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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Abstract
Ecotourism can fuel an important source of financial income for African countries and can therefore help biodiversity policies in the continent. Translocations can be a powerful tool to spread economic benefits among countries and communities; yet, to be positive for biodiversity conservation, they require a basic knowledge of conservation units through appropriate taxonomic research. This is not always the case, as taxonomy was considered an outdated discipline for almost a century, and some plurality in taxonomic approaches is incorrectly considered as a disadvantage for conservation work. As an example, diversity of the genus Giraffa and its recent taxonomic history illustrate the importance of such knowledge for a sound conservation policy that includes translocations. We argue that a fine-grained conservation perspective that prioritizes all remaining populations along the Nile Basin is needed. Translocations are important tools for giraffe diversity conservation, but more discussion is needed, especially for moving new giraffes to regions where the autochthonous taxa/populations are no longer existent. As the current discussion about the giraffe taxonomy is too focused on the number of giraffe species, we argue that the plurality of taxonomic and conservation approaches might be beneficial, i.e., for defining the number of units requiring separate management using a (majority) consensus across different concepts (e.g., MU—management unit, ESU—evolutionary significant unit, and ECU—elemental conservation unit). The taxonomically sensitive translocation policy/strategy would be important for the preservation of current diversity, while also supporting the ecological restoration of some regions within rewilding. A summary table of the main translocation operations of African mammals that have underlying problems is included. Therefore, we call for increased attention toward the taxonomy of African mammals not only as the basis for sound conservation but also as a further opportunity to enlarge the geographic scope of ecotourism in Africa.
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Abstract
The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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Affiliation(s)
- Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
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Kotzé A, Smith RM, Moodley Y, Luikart G, Birss C, Van Wyk AM, Grobler JP, Dalton DL. Lessons for conservation management: Monitoring temporal changes in genetic diversity of Cape mountain zebra (Equus zebra zebra). PLoS One 2019; 14:e0220331. [PMID: 31365543 PMCID: PMC6668792 DOI: 10.1371/journal.pone.0220331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/12/2019] [Indexed: 11/23/2022] Open
Abstract
The Cape mountain zebra (Equus zebra zebra) is a subspecies of mountain zebra endemic to South Africa. The Cape mountain zebra experienced near extinction in the early 1900's and their numbers have since recovered to more than 4,800 individuals. However, there are still threats to their long-term persistence. A previous study reported that Cape mountain zebra had low genetic diversity in three relict populations and that urgent conservation management actions were needed to mitigate the risk of further loss. As these suggestions went largely unheeded, we undertook the present study, fifteen years later to determine the impact of management on genetic diversity in three key populations. Our results show a substantial loss of heterozygosity across the Cape mountain zebra populations studied. The most severe losses occurred at De Hoop Nature Reserve where expected heterozygosity reduced by 22.85% from 0.385 to 0.297. This is alarming, as the De Hoop Nature Reserve was previously identified as the most genetically diverse population owing to its founders originating from two of the three remaining relict stocks. Furthermore, we observed a complete loss of multiple private alleles from all populations, and a related reduction in genetic structure across the subspecies. These losses could lead to inbreeding depression and reduce the evolutionary potential of the Cape mountain zebra. We recommend immediate implementation of evidence-based genetic management and monitoring to prevent further losses, which could jeopardise the long term survival of Cape mountain zebra, especially in the face of habitat and climate change and emerging diseases.
