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Tensen L, Fischer K. Heterozygosity is low where rare color variants in wild carnivores prevail. Ecol Evol 2024; 14:e10881. [PMID: 38327687 PMCID: PMC10847885 DOI: 10.1002/ece3.10881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/04/2023] [Indexed: 02/09/2024] Open
Abstract
Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average A R was 4.18, H O = 0.59, and H E = 0.66, and F IS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.
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Affiliation(s)
- Laura Tensen
- Zoology, Institute for Integrated Natural SciencesKoblenz UniversityKoblenzGermany
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Klaus Fischer
- Zoology, Institute for Integrated Natural SciencesKoblenz UniversityKoblenzGermany
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Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 2023; 5:lqad033. [PMID: 37025970 PMCID: PMC10071556 DOI: 10.1093/nargab/lqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Melissa Drown
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Carrie Walls
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jay Pratte
- Bloomington Parks and Recreation, Miller Park Zoo, Bloomington, IL 61701, USA
| | - Adam McLain
- Department of Biology and Chemistry, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
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Conservation importance of the strategic, centrally located snow leopard population in the western Himalayas, India: a genetic perspective. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00275-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Tensen L, Power J, Camacho G, Godinho R, Jansen van Vuuren B, Fischer K. Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa. Evol Appl 2022; 15:1028-1041. [PMID: 35782007 PMCID: PMC9234631 DOI: 10.1111/eva.13423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off-take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour-associated genes and 20 microsatellite loci in twenty Wild-type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase-related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human-induced mortality rate.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, ZoologyUniversity of Koblenz‐LandauKoblenzGermany
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - John Power
- Directorate of Biodiversity Management, Department of Economic Development, Environment, Conservation and TourismNorth West Provincial GovernmentMmabathoSouth Africa
| | - Gerrie Camacho
- Mpumalanga Tourism and Parks AgencyNelspruitSouth Africa
| | - Raquel Godinho
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório AssociadoCampus de Vairão, Universidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO, Campus de VairãoVairãoPortugal
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity of Koblenz‐LandauKoblenzGermany
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Cross-amplification of ungulate microsatellite markers in the endemic Indian antelope or blackbuck (Antilope cervicapra) for population monitoring and conservation genetics studies in south Asia. Mol Biol Rep 2021; 48:5151-5160. [PMID: 34213708 DOI: 10.1007/s11033-021-06514-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/25/2021] [Indexed: 01/01/2023]
Abstract
The Indian antelope or blackbuck (Antilope cervicapra) is endemic to the Indian subcontinent, inhabiting scrublands and dry grasslands. Most of the blackbuck populations are small, isolated, and threatened by habitat fragmentation and degradation. Management of such disjunct populations requires genetic characterization, which is critical for assessing hazards of stochastic events and inbreeding. Addressing the scarcity of such information on the blackbuck, we describe a novel panel of microsatellite markers that could be used to monitor blackbuck demography and population genetic parameters using non-invasive faecal sampling. We screened microsatellites (n = 40) that had been reported to amplify in bovid and cervid species using faecal samples of the blackbuck collected from Kaimoor Wildlife Sanctuary, Uttar Pradesh, India and its vicinities. We selected 12 markers for amplification using faecal DNA extracts (n = 140) in three multiplex reactions. We observed a mean amplification success rate of 72.4% across loci (92.1-25.7%) with high allele diversity (mean number of alleles/locus = 8.67 ± 1.03). Mean genotyping error rates across the markers were low to moderate (allelic drop-out rate = 0.09; false allele rate = 0.11). The proportions of first- and second-order relatives in the study population were 0.69% and 6.21%, respectively. Based on amplification success, genotyping error rates and the probability of identity (PID), we suggest (i) a panel of five microsatellite markers (cumulative PID = 1.24 × 10-5) for individual identification and population monitoring and (ii) seven additional markers for conservation genetics studies. This study provides essential tools capable of augmenting blackbuck conservation strategies at the landscape level, integral to protecting the scrubland-grassland ecosystem.
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Bhatt S, Biswas S, Karanth K, Pandav B, Mondol S. Genetic analyses reveal population structure and recent decline in leopards ( Panthera pardus fusca) across the Indian subcontinent. PeerJ 2020; 8:e8482. [PMID: 32117616 PMCID: PMC7006512 DOI: 10.7717/peerj.8482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/29/2019] [Indexed: 11/21/2022] Open
Abstract
Background Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. Methods We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. Results Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. Conclusions Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.
