1
|
Hess J, Braude S, Ingram C, Templeton A. Population genetics of the naked mole-rat Heterocephalus glaber: The role of rivers in shaping genetic structure. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.857660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We used nested clade phylogeographic analysis (NCPA) of mitochondrial DNA sequence data to examine the processes contributing to population structure in naked mole-rats. We examined sequence variation in the (1097 bp) control region D-loop of the mitochondrial genome in 303 individuals from 174 colonies of naked mole-rats (Heterocephalus glaber) located mainly within an 870 km2 area in Meru National Park, Kenya. Four rivers were found to be correlated to a significant fragmentation inference in the NCPA. The largest pairwise divergence between haplotypes from populations separated by rivers was 2.74%, which was well over half of the divergence reported between the extremes of the distribution from southern Ethiopia to southern Kenya (4.6%). However, the size of the river (measured in current discharge) was not a good predictor of the amount of sequence divergence between populations separated by a river. It appears that a large-scale historical fragmentation event may have conflated fragmentation patterns on a smaller scale, when recent colonization and range expansion brought two old lineages together at a location with a relatively small river separating them.
Collapse
|
2
|
Lokasola AL, Lotana CB, Tungaluna GCG, Akaibe BD, Jirků M, Gvoždík V. New distributional data and genetic variation of Panaspis breviceps (Squamata: Scincidae) indicate a biogeographic connection across the Congo Basin. AFRICAN ZOOLOGY 2021. [DOI: 10.1080/15627020.2021.2007418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Albert L Lokasola
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Cédric Botshuna Lotana
- Department of Waters & Forests, Djolu Technical College, Djolu, Democratic Republic of the Congo
| | | | - Benjamin Dudu Akaibe
- Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Miloslav Jirků
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Václav Gvoždík
- National Museum, Department of Zoology, Prague, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| |
Collapse
|
3
|
Role of Geographical Gaps in the Western Ghats in Shaping Intra- and Interspecific Genetic Diversity. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00241-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
4
|
The origin of island populations of the African malaria mosquito, Anopheles coluzzii. Commun Biol 2021; 4:630. [PMID: 34040154 PMCID: PMC8155153 DOI: 10.1038/s42003-021-02168-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/21/2021] [Indexed: 11/09/2022] Open
Abstract
Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome study of 142 specimens from nine countries in continental Africa and three islands in the Gulf of Guinea. This sample set covers a large part of this species' geographic range. Our population genomic analyses included a description of the structure of mainland populations, island populations, and connectivity between them. Three genetic clusters are identified among mainland populations and genetic distances (FST) fits an isolation-by-distance model. Genomic analyses are applied to estimate the demographic history and ancestry for each island. Taken together with the unique biogeography and history of human occupation for each island, they present a coherent explanation underlying levels of genetic isolation between mainland and island populations. We discuss the relationship of our findings to the suitability of São Tomé and Príncipe islands as candidate sites for potential field trials of genetic-based malaria control strategies.