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Affiliation(s)
- Antoinette Kotzé
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Rae M. Smith
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Gordon Luikart
- Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Program, Fish and Wildlife Genomics Group, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | | | - Anna M. Van Wyk
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - J. Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Desiré L. Dalton
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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Spaan RS, Epps CW, Ezenwa VO, Jolles AE. Why did the buffalo cross the park? Resource shortages, but not infections, drive dispersal in female African buffalo ( Syncerus caffer). Ecol Evol 2019; 9:5651-5663. [PMID: 31160988 PMCID: PMC6540691 DOI: 10.1002/ece3.5145] [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: 12/18/2018] [Revised: 03/06/2019] [Accepted: 03/13/2019] [Indexed: 12/04/2022] Open
Abstract
Dispersal facilitates population health and maintains resilience in species via gene flow. Adult dispersal occurs in some species, is often facultative, and is poorly understood, but has important management implications, particularly with respect to disease spread. Although the role of adult dispersal in spreading disease has been documented, the potential influence of disease on dispersal has received little attention. African buffalo (Syncerus caffer) are wide-ranging and harbor many pathogens that can affect nearby livestock. Dispersal of adult buffalo has been described, but ecological and social drivers of buffalo dispersal are poorly understood. We investigated drivers of adult buffalo dispersal during a 4-year longitudinal study at Kruger National Park, South Africa. We monitored the spatial movement of 304 female buffalo in two focal areas using satellite and radio collars, capturing each buffalo every 6 months to assess animal traits and disease status. We used generalized linear mixed models to determine whether likelihood of dispersal for individual female buffalo was influenced by animal traits, herd identity, environmental variables, gastrointestinal parasites, or microparasite infections. The likelihood and drivers of buffalo dispersal varied by herd, area, and year. In the Lower Sabie herd, where resources were abundant, younger individuals were more likely to disperse, with most dispersal occurring in the early wet season and during an unusually dry year, 2009. In the resource-poor Crocodile Bridge area, buffalo in poor condition were most likely to disperse. Our findings suggest that dispersal of female buffalo is driven by either seasonal (Lower Sabie) or perhaps social (Crocodile Bridge) resource restriction, indicating resource limitation and dispersal decisions are tightly linked for this social ungulate. We found no direct effects of infections on buffalo dispersal, assuaging fears that highly infectious individuals might be more prone to dispersing, which could accelerate the spatial spread of infectious diseases.
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Affiliation(s)
- Robert S. Spaan
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOregon
| | - Clinton W. Epps
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOregon
| | - Vanessa O. Ezenwa
- Department of Infectious Diseases, Odum School of EcologyUniversity of GeorgiaAthensGeorgia
| | - Anna E. Jolles
- Department of Biomedical SciencesOregon State UniversityCorvallisOregon
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
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7
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Kaczensky P, Kovtun E, Habibrakhmanov R, Hemami MR, Khaleghi A, Linnell JDC, Rustamov E, Sklyarenko S, Walzer C, Zuther S, Kuehn R. Genetic characterization of free-ranging Asiatic wild ass in Central Asia as a basis for future conservation strategies. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1086-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Pedersen CET, Albrechtsen A, Etter PD, Johnson EA, Orlando L, Chikhi L, Siegismund HR, Heller R. A southern African origin and cryptic structure in the highly mobile plains zebra. Nat Ecol Evol 2018; 2:491-498. [PMID: 29358610 DOI: 10.1038/s41559-017-0453-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/14/2017] [Indexed: 12/30/2022]
Abstract
The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi). Surprisingly, the population genetic structure does not mirror the morphology-based subspecies delineation, underlining the dangers of basing management units exclusively on morphological variation. We use demographic modelling to provide insights into the past phylogeography of the species. The results identify a southern African location as the most likely source region from which all extant populations expanded around 370,000 years ago. We show evidence for inclusion of the extinct and phenotypically divergent quagga (Equus quagga quagga) in the plains zebra variation and reveal that it was less divergent from the other subspecies than the northernmost (Ugandan) extant population.
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Affiliation(s)
- Casper-Emil T Pedersen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lounes Chikhi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Centre National de la Recherche Scientifique, Université Paul Sabatier, École Nationale de Formation Agronomique, UMR 5174 Laboratoire Évolution et Diversité Biologique, Toulouse, France
| | - Hans R Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark.
