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de Flamingh A, Ishida Y, Pečnerová P, Vilchis S, Siegismund HR, van Aarde RJ, Malhi RS, Roca AL. Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. Front Genet 2023; 13:1021004. [PMID: 36712847 PMCID: PMC9876978 DOI: 10.3389/fgene.2022.1021004] [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: 08/16/2022] [Accepted: 12/05/2022] [Indexed: 01/13/2023] Open
Abstract
Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
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Affiliation(s)
- Alida de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sahara Vilchis
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Hans R. Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rudi J. van Aarde
- Department of Zoology and Entomology, Conservation Ecology Research Unit, University of Pretoria, Pretoria, South Africa
| | - Ripan S. Malhi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
| | - Alfred L. Roca
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
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Lohay GG, Weathers TC, Estes AB, McGrath BC, Cavener DR. Genetic connectivity and population structure of African savanna elephants ( Loxodonta africana) in Tanzania. Ecol Evol 2020; 10:11069-11089. [PMID: 33144949 PMCID: PMC7593188 DOI: 10.1002/ece3.6728] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 11/07/2022] Open
Abstract
Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals sampled in 2015 and 2017. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. In northern Tanzania, elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean F ST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean A R = 9.96), heterozygosity (mean µH E = 0.73), and effective population sizes (mean N e = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.
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Affiliation(s)
- George G. Lohay
- Biology DepartmentThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Thomas Casey Weathers
- Ecosystem Science and ManagementThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Anna B. Estes
- Environmental Studies DepartmentCarleton CollegeNorthfieldMNUSA
- The Nelson Mandela African Institution of Science and TechnologyArushaTanzania
| | | | - Douglas R. Cavener
- Biology DepartmentThe Pennsylvania State UniversityUniversity ParkPAUSA
- The Nelson Mandela African Institution of Science and TechnologyArushaTanzania
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Visser J, Robinson T, Jansen van Vuuren B. Spatial genetic structure in the rock hyrax (Procavia capensis) across the Namaqualand and western Fynbos areas of South Africa — a mitochondrial and microsatellite perspective. CAN J ZOOL 2020. [DOI: 10.1139/cjz-2019-0154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interplay between biotic and abiotic environments is increasingly recognized as a major determinant of spatial genetic patterns. Among spatial genetic studies, saxicolous or rock-dwelling species remain underrepresented in spite of their strict dependence on landscape structure. Here we investigated patterns and processes operating at different spatial (fine and regional scales) and time scales (using mitochondrial and microsatellite markers) in the rock hyrax (Procavia capensis (Pallas, 1766)). Our focus was on the western seaboard of South Africa and included two recognized biodiversity hotspots (Cape Floristic Region and Succulent Karoo). At fine spatial scale, significant genetic structure was present between four rocky outcrops in an isolated population, likely driven by the social system of this species. At a broader spatial scale, ecological dependence on rocky habitat and population-level processes, in conjunction with landscape structure, appeared to be the main drivers of genetic diversity and structure. Large areas devoid of suitable rocky habitat (e.g., the Knersvlakte, Sandveld, and Cape Flats, South Africa) represent barriers to gene flow in the species, although genetic clusters closely follow climatic, geological, and phytogeographic regions, possibly indicating ecological specialization or adaptation as contributing factors enforcing isolation. Taken together, our study highlights the need to consider both intrinsic and extrinsic factors when investigating spatial genetic structures within species.
