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Dalui S, Sharma LK, Thakur M. Barriers and corridors: Assessment of gene flow and movement among red panda populations in eastern Himalayas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172523. [PMID: 38657804 DOI: 10.1016/j.scitotenv.2024.172523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/14/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Landscape features can impede dispersal, gene flow, and population demography, resulting in the formation of several meta-populations within a continuous landscape. Understanding a species' ability to overcome these barriers is critical for predicting genetic connectivity and population persistence, and implementing effective conservation strategies. In the present study, we conducted a fine-scale spatial genetic analysis to understand the contemporary gene flow within red panda populations in the Eastern Himalayas. Employing geometric aspects of reserve design, we delineated the critical core habitats for red pandas, which comprise 14.5 % of the landscape (12,189.75 Km2), with only a mere 443 Km2 falling within the protected areas. We identified corridors among the core habitats, which may be vital for the species' long-term genetic viability. Furthermore, we identified substantial landscape barriers, including Sela Pass in the western region, Siang river in the central region, and the Dibang river, Lohit river, along with Dihang, Dipher, and Kumjawng passes in the eastern region, which hinder gene flow. We suggest managing red panda populations through the creation of Community Conservation Reserves in the identified core habitats, following landscape-level management planning based on the core principles of geometric reserve design. This includes a specific emphasis on identified core habitats of red panda (CH-RP 5 and CH-RP 8) to facilitate corridors and implement meta-population dynamics. We propose the development of a comprehensive, long-term conservation and management plan for red pandas in the transboundary landscape, covering China, Nepal, and Bhutan.
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Affiliation(s)
- Supriyo Dalui
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India; Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India.
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Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proc Natl Acad Sci U S A 2022; 119:e2121388119. [PMID: 35759654 PMCID: PMC9282390 DOI: 10.1073/pnas.2121388119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although biodiversity in East Africa is overall extremely high, species richness is not geographically uniform for fishes and mammals. We investigated the biogeographic relevance of past river activity in the Kenya Rift. We show that during a humid period 12,000 to 8,000 years ago, a river system connected currently isolated rift lakes and was partly connected to the Nile. While this river system formed pathways for the dispersal of fishes between lakes, it also acted as a barrier to the range expansion of forest mammals. This fairly recent hydrological connectivity between lakes has been a key driver of modern biodiversity patterns in East Africa. Climate-driven changes in drainage networks on multimillennial timescales are an important hypothesis in biodiversity research. East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
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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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Pacifici M, Di Marco M, Watson JEM. Protected areas are now the last strongholds for many imperiled mammal species. Conserv Lett 2020. [DOI: 10.1111/conl.12748] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Michela Pacifici
- Global Mammal Assessment Programme, Department of Biology and Biotechnologies Sapienza Università di Roma Rome Italy
| | - Moreno Di Marco
- Department of Biology and Biotechnologies Sapienza Università di Roma Rome Italy
- School for Earth and Environmental Sciences University of Queensland Brisbane Australia
| | - James E. M. Watson
- School for Earth and Environmental Sciences University of Queensland Brisbane Australia
- Wildlife Conservation Society Global Conservation Program Bronx New York
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Dures SG, Carbone C, Savolainen V, Maude G, Gottelli D. Ecology rather than people restrict gene flow in Okavango‐Kalahari lions. Anim Conserv 2020. [DOI: 10.1111/acv.12562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- S. G. Dures
- Institute of Zoology Zoological Society of London London UK
- Department of Life Sciences Imperial College London Ascot UK
| | - C. Carbone
- Institute of Zoology Zoological Society of London London UK
| | - V. Savolainen
- Department of Life Sciences Imperial College London Ascot UK
| | - G. Maude
- Kalahari Research and Conservation Maun Botswana
| | - D. Gottelli
- Institute of Zoology Zoological Society of London London UK