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Affiliation(s)
- Supriya Bhatt
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| | - Suvankar Biswas
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| | - Krithi Karanth
- Centre for Wildlife Studies, Bengaluru, India.,Nicholas School of Environment, Duke University, Durham, United States of America
| | - Bivash Pandav
- Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Samrat Mondol
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
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Asad M, Waseem M, Ross JG, Paterson AM. The Un-Common Leopard: presence, distribution and abundance in Gallies and Murree Forest Division, Northern Pakistan. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.37.32748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The leopard Panthera pardus is thought to be sparsely distributed across Pakistan and there is limited understanding of the demographic structure and distribution of the species in this country. We conducted a study, from April to July 2017, and, from March to June 2018, in the northern Pakistan region to establish the presence and distribution of leopards, mindful at the outset of their abundance in that region. The presence of leopards was confirmed in the Swat, Dir and Margalla Hills region. The leopard population in Gallies and Murree Forest Division was preliminarily assessed via camera-trapping. As a result, a total of 63 potential areas of leopard population were identified initially. The leopard was photo captured at 27 locations (hotspots) with 34 capture events yielding 195 images over the course of 3,022 active trap-nights. Camera trap images were examined to identify leopard individuals using their rosette patterns on both the left and right flanks and the dorsal side of the tail. Ultimately, 15 leopard individuals were identified during the first survey period of the study and four individuals were recaptured in the second survey period, together with three new individuals. The detection probability of individual leopards from MARK varied from 0.10 and 0.20 with a population size (preliminarily estimated to be 16–25 (SE = 3.18) in 2107 and 7–13 (SE = 1.87) in 2018. This gave a density of 4.5 to 9.5 leopards/100 km2, respectively. A home range of various individual leopards was found to extend from the Gallies Reserved Forest to the extended corridors of Guzara Forest. In general, this study suggests that the Guzara Forest is crucially important for the conservation of leopards in the region as this area allows them extended movement while searching for food and mates.
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Paijmans JLA, Barlow A, Förster DW, Henneberger K, Meyer M, Nickel B, Nagel D, Worsøe Havmøller R, Baryshnikov GF, Joger U, Rosendahl W, Hofreiter M. Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations. BMC Evol Biol 2018; 18:156. [PMID: 30348080 PMCID: PMC6198532 DOI: 10.1186/s12862-018-1268-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1268-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Daniel W Förster
- Leibniz Institute for Zoo- and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Doris Nagel
- Institute for Paleontology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Rasmus Worsøe Havmøller
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Gennady F Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034, St. Petersburg, Russia
| | - Ulrich Joger
- State Natural History Museum, Pockelsstr. 10, 38106, Braunschweig, Germany
| | - Wilfried Rosendahl
- Reiss-Engelhorn Museen and Curt-Engelhorn-Centre for Archaeometry, C4 8, 68159, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
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Ko BJ, An J, Seomun H, Lee MY, Eo SH. Microsatellite DNA analysis reveals lower than expected genetic diversity in the threatened leopard cat (Prionailurus bengalensis) in South Korea. Genes Genomics 2018; 40:521-530. [PMID: 29892957 DOI: 10.1007/s13258-018-0654-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/09/2018] [Indexed: 11/25/2022]
Abstract
To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which population size and habitat area data are unknown in the country, to assess its conservation status. The average number of alleles and the observed heterozygosity of the species were 3.8 and 0.41, respectively, and microsatellite diversity was lower than the average genetic diversity of 57 populations of 12 other felid species, and lower than that of other mammal populations occurring in South Korea, including the raccoon dog (Nyctereutes procyonoides), water deer (Hydropotes inermis), and endangered long-tailed goral (Naemorhedus caudatus). Furthermore, analysis of genetic structure in the national leopard cat population showed no clear genetic differentiation, suggesting that it is not necessary to divide the South Korean leopard cat population into multiple management units for the purposes of conservation. These results indicate that the genetic diversity of the leopard cat in South Korea is unexpectedly low, and that the risk of local extinction is, as a result, substantial. Thus, it is necessary to begin appropriate conservation efforts at a national level to conserve the leopard cat population in South Korea.
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Affiliation(s)
- Byung June Ko
- Department of Forest Resources, Kongju National University, Yesan, Chungnam, South Korea
| | - Junghwa An
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Hong Seomun
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Mu-Yeong Lee
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Soo Hyung Eo
- Department of Forest Resources, Kongju National University, Yesan, Chungnam, South Korea.
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Heinrich SK, Hofer H, Courtiol A, Melzheimer J, Dehnhard M, Czirják GÁ, Wachter B. Cheetahs have a stronger constitutive innate immunity than leopards. Sci Rep 2017; 7:44837. [PMID: 28333126 PMCID: PMC5363065 DOI: 10.1038/srep44837] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 02/14/2017] [Indexed: 11/21/2022] Open
Abstract
As a textbook case for the importance of genetics in conservation, absence of genetic variability at the major histocompatibility complex (MHC) is thought to endanger species viability, since it is considered crucial for pathogen resistance. An alternative view of the immune system inspired by life history theory posits that a strong response should evolve in other components of the immune system if there is little variation in the MHC. In contrast to the leopard (Panthera pardus), the cheetah (Acinonyx jubatus) has a relatively low genetic variability at the MHC, yet free-ranging cheetahs are healthy. By comparing the functional competence of the humoral immune system of both species in sympatric populations in Namibia, we demonstrate that cheetahs have a higher constitutive innate but lower induced innate and adaptive immunity than leopards. We conclude (1) immunocompetence of cheetahs is higher than previously thought; (2) studying both innate and adaptive components of immune systems will enrich conservation science.