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Affiliation(s)
- J.H. Visser
- Department of Botany and Zoology, University of Stellenbosch, Private Bag XI, Matieland 7602, South Africa
| | - T.J. Robinson
- Department of Botany and Zoology, University of Stellenbosch, Private Bag XI, Matieland 7602, South Africa
| | - B. Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, P.O. Box 524, Auckland Park 2000, South Africa
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Cosenza M, La Rosa V, Rosati R, Chiofalo V. Genetic diversity of the Italian thoroughbred horse population. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2018.1547128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mario Cosenza
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
| | - Valentina La Rosa
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
| | - Raffaella Rosati
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
| | - Vincenzo Chiofalo
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
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Sabino-Marques H, Ferreira CM, Paupério J, Costa P, Barbosa S, Encarnação C, Alpizar-Jara R, Alves PC, Searle JB, Mira A, Beja P, Pita R. Combining genetic non-invasive sampling with spatially explicit capture-recapture models for density estimation of a patchily distributed small mammal. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1206-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Effect of landscape features on genetic structure of the goitered gazelle (Gazella subgutturosa) in Central Iran. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1002-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Noble CW, Bono JM, Pigage HK, Hale DW, Pigage JC. Fine-Scale Genetic Structure in Female Mule Deer (Odocoileus hemionus). WEST N AM NATURALIST 2016. [DOI: 10.3398/064.076.0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Roca AL, Ishida Y, Brandt AL, Benjamin NR, Zhao K, Georgiadis NJ. Elephant Natural History: A Genomic Perspective. Annu Rev Anim Biosci 2015; 3:139-67. [DOI: 10.1146/annurev-animal-022114-110838] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfred L. Roca
- Department of Animal Sciences,
- Institute for Genomic Biology, and
| | | | | | - Neal R. Benjamin
- Department of Animal Sciences,
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; , , , , ,
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Hess MA, Rhydderch JG, LeClair LL, Buckley RM, Kawase M, Hauser L. Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus). Mol Ecol Resour 2012; 12:1114-23. [PMID: 22958648 DOI: 10.1111/1755-0998.12002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 07/20/2012] [Accepted: 07/28/2012] [Indexed: 11/25/2022]
Abstract
Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent-offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop-out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent-offspring pairs and unintentionally recaptured individuals, respectively. By direct-count error estimates, the recapture and known parent-offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent-offspring comparisons. Furthermore, there was no correlation in locus-specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus-specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent-offspring comparisons in parentage studies).
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Affiliation(s)
- Maureen A Hess
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.
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Archie EA, Chiyo PI. Elephant behaviour and conservation: social relationships, the effects of poaching, and genetic tools for management. Mol Ecol 2011; 21:765-78. [PMID: 21880086 DOI: 10.1111/j.1365-294x.2011.05237.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic tools are increasingly valuable for understanding the behaviour, evolution, and conservation of social species. In African elephants, for instance, genetic data provide basic information on the population genetic causes and consequences of social behaviour, and how human activities alter elephants' social and genetic structures. As such, African elephants provide a useful case study to understand the relationships between social behaviour and population genetic structure in a conservation framework. Here, we review three areas where genetic methods have made important contributions to elephant behavioural ecology and conservation: (1) understanding kin-based relationships in females and the effects of poaching on the adaptive value of elephant relationships, (2) understanding patterns of paternity in elephants and how poaching can alter these patterns, and (3) conservation genetic tools to census elusive populations, track ivory, and understand the behavioural ecology of crop-raiding. By comparing studies from populations that have experienced a range of poaching intensities, we find that human activities have a large effect on elephant behaviour and genetic structure. Poaching disrupts kin-based association patterns, decreases the quality of elephant social relationships, and increases male reproductive skew, with important consequences for population health and the maintenance of genetic diversity. In addition, we find that genetic tools to census populations or gather forensic information are almost always more accurate than non-genetic alternatives. These results contribute to a growing understanding of poaching on animal behaviour, and how genetic tools can be used to understand and conserve social species.
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Affiliation(s)
- Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
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Ishida Y, Demeke Y, van Coeverden de Groot PJ, Georgiadis NJ, Leggett KEA, Fox VE, Roca AL. Distinguishing forest and savanna African elephants using short nuclear DNA sequences. ACTA ACUST UNITED AC 2011; 102:610-6. [PMID: 21775678 DOI: 10.1093/jhered/esr073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A more complete description of African elephant phylogeography would require a method that distinguishes forest and savanna elephants using DNA from low-quality samples. Although mitochondrial DNA is often the marker of choice for species identification, the unusual cytonuclear patterns in African elephants make nuclear markers more reliable. We therefore designed and utilized genetic markers for short nuclear DNA regions that contain fixed nucleotide differences between forest and savanna elephants. We used M13 forward and reverse sequences to increase the total length of PCR amplicons and to improve the quality of sequences for the target DNA. We successfully sequenced fragments of nuclear genes from dung samples of known savanna and forest elephants in the Democratic Republic of Congo, Ethiopia, and Namibia. Elephants at previously unexamined locations were found to have nucleotide character states consistent with their status as savanna or forest elephants. Using these and results from previous studies, we estimated that the short-amplicon nuclear markers could distinguish forest from savanna African elephants with more than 99% accuracy. Nuclear genotyping of museum, dung, or ivory samples will provide better-informed conservation management of Africa's elephants.