Collapse
|
5
|
Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
Collapse
Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
| |
Collapse
|
6
|
Peek RA, O'Rourke SM, Miller MR. Flow modification associated with reduced genetic health of a river‐breeding frog,
Rana boylii. Ecosphere 2021. [DOI: 10.1002/ecs2.3496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis California95616USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis California95616USA
| | - Michael R. Miller
- Department of Animal Science University of California Davis California95616USA
| |
Collapse
|
7
|
Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
Collapse
Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
| |
Collapse
|
8
|
Kopuchian C, Campagna L, Lijtmaer DA, Cabanne GS, García NC, Lavinia PD, Tubaro PL, Lovette I, Di Giacomo AS. A test of the riverine barrier hypothesis in the largest subtropical river basin in the Neotropics. Mol Ecol 2020; 29:2137-2149. [DOI: 10.1111/mec.15384] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Cecilia Kopuchian
- Laboratorio de Biología de la ConservaciónCECOAL (Centro de Ecología Aplicada del Litoral) CONICET Corrientes Argentina
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program Cornell Laboratory of Ornithology Cornell University Ithaca New York USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Darío A. Lijtmaer
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Gustavo S. Cabanne
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Natalia C. García
- Fuller Evolutionary Biology Program Cornell Laboratory of Ornithology Cornell University Ithaca New York USA
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Pablo D. Lavinia
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Pablo L. Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Irby Lovette
- Fuller Evolutionary Biology Program Cornell Laboratory of Ornithology Cornell University Ithaca New York USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Adrián S. Di Giacomo
- Laboratorio de Biología de la ConservaciónCECOAL (Centro de Ecología Aplicada del Litoral) CONICET Corrientes Argentina
| |
Collapse
|
9
|
Schmidt H, Lee Y, Collier TC, Hanemaaijer MJ, Kirstein OD, Ouledi A, Muleba M, Norris DE, Slatkin M, Cornel AJ, Lanzaro GC. Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events. Commun Biol 2019; 2:473. [PMID: 31886413 PMCID: PMC6923408 DOI: 10.1038/s42003-019-0717-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/28/2019] [Indexed: 01/20/2023] Open
Abstract
The mosquito Anopheles gambiae s.s. is distributed across most of sub-Saharan Africa and is of major scientific and public health interest for being an African malaria vector. Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros. Genetic distances between populations of A. gambiae are discordant with geographic distances but are consistent with a stepwise migration scenario in which the species increases its range from west to east Africa through consecutive founder events over the last ~200,000 years. Geological barriers like the Congo River basin and the East African rift seem to play an important role in shaping this process. Moreover, we find a high degree of genetic isolation of populations on the Comoros, confirming the potential of these islands as candidate sites for potential field trials of genetically engineered mosquitoes for malaria control.
Collapse
Affiliation(s)
- Hanno Schmidt
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Travis C. Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Mark J. Hanemaaijer
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Oscar D. Kirstein
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Ahmed Ouledi
- Université des Comores, Grande Comore, Union of the Comoros
| | | | - Douglas E. Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA 94720 USA
| | - Anthony J. Cornel
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
- Mosquito Control Research Laboratory, Department of Entomology and Nematology, University of California - Kearney Research and Extension Center, Parlier, CA 93648 USA
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| |
Collapse
|
10
|
Barratt CD, Bwong BA, Jehle R, Liedtke HC, Nagel P, Onstein RE, Portik DM, Streicher JW, Loader SP. Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians. Mol Ecol 2018; 27:4289-4308. [DOI: 10.1111/mec.14862] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/08/2018] [Accepted: 08/29/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Christopher D. Barratt
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Beryl A. Bwong
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- Herpetology Section; National Museums of Kenya; Nairobi Kenya
| | - Robert Jehle
- School of Environment and Life Sciences; University of Salford; Salford UK
| | - H. Christoph Liedtke
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- Ecology, Evolution and Developmental Group; Department of Wetland Ecology; Estación Biológica de Doñana (CSIC); Sevilla Spain
| | - Peter Nagel
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | - Renske E. Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Daniel M. Portik
- Department of Biology; The University of Texas at Arlington; Arlington Texas
- Department of Ecology and Evolutionary Biology; University of Arizona; Tucson Arizona
| | | | - Simon P. Loader
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- Department of Life Sciences; Natural History Museum; London UK
| |
Collapse
|
11
|
Naka LN, Brumfield RT. The dual role of Amazonian rivers in the generation and maintenance of avian diversity. SCIENCE ADVANCES 2018; 4:eaar8575. [PMID: 30083603 PMCID: PMC6070317 DOI: 10.1126/sciadv.aar8575] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 06/19/2018] [Indexed: 05/04/2023]
Abstract
The Amazon River and its major tributaries delimit the distributions of hundreds of terrestrial taxa. It remains unclear whether river-bounded distributions and taxon replacements reflect the historical role of rivers in generating species diversity as vicariant forces, or are the result of their role as secondary barriers, maintaining current levels of species diversity by inhibiting gene flow and population introgression. We use a community-wide comparative phylogeographic and phylogenetic approach to address the roles that the Rio Negro and the Rio Branco play in the avian speciation process in the Guiana Shield. Examining 74 pairs of ecologically similar geographic replacements that turn over across the lower Negro, we found substantial variation in the levels of genetic divergence and the inferred timing of diversification among pairs, ranging from ~0.24 to over 8 million years (Ma ago). The breadth of this variation is inconsistent with a single, shared speciation event. Coalescent simulations also rejected a simultaneous divergence scenario for pairs divided by the Rio Branco but could not reject a single diversification pulse for a subset of 12 pairs of taxa divided by the upper Negro. These results are consistent with recent geomorphological hypotheses regarding the origins of these rivers. Phylogenetically, taxon pairs represent a blend of sister (~40%) and nonsister taxa (~60%), consistent with river-associated allopatric or peripatric speciation and secondary contact, respectively. Our data provide compelling evidence that species turnover across the Rio Negro basin encompasses a mixture of histories, supporting a dual role for Amazonian rivers in the generation and maintenance of biological diversity.