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Affiliation(s)
- Sonja K. Heinrich
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Heribert Hofer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alexandre Courtiol
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Jörg Melzheimer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Martin Dehnhard
- Department of Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Bettina Wachter
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
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Assessing temporal genetic variation in a cougar population: influence of harvest and neighboring populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0790-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mondol S, Sridhar V, Yadav P, Gubbi S, Ramakrishnan U. Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:556-564. [PMID: 25376464 DOI: 10.1111/cobi.12393] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/17/2014] [Indexed: 06/04/2023]
Abstract
Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond.
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Affiliation(s)
- Samrat Mondol
- Centre for Cellular and Molecular Platforms, GKVK Post, Bangalore, 56065, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India; Department of Biology, Center for Conservation Biology, University of Washington, Box 351800, Seattle, WA, 98195-1800, U.S.A.; Postgraduate Program in Wildlife Biology and Conservation, Wildlife Conservation Society-India Program, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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Farhadinia MS, Farahmand H, Gavashelishvili A, Kaboli M, Karami M, Khalili B, Montazamy S. Molecular and craniological analysis of leopard,Panthera pardus(Carnivora: Felidae) in Iran: support for a monophyletic clade in Western Asia. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12473] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohammad S. Farhadinia
- Department of Fisheries and Environment; Faculty of Natural Resources; University of Tehran; Karaj Iran
- Iranian Cheetah Society (ICS); P.O. Box 14155-8549 Tehran Iran
- Wildlife Conservation Research Unit (WildCRU); The Recanati-Kaplan Centre; University of Oxford; Tubney House, Abingdon Road Tubney Abingdon OX13 5QL UK
| | - Hamid Farahmand
- Department of Fisheries and Environment; Faculty of Natural Resources; University of Tehran; Karaj Iran
| | - Alexander Gavashelishvili
- Center of Biodiversity Studies; Institute of Ecology; Ilia State University; Cholokashvili Str. 5 0162 Tbilisi Georgia
| | - Mohammad Kaboli
- Department of Fisheries and Environment; Faculty of Natural Resources; University of Tehran; Karaj Iran
| | - Mahmoud Karami
- Department of Fisheries and Environment; Faculty of Natural Resources; University of Tehran; Karaj Iran
| | - Bita Khalili
- Department of Fisheries and Environment; Faculty of Natural Resources; University of Tehran; Karaj Iran
| | - Shahab Montazamy
- Natural History Museum and Genetic Resources Bureau; Iranian Department of Environment (DoE); Tehran Iran
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Welch AJ, Bedoya-Reina OC, Carretero-Paulet L, Miller W, Rode KD, Lindqvist C. Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment. Genome Biol Evol 2015; 6:433-50. [PMID: 24504087 PMCID: PMC3942037 DOI: 10.1093/gbe/evu025] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate whether polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide (NO), which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of NO as an adaptive response to control trade-offs between energy production in the form of adenosine triphosphate versus generation of heat (thermogenesis).
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Affiliation(s)
- Andreanna J Welch
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo
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15
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McManus JS, Dalton DL, Kotzé A, Smuts B, Dickman A, Marshal JP, Keith M. Gene flow and population structure of a solitary top carnivore in a human-dominated landscape. Ecol Evol 2015; 5:335-44. [PMID: 25691961 PMCID: PMC4314266 DOI: 10.1002/ece3.1322] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/20/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022] Open
Abstract
While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free-roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human-carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human-caused extinctions.
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Affiliation(s)
- Jeannine S McManus
- School of Animal, Plant and Environmental SciencesUniversity of the Witwatersrand Private Bag X3, Johannesburg, 2050, South Africa
- Landmark FoundationP.O. Box 22, Riversdale, 6670, South Africa
| | - Desiré L Dalton
- National Zoological Gardens of South AfricaP.O. Box 754, Pretoria, 0001, South Africa
- Genetics Department, University of the Free StateP.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- National Zoological Gardens of South AfricaP.O. Box 754, Pretoria, 0001, South Africa
- Genetics Department, University of the Free StateP.O. Box 339, Bloemfontein, 9300, South Africa
| | - Bool Smuts
- Landmark FoundationP.O. Box 22, Riversdale, 6670, South Africa
| | - Amy Dickman
- WildCRU, Oxford UniversityAbingdon Road, Tubney, Abingdon, OX13 5QL, UK
| | - Jason P Marshal
- School of Animal, Plant and Environmental SciencesUniversity of the Witwatersrand Private Bag X3, Johannesburg, 2050, South Africa
| | - Mark Keith
- School of Animal, Plant and Environmental SciencesUniversity of the Witwatersrand Private Bag X3, Johannesburg, 2050, South Africa
- Centre for Wildlife Management, University of PretoriaPrivate Bag X20 Hatfield, Pretoria 0028, South Africa
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Pinho GM, Gonçalves da Silva A, Hrbek T, Venticinque EM, Farias IP. Kinship and social behavior of lowland tapirs (Tapirus terrestris) in a central Amazon landscape. PLoS One 2014; 9:e92507. [PMID: 24671057 PMCID: PMC3966805 DOI: 10.1371/journal.pone.0092507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/23/2014] [Indexed: 11/29/2022] Open
Abstract
We tested the hypothesis that tapirs tolerate individuals from adjacent and overlapping home ranges if they are related. We obtained genetic data from fecal samples collected in the Balbina reservoir landscape, central Amazon. Samples were genotyped at 14 microsatellite loci, of which five produced high quality informative genotypes. Based on an analysis of 32 individuals, we inferred a single panmictic population with high levels of heterozygosity. Kinship analysis identified 10 pairs of full siblings or parent-offspring, 10 pairs of half siblings and 25 unrelated pairs. In 10 cases, the related individuals were situated on opposite margins of the reservoir, suggesting that tapirs are capable of crossing the main river, even after damming. The polygamous model was the most likely mating system for Tapirus terrestris. Moran's I index of allele sharing between pairs of individuals geographically close (<3 km) was similar to that observed between individual pairs at larger distances (>3 km). Confirming this result, the related individuals were not geographically closer than unrelated ones (W = 188.5; p = 0.339). Thus, we found no evidence of a preference for being close to relatives and observed a tendency for dispersal. The small importance of relatedness in determining spatial distribution of individuals is unusual in mammals, but not unheard of. Finally, non-invasive sampling allowed efficient access to the genetic data, despite the warm and humid climate of the Amazon, which accelerates DNA degradation.