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Groves CP, Cotterill FPD, Gippoliti S, Robovský J, Roos C, Taylor PJ, Zinner D. Species definitions and conservation: a review and case studies from African mammals. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0976-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Ito H, Ogden R, Langenhorst T, Inoue-Murayama M. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations. Zoo Biol 2016; 36:87-94. [PMID: 27981608 DOI: 10.1002/zoo.21342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 11/12/2022]
Abstract
Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hideyuki Ito
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Kyoto City Zoo, Kyoto, Japan
| | - Rob Ogden
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | | | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
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11
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Niedziałkowska M, Jędrzejewska B, Danyłow J, Niedziałkowski K. Diverse rates of gene flow and long-distance migration in two moose Alces alces subpopulations in Europe. MAMMAL RES 2016. [DOI: 10.1007/s13364-016-0274-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Population genetic diversity and hybrid detection in captive zebras. Sci Rep 2015; 5:13171. [PMID: 26294133 PMCID: PMC4544005 DOI: 10.1038/srep13171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/20/2015] [Indexed: 01/24/2023] Open
Abstract
Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy’s zebra E. grevyi and the mountain zebra E. zebra. The Grevy’s zebra and the mountain zebra are endangered, and hybridization between the Grevy’s zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy’s zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy’s and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy’s zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy’s zebra.
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Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L. Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene. Mol Ecol 2015; 24:2507-20. [PMID: 25827243 DOI: 10.1111/mec.13179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/11/2015] [Accepted: 03/18/2015] [Indexed: 11/30/2022]
Abstract
Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.
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Affiliation(s)
- Céline Stoffel
- Department of Ecology and Evolution, Laboratory for Conservation Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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Renan S, Greenbaum G, Shahar N, Templeton AR, Bouskila A, Bar-David S. Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass. Mol Ecol 2015; 24:1433-46. [PMID: 25728575 DOI: 10.1111/mec.13131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
Abstract
Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.
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Affiliation(s)
- Sharon Renan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 85104, Israel; Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 84990, Israel
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Tong W, Shapiro B, Rubenstein DI. Genetic relatedness in two-tiered plains zebra societies suggests that females choose to associate with kin. BEHAVIOUR 2015. [DOI: 10.1163/1568539x-00003314] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
How kinship structures alter inclusive fitness benefits or competition costs to members of a group can explain variation in animal societies. We present rare data combining behavioural associations and genetic relatedness to determine the influence of sex differences and kinship in structuring a two-tiered zebra society. We found a significantly positive relationship between the strength of behavioural association and relatedness. Female relatedness within herds was higher than chance, suggesting that female kin drive herd formation, and consistent with evidence that lactating females preferentially group into herds to dilute predation risk. In contrast, male relatedness across harems in a herd was no different from relatedness across herds, suggesting that although stallions benefit from associating to fend off bachelors, they do not preferentially form kin coalitions. Although both sexes disperse, we found that most harems contained adult relatives, implying limited female dispersal distances and inbreeding in this population, with potential conservation consequences.
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Affiliation(s)
- Wenfei Tong
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Beth Shapiro
- Department of Biology, The Pennsylvania State University, 326 Mueller Laboratory, University Park, PA 16802, USA
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, 106A Guyot Hall, Princeton University, Princeton, NJ 08544-2016, USA
- Mpala Research Center, PO Box 155, Nanyuki, Kenya
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Larison B, Harrigan RJ, Thomassen HA, Rubenstein DI, Chan-Golston AM, Li E, Smith TB. How the zebra got its stripes: a problem with too many solutions. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140452. [PMID: 26064590 PMCID: PMC4448797 DOI: 10.1098/rsos.140452] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/15/2014] [Indexed: 05/30/2023]