Collapse
Affiliation(s)
- Luciano N. Naka
- Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
- Corresponding author.
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| |
Collapse
|
12
|
Integrative taxonomy of Afrotropical Ornithodoros (Ornithodoros) (Acari: Ixodida: Argasidae). Ticks Tick Borne Dis 2018; 9:1006-1037. [DOI: 10.1016/j.ttbdis.2018.03.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 01/26/2023]
|
13
|
Hughes DF, Tolley KA, Behangana M, Lukwago W, Menegon M, Dehling JM, Stipala J, Tilbury CR, Khan AM, Kusamba C, Greenbaum E. Cryptic diversity in Rhampholeon boulengeri (Sauria: Chamaeleonidae), a pygmy chameleon from the Albertine Rift biodiversity hotspot. Mol Phylogenet Evol 2018; 122:125-141. [PMID: 29199108 PMCID: PMC6010225 DOI: 10.1016/j.ympev.2017.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 10/03/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022]
Abstract
Several biogeographic barriers in the Central African highlands have reduced gene flow among populations of many terrestrial species in predictable ways. Yet, a comprehensive understanding of mechanisms underlying species divergence in the Afrotropics can be obscured by unrecognized levels of cryptic diversity, particularly in widespread species. We implemented a multilocus phylogeographic approach to examine diversity within the widely distributed Central African pygmy chameleon, Rhampholeon boulengeri. Gene-tree analyses coupled with a comparative coalescent-based species delimitation framework revealed R. boulengeri as a complex of at least six genetically distinct species. The spatiotemporal speciation patterns for these cryptic species conform to general biogeographic hypotheses supporting vicariance as the main factor behind patterns of divergence in the Albertine Rift, a biodiversity hotspot in Central Africa. However, we found that parapatric species and sister species inhabited adjacent habitats, but were found in largely non-overlapping elevational ranges in the Albertine Rift, suggesting that differentiation in elevation was also an important mode of divergence. The phylogeographic patterns recovered for the genus-level phylogeny provide additional evidence for speciation by isolation in forest refugia, and dating estimates indicated that the Miocene was a significant period for this diversification. Our results highlight the importance of investigating cryptic diversity in widespread species to improve understanding of diversification patterns in environmentally diverse regions such as the montane Afrotropics.
