Microsatellite analysis of genetic diversity in fragmented South African buffalo populations

O’Ryan, Colleen; Harley, Eric H.; Bruford, Michael William; Beaumont, Mark A.; Wayne, Robert K.; Cherry, Michael

doi:10.1017/s136794309800002x

Cited by 35 publications

(72 citation statements)

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“…The level of variation in the black‐faced impala is, however, comparable to that of cattle Bos taurus and Bos indicus (MacHugh et al . 1997), African buffalo populations Syncerus caffer (O’Ryan et al . 1998; Simonsen et al .…”

Section: Discussionmentioning

confidence: 99%

No suggestion of hybridization between the vulnerable black‐faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia

Lorenzen

Siegismund

2004

Molecular Ecology

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There are two recognized subspecies of impala in sub-Saharan Africa: the common impala (Aepyceros melampus melampus) -- widespread in southern and east Africa -- and the vulnerable black-faced impala (A. m. petersi) -- found naturally in only a small enclave in southwest Africa. The Etosha National Park (NP) in Namibia harbours the largest and only protected-area population of black-faced impala, numbering some 1500 individuals. Due to translocations of the exotic common impala to commercial farms in Namibia during the past decades, the black-faced impala in Etosha is faced with the potentially serious threat of hybridization posed by secondary contact with the common impala inhabiting bordering farms. Using eight microsatellite DNA markers, we analysed 127 black-faced impala individuals from the five subpopulations in Etosha NP, to determine the degree, if any, of hybridization within the park. We found that (a) the black-faced impala were highly genetically differentiated from the common impala (pairwise theta-values ranged from 0.18 to 0.39 between subspecies; overall value = 0.27) and (b) black-faced samples showed high levels of genetic variability [average expected heterozygosity (H(E)) = 0.61 +/- 0.01 SE], although not as high as that observed in the common impala (average H(E) = 0.69 +/- 0.02 SE). (c) No hybridization between the subspecies in Etosha was suggested. A Bayesian Markov Chain Monte Carlo approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of 'genetic admixture' among subspecies.

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Section: Discussionmentioning

confidence: 99%

No suggestion of hybridization between the vulnerable black‐faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia

Lorenzen

Siegismund

2004

Molecular Ecology

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“…To avoid large numerical errors in calculating (2) and thus (7) for large genealogies (a sample of $100 sequences), I conduct computations using high precision of hundreds of significant digits (depending on sample size). An alternative option is to adopt a Markov chain Monte Carlo method proposed by Griffiths and Tavaré (1994) as in O'Ryan et al (1998).…”

Section: Methodsmentioning

confidence: 99%

A Coalescent-Based Estimator of Admixture From DNA Sequences

Wang

2006

Genetics

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A variety of estimators have been developed to use genetic marker information in inferring the admixture proportions (parental contributions) of a hybrid population. The majority of these estimators used allele frequency data, ignored molecular information that is available in markers such as microsatellites and DNA sequences, and assumed that mutations are absent since the admixture event. As a result, these estimators may fail to deliver an estimate or give rather poor estimates when admixture is ancient and thus mutations are not negligible. A previous molecular estimator based its inference of admixture proportions on the average coalescent times between pairs of genes taken from within and between populations. In this article I propose an estimator that considers the entire genealogy of all of the sampled genes and infers admixture proportions from the numbers of segregating sites in DNA sequence samples. By considering the genealogy of all sequences rather than pairs of sequences, this new estimator also allows the joint estimation of other interesting parameters in the admixture model, such as admixture time, divergence time, population size, and mutation rate. Comparative analyses of simulated data indicate that the new coalescent estimator generally yields better estimates of admixture proportions than the previous molecular estimator, especially when the parental populations are not highly differentiated. It also gives reasonably accurate estimates of other admixture parameters. A human mtDNA sequence data set was analyzed to demonstrate the method, and the analysis results are discussed and compared with those from previous studies.

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“…R st is expected to be larger than F st when populations have evolved independently (e.g., low historical Nm between populations). On the other hand, when the values between R st and F st are nearly equal, Nm has been historically large between populations and drift has been the predominant factor in creating differences between populations, not mutation (Slatkin 1995;O'Ryan et al 1998). In this study, R st was lower than F st suggesting that (1) drift has been more important than mutation historically, and (2) Nm has been large.…”

Section: Current Versus Historical Gene Flowmentioning

confidence: 55%

“…Unfortunately, migration rates calculated by these methods may be more reflective of historical migration than current migration (Whitlock and McCauley 1999), even when based on highly variable DNA markers such as microsatellites. Several authors have suggested ways to separate historical versus current gene flow (Slatkin 1995;O'Ryan et al 1998). We use these approaches, plus combined field and laboratory data to make inferences about current versus historical gene flow of kit fox in the San Joaquin Valley.…”

Section: Introductionmentioning

confidence: 99%

Gene flow among San Joaquin kit fox populations in a severely changed ecosystem

et al. 2005

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The San Joaquin kit fox (Vulpes macrotis mutica) was once ubiquitous throughout California's San Joaquin Valley and its surrounds. However, most of its habitat has been lost to irrigated agriculture, urban development, and oil fields. The remaining foxes are concentrated in six areas, although there are several small pockets of foxes throughout the Valley. To help conserve kit foxes, we sought an ecological understanding of the level of genetic variation remaining in these locations and the extent of gene flow among them. We collected tissue from 317 kit foxes from 8 sites and estimated genetic variability in and gene flow among sites using data from 8 polymorphic, microsatellite markers. We found no differences in both observed and expected heterozygosity between locations using Bonferonni corrected paired t-tests. We found differences in mean number of alleles per locus, even after we used Monte Carlo simulations to adjust for sample size differences. Population subdivision was low among sites (F st ¼ 0.043), yet a matrix of pairwise F st values was correlated with a matrix of pairwise geographic distances. An assignment test classified only 45% of the individuals to the site where they were captured. Overall, these data suggest that kit fox dispersal between locations may still maintain genetic variation throughout most of the areas we sampled.

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Microsatellite analysis of genetic diversity in fragmented South African buffalo populations

Cited by 35 publications

References 0 publications

No suggestion of hybridization between the vulnerable black‐faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia

No suggestion of hybridization between the vulnerable black‐faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia

A Coalescent-Based Estimator of Admixture From DNA Sequences

Gene flow among San Joaquin kit fox populations in a severely changed ecosystem

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