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Affiliation(s)
- Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Zemanová B, Hájková P, Bryja J, Zima J, Hájková A, Zima J. Development of multiplex microsatellite sets for noninvasive population genetic study of the endangered Tatra chamois. FOLIA ZOOLOGICA 2011. [DOI: 10.25225/fozo.v60.i1.a11.2011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Barbora Zemanová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petra Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Andrea Hájková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Jan Zima
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Department of Population Biology, Květná 8, 603 65 Brno, Czech Republic; e-mails: , , , , ,
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Development of a microsatellite library for the flightless moth Pringleophaga marioni Viette (Lepidoptera: Tineidae). CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9344-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wittemyer G, Okello JBA, Rasmussen HB, Arctander P, Nyakaana S, Douglas-Hamilton I, Siegismund HR. Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants. Proc Biol Sci 2009; 276:3513-21. [PMID: 19605399 PMCID: PMC2817196 DOI: 10.1098/rspb.2009.0941] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/24/2009] [Indexed: 11/12/2022] Open
Abstract
Hierarchical properties characterize elephant fission-fusion social organization whereby stable groups of individuals coalesce into higher order groups or split in a predictable manner. This hierarchical complexity is rare among animals and, as such, an examination of the factors driving its emergence offers unique insight into the evolution of social behaviour. Investigation of the genetic basis for such social affiliation demonstrates that while the majority of core social groups (second-tier affiliates) are significantly related, this is not exclusively the case. As such, direct benefits received through membership of these groups appear to be salient to their formation and maintenance. Further analysis revealed that the majority of groups in the two higher social echelons (third and fourth tiers) are typically not significantly related. The majority of third-tier members are matrilocal, carrying the same mtDNA control region haplotype, while matrilocality among fourth-tier groups was slightly less than expected at random. Comparison of results to those from a less disturbed population suggests that human depredation, leading to social disruption, altered the genetic underpinning of social relations in the study population. These results suggest that inclusive fitness benefits may crystallize elephant hierarchical social structuring along genetic lines when populations are undisturbed. However, indirect benefits are not critical to the formation and maintenance of second-, third- or fourth-tier level bonds, indicating the importance of direct benefits in the emergence of complex, hierarchical social relations among elephants. Future directions and conservation implications are discussed.
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Affiliation(s)
- George Wittemyer
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA.
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Rivière-Dobigny T, Doan LP, Quang NL, Maillard JC, Michaux J. Species identification, molecular sexing and genotyping using non-invasive approaches in two wild bovids species: Bos gaurus and Bos javanicus. Zoo Biol 2009; 28:127-36. [PMID: 19367625 DOI: 10.1002/zoo.20211] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since the second Indochina war, habitat destruction and overhunting has resulted in fragmentation of the remaining populations of Bos javanicus and B. gaurus. Nowadays, both species are in serious danger, especially the gaur. In Vietnam, where these species have become almost impossible to capture in the wild, non-invasive investigations are the only feasible approach to obtain data on populations. However, non-invasive derived DNA, especially in tropical areas, is usually characterized by low concentrations, poor quality and/or contamination from alien DNA. To assist in tropical conservation management, baseline information is provided here on assessing the reliability of species identification, molecular sexing and microsatellite genotyping using fecal DNA from B. gaurus and B. javanicus. For species identification using bovine fecal samples, cytochrome b fragment between positions 867 and 1140 was found to contain species diagnostic sites, which distinguishes the four species encountered in the region: B. gaurus, B. indicus, B. javanicus and B. taurus. For sex determination, primers were initially tested on DNA obtained from blood. Then, these primers were successfully used on DNA derived from fecal material. Finally, we also evaluate the feasibility of non-invasive microsatellite genotyping on fecal samples collected in Vietnamese nature reserves. The results presented here improve on current molecular methods based on fecal material obtained from tropical areas.