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Affiliation(s)
- Gabriela M Pinho
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil; Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | - Anders Gonçalves da Silva
- Division of Marine and Atmospheric Research, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, Tasmania, Australia; School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | - Eduardo M Venticinque
- Laboratório de Ecologia e Conservação da Biodiversidade, Centro de Biociências, Universidade Federal do Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, Brasil
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
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Philopatry and dispersal patterns in tiger (Panthera tigris). PLoS One 2013; 8:e66956. [PMID: 23843973 PMCID: PMC3699573 DOI: 10.1371/journal.pone.0066956] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Background Tiger populations are dwindling rapidly making it increasingly difficult to study their dispersal and mating behaviour in the wild, more so tiger being a secretive and solitary carnivore. Methods We used non-invasively obtained genetic data to establish the presence of 28 tigers, 22 females and 6 males, within the core area of Pench tiger reserve, Madhya Pradesh. This data was evaluated along with spatial autocorrelation and relatedness analyses to understand patterns of dispersal and philopatry in tigers within this well-managed and healthy tiger habitat in India. Results We established male-biased dispersal and female philopatry in tigers and reiterated this finding with multiple analyses. Females show positive correlation up to 7 kms (which corresponds to an area of approximately 160 km2) however this correlation is significantly positive only upto 4 kms, or 50 km2 (r = 0.129, p<0.0125). Males do not exhibit any significant correlation in any of the distance classes within the forest (upto 300 km2). We also show evidence of female dispersal upto 26 kms in this landscape. Conclusions Animal movements are important for fitness, reproductive success, genetic diversity and gene exchange among populations. In light of the current endangered status of tigers in the world, this study will help us understand tiger behavior and movement. Our findings also have important implications for better management of habitats and interconnecting corridors to save this charismatic species.
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Abstract
Panthera pardus (leopard; Linnaeus, 1758) is the smallest of the 4 large felids in the genus Panthera. A solitary and adaptable species, P. pardus is the widest ranging of all wild felids, inhabiting rain forests, mountains, semiarid environments, and suburban areas throughout sub-Saharan Africa, the Middle East, and South Asia to the Russian Far East. Despite this distribution, P. pardus is listed as “Near Threatened” by the International Union for Conservation of Nature and Natural Resources and several Asian subspecies are listed as endangered. P. pardus primarily feeds on small to medium-sized ungulates, but has a varied diet including fish, reptiles, birds, and small mammals.