Collapse
Affiliation(s)
- Daniel F Hughes
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA.
| | - Krystal A Tolley
- South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2000, Johannesburg, South Africa
| | - Mathias Behangana
- Department of Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Wilber Lukwago
- Department of Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Michele Menegon
- Tropical Biodiversity Section, MUSE - The Science Museum of Trento, Corso del Lavoro e della Scienza 3, Trento 38123, Italy
| | - J Maximilian Dehling
- Institut für Integrierte Naturwissenschaften, Abteilung Biologie, AG Zoologie, Universität Koblenz-Landau, Universitätsstraße 1, 56070 Koblenz, Germany
| | - Jan Stipala
- School of Biosciences, University of Exeter, Tremough Campus, Penryn, Cornwall TR10 9EZ, United Kingdom
| | - Colin R Tilbury
- Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - Arshad M Khan
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, Democratic Republic of the Congo
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| |
Collapse
|
14
|
Jongsma GF, Barej MF, Barratt CD, Burger M, Conradie W, Ernst R, Greenbaum E, Hirschfeld M, Leaché AD, Penner J, Portik DM, Zassi-Boulou AG, Rödel MO, Blackburn DC. Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa. Mol Phylogenet Evol 2018; 120:274-285. [DOI: 10.1016/j.ympev.2017.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
|
15
|
Fuchs J, De Swardt DH, Oatley G, Fjeldså J, Bowie RCK. Habitat‐driven diversification, hybridization and cryptic diversity in the Fork‐tailed Drongo (Passeriformes: Dicruridae:
Dicrurus adsimilis
). ZOOL SCR 2018. [DOI: 10.1111/zsc.12274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité UMR7205 CNRS MNHN UPMC EPHE Sorbonne Universités, Muséum National d'Histoire Naturelle Paris France
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch South Africa
| | | | - Graeme Oatley
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch South Africa
- Department of Zoology and Lab of Ornithology Faculty of Science Palacky University Olomouc Czech Republic
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch South Africa
| |
Collapse
|
16
|
|
17
|
Huntley JW, Harvey JA, Pavia M, Boano G, Voelker G. The systematics and biogeography of the Bearded Greenbuls (Aves: Criniger) reveals the impact of Plio-Pleistocene forest fragmentation on Afro-tropical avian diversity. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jerry W Huntley
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TX, USA
| | - Johanna A Harvey
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TX, USA
| | - Marco Pavia
- University of Torino, DST, via Valperga Caluso Torino, Italy
| | - Giovanni Boano
- Museo Civico di Storia Naturale, Cascina Vigna, Carmagnola, Italy
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TX, USA
| |
Collapse
|
18
|
Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot. Mol Phylogenet Evol 2017; 116:157-171. [DOI: 10.1016/j.ympev.2017.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 11/21/2022]
|
19
|
Bell RC, Parra JL, Badjedjea G, Barej MF, Blackburn DC, Burger M, Channing A, Dehling JM, Greenbaum E, Gvoždík V, Kielgast J, Kusamba C, Lötters S, McLaughlin PJ, Nagy ZT, Rödel M, Portik DM, Stuart BL, VanDerWal J, Zassi‐Boulou AG, Zamudio KR. Idiosyncratic responses to climate‐driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands. Mol Ecol 2017; 26:5223-5244. [DOI: 10.1111/mec.14260] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/03/2017] [Accepted: 07/12/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
- Museum of Vertebrate Zoology University of California, Berkeley CA USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados Instituto de Biología Universidad de Antioquia Medellín Colombia
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des ressources Aquatiques Centre de Surveillance de la Biodiversité Kisangani Democratic Republic of the Congo
| | - Michael F. Barej
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - David C. Blackburn
- Florida Museum of Natural History University of Florida Gainesville FL USA
- Department of Herpetology California Academy of Sciences San Francisco CA USA
| | - Marius Burger
- African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
- Flora Fauna & Man, Ecological Services Ltd. Tortola British Virgin Islands
| | - Alan Channing
- Biodiversity and Conservation Biology Department University of the Western Cape Bellville South Africa
| | - Jonas Maximilian Dehling
- Abteilung Biologie Institut für Integrierte Naturwissenschaften Universität Koblenz‐Landau Koblenz Germany
| | - Eli Greenbaum
- Department of Biological Sciences University of Texas at El Paso El Paso TX USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology Czech Academy of Sciences Brno Czech Republic
- Department of Zoology National Museum Prague Czech Republic
