Characterization of microsatellite loci in the black rhinoceros (Diceros bicornis) and white rhinoceros (Ceratotherium simum): their use for cross-species amplification and differentiation between the two species

Nielsen, Lindsey; Meehan-Meola, Dawn; Kilbourn, Annelisa M.; Alcivar–Warren, Acacia

doi:10.1007/s10592-007-9321-3

Cited by 10 publications

(10 citation statements)

References 8 publications

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“…It is apparent that low levels of genetic diversity characterize southern white rhinoceros populations, and the results from our study are consistent with other microsatellite studies in this species (Seror et al 2002;Florescu et al 2003;Nielsen et al 2008 To date, our study population has produced just one inbred F 2 individual from seven offspring in the F 2 cohort. While many species demonstrate deleterious effects from inbreeding depression (Frankham et al 2002), in both managed and natural populations of free-ranging, long-lived species these effects are very difficult to measure.…”

Section: Discussionsupporting

confidence: 91%

“…Loci were selected based on data from Coutts (2009) and included 7B and 7C (Florescu et al 2003), WR1 and WR2 (reported in Nielsen et al 2008, redesigned from loci reported in Florescu et al 2003), BR6 (Cunningham et al 1999), DB1, DB44 and DB49 (Brown and Houlden 1999) and Rh7, Rh8 and Rh9 (Zschokke et al 2003). PCR conditions followed Coutts (2009) and Menotti-Raymond et al (2005) and cycle conditions were 5 adapted where needed (see Online Resource S2 for details).…”

Section: Dna Extraction and Microsatellite Genotypingmentioning

confidence: 99%

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Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management

Guerier

Bishop

Crawford³

et al. 2012

Conserv Genet

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Small populations are vulnerable to the consequences of breeding within closed groups as the loss of genetic variability can lead to inbreeding depression. Here, we use microsatellite genotypes to assess variability and parentage within a small, managed population of southern white rhinoceros in northern Namibia. Tissue samples gathered from either a modified biopsy darting technique or ear notches allowed us to obtain genotypic data for all individuals in the population. As expected for this species, genetic variability in the population was relatively low (overall H obs 0.45). In combination with detailed management records for the period 1993-2009, we were able to assign both parents for all 23 offspring. Only one calf of seven in the F 2 generation arose from father-daughter inbreeding within the population. Our analysis revealed that paternity was initially dominated by a single founder bull siring 10 of 13 calves over nine years; paradoxically, the other founder bull was selected for removal based on observations suggesting he was behaviourally dominant and therefore the likely sire of most calves. We also found that young introduced bulls were breeding successfully within six months of their arrival, well before having established their home ranges. We argue that in order to optimally manage and conserve the southern African rhino metapopulation it is essential to have accurate pedigree information and genetic data for all individuals in the numerous small populations that are key to the survival of the species.(379 words) Keywords Microsatellites, tissue biopsy, biopsy dart method, inbreeding, Ceratotherium simum simumElectronic supplementary material The online version of this article (doi: to come) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 91%

Section: Dna Extraction and Microsatellite Genotypingmentioning

confidence: 99%

Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management

Guerier

Bishop

Crawford³

et al. 2012

Conserv Genet

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“…Within our study, the average H E for D. b. minor was estimated at 0.44 compared with 0.51 reported for D. b. bicornis (Harley et al, 2005) and 0.68 for D. b. michaeli (see also Brown & Houlden, 1999) (in our study, H E was estimated at 0.43 for D. b. bicornis and 0.54 for D. b. michaeli based on a sample size of four individuals per subspecies). Although the lower heterozygosity for D. b. minor may reflect a sampling bias in our study, we do not believe this to be the case as our finding are in line with previous studies which similarly documented lower diversity within D. b. minor (H E = 0.46, Harley et al, 2005; H E = 0.37, Nielsen et al, 2008). Rather, these lower diversity values may reflect past demography and a small founding population (both in terms of number of individuals as well as the geographic area from which samples were taken) where all extant South African D. b. minor individuals are descendants from populations on only two reserves namely Hluhluwe-iMfolozi Park and Mkhuze Game Reserve.…”