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Affiliation(s)
- Andrew B. Stein
- Department of Natural Resources Conservation, University of Massachusetts, Amherst, MA 01003, USA;
| | - Virginia Hayssen
- Department of Biology, Smith College, Northampton, MA 01063, USA;
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Dutta T, Sharma S, Maldonado JE, Wood TC, Panwar HS, Seidensticker J. Fine-scale population genetic structure in a wide-ranging carnivore, the leopard (Panthera pardus fusca)in central India. DIVERS DISTRIB 2012. [DOI: 10.1111/ddi.12024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | - Jesús E. Maldonado
- Smithsonian Conservation Biology Institute; National Zoological Park; Washington; DC; 20013-7012; USA
| | - Thomas C. Wood
- Department of Environmental Science and Policy; George Mason University; 4400 University Dr, David King Hall MSN 5F2; Fairfax; VA; 22030; USA
| | - H. S. Panwar
- Peace Institute Charitable Trust; 178-F, Pocket-4,Mayur Vihar, Phase-I; Delhi; 110091; India
| | - John Seidensticker
- Smithsonian Conservation Biology Institute; National Zoological Park; Washington; DC; 20013-7012; USA
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20
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Applications and techniques for non-invasive faecal genetics research in felid conservation. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0675-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Holbrook JD, DeYoung RW, Janecka JE, Tewes ME, Honeycutt RL, Young JH. Genetic diversity, population structure, and movements of mountain lions (Puma concolor) in Texas. J Mammal 2012. [DOI: 10.1644/11-mamm-a-326.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Holbrook JD, Deyoung RW, Tewes ME, Young JH. Demographic history of an elusive carnivore: using museums to inform management. Evol Appl 2012; 5:619-28. [PMID: 23028402 PMCID: PMC3461144 DOI: 10.1111/j.1752-4571.2012.00241.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 12/20/2011] [Indexed: 11/29/2022] Open
Abstract
Elusive carnivores present a challenge to managers because traditional survey methods are not suitable. We applied a genetic approach using museum specimens to examine how historical and recent conditions influenced the demographic history of Puma concolor in western and southern Texas, USA. We used 10 microsatellite loci and indexed population trends by estimating historical and recent genetic diversity, genetic differentiation and effective population size. Mountain lions in southern Texas exhibited a 9% decline in genetic diversity, whereas diversity remained stable in western Texas. Genetic differentiation between western and southern Texas was minimal historically (F(ST) = 0.04, P < 0.01), but increased 2-2.5 times in our recent sample. An index of genetic drift for southern Texas was seven to eight times that of western Texas, presumably contributing to the current differentiation between western and southern Texas. Furthermore, southern Texas exhibited a >50% temporal decline in effective population size, whereas western Texas showed no change. Our results illustrate that population declines and genetic drift have occurred in southern Texas, likely because of contemporary habitat loss and predator control. Population monitoring may be needed to ensure the persistence of mountain lions in the southern Texas region. This study highlights the utility of sampling museum collections to examine demographic histories and inform wildlife management.
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Affiliation(s)
- Joseph D Holbrook
- Caesar Kleberg Wildlife Research Institute, MSC 218, Texas A&M University-Kingsville Kingsville, TX, USA
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23
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Castro-Prieto A, Wachter B, Melzheimer J, Thalwitzer S, Sommer S. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus). ACTA ACUST UNITED AC 2011; 102:653-65. [PMID: 21914667 DOI: 10.1093/jhered/esr097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.
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Affiliation(s)
- Aines Castro-Prieto
- Evolutionary Genetics, Research Groups at the Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany
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Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics 2011; 188:151-64. [PMID: 21385725 PMCID: PMC3120151 DOI: 10.1534/genetics.110.125260] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We provide a framework for Bayesian coalescent inference from microsatellite data that enables inference of population history parameters averaged over microsatellite mutation models. To achieve this we first implemented a rich family of microsatellite mutation models and related components in the software package BEAST. BEAST is a powerful tool that performs Bayesian MCMC analysis on molecular data to make coalescent and evolutionary inferences. Our implementation permits the application of existing nonparametric methods to microsatellite data. The implemented microsatellite models are based on the replication slippage mechanism and focus on three properties of microsatellite mutation: length dependency of mutation rate, mutational bias toward expansion or contraction, and number of repeat units changed in a single mutation event. We develop a new model that facilitates microsatellite model averaging and Bayesian model selection by transdimensional MCMC. With Bayesian model averaging, the posterior distributions of population history parameters are integrated across a set of microsatellite models and thus account for model uncertainty. Simulated data are used to evaluate our method in terms of accuracy and precision of θ estimation and also identification of the true mutation model. Finally we apply our method to a red colobus monkey data set as an example.
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25
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Charruau P, Fernandes C, Orozco-Terwengel P, Peters J, Hunter L, Ziaie H, Jourabchian A, Jowkar H, Schaller G, Ostrowski S, Vercammen P, Grange T, Schlötterer C, Kotze A, Geigl EM, Walzer C, Burger PA. Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates. Mol Ecol 2011; 20:706-24. [PMID: 21214655 PMCID: PMC3531615 DOI: 10.1111/j.1365-294x.2010.04986.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
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Affiliation(s)
- P Charruau
- Department of Biomedical Sciences, Institute of Population Genetics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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Krafsur ES. Tsetse flies: genetics, evolution, and role as vectors. INFECTION GENETICS AND EVOLUTION 2008; 9:124-41. [PMID: 18992846 DOI: 10.1016/j.meegid.2008.09.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 08/27/2008] [Accepted: 09/25/2008] [Indexed: 10/21/2022]
Abstract
Tsetse flies (Diptera: Glossinidae) are an ancient taxon of one genus, Glossina, and limited species diversity. All are exclusively haematophagous and confined to sub-Saharan Africa. The Glossina are the principal vectors of African trypanosomes Trypanosoma sp. (Kinetoplastida: Trypanosomatidae) and as such, are of great medical and economic importance. Clearly tsetse flies and trypanosomes are coadapted and evolutionary interactions between them are manifest. Numerous clonally reproducing strains of Trypanosoma sp. exist and their genetic diversities and spatial distributions are inadequately known. Here I review the breeding structures of the principle trypanosome vectors, G. morsitans s.l., G. pallidipes, G. palpalis s.l. and G. fuscipes fuscipes. All show highly structured populations among which there is surprisingly little detectable gene flow. Rather less is known of the breeding structure of T. brucei sensu lato vis à vis their vector tsetse flies but many genetically differentiated strains exist in nature. Genetic recombination in Trypanosoma via meiosis has recently been demonstrated in the laboratory thereby furnishing a mechanism of strain differentiation in addition to that of simple mutation. Spatially and genetically representative sampling of both trypanosome species and strains and their Glossina vectors is a major barrier to a comprehensive understanding of their mutual relationships.
