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:10.1111/j.1469-1795.1998.tb00015.x

Cited by 99 publications

(84 citation statements)

References 24 publications

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“…In the immigration-drift-equilibrium model, the degree of differentiation is a measure of the relative strength of drift versus immigration (Rannala and Hartigan 1996), while in the non-equilibrium drift model it is related to the time since fragmentation (scaled by population size) (O'Ryan et al 1998). 2mod first estimates the probability of obtaining each dataset assuming that the mutation rate is much smaller than the immigration rate in the gene flow model, and that the reciprocal of the mutation rate is much longer than the divergence time in the drift model.…”

Section: Demographic Historymentioning

confidence: 99%

Fine-scale genetic structure in Ethiopian wolves imposed by sociality, migration, and population bottlenecks

Randall

Pollinger

Argaw³

et al. 2009

Conserv Genet

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We used demographic, spatial, and microsatellite data to assess fine-scale genetic structure in Ethiopian wolves found in the Bale Mountains and evaluated the impact of historical versus recent demographic processes on genetic variation. We applied several analytical methods, assuming equilibrium and nonequilibrium conditions, to assess demography and genetic structure. Genetic variation (H E = 0.584-0.607, allelic richness = 4.2-4.3) was higher than previously reported for this species and genetic structure was influenced by geography and social structure. Statistically significant F ST values (0.06-0.08) implied differentiation among subpopulations. STRUCTURE analyses showed that neighbouring packs often have shared coancestry and spatial autocorrelation showed higher genetic similarity between individuals within packs and between individuals in neighbouring packs compared to random pairs of individuals. Recent effective population sizes were lower than 2n (where n is the number of packs) and lower than the number of breeding individuals with N e /N ratios near 0.20. All subpopulations have experienced bottlenecks, one occurring due to a rabies outbreak in 2003. Nevertheless, differentiation among these subpopulations is consistent with long-term migration rates and fragmentation at the end of the Pleistocene. Enhanced drift due to population bottlenecks may be countered by higher migration into disease-affected subpopulations. Contemporary factors such as social structure and population bottlenecks are clearly influencing the level and distribution of genetic variation in this population, which has implications for its conservation.

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Section: Demographic Historymentioning

confidence: 99%

Fine-scale genetic structure in Ethiopian wolves imposed by sociality, migration, and population bottlenecks

Randall

Pollinger

Argaw³

et al. 2009

Conserv Genet

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“…The effective population size (N e ) of both wild and captive populations was estimated with the program DLIK (available at: http://www.rubic.rdg.ac.uk/~mab/software.html). This program uses coalescent theory and Monte Carlo sampling of gene frequencies to generate a probability distribution of the parameter T/N e , where T is the number of generations that have elapsed since the population was founded and N e is the effective population size over that period (O'Ryan et al 1998). A generation time of 8.34 for Cynopterus bats (Storz et al 2001b) was used as a best estimate for Pteropus bats and a maximum effective population size of 1,000 was assumed based on previous census data (Fig.…”

Section: Discussionmentioning

confidence: 99%

Rodrigues fruit bats (Pteropus rodricensis, Megachiroptera: Pteropodidae) retain genetic diversity despite population declines and founder events

et al. 2007

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Fruit bats of the genus Pteropus are important contributors to ecosystem maintenance on islands through their roles as pollinators and seed dispersers. However, island faunas are the most prone to extinction and there is a real need to assess the possible genetic implications of population reductions in terms of extinction risk. An effective method of ameliorating extinction risk in endangered species is the establishment of captive populations ex situ. The effectiveness of captive breeding programmes may be assessed by comparing the genetic variability of captive colonies to that of wild counterparts. Here, we use polymorphic microsatellite loci to assess genetic variability in wild, critically endangered Rodrigues fruit bats (Pteropus rodricensis, Dobson 1878) and we compare this variability to that in a captive colony. We document remarkable conservation of genetic variability in both the wild and captive populations, despite population declines and founder events. Our results demonstrate that the wild population has withstood the negative effects of population reductions and that captive breeding programmes can fulfil the goals of retaining genetic diversity and limiting inbreeding.

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“…For example, information on census size is often available, and if the rate of inbreeding for a given census size can be calibrated for one population then predictions may be made about other (comparable) populations on other (comparable) timescales (e.g. O'Ryan et al, 1998).…”

Section: Estimating Effective Population Sizementioning

confidence: 99%

“…An additional problem is that the evaluation of p(n c |T /(2N e ), n s ) can be numerically unstable. O'Ryan et al (1998) use importance sampling (Griffiths and Tavaré, 1994) as an alternative method of evaluation, and this is embedded within a Markov chain Monte Carlo (MCMC) sampler to infer marginal posterior densities for individual parameters (see Beaumont, 2003a, for a detailed description of this general approach). The general scheme for two populations is illustrated in Figure 30.1.…”

Section: Estimating N E From Two Derived Populationsmentioning

confidence: 99%

“…Using the MCMC scheme, marginal posterior distributions for T /(2N e ) can be obtained. In the study of O'Ryan et al (1998) a number of isolated populations were modelled in this way and the effective population size could be estimated because the splitting times were known. As an example, one population, (St. Lucia), was seeded from another umfolozi-hluhluwe complex (UHC) 16 years prior to sampling.…”

Section: Estimating N E From Two Derived Populationsmentioning

confidence: 99%

See 1 more Smart Citation

Conservation Genetics

Beaumont¹

2007

Handbook of Statistical Genetics

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This chapter reviews some of the statistical methodologies used in the genetic analysis of endangered and managed populations. The topics covered include the estimation of effective population size, N e , the detection of past changes in population size, the estimation of admixture proportions, and the analysis of local population structure, kinship, and relatedness through genotypic methods. The reasons why it may be useful to measure N e are discussed. Using genetic information it is possible to estimate N e from changes in gene frequencies between samples taken at different times, or from genotypic disequilibria in one sample, or from differences in gene frequencies between two recently descended populations. The different statistical methodologies that have been applied are discussed in some detail. The ability to detect past changes in population size may also be useful in conservation management, and some of the more recent approaches are described. Another area of concern in conservation biology is introgressive hybridisation. At the population level it is possible to infer admixture proportions by comparing the gene frequencies in the admixed and non-admixed populations, providing they are available, and the different statistical approaches to analysing this problem are reviewed. Statistical methods have also been developed to detect immigrant and hybrid individuals from their multi-locus genotype, and the main methods developed in this area are also discussed.

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Microsatellite analysis of genetic diversity in fragmented South African buffalo populations

Cited by 99 publications

References 24 publications

Fine-scale genetic structure in Ethiopian wolves imposed by sociality, migration, and population bottlenecks

Fine-scale genetic structure in Ethiopian wolves imposed by sociality, migration, and population bottlenecks

Rodrigues fruit bats (Pteropus rodricensis, Megachiroptera: Pteropodidae) retain genetic diversity despite population declines and founder events

Conservation Genetics

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