Section: Discussionsupporting

confidence: 81%

The history and management of black rhino in KwaZulu‐Natal: a population genetic approach to assess the past and guide the future

Karsten

Vuuren

Goodman³

et al. 2011

Animal Conservation

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The numbers of black rhino Diceros bicornis in Africa declined dramatically during the last century due primarily to poaching and latterly habitat transformation and fragmentation and as such, significant concerns exist with regard to the long-term population viability and the management of these fragmented populations. A considerable proportion of the remaining black rhino (ssp. minor) are found within South Africa where they largely fall under the protection and management of Ezemvelo KwaZulu-Natal (KZN) Wildlife. Here we provide information on the genetic diversity, population differentiation and level of inbreeding among 77 Diceros bicornis minor individuals sampled in seven protected areas within the KZN Province of South Africa and a single population from Zimbabwe founded from the KZN population. For reference purposes with the cluster analyses, we included four individuals from ssp. bicornis and four individuals from ssp. michaeli. We found low levels of differentiation among ssp. minor populations across the KZN Province; this result is not unexpected given the history of establishments and translocations between reserves. In fact, we argue that the translocations conducted by Ezemvelo KZN Wildlife have contributed to the acceptable levels of heterozygosity and minimal inbreeding which characterize the majority of protected areas in the province. Although the overall genetic diversity in D. b. minor is lower than that present in both Diceros bicornis bicornis and Diceros bicornis michaeli, we do not feel that it is any cause for concern at this stage as it still falls within the range reported for other large mammals across Africa. The information presented here forms the basis of an ongoing monitoring programme aimed at providing vital information which, when taken with ecological and other data, will direct the future management decisions regarding translocations between reserves in South Africa and the exchange of individuals with other countries.

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“…Earlier genetic studies of black rhinoceros have examined various aspects of ex-situ conservation using mitochondrial (mt; Ashley et al 1990;Jama et al 1993; Morales and Melnick 1994;O'Ryan et al 1994) and nuclear DNA (Brown and Houlden 1999;Garnier et al 2001;Zschokke et al 2003;Nielsen et al 2008;Scott 2008). For example, Swart et al (1994), using mtDNA, demonstrated the persistence of genetic diversity in small populations of black rhinoceros that had undergone demographic contraction; highlighting the need to conserve even small populations.…”

Section: Introductionmentioning

confidence: 99%

Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation

et al. 2011

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Kenya's black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management exercise translocated the survivors into four high security sanctuaries to control poaching and enhance breeding, and this measure successfully arrested the decline. Subsequently, new sanctuaries were established and the metapopulation size reached 650 animals by 2008. However, translocations and the current management strategy that partitions the metapopulation into 'montane' and 'lowland' rhinoceros may have substantial consequences at the population level and their impact on population genetic diversity has not been investigated. In this study, 12 of the 16 extant subpopulations were analysed using 408 bp of mitochondrial control region sequence (n = 170) and nine microsatellite loci (n = 145). Both markers detected moderate to high genetic diversity (h = 0.78 ± 0.027, n = 170; H O = 0.70 ± 0.087, n = 145) consistent with previous studies on Diceros bicornis michaeli. However, mtDNA and nDNA diversity varied substantially between subpopulations. The results suggest that the Masai Mara is more differentiated, inbred and isolated than other subpopulations. It also suggests that there are neither distinct montane and lowland groups nor other detectable historical barriers to gene flow. Instead the large majority of genetic diversity was partitioned at the level of individuals; highlighting the need to conserve as many individuals as possible. Future translocations should consider the genetic profile of individuals and the demographic history of both the donor and recipient subpopulations.

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Characterization of microsatellite loci in the black rhinoceros (Diceros bicornis) and white rhinoceros (Ceratotherium simum): their use for cross-species amplification and differentiation between the two species

Cited by 10 publications

References 8 publications

Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management

Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management

The history and management of black rhino in KwaZulu‐Natal: a population genetic approach to assess the past and guide the future

Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation

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