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Affiliation(s)
- E S Krafsur
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
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BİLGİN RAİT. PROGRAM NOTE: Kgtests: a simple Excel Macro program to detect signatures of population expansion using microsatellites. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2006.01671.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Hansen H, Hess SC, Cole D, Banko PC. Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i. WILDLIFE RESEARCH 2007. [DOI: 10.1071/wr07043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai‘i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools.
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Ruiz-Garcia M, Escobar-Armel P, Alvarez D, Mudry M, Ascunce M, Gutierrez-Espeleta G, Shostell JM. Genetic Variability in Four Alouatta Species Measured by Means of Nine DNA Microsatellite Markers: Genetic Structure and Recent Bottlenecks. Folia Primatol (Basel) 2007; 78:73-87. [PMID: 17303937 DOI: 10.1159/000097058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 04/12/2006] [Indexed: 11/19/2022]
Abstract
We used microsatellite DNA to study the population genetics of 4 Alouatta species from Central and South America. Our main findings include the following: (1) A. seniculus had the highest level of microsatellite variability while A. caraya and A. palliata had the lowest mean number of alleles per locus and the lowest expected heterozygosity, respectively; (2) the samples of A. seniculus and A. palliata came from different regions and were not in Hardy-Weinberg equilibrium (HWE) which may indicate a Wahlund effect and differentiated gene pools -- in contrast, A. macconnelli and A. caraya were in HWE; (3) the microsatellite genetic heterogeneity of the 4 Alouatta species was similar to the karyotype divergence found among these Alouatta species; the species pair with the lowest level of heterogeneity (genetic differentiation) was A. seniculus/A. caraya, while the Central American species, A. palliata, was highly differentiated from the other 3 South American species; (4) we recommend the establishment of a conservation plan to help protect A. caraya because the Cornuet and Luikart procedure demonstrated a recent bottleneck for this species.
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Affiliation(s)
- M Ruiz-Garcia
- Unidad de Genética (Grupo de Genética de Poblaciones-Biología Evolutiva), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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Ruiz-Garcia M, Payán E, Murillo A, Alvarez D. DNA microsatellite characterization of the jaguar (Panthera onca) in Colombia. Genes Genet Syst 2006; 81:115-27. [PMID: 16755135 DOI: 10.1266/ggs.81.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Colombian jaguar population is thought to contain two different subspecies, Panthera onca centralis and Panthera onca onca. The genetic structure of this population was evaluated using 12 microsatellite loci (n = 62 samples). In addition, 22 jaguar DNA samples from Guatemala, Paraguay, Perú, Bolivia, Venezuela and Brazil were analyzed for these microsatellite loci (n = 84 samples). The results of this study indicate six primary themes. First, the levels of gene diversity were very high. Second, the majority of the loci analyzed showed an absence of Hardy-Weinberg equilibrium, probably due to the Wahlund effect (= population subdivision). Third, several microsatellite loci showed significant heterogeneity between the two supposed subspecies in the country. Nevertheless, gene flow was present between them, and heterogeneity was relatively low, although the assignment analyses showed good classification of the jaguars studied into their respective subspecies. Fourth, the long-term historical effective population sizes were calculated through a maximum likelihood procedure for single and multi-step mutation models. Fifth, seven out of twelve DNA microsatellites studied significantly deviated from a single-step mutation model. However, the overall mean multi-step mutation percentage for these 12 DNA microsatellites was only 6%. Therefore, 94% of mutations were uni-step. Sixth, no bottleneck events were detected in the Colombian jaguar population overall.
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Affiliation(s)
- Manuel Ruiz-Garcia
- Laboratory of Molecular Population Genetics (Grupo de Genética de Poblaciones-Biología Evolutiva), Unidad de Genética, Departamento de Biología. Facultad de Ciencias, Pontificia Universidad Javeriana, Colombia.
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Abstract
Population bottlenecks wield a powerful influence on the evolution of species and populations by reducing the repertoire of responses available for stochastic environmental events. Although modern contractions of wild populations due to human-related impacts have been documented globally, discerning historic bottlenecks for all but the most recent and severe events remains a serious challenge. Genetic samples dating to different points in time may provide a solution in some cases. We conducted serial coalescent simulations to assess the extent to which temporal genetic data are informative regarding population bottlenecks. These simulations demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based solely on modern data. The difference in power between the modern and temporal DNA approaches depends significantly on effective population size and bottleneck intensity and less significantly on sample size. The temporal approach provides more power in cases of genetic recovery (via migration) from a bottleneck than in cases of demographic recovery (via population growth). Choice of genetic region is critical, as mutation rate heavily influences the extent to which temporal sampling yields novel information regarding the demographic history of populations.