| | - Jos Kielgast
- Section of Freshwater Biology Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark Copenhagen Denmark
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie Département de Biologie Centre de Recherche en Sciences Naturelles Lwiro Democratic Republic of the Congo
| | | | | | - Zoltán T. Nagy
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
- Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Mark‐Oliver Rödel
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Daniel M. Portik
- Museum of Vertebrate Zoology University of California, Berkeley CA USA
- Department of Biology University of Texas Arlington TX USA
| | | | - Jeremy VanDerWal
- Centre for Tropical Biodiveristy & Climate Change College of Science and Engineering James Cook University Townsville Qld Australia
- Division of Research and Innovation eResearch Centre James Cook University Townsville Qld Australia
| | | | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| |
Collapse
|
20
|
Herrera JP. The Effects of Biogeography and Biotic Interactions on Lemur Community Assembly. INT J PRIMATOL 2017. [DOI: 10.1007/s10764-017-9974-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
21
|
Voelker G, Tobler M, Prestridge HL, Duijm E, Groenenberg D, Hutchinson MR, Martin AD, Nieman A, Roselaar CS, Huntley JW. Three new species of Stiphrornis (Aves: Muscicapidae) from the Afro-tropics, with a molecular phylogenetic assessment of the genus. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1226978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Heather L. Prestridge
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Elza Duijm
- Naturalis Biodiversity Center, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Dick Groenenberg
- Naturalis Biodiversity Center, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Mark R. Hutchinson
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Alyssa D. Martin
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Aline Nieman
- Naturalis Biodiversity Center, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Cees S. Roselaar
- Naturalis Biodiversity Center, Vertebrate Department, PO Box 9517, 2300 RA Leiden, the Netherlands
| | - Jerry W. Huntley
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
22
|
Fuchs J, Fjeldså J, Bowie RCK. Diversification across major biogeographic breaks in the African Shining/Square‐tailed Drongos complex (Passeriformes: Dicruridae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12191] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité UMR7205 CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d'Histoire Naturelle CP 51, 57 rue Cuvier F‐75231 Paris Cedex 05 France
| | - Jon Fjeldså
- Centre of Macroecology, Evolution and Climate Zoological Museum University of Copenhagen Universitetsparken 15 DK‐2100 Copenhagen Denmark
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California 3101 Valley Life Science Building Berkeley CA 94720‐3160 USA
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch 7701 South Africa
| |
Collapse
|
23
|
Huntley JW, Voelker G. Cryptic diversity in Afro-tropical lowland forests: The systematics and biogeography of the avian genus Bleda. Mol Phylogenet Evol 2016; 99:297-308. [DOI: 10.1016/j.ympev.2016.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/28/2016] [Accepted: 04/02/2016] [Indexed: 01/18/2023]
|
24
|
Takemoto H, Kawamoto Y, Furuichi T. How did bonobos come to range south of the congo river? Reconsideration of the divergence of Pan paniscus from other Pan populations. Evol Anthropol 2016; 24:170-84. [PMID: 26478139 DOI: 10.1002/evan.21456] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
While investigating the genetic structure in wild bonobos,(1) we realized that the widely accepted scenario positing that the Pleistocene appearance of the Congo River separated the common ancestor of chimpanzees (Pan troglodytes) and bonobos (P. paniscus) into two species is not supported by recent geographical knowledge about the formation of the Congo River. We explored the origin of bonobos using a broader biogeographical perspective by examining local faunas in the central African region. The submarine Congo River sediments and paleotopography of central Africa show that the Congo River has functioned as a geographical barrier for the last 34 million years. This evidence allows us to hypothesize that when the river was first formed, the ancestor of bonobos did not inhabit the current range of the species on the left bank of the Congo River but that, during rare times when the Congo River discharge decreased during the Pleistocene, one or more founder populations of ancestral Pan paniscus crossed the river to its left bank. The proposed scenario for formation of the Congo River and the corridor hypothesis for an ancestral bonobo population is key to understanding the distribution of great apes and their evolution.
