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Kazufumi Atsumi
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Takashi Kamiya
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Aoi Nozawa
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Yuma Aoki
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Satoshi Tasumi
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Takashi Koyama
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Osamu Nakamura
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Yuzuru Suzuki
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan
- * E-mail:
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45
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Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proc Natl Acad Sci U S A 2017; 113:7978-85. [PMID: 27432951 DOI: 10.1073/pnas.1601063113] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.
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46
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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47
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Chan KO, Alexander AM, Grismer LL, Su YC, Grismer JL, Quah ESH, Brown RM. Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs. Mol Ecol 2017; 26:5435-5450. [DOI: 10.1111/mec.14296] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - Alana M. Alexander
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology; Kaohsiung Medical University; Kaohsiung City Taiwan
| | - Jesse L. Grismer
- Department of Biological Sciences; Auburn University; Auburn AL USA
- La Kretz Center for Californian Conservation Science; Institute of the Environment and Sustainability; University of California Los Angeles; Los Angeles CA USA
| | - Evan S. H. Quah
- School of Biological Sciences; Universiti Sains Malaysia; Penang Malaysia
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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48
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Leavitt DH, Marion AB, Hollingsworth BD, Reeder TW. Multilocus phylogeny of alligator lizards ( Elgaria , Anguidae): Testing mtDNA introgression as the source of discordant molecular phylogenetic hypotheses. Mol Phylogenet Evol 2017; 110:104-121. [DOI: 10.1016/j.ympev.2017.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 12/25/2022]
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49
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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50
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Mao X, Tsagkogeorga G, Bailey SE, Rossiter SJ. Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Sebastian E. Bailey
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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