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Affiliation(s)
- Uma Ramakrishnan
- Department of Biological Sciences, Stanford University, Stanford, CA 94035-5020, USA.
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Ruiz-García M, Orozco-terWengel P, Castellanos A, Arias L. Microsatellite Analysis of the Spectacled Bear (Tremarctos ornatus) Across its Range Distribution. Genes Genet Syst 2005; 80:57-69. [PMID: 15824457 DOI: 10.1266/ggs.80.57] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA samples of the spectacled bear (Tremarctos ornatus) from five Andean countries, Venezuela, Colombia, Ecuador, Peru and Bolivia, were analyzed for nine microsatellite loci. Seven of them were polymorphic, which led us to investigate several population-genetic parameters. Private alleles and significant differences in gene frequencies were found among the populations studied, which demonstrated the extent of genetic differentiation among the spectacled bear populations. The levels of gene diversity measured with these microsatellites were rather modest in this species. Hardy-Weinberg disequilibrium was especially found for the overall and the Ecuadorian samples, and might be due to the Wahl-und effect or consanguinity. Significant genetic heterogeneity was mainly observed among the Colombian and the Ecuadorian populations. Markov chain Monte Carlo simulations clearly showed that two different gene pools were present, one present in the Venezuelan-Colombian bears and other in the Ecuadorian ones.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratory of Molecular Population Genetics (Grupo de Genética de Poblaciones-Biología Evolutiva), Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogota DC, Colombia
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Anderson CR, Lindzey FG, McDonald DB. GENETIC STRUCTURE OF COUGAR POPULATIONS ACROSS THE WYOMING BASIN: METAPOPULATION OR MEGAPOPULATION. J Mammal 2004. [DOI: 10.1644/bel-111.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Thuillet AC, Bataillon T, Poirier S, Santoni S, David JL. Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics 2004; 169:1589-99. [PMID: 15545658 PMCID: PMC1449565 DOI: 10.1534/genetics.104.029553] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Estimation of long-term effective population size (N(e)) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate N(e) because their high mutation rate can be estimated from observed mutations. We used this property to estimate N(e) in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates mu were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter theta = 4N(e)mu. We demonstrated from simulations that the unbiased estimator of theta based on Nei's heterozygosity is the most appropriate for estimating N(e) because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a N(e) of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.
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Affiliation(s)
- A-C Thuillet
- Institut National de la Recherche Agronomique-UMR 1097 Diversité et Génomes des Plantes Cultivées, Mauguio, France
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Onorato DP, Hellgren EC, Van Den Bussche RA, Skiles, Jr. JR. Paternity and relatedness of American black bears recolonizing a desert montane island. CAN J ZOOL 2004. [DOI: 10.1139/z04-097] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
American black bears (Ursus americanus (Pallas, 1780)) are characterized by female philopatry and male-biased dispersal, with predictable consequences for genetic structure of populations. We studied a recolonizing population of black bears on a desert montane island to test genetic-based predictions of bear social behavior. We assessed genetic paternity and relatedness among bears within Big Bend National Park, Texas, from 1998 to 2001 via maternally and biparentally inherited markers and field observations. Data from seven microsatellite loci permitted us to assign paternity for 7 of 12 cubs, and multiple paternity was revealed in one litter. Levels of relatedness in the Park were comparable to those found in a nearby large population in Coahuila, Mexico. Adult female bears in the Park were more closely related to each other than males were to each other. Microsatellite data were consistent with previous analyses of mtDNA sequences that indicated bears in the Mexico-Texas metapopulation exhibit male-biased dispersal. Demographic and genetic data provided a pedigree for 23 of 31 sampled bears and depicted the matriarchal structure of this recently recolonized population. Although females in this insular population are closely related to each other, as predicted by characteristics of ursine social ecology, incoming dispersal by unrelated males results in periodic supplementation of genetic variation.
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Kaeuffer R, Pontier D, Devillard S, Perrin N. Effective size of two feral domestic cat populations (Felis catus L.): effect of the mating system. Mol Ecol 2004; 13:483-90. [PMID: 14717902 DOI: 10.1046/j.1365-294x.2003.02046.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A variety of behavioural traits have substantial effects on the gene dynamics and genetic structure of local populations. The mating system is a plastic trait that varies with environmental conditions in the domestic cat (Felis catus) allowing an intraspecific comparison of the impact of this feature on genetic characteristics of the population. To assess the potential effect of the heterogenity of males' contribution to the next generation on variance effective size, we applied the ecological approach of Nunney & Elam (1994) based upon a demographic and behavioural study, and the genetic 'temporal methods' of Waples (1989) and Berthier et al. (2002) using microsatellite markers. The two cat populations studied were nearly closed, similar in size and survival parameters, but differed in their mating system. Immigration appeared extremely restricted in both cases due to environmental and social constraints. As expected, the ratio of effective size to census number (Ne/N) was higher in the promiscuous cat population (harmonic mean = 42%) than in the polygynous one (33%), when Ne was calculated from the ecological method. Only the genetic results based on Waples' estimator were consistent with the ecological results, but failed to evidence an effect of the mating system. Results based on the estimation of Berthier et al. (2002) were extremely variable, with Ne sometimes exceeding census size. Such low reliability in the genetic results should retain attention for conservation purposes.