Collapse
|
25
|
Robin VV, Vishnudas CK, Gupta P, Ramakrishnan U. Deep and wide valleys drive nested phylogeographic patterns across a montane bird community. Proc Biol Sci 2016; 282:rspb.2015.0861. [PMID: 26085588 DOI: 10.1098/rspb.2015.0861] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Montane species distributions interrupted by valleys can lead to range fragmentation, differentiation and ultimately speciation. Paleoclimatic fluctuations may accentuate or reduce such diversification by temporally altering the extent of montane habitat and may affect species differentially. We examined how an entire montane bird community of the Western Ghats--a linear, coastal tropical mountain range--responds to topographic valleys that host different habitats. Using genetic data from 23 species (356 individuals) collected across nine locations, we examined if different species in the community reveal spatial concordance in population differentiation, and whether the timing of these divergences correlate with climatic events. Our results reveal a nested effect of valleys, with several species (10 of 23) demonstrating the oldest divergences associated with the widest and deepest valley in the mountain range, the Palghat Gap. Further, a subset of these 10 species revealed younger divergences across shallower, narrower valleys. We recovered discordant divergence times for all valley-affected montane birds, mostly in the Pleistocene, supporting the Pliestocene-pump hypotheses and highlighting the role of climatic fluctuations during this period in driving species evolution. A majority of species remain unaffected by valleys, perhaps owing to geneflow or extinction-recolonization dynamics. Studying almost the entire community allowed us to uncover a range of species' responses, including some generalizable and other unpredicted patterns.
Collapse
Affiliation(s)
- V V Robin
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - C K Vishnudas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Pooja Gupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| |
Collapse
|
26
|
Light JE, Nessner CE, Gustafsson DR, Wise SR, Voelker G. Remarkable levels of avian louse (Insecta: Phthiraptera) diversity in the Congo Basin. ZOOL SCR 2016. [DOI: 10.1111/zsc.12170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jessica E. Light
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
| | - Caitlin E. Nessner
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
| | - Daniel R. Gustafsson
- Department of Biology; University of Utah; 257 South 1400 East, Room 201 Salt Lake City UT 84112 USA
| | - Samantha R. Wise
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
| |
Collapse
|
27
|
Hirschfeld M, Blackburn DC, Burger M, Greenbaum E, Zassi-Boulou AG, Rödel MO. Two new species of long-fingered frogs of the genus Cardioglossa (Anura: Arthroleptidae) from Central African rainforests. AFR J HERPETOL 2015. [DOI: 10.1080/21564574.2015.1052102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Mareike Hirschfeld
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - David C. Blackburn
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Marius Burger
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
- Flora Fauna & Man, Ecological Services Ltd. Tortola, British Virgin Islands
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX 79968, USA
| | - Ange-Ghislain Zassi-Boulou
- Institut National de Recherche en Sciences Exactes et Naturelles, BP 2400 Brazzaville, République du Congo
| | - Mark-Oliver Rödel
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| |
Collapse
|
28
|
Koen E, Bowman J, Wilson P. Isolation of peripheral populations of Canada lynx (Lynx canadensis). CAN J ZOOL 2015. [DOI: 10.1139/cjz-2014-0227] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Landscape barriers to gene flow, such as rivers, can affect animal populations by limiting the potential for rescue of these isolated populations. We tested the riverine barrier hypothesis, predicting that the St. Lawrence River in eastern Canada would cause genetic divergence of Canada lynx (Lynx canadensis Kerr, 1792) populations by restricting dispersal and gene flow. We sampled 558 lynx from eastern Canada and genotyped these at 14 microsatellite loci. We found three genetic clusters, defined by the St. Lawrence River and the Strait of Belle Isle, a waterway separating Newfoundland from mainland Canada. However, these waterways were not absolute barriers, as we found 24 individuals that appeared to have crossed them. Peripheral populations of lynx are threatened in parts of Canada and the USA, and it is thought that these populations are maintained by immigration from the core. Our findings suggest that in eastern North America, rescue might be less likely because the St. Lawrence River restricts dispersal. We found that ice cover was often sufficient to allow lynx to walk across the ice in winter. If lynx used ice bridges in winter, then climate warming could cause a reduction in the extent and longevity of river and sea ice, further isolating these peripheral lynx populations.