Abstract
The adaptive significance of zebra stripes has thus far eluded understanding. Many explanations have been suggested, including social cohesion, thermoregulation, predation evasion and avoidance of biting flies. Identifying the associations between phenotypic and environmental factors is essential for testing these hypotheses and substantiating existing experimental evidence. Plains zebra striping pattern varies regionally, from heavy black and white striping over the entire body in some areas to reduced stripe coverage with thinner and lighter stripes in others. We examined how well 29 environmental variables predict the variation in stripe characteristics of plains zebra across their range in Africa. In contrast to recent findings, we found no evidence that striping may have evolved to escape predators or avoid biting flies. Instead, we found that temperature successfully predicts a substantial amount of the stripe pattern variation observed in plains zebra. As this association between striping and temperature may be indicative of multiple biological processes, we suggest that the selective agents driving zebra striping are probably multifarious and complex.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Ryan J. Harrigan
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Henri A. Thomassen
- Institute for Evolution and Ecology, University of Tübingen, Building E, Floor 4, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Alec M. Chan-Golston
- Department of Mathematics, University of California, 520 Portola Plaza, Math Sciences Building 6363, Los Angeles, CA 90095, USA
| | - Elizabeth Li
- Department of Mathematics, University of California, 520 Portola Plaza, Math Sciences Building 6363, Los Angeles, CA 90095, USA
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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17
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Mager KH, Colson KE, Groves P, Hundertmark KJ. Population structure over a broad spatial scale driven by nonanthropogenic factors in a wide-ranging migratory mammal, Alaskan caribou. Mol Ecol 2014; 23:6045-57. [DOI: 10.1111/mec.12999] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Karen H. Mager
- Department of Biology and Wildlife; University of Alaska Fairbanks; P. O. Box 756100 Fairbanks AK 99775 USA
| | - Kevin E. Colson
- Institute of Arctic Biology; University of Alaska Fairbanks; P. O. Box 757000 Fairbanks AK 99775 USA
| | - Pam Groves
- Institute of Arctic Biology; University of Alaska Fairbanks; P. O. Box 757000 Fairbanks AK 99775 USA
| | - Kris J. Hundertmark
- Department of Biology and Wildlife; University of Alaska Fairbanks; P. O. Box 756100 Fairbanks AK 99775 USA
- Institute of Arctic Biology; University of Alaska Fairbanks; P. O. Box 757000 Fairbanks AK 99775 USA
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18
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Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci U S A 2014; 111:18655-60. [PMID: 25453089 DOI: 10.1073/pnas.1412627111] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.
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Heller R, Frandsen P, Lorenzen ED, Siegismund HR. Is diagnosability an indicator of speciation? Response to "Why one century of phenetics is enough". Syst Biol 2014; 63:833-7. [PMID: 24831669 DOI: 10.1093/sysbio/syu034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, DenmarkDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
| | - Eline Deirdre Lorenzen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, DenmarkDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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Kebede F, Rosenbom S, Khalatbari L, Moehlman PD, Beja-Pereira A, Bekele A. Genetic diversity of the Ethiopian Grevy's zebra (Equus grevyi) populations that includes a unique population of the Alledeghi Plain. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:397-400. [PMID: 24660908 DOI: 10.3109/19401736.2014.898276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The endangered Grevy's Zebra (Equus grevyi) is confined to the Horn of Africa, specifically Ethiopia and Kenya. It is threatened by habitat loss and fragmentation due to human encroachment of historic range. Knowledge of population genetics is essential for the development of appropriate conservation actions and management. The focus of this study was to assess the heterogeneity and genetic distinctiveness of the two Grevy's zebra populations in Ethiopia. Non-invasive fecal samples (N = 120) were collected during 2009-2010 from Grevy's zebra populations in the Alledeghi Wildlife Reserve and the Sarite area, Ethiopia. Analyses of a 329 bp of the mtDNA control region of 47 sequences, revealed the existence of two unreported haplotypes in the northern population of Alledeghi, that were not shared with the southern population of Sarite. The Sarite population is contiguous with the Grevy's zebra population in Kenya. The nucleotide diversity levels found in both the populations are extremely low.