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Affiliation(s)
- R Kaeuffer
- UMR-CNRS 5558 'Biométrie et biologie évolutive', Université C. Bernard Lyon 1, 43 Bd du 11 novembre 1918, 69622 Villeurbanne cedex, France
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Ciofi C, Milinkovitch MC, Gibbs JP, Caccone A, Powell JR. Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises. Mol Ecol 2002; 11:2265-83. [PMID: 12406238 DOI: 10.1046/j.1365-294x.2002.01617.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Giant Galápagos tortoises represent an interesting model for the study of patterns of genetic divergence and adaptive differentiation related to island colonization events. Recent mitochondrial DNA work elucidated the evolutionary history of the species and helped to clarify aspects of nomenclature. We used 10 microsatellite loci to assess levels of genetic divergence among and within island populations. In particular, we described the genetic structure of tortoises on the island of Isabela, where discrimination of different taxa is still subject of debate. Individual island populations were all genetically distinct. The island of Santa Cruz harboured two distinct populations. On Isabela, populations of Volcan Wolf, Darwin and Alcedo were significantly different from each other. On the other hand, Volcan Wolf showed allelic similarity with the island of Santiago. On Southern Isabela, lower genetic divergence was found between Northeast Sierra Negra and Volcan Alcedo, while patterns of gene flow were recorded among tortoises of Cerro Azul and Southeast Sierra Negra. These tortoises have endured heavy exploitation during the last three centuries and recently attracted much concern due to the current number of stochastic and deterministic threats to extant populations. Our study complements previous investigation based on mtDNA diversity and provides further information that may help devising tortoise management plans.
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Affiliation(s)
- Claudio Ciofi
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA.
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Larson S, Jameson R, Etnier M, Fleming M, Bentzen P. Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18th and 19th centuries. Mol Ecol 2002; 11:1899-903. [PMID: 12296934 DOI: 10.1046/j.1365-294x.2002.01599.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sea otter (Enhydra lutris) populations experienced widespread reduction and extirpation due to the fur trade of the 18th and 19th centuries. We examined genetic variation within four microsatellite markers and the mitochondrial DNA (mtDNA) d-loop in one prefur trade population and compared it to five modern populations to determine potential losses in genetic variation. While mtDNA sequence variability was low within both modern and extinct populations, analysis of microsatellite allelic data revealed that the prefur trade population had significantly more variation than all the extant sea otter populations. Reduced genetic variation may lead to inbreeding depression and we believe sea otter populations should be closely monitored for potential associated negative effects.
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Affiliation(s)
- Shawn Larson
- The Seattle Aquarium, 1483 Alaskan Way, Pier 59, Seattle, WA 98101, USA.
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Larson S, Jameson R, Bodkin J, Staedler M, Bentzen P. MICROSATELLITE DNA AND MITOCHONDRIAL DNA VARIATION IN REMNANT AND TRANSLOCATED SEA OTTER (ENHYDRA LUTRIS) POPULATIONS. J Mammal 2002. [DOI: 10.1644/1545-1542(2002)083<0893:mdamdv>2.0.co;2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Uphyrkina O, Johnson WE, Quigley H, Miquelle D, Marker L, Bush M, O'Brien SJ. Phylogenetics, genome diversity and origin of modern leopard, Panthera pardus. Mol Ecol 2001; 10:2617-33. [PMID: 11883877 DOI: 10.1046/j.0962-1083.2001.01350.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Leopards, Panthera pardus, are widely distributed across southern Asia and sub-Saharan Africa. The extent and phylogeographic patterns of molecular genetic diversity were addressed in a survey of 77 leopards from known geographical locales representing 13 of the 27 classical trinomial subspecies. Phylogenetic analysis of mitochondrial DNA sequences (727 bp of NADH5 and control region) and 25 polymorphic microsatellite loci revealed abundant diversity that could be partitioned into a minimum of nine discrete populations, tentatively named here as revised subspecies: P. pardus pardus, P. p. nimr, P. p. saxicolor, P. p. fusca, P. p. kotiya, P. p. delacouri, P. p. japonensis, P. p. orientalis and P. p. melas. However, because of limited sampling of African populations, this may be an underestimate of modern phylogeographic population structure. Combined phylogeographic and population diversity estimates support an origin for modern leopard lineages 470,000-825,000 years ago in Africa followed by their migration into and across Asia more recently (170,000-300,000 years ago). Recent demographic reductions likely have led to genetic impoverishment in P. p. orientalis and in the island subspecies P. p. kotiya.
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Affiliation(s)
- O Uphyrkina
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA
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