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Wright JA, Barker RJ, Schofield MR, Frantz AC, Byrom AE, Gleeson DM. Incorporating Genotype Uncertainty into Mark-Recapture-Type Models For Estimating Abundance Using DNA Samples. Biometrics 2009; 65:833-40. [DOI: 10.1111/j.1541-0420.2008.01165.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Okello JBA, Wittemyer G, Rasmussen HB, Arctander P, Nyakaana S, Douglas-Hamilton I, Siegismund HR. Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants. Mol Ecol 2008; 17:3788-99. [PMID: 18643879 DOI: 10.1111/j.1365-294x.2008.03871.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two hundred years of elephant hunting for ivory, peaking in 1970-1980s, caused local extirpations and massive population declines across Africa. The resulting genetic impacts on surviving populations have not been studied, despite the importance of understanding the evolutionary repercussions of such human-mediated events on this keystone species. Using Bayesian coalescent-based genetic methods to evaluate time-specific changes in effective population size, we analysed genetic variation in 20 highly polymorphic microsatellite loci from 400 elephants inhabiting the greater Samburu-Laikipia region of northern Kenya. This area experienced a decline of between 80% and 90% in the last few decades when ivory harvesting was rampant. The most significant change in effective population size, however, occurred approximately 2500 years ago during a mid-Holocene period of climatic drying in tropical Africa. Contrary to expectations, detailed analyses of four contemporary age-based cohorts showed that the peak poaching epidemic in the 1970s caused detectable temporary genetic impacts, with genetic diversity rebounding as juveniles surviving the poaching era became reproductively mature. This study demonstrates the importance of climatic history in shaping the distribution and genetic history of a keystone species and highlights the utility of coalescent-based demographic approaches in unravelling ancestral demographic events despite a lack of ancient samples. Unique insights into the genetic signature of mid-Holocene climatic change in Africa and effects of recent poaching pressure on elephants are discussed.
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Affiliation(s)
- J B A Okello
- Biotechnology and Molecular Genetics, FB2-UFT, University of Bremen, Leobenerstrasse UFT, 28359 Bremen, Germany.
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Okello JBA, Masembe C, Rasmussen HB, Wittemyer G, Omondi P, Kahindi O, Muwanika VB, Arctander P, Douglas-Hamilton I, Nyakaana S, Siegismund HR. Population genetic structure of savannah elephants in Kenya: conservation and management implications. J Hered 2008; 99:443-52. [PMID: 18477589 DOI: 10.1093/jhered/esn028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of alleles, expected and observed heterozygosities in the total study population of 10.20, 0.75, and 0.69, respectively. Hierarchical analysis of molecular variance of mtDNA variation revealed significant differentiation among the 3 geographical regions studied (F(CT) = 0.264; P < 0.05) and a relatively lower differentiation among populations within regions (F(SC) = 0.218; P < 0.0001). Microsatellite variation significantly differentiated among populations within regions (F(SC) = 0.019; P < 0.0001) but not at the regional levels (F(CT) = 0.000; P > 0.500). We attribute the high differentiation at the mitochondrial genome to the matrilineal social structure of elephant populations, female natal philopatry, and probably ancient vicariance. Lack of significant regional differentiation at the nuclear loci vis-a-vis strong differences at mtDNA loci between regions is likely the effect of subsequent homogenization through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.
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Affiliation(s)
- John B A Okello
- Molecular Biology Laboratory, Makerere University Institute of Environment and Natural Resources, PO Box 7298, Kampala, Uganda
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GREEN MICHELLEL, HERZING DENISEL, BALDWIN JOHND. Noninvasive methodology for the sampling and extraction of DNA from free-ranging Atlantic spotted dolphins (Stenella frontalis). ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01858.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rasmussen H, Okello J, Wittemyer G, Siegismund H, Arctander P, Vollrath F, Douglas-Hamilton I. Age- and tactic-related paternity success in male African elephants. Behav Ecol 2007. [DOI: 10.1093/beheco/arm093] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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