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Affiliation(s)
- Fanuel Kebede
- a Ethiopian Wildlife Conservation Authority , Addis Ababa , Ethiopia
| | - Sonia Rosenbom
- b Research Centre for Biodiversity and Genetic Resources (CIBIO), University of Porto , Vairão , Portugal
| | - Leili Khalatbari
- b Research Centre for Biodiversity and Genetic Resources (CIBIO), University of Porto , Vairão , Portugal
| | | | - Albano Beja-Pereira
- b Research Centre for Biodiversity and Genetic Resources (CIBIO), University of Porto , Vairão , Portugal
| | - Afework Bekele
- d Department of Zoological Sciences , Addis Ababa University , Addis Ababa , Ethiopia
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Liu G, Xu CQ, Cao Q, Zimmermann W, Songer M, Zhao SS, Li K, Hu DF. Mitochondrial and pedigree analysis in Przewalski's horse populations: implications for genetic management and reintroductions. ACTA ACUST UNITED AC 2013; 25:313-8. [PMID: 23808923 DOI: 10.3109/19401736.2013.800487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS Przewalski's horses have been imported from the western zoos to China since 1985. Yet the genetic diversity in China's populations has not been studied, thus lacking of such knowledge inevitably affects this population's management. The aim of this study was to assess genetic diversity in Chinese population of Przewalski's horses via mitochondrial DNA (mtDNA) control region and pedigree analysis. MATERIALS AND METHODS Two captive and one reintroduced populations were examined based on mitochondrial DNA control region variation via fecal sampling from 2010 to 2012, together with pedigree analysis. RESULTS Amplification success rates of fecal mtDNA were as high as 96.2% (93.8%-100%), and were higher for sample in winter than in summer and autumn. Two haplotypes were identified and shared among three populations, but the proportion of individuals with each haplotype varied among the three populations (F(ST) = 0.10874, p = 0.00978). Haplotype diversity in the released population (0.153) was much lower than that in the two captive populations (0.4011 and 0.4966), in accordance with the direction of increase in probability of identity at the dam lines. CONCLUSION Future concerns in Przewalski's horse population management should emphasize on strict reproduction control to minimize inbreeding in captivity, followed by long-term genetic diversity guidelines and non-invasive monitoring in the reintroduction programmes.
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Affiliation(s)
- Gang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Biological Science and Technology, Beijing Forestry University , Beijing , China
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Mager KH, Colson KE, Hundertmark KJ. High genetic connectivity and introgression from domestic reindeer characterize northern Alaska caribou herds. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0499-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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D’Amato ME, Alechine E, Cloete KW, Davison S, Corach D. Where is the game? Wild meat products authentication in South Africa: a case study. INVESTIGATIVE GENETICS 2013; 4:6. [PMID: 23452350 PMCID: PMC3621286 DOI: 10.1186/2041-2223-4-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/14/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species. RESULTS The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species. CONCLUSIONS The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
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Affiliation(s)
- Maria Eugenia D’Amato
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Evguenia Alechine
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
| | - Kevin Wesley Cloete
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
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Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SCA, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids. PLoS One 2013; 8:e55950. [PMID: 23437078 PMCID: PMC3577844 DOI: 10.1371/journal.pone.0055950] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
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Affiliation(s)
- Julia T. Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Aurelien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sandra C. A. Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jacobo Weinstock
- Faculty of Humanities, University of Southampton, Southampton, United Kingdom
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Alberta, Canada
| | - Sergei K. Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolai D. Ovodov
- Laboratory of Archaeology and Paleogeography of Central Siberia, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Joel Clary
- Centre de Conservation et d’Étude des Collections, Musée des Confluences, Lyon, France
| | - Kristofer M. Helgen
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington D.C., United States of America
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian National Zoological Park, Smithsonian Institution, Washington D.C., United States of America
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, The University of Adelaide, South Australia, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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25
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Epps CW, Castillo JA, Schmidt-Küntzel A, du Preez P, Stuart-Hill G, Jago M, Naidoo R. Contrasting historical and recent gene flow among African buffalo herds in the Caprivi Strip of Namibia. ACTA ACUST UNITED AC 2013; 104:172-81. [PMID: 23341534 DOI: 10.1093/jhered/ess142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Population genetic structure is often used to infer population connectivity, but genetic structure may largely reflect historical rather than recent processes. We contrasted genetic structure with recent gene-flow estimates among 6 herds of African buffalo (Syncerus caffer) in the Caprivi Strip, Namibia, using 134 individuals genotyped at 10 microsatellite loci. We tested whether historical and recent gene flows were influenced by distance, potential barriers (rivers), or landscape resistance (distance from water). We also tested at what scales individuals were more related than expected by chance. Genetic structure across the Caprivi Strip was weak, indicating that historically, gene flow was strong and was not affected by distance, barriers, or landscape resistance. Our analysis of simulated data suggested that genetic structure would be unlikely to reflect human disturbances in the last 10-20 generations (75-150 years) because of slow predicted rates of genetic drift, but recent gene-flow estimates would be affected. Recent gene-flow estimates were not consistently affected by rivers or distance to water but showed that isolation by distance appears to be developing. Average relatedness estimates among individuals exceeded random expectations only within herds. We conclude that historically, African buffalo moved freely throughout the Caprivi Strip, whereas recent gene flow has been more restricted. Our findings support efforts to maintain the connectivity of buffalo herds across this region and demonstrate the utility of contrasting genetic inferences from different time scales.