Collapse
Affiliation(s)
- E.L. Koen
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - J. Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - P.J. Wilson
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| |
Collapse
|
29
|
Fuchs J, Bowie RC. Concordant genetic structure in two species of woodpecker distributed across the primary West African biogeographic barriers. Mol Phylogenet Evol 2015; 88:64-74. [DOI: 10.1016/j.ympev.2015.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 12/21/2022]
|
30
|
Khan NF, Murdoch KC, Feldheim KA, Marks BD, Cordeiro NJ. Isolation and development of microsatellite loci in an African Woodpecker (Campethera nivosa) using polymerase chain reaction and DNA sequencing. BMC Res Notes 2015; 8:201. [PMID: 26025432 PMCID: PMC4449581 DOI: 10.1186/s13104-015-1165-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Buff-spotted Woodpecker (Campethera nivosa) is a resident bird species that is distributed in lowland rainforest habitats from western to eastern Africa. We developed species-specific microsatellite markers to examine the population genetics of this species. FINDINGS Twenty-one microsatellite loci were isolated from C. nivosa. Of these, 15 were found to amplify consistently. These loci were then tested for variability in 15 individuals from different lowland forest localities. The number of alleles ranged from 3 to 13 per locus, with observed and expected heterozygosity ranging from 0.100 to 0.917 and 0.485 to 0.901, respectively. Four loci exhibited significant heterozygote deficiency while one had an excess of heterozygotes. None of the loci exhibited linkage disequilibrium. CONCLUSION These polymorphic microsatellite markers will be used to study genetic variability in populations of C. nivosa across either sides of the Congo River to evaluate the effect of the river as a barrier to gene flow.
Collapse
Affiliation(s)
- Nausheen F Khan
- Department of Biological and Chemical Sciences, Roosevelt University, 430S Michigan Ave, Chicago, USA.
| | - Kellie C Murdoch
- Pritzker Laboratory for Molecular Systematics and Evolution, Integrative Research Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA. .,Gantz Family Collections Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Integrative Research Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| | - Ben D Marks
- Gantz Family Collections Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| | - Norbert J Cordeiro
- Department of Biological and Chemical Sciences, Roosevelt University, 430S Michigan Ave, Chicago, USA. .,Pritzker Laboratory for Molecular Systematics and Evolution, Integrative Research Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| |
Collapse
|
31
|
Link A, Valencia LM, Céspedes LN, Duque LD, Cadena CD, Di Fiore A. Phylogeography of the Critically Endangered Brown Spider Monkey (Ateles hybridus): Testing the Riverine Barrier Hypothesis. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9840-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
32
|
Anthony NM, Atteke C, Bruford MW, Dallmeier F, Freedman A, Hardy O, Ibrahim B, Jeffery KJ, Johnson M, Lahm SA, Lepengue N, Lowenstein JH, Maisels F, Mboumba JF, Mickala P, Morgan K, Ntie S, Smith TB, Sullivan JP, Verheyen E, Gonder MK. Evolution and Conservation of Central African Biodiversity: Priorities for Future Research and Education in the Congo Basin and Gulf of Guinea. Biotropica 2014. [DOI: 10.1111/btp.12188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicola M. Anthony
- Department of Biological Sciences; University of New Orleans; New Orleans Louisiana 70148 U.S.A
| | - Christiane Atteke
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Michael W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff CF10 3TL U.K
| | - Francisco Dallmeier
- Smithsonian Conservation Biology Institute; Center for Conservation Education and Sustainability; Box 37012 MRC 705 Washington DC 20013-7012 U.S.A
| | - Adam Freedman
- Department of Ecology and Evolutionary Biology and Center for Tropical Research; Institute of Environment and Sustainability; University of California Los Angeles; Los Angeles California 90092 U.S.A
- Department of Organismic and Evolutionary Biology; Harvard University; Boston Massachusetts U.S.A
| | - Olivier Hardy