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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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Portanier E, Garel M, Devillard S, Maillard D, Poissant J, Galan M, Benabed S, Poirel MT, Duhayer J, Itty C, Bourgoin G. Both candidate gene and neutral genetic diversity correlate with parasite resistance in female Mediterranean mouflon. BMC Ecol 2019; 19:12. [PMID: 30836982 PMCID: PMC6402107 DOI: 10.1186/s12898-019-0228-x] [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: 09/03/2018] [Accepted: 02/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parasite infections can have substantial impacts on population dynamics and are accordingly a key challenge for wild population management. Here we studied genetic mechanisms driving parasite resistance in a large herbivore through a comprehensive approach combining measurements of neutral (16 microsatellites) and adaptive (MHC DRB1 exon 2) genetic diversity and two types of gastrointestinal parasites (nematodes and coccidia). RESULTS While accounting for other extrinsic and intrinsic predictors known to impact parasite load, we show that both neutral genetic diversity and DRB1 are associated with resistance to gastrointestinal nematodes. Intermediate levels of multi-locus heterozygosity maximized nematodes resistance, suggesting that both in- and outbreeding depression might occur in the population. DRB1 heterozygosity and specific alleles effects were detected, suggesting the occurrence of heterozygote advantage, rare-allele effects and/or fluctuating selection. On the contrary, no association was detected between genetic diversity and resistance to coccidia, indicating that different parasite classes are impacted by different genetic drivers. CONCLUSIONS This study provides important insights for large herbivores and wild sheep pathogen management, and in particular suggests that factors likely to impact genetic diversity and allelic frequencies, including global changes, are also expected to impact parasite resistance.
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Affiliation(s)
- Elodie Portanier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive, 69100 Villeurbanne, France
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
| | - Mathieu Garel
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Sébastien Devillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive, 69100 Villeurbanne, France
| | - Daniel Maillard
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Jocelyn Poissant
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34980 Montferrier Sur Lez, France
| | - Slimania Benabed
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
| | - Marie-Thérèse Poirel
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
| | - Jeanne Duhayer
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Christian Itty
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Gilles Bourgoin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive, 69100 Villeurbanne, France
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
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Srbek-Araujo AC, Haag T, Chiarello AG, Salzano FM, Eizirik E. Worrisome isolation: noninvasive genetic analyses shed light on the critical status of a remnant jaguar population. J Mammal 2018. [DOI: 10.1093/jmammal/gyy007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ana Carolina Srbek-Araujo
- Programa de Pós-graduação em Ecologia de Ecossistemas, Universidade Vila Velha, Boa Vista, Vila Velha, Espírito Santo, Brazil
- Instituto SerraDiCal de Pesquisa e Conservação, Belo Horizonte, Minas Gerais, Brazil
| | - Taiana Haag
- PUCRS, Faculdade de Biociências, Laboratório de Biologia Genômica e Molecular, Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
| | - Adriano Garcia Chiarello
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Eduardo Eizirik
- PUCRS, Faculdade de Biociências, Laboratório de Biologia Genômica e Molecular, Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
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Gippoliti S, Cotterill FPD, Zinner D, Groves CP. Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview. Biol Rev Camb Philos Soc 2017; 93:115-130. [PMID: 28429851 DOI: 10.1111/brv.12335] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 01/27/2023]
Abstract
We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.
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Affiliation(s)
- Spartaco Gippoliti
- Società Italiana di Storia della Fauna 'G. Altobello' Viale Liegi 48, 00198, Roma, Italy
| | - Fenton P D Cotterill
- Geoecodynamics Research Hub, Department of Earth Sciences, University of Stellenbosch, Stellenbosch, 7602, South Africa
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, 37077, Göttingen, Germany
| | - Colin P Groves
- School of Archaeology & Anthropology, Australian National University, Canberra, Australia
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Montiel-Reyes F, Maldonado JE, del Real-Monroy M, Martínez-Méndez N, Ortega J. Non-invasive sampling reveals fine-scale genetic structure in black bear Ursus americanus populations from northeastern Mexico. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Smitz N, Cornélis D, Chardonnet P, Caron A, de Garine-Wichatitsky M, Jori F, Mouton A, Latinne A, Pigneur LM, Melletti M, Kanapeckas KL, Marescaux J, Pereira CL, Michaux J. Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer). BMC Evol Biol 2014; 14:203. [PMID: 25367154 PMCID: PMC4232705 DOI: 10.1186/s12862-014-0203-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/16/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the "genetic health" of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. RESULTS The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (A r ) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (P a ) of 11), low differentiation, and an absence of an inbreeding depression signal (mean F IS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (F IS = 0.062, mean A r = 6.160, P a = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. CONCLUSIONS We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.