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Affiliation(s)
- Clinton W Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.
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26
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Kamath PL, Getz WM. Unraveling the effects of selection and demography on immune gene variation in free-ranging plains zebra (Equus quagga) populations. PLoS One 2012; 7:e50971. [PMID: 23251409 PMCID: PMC3522668 DOI: 10.1371/journal.pone.0050971] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
Demography, migration and natural selection are predominant processes affecting the distribution of genetic variation among natural populations. Many studies use neutral genetic markers to make inferences about population history. However, the investigation of functional coding loci, which directly reflect fitness, is critical to our understanding of species' ecology and evolution. Immune genes, such as those of the Major Histocompatibility Complex (MHC), play an important role in pathogen recognition and provide a potent model system for studying selection. We contrasted diversity patterns of neutral data with MHC loci, ELA-DRA and -DQA, in two southern African plains zebra (Equus quagga) populations: Etosha National Park, Namibia, and Kruger National Park, South Africa. Results from neutrality tests, along with observations of elevated diversity and low differentiation across populations, supported previous genus-level evidence for balancing selection at these loci. Despite being low, MHC divergence across populations was significant and may be attributed to drift effects typical of geographically separated populations experiencing little to no gene flow, or alternatively to shifting allele frequency distributions driven by spatially variable and fluctuating pathogen communities. At the DRA, zebra exhibited geographic differentiation concordant with microsatellites and reduced levels of diversity in Etosha due to highly skewed allele frequencies that could not be explained by demography, suggestive of spatially heterogeneous selection and local adaptation. This study highlights the complexity in which selection affects immune gene diversity and warrants the need for further research on the ecological mechanisms shaping patterns of adaptive variation among natural populations.
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Affiliation(s)
- Pauline L Kamath
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America.
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27
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Odee DW, Telford A, Wilson J, Gaye A, Cavers S. Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion. Heredity (Edinb) 2012; 109:372-82. [PMID: 22929152 DOI: 10.1038/hdy.2012.52] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (h(T(cpSSR))=0.903-0.948) and population differentiation (G(ST(RFLP))=0.700-0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (G(ST(cpSSR))=0.392; R(ST)=0.673; R(ST)>R(ST) (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.
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Affiliation(s)
- D W Odee
- Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian, Scotland, UK.
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28
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Abstract
The savannah biome of sub-Saharan Africa harbours the highest diversity of ungulates (hoofed mammals) on Earth. In this review, we compile population genetic data from 19 codistributed ungulate taxa of the savannah biome and find striking concordance in the phylogeographic structuring of species. Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene. Data from taxa across trophic levels suggest distinct savannah refugia were present in West, East, Southern and South-West Africa. Furthermore, differing Pleistocene evolutionary biogeographic scenarios are proposed for East and Southern Africa, supported by palaeoclimatic data and the fossil record. Environmental instability in East Africa facilitated several spatial and temporal refugia and is reflected in the high inter- and intraspecific diversity of the region. In contrast, phylogeographic data suggest a stable, long-standing savannah refuge in the south.
