Noninvasive Genotyping and Mendelian Analysis of Microsatellites in African Savannah Elephants (original) (raw)
Related papers
Patterns of molecular genetic variation among African elephant populations
Molecular Ecology, 2002
The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant populations show modest levels of phylogeographic subdivision based on composite microsatellite genotype, an indication of recent population isolation and restricted gene flow between locales. The savannah elephants show significantly lower genetic diversity than forest elephants, probably reflecting a founder effect in the recent history of the savannah species.
European Journal of Wildlife …, 2007
Habitat fragmentation often promotes increased inbreeding depression due to interrupted gene flow between populations. In this study, we demonstrate that Asian elephants most likely also suffer from outbreeding depression due to cryptic speciation. We analysed mitochondrial and nuclear DNA loci from 78 Asian elephants. Haplotype genealogy and analysis of molecular variance revealed two matrilinear clades (α h , β h ). Microsatellite analyses of individuals grouped according to their haplotype clade (corresponding group of nuclear genotypes called α nuc and β nuc ) revealed significant genotypic differentiation between α nuc and β nuc . Such genealogically differentiated forms in a morphologically uniform species are considered indicative of cryptic speciation. The differentiation was caused by bulls, whereas considering cows only resulted in no differentiation. Such result is best explained by Haldane's rule whereby hybrid formation between genealogical forms causes lower viability and fertility of heterogametic hybrids. Although the lack of hybrid-specific morphological characteristics renders direct testing of reduced hybrid fitness under natural conditions unfeasible, the effects of Haldane's rule are demonstrated by reduced male-mediated gene flow between genealogical forms under sympatric conditions, as was indeed suggested by the data found in Asian elephants: male-mediated gene flow between groups α nuc and β nuc was much lower than female-mediated gene flow.
Conservation Genetics, 2008
Numbers of the Asian elephants (Elephas maximus) population are declining due to poaching, human-elephant conflicts, capture of wild calves for tourism and export and habitat destruction, which also may cause inbreeding in fragmented populations. In order to contribute to a reversal of this trend, we have developed an identification and parentage test by evaluation and selection of markers from 43 microsatellite loci that have been previously described for Asian or African elephants. Testing these markers on a panel of 169 Asian elephants comprising the 23 mother-offspring, 13 father-offspring and 13 parents-offspring pairs yielded 26 polymorphic markers. However, only 14 of these were found to be suitable for an analysis of molecular diversity, 12 of which will be implemented for an identification and parentage test to control the capture of wild calves in Thailand and neighboring countries.
2002
Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and southern Africa. In the total sample, 43 haplotypes were identified and an overall nucleotide diversity of 2.0% was observed. High levels of polymorphism were also observed at the microsatellite loci both at the level of number of alleles and gene diversity. Nine to 14 alleles per locus across populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72
Journal of Heredity, 2008
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 5 0.264; P , 0.05) and a relatively lower differentiation among populations within regions (F SC 5 0.218; P , 0.0001). Microsatellite variation significantly differentiated among populations within regions (F SC 5 0.019; P , 0.0001) but not at the regional levels (F CT 5 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.
Genes
Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination ...
2014
Earlier studies investigated the genetic structure of fragmented or isolated elephant populations by comparing the genetic characteristics of pre-defined populations. This study aimed to determine if there was genetic evidence for spatial structuring in a continuous elephant population in the Kavango-Zambezi Transfrontier Conservation Area (KAZA-TFCA). I sequenced one mtDNA gene region for 88 individuals and genotyped 100 individuals for 10 nuclear microsatellite loci. Bayesian Clustering Algorithms incorporated in the program Geneland were used to identify groups of genetically similar individuals. An Analysis of Molecular Variance (AMOVA) determined if these groups (henceforth referred to as subpopulations) were significantly differentiated. I used a Geographic Information System (GIS) © University of Pretoria ii landscape genetic toolbox to identify areas in the landscape with high genetic divergence between individual samples to determine if there were identifiable genetic barri...
Habitat fragmentation plays a major role in the reduction of genetic diversity among wildlife populations. The African savannah elephant population of the Ruaha-Rungwa and Katavi-Rukwa ecosystems in south-western Tanzania, comprises one of the world’s largest remaining elephant populations, but is increasingly threatened by loss of connectivity and poaching for ivory. We investigate whether there are incipient signs of genetic isolation (loss of heterozygosity) within the younger cohort as a result of habitat loss between the two ecosystems. To investigate the genetic structure of populations, we compared the genotypes for 11 microsatellite loci in the western (n = 81 individuals from Katavi-Rukwa), central (n = 36 individuals from Lukwati and Piti), and eastern populations (n = 193, individuals from Ruaha-Rungwa). We found evidence of significant genetic differentiation among the three populations, but the levels were low, suggesting recent divergence. Furthermore, we identified we...
Systematic review on the conservation genetics of African savannah elephants
In this paper we review the conservation genetics of African savannah elephants, aiming to understand the spatio-temporal research trends and their underlying factors. As such, we explore three questions associated to the conservation genetics and molecular ecology of these elephants: (1) what are the research trends concerning the conservation genetics of Loxodonta africana? (2) Do richer countries conduct more research on the genetics of African elephants? (3) Which attributes influence where scholars conduct their research? We examined available peer-reviewed publications from 1993 to 2014 in complementary online databases, including the ISI/Web of Science (WoS), Scopus and Google Scholar (GS), and searched for publications in scientific journals as well as in the reference section of these publications. We analyzed the annual trend of publications in this field of research, including the number of authors, levels of collaboration among authors, year of publication, publishing journal and the countries from where genetic samples were collected. Additionally, we identified main research clusters, authors, and institutional collaborations, based on co-citation and co-occurrence networks. We found that during the study period there was a positive trend in the number of publications and a reduction in the number of authors per paper. Twenty-five countries contributed, with the majority of publications authored by researchers in the USA, Kenya and South Africa. The majority of samples were collected in Kenya, Tanzania and South Africa. Research outputs are associated with the existence of long-term conservation/research projects and research potential as measured by the literacy rate and the number of higher education institutions in a country. Five research clusters were identified, focusing on the origin and evolution of the species, methodological issues and the relatedness among elephant species. Research in this field should be expanded to additional countries harboring elephant populations to enable a more comprehensive understanding of the population structure and genetic differentiation of the species, and to cope with challenges associated with the conservation of the species such as illegal hunting, habitat fragmentation, species reintroduction and climate change.
Sustainability
Illegal wildlife trade is a major threat to global biodiversity. Asian elephants (Elephas maximus) are highly valued by various cultures as religious symbols and tourist attractions, which has led to a high demand for captive elephants. Owing to the unviability of captive breeding programs, several captive elephant populations are maintained by illegally obtaining wild Asian elephants. Morbidity and mortality rates among captive populations are high, whereas reproduction is low. In this study, we examined the genetic diversity among elephants using microsatellite genotyping and mitochondrial D-loop sequences of three captive elephant populations. The study results showed very low nucleotide diversity D-loop sequences and high variations in microsatellite genotyping, with an extensive variation of the gene pool estimates from different populations. This suggests that the optimal male selection during breeding could aid in maintaining the genetic diversity among captive populations. F...