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Affiliation(s)
- Nathalie Smitz
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
| | - Daniel Cornélis
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | | | - Alexandre Caron
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCP, University of Zimbabwe, Harare, Zimbabwe
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Michel de Garine-Wichatitsky
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-RP-PCP, University of Zimbabwe, Harare, Zimbabwe
- />Department of Biological Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Ferran Jori
- />Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- />Department of Animal Science and Production, Botswana College of Agriculture, Gaborone, Botswana
| | - Alice Mouton
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
| | - Alice Latinne
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
- />Institut des Sciences de l’Evolution-CNRS-IRD, Université de Montpellier 2, Montpellier, France
- />Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Lise-Marie Pigneur
- />Research Unit in Environmental and Evolutionary Biology, University of Namur, Namur, Belgium
| | - Mario Melletti
- />Independent researcher, Via Di Villa Chigi, Rome, Italy
| | - Kimberly L Kanapeckas
- />Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- />Department of Genetics and Biochemistry, Clemson University, Clemson, USA
| | - Jonathan Marescaux
- />Research Unit in Environmental and Evolutionary Biology, University of Namur, Namur, Belgium
| | | | - Johan Michaux
- />Departement of Life Sciences-Conservation Genetics, University of Liège, Liège, Belgium
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Radespiel U, Bruford MW. Fragmentation genetics of rainforest animals: insights from recent studies. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0550-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Mondol S, Bruford MW, Ramakrishnan U. Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc Biol Sci 2013; 280:20130496. [PMID: 23677341 PMCID: PMC3673047 DOI: 10.1098/rspb.2013.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/23/2013] [Indexed: 11/12/2022] Open
Abstract
India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.
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Affiliation(s)
- Samrat Mondol
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | | | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
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Pan-African genetic structure in the African buffalo (Syncerus caffer): investigating intraspecific divergence. PLoS One 2013; 8:e56235. [PMID: 23437100 PMCID: PMC3578844 DOI: 10.1371/journal.pone.0056235] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
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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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Ahlering MA, Eggert LS, Western D, Estes A, Munishi L, Fleischer R, Roberts M, Maldonado JE. Identifying source populations and genetic structure for savannah elephants in human-dominated landscapes and protected areas in the Kenya-Tanzania borderlands. PLoS One 2012; 7:e52288. [PMID: 23300634 PMCID: PMC3530563 DOI: 10.1371/journal.pone.0052288] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/13/2012] [Indexed: 11/19/2022] Open
Abstract
We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.
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Affiliation(s)
- Marissa A Ahlering
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America.
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Guerier AS, Bishop JM, Crawford SJ, Schmidt-Küntzel A, Stratford KJ. Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0331-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Influence of habitat fragmentation on the genetic structure of large mammals: evidence for increased structuring of African buffalo (Syncerus caffer) within the Serengeti ecosystem. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0291-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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KOBLMÜLLER STEPHAN, SALZBURGER WALTER, OBERMÜLLER BEATE, EIGNER EVA, STURMBAUER CHRISTIAN, SEFC KRISTINAM. Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations in Lake Tanganyika. Mol Ecol 2011; 20:2272-90. [DOI: 10.1111/j.1365-294x.2011.05088.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Haag T, Santos AS, Sana DA, Morato RG, Cullen L, Crawshaw PG, De Angelo C, Di Bitetti MS, Salzano FM, Eizirik E. The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca). Mol Ecol 2010; 19:4906-21. [PMID: 21040050 DOI: 10.1111/j.1365-294x.2010.04856.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Habitat fragmentation may disrupt original patterns of gene flow and lead to drift-induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar's high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large-scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars' ability to effectively disperse across the human-dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift.
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Affiliation(s)
- T Haag
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, CP 15053, Porto Alegre, RS 91501-970, Brazil
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