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Affiliation(s)
- E D Lorenzen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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29
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Colli L, Perrotta G, Negrini R, Bomba L, Bigi D, Zambonelli P, Verini Supplizi A, Liotta L, Ajmone-Marsan P. Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys. Anim Genet 2012; 44:69-78. [DOI: 10.1111/j.1365-2052.2012.02356.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2012] [Indexed: 11/29/2022]
Affiliation(s)
- L. Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - G. Perrotta
- Laboratorio di Genetica e Servizi L.G.S.; I-26100; Cremona; Italy
| | - R. Negrini
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - L. Bomba
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - D. Bigi
- Dipartimento di Protezione e Valorizzazione Agro-Alimentare; Università di Bologna - Sede di Reggio Emilia; I-42123; Reggio Emilia; Italy
| | - P. Zambonelli
- Dipartimento di Protezione e Valorizzazione Agro-Alimentare; Università di Bologna - Sede di Reggio Emilia; I-42123; Reggio Emilia; Italy
| | - A. Verini Supplizi
- Dipartimento di Patologia; Diagnostica e Clinica Veterinaria; Università di Perugia; I-06126; Perugia; Italy
| | - L. Liotta
- Dipartimento di Morfologia, Biochimica; Fisiologia e Produzioni Animali; Università di Messina; I-98168; Messina; Italy
| | - P. Ajmone-Marsan
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
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Damm S, Hadrys H. A dragonfly in the desert: genetic pathways of the widespread Trithemis arteriosa (Odonata: Libellulidae) suggest male-biased dispersal. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0079-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Loss of genetic diversity means loss of geological information: the endangered Japanese crayfish exhibits remarkable historical footprints. PLoS One 2012; 7:e33986. [PMID: 22470505 PMCID: PMC3314697 DOI: 10.1371/journal.pone.0033986] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 02/24/2012] [Indexed: 11/19/2022] Open
Abstract
Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall FST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events.
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The genetic legacy of aridification: Climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate. Mol Phylogenet Evol 2011; 61:750-9. [DOI: 10.1016/j.ympev.2011.08.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 07/22/2011] [Accepted: 08/04/2011] [Indexed: 11/18/2022]
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Schwab P, Debes PV, Witt T, Hartl GB, Hmwe SS, Zachos FE, Grobler JP. Genetic structure of the common impala (Aepyceros melampus melampus) in South Africa: phylogeography and implications for conservation. J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00638.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Heupink TH, Huynen L, Lambert DM. Ancient DNA suggests dwarf and 'giant' emu are conspecific. PLoS One 2011; 6:e18728. [PMID: 21494561 PMCID: PMC3073985 DOI: 10.1371/journal.pone.0018728] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 03/14/2011] [Indexed: 11/19/2022] Open
Abstract
Background The King Island Emu (Dromaius ater) of Australia is one of several extinct emu taxa whose taxonomic relationship to the modern Emu (D. novaehollandiae) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu. Methodology and Results We investigated the evolutionary relationships between the King Island and modern Emu by the recovery of both nuclear and mitochondrial DNA sequences from sub-fossil remains. The complete mitochondrial control (1,094 bp) and cytochrome c oxidase subunit I (COI) region (1,544 bp), as well as a region of the melanocortin 1 receptor gene (57 bp) were sequenced using a multiplex PCR approach. The results show that haplotypes for King Island Emu fall within the diversity of modern Emu. Conclusions These data show the close relationship of these emu when compared to other congeneric bird species and indicate that the King Island and modern Emu share a recent common ancestor. King Island emu possibly underwent insular dwarfism as a result of phenotypic plasticity. The close relationship between the King Island and the modern Emu suggests it is most appropriate that the former should be considered a subspecies of the latter. Although both taxa show a close genetic relationship they differ drastically in size. This study also suggests that rates of morphological and neutral molecular evolution are decoupled.