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP 160/12 1050 Brussels Belgium
| | - Brama Ibrahim
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux; Libreville BP 20379 Gabon
- School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
- Institut de Recherche en Écologie Tropicale; BP13354 Libreville Gabon
| | - Mireille Johnson
- Gabon Biodiversity Program; Center for Conservation Education and Sustainability; Smithsonian Conservation Biology Institute; B.P. 48 Gamba Gabon
| | - Sally A. Lahm
- Department of Global Health; George Washington University; Washington DC 20037 U.S.A
| | - Nicaise Lepengue
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Jacob H. Lowenstein
- Department of Ecology Evolution and Environmental Biology; Columbia University; New York New York 10027 U.S.A
- Division of Vertebrate Zoology; American Museum of Natural History; New York New York 10024 U.S.A
| | - Fiona Maisels
- School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
- Wildlife Conservation Society; 2300 Southern Boulevard New York New York 10460 U.S.A
| | - Jean-François Mboumba
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
- Equipe Biodiversité et Gestion des Territoires; UMR 7204 Muséum National d'Histoire Naturelle; Université de Rennes 1; Rennes France
| | - Patrick Mickala
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Katy Morgan
- Department of Biological Sciences; University of New Orleans; New Orleans Louisiana 70148 U.S.A
| | - Stephan Ntie
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology and Center for Tropical Research; Institute of Environment and Sustainability; University of California Los Angeles; Los Angeles California 90092 U.S.A
| | - John P. Sullivan
- Cornell University Museum of Vertebrates; Ithaca New York 14850 U.S.A
| | - Erik Verheyen
- OD Taxonomy and Phylogeny; Vertebrates; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
- Evolutionary Biology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171 2020 Antwerpen Belgium
| | - Mary K. Gonder
- Department of Biology; Drexel University; Philadelphia Pennsylvannia 19104 U.S.A
| |
Collapse
|
33
|
Amei A, Smith BT. Robust estimates of divergence times and selection with a poisson random field model: a case study of comparative phylogeographic data. Genetics 2014; 196:225-33. [PMID: 24142896 PMCID: PMC3872187 DOI: 10.1534/genetics.113.157776] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 10/11/2013] [Indexed: 11/18/2022] Open
Abstract
Mutation frequencies can be modeled as a Poisson random field (PRF) to estimate speciation times and the degree of selection on newly arisen mutations. This approach provides a quantitative theory for comparing intraspecific polymorphism with interspecific divergence in the presence of selection and can be used to estimate population genetic parameters. Although the original PRF model has been extended to more general biological settings to make statistical inference about selection and divergence among model organisms, it has not been incorporated into phylogeographic studies that focus on estimating population genetic parameters for nonmodel organisms. Here, we modified a recently developed time-dependent PRF model to independently estimate genetic parameters from a nuclear and mitochondrial DNA data set of 22 sister pairs of birds that have diverged across a biogeographic barrier. We found that species that inhabit humid habitats had more recent divergence times and larger effective population sizes than those that inhabit drier habitats, and divergence time estimated from the PRF model were similar to estimates from a coalescent species-tree approach. Selection coefficients were higher in sister pairs that inhabited drier habitats than in those in humid habitats, but overall the mitochondrial DNA was under weak selection. Our study indicates that PRF models are useful for estimating various population genetic parameters and serve as a framework for incorporating estimates of selection into comparative phylogeographic studies.
Collapse
Affiliation(s)
- Amei Amei
- Department of Mathematical Sciences, University of Nevada, Las Vegas, Nevada 89154
| | - Brian Tilston Smith
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803
| |
Collapse
|