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Affiliation(s)
- Tim H. Heupink
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
| | - Leon Huynen
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
- * E-mail:
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BRYJA J, GRANJON L, DOBIGNY G, PATZENHAUEROVÁ H, KONEČNÝ A, DUPLANTIER JM, GAUTHIER P, COLYN M, DURNEZ L, LALIS A, NICOLAS V. Plio‐Pleistocene history of West African Sudanian savanna and the phylogeography of the
Praomys daltoni
complex (Rodentia): the environment/geography/genetic interplay. Mol Ecol 2010; 19:4783-99. [DOI: 10.1111/j.1365-294x.2010.04847.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. BRYJA
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - L. GRANJON
- IRD, CBGP (UMR IRD / INRA / CIRAD / MontpellierSupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
| | - G. DOBIGNY
- IRD, CBGP (UMR IRD / INRA / CIRAD / MontpellierSupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
| | - H. PATZENHAUEROVÁ
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - A. KONEČNÝ
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
- IRD, CBGP (UMR IRD / INRA / CIRAD / MontpellierSupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
| | - J. M. DUPLANTIER
- IRD, CBGP (UMR IRD / INRA / CIRAD / MontpellierSupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
| | - P. GAUTHIER
- IRD, CBGP (UMR IRD / INRA / CIRAD / MontpellierSupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
| | - M. COLYN
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Station Biologique, 35380 Paimpont, France
| | - L. DURNEZ
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B‐2020 Antwerp, Belgium & Mycobacteriology Unit, Department of Microbiology, Institute of Tropical Medicine, Nationalestraat 155, B‐2000 Antwerp, Belgium
| | - A. LALIS
- Muséum National d’Histoire Naturelle, Département de Systématique et Evolution, UMR CNRS 7205, Laboratoire Mammifères et Oiseaux, 47 rue Cuvier, CP 51, 75005 Paris, France
| | - V. NICOLAS
- Muséum National d’Histoire Naturelle, Département de Systématique et Evolution, UMR CNRS 7205, Laboratoire Mammifères et Oiseaux, 47 rue Cuvier, CP 51, 75005 Paris, France
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HELLER R, OKELLO JBA, SIEGISMUND H. Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa. Mol Ecol 2010; 19:1324-34. [DOI: 10.1111/j.1365-294x.2010.04589.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Revising the recent evolutionary history of equids using ancient DNA. Proc Natl Acad Sci U S A 2009; 106:21754-9. [PMID: 20007379 DOI: 10.1073/pnas.0903672106] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
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Harley EH, Knight MH, Lardner C, Wooding B, Gregor M. The Quagga Project: Progress Over 20 Years of Selective Breeding. ACTA ACUST UNITED AC 2009. [DOI: 10.3957/056.039.0206] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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39
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Heller R, Siegismund HR. Relationship between three measures of genetic differentiation G(ST), D(EST) and G'(ST): how wrong have we been? Mol Ecol 2009; 18:2080-3; discussion 2088-91. [PMID: 19645078 DOI: 10.1111/j.1365-294x.2009.04185.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R Heller
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark.
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Neaves LE, Zenger KR, Prince RIT, Eldridge MDB, Cooper DW. Landscape discontinuities influence gene flow and genetic structure in a large, vagile Australian mammal, Macropus fuliginosus. Mol Ecol 2009; 18:3363-78. [PMID: 19659477 DOI: 10.1111/j.1365-294x.2009.04293.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large vagile mammals typically exhibit little genetic structuring across their range, particularly when their habitat is essentially continuous. We investigated the population genetic structure of a large vagile Australian macropodid, Macropus fuliginosus, which is continuously distributed across most of southern Australia, using nine highly polymorphic nuclear microsatellite loci. Five distinct genetic units were identified across the range, four on the mainland and one on Kangaroo Island. In addition to the predicted historic Nullarbor Plain Barrier, two unexpected mainland barriers to gene flow were identified. Both were associated with landscape discontinuities (Swan River, Flinders Ranges), which appear within the dispersal capabilities of M. fuliginosus. Typical of large vagile mammals, M. fuliginosus displays high genetic diversity (with the exception of an insular population) and weak genetic structuring (within genetic units). However, the expansion of M. fuliginosus from southwestern Australia during the Pleistocene has resulted in significantly reduced genetic diversity in eastern populations. No significant sex-biased dispersal was detected, although differences in habitat, densities and climatic conditions between the eastern and western regions of the range appear to influence dispersal with the effects of isolation by distance only evident in the west. These results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.
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Affiliation(s)
- Linda E Neaves
- Department of Biological Sciences, Macquarie University, NSW, Australia.
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