Computational protocol: Identifying Source Populations and Genetic Structure for Savannah Elephants in Human-Dominated Landscapes and Protected Areas in the Kenya-Tanzania Borderlands

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Protocol publication

[…] We performed calculations of expected (HE) and observed heterozygosity (HO) values and tests for deviations from expectations under Hardy-Weinberg equilibrium and linkage disequilibrium using Genepop 4.0 , . In Arlequin v. 3.11 , we quantified microsatellite diversity using the number of alleles, the expected and the observed heterozygosity for each population, and we quantified levels of mtDNA variation using indices of nucleotide diversity. We used the program Geneious Pro 5.5.6 to estimate phylogenetic relationships among the mtDNA haplotypes by constructing a neighbor joining tree using the HKY model as indicated by jModelTest 2.02 , . To place our haplotypes in a larger phylogenetic framework, we included published sequences from Okello et al. , Eggert et al. and Debruyne ().To evaluate genetic metapopulation structure and determine the source population for the elephants in the CCA, we used two different statistical approaches. We calculated population pairwise FST values in Arlequin v. 3.11 for both mtDNA haplotypes (using the Kimura 2-parameter model) and microsatellite allele frequency data. We also used STRUCTURE 2.3.3 to assign the individuals from the CCA to their source population using the microsatellite data. We ran STRUCTURE for values of K from 1 through 9 with 20 replicates for each level of K, a burn-in period of 100,000, and a run length of 1,000,000 under the admixture model and updating for population location. Because we had low FST values among populations, we used the LOCPRIOR option , and we coded the data for five populations: Amboseli, Tarangire, the CCA, Maasai Mara and Serengeti. For comparison, we ran the same STRUCTURE models without any prior information as well as using the POPFLAG option for all populations except the CCA. The Evanno method , as visualized using Structure Harvester , was used to determine the number of populations (K). […]

Pipeline specifications

Software tools Genepop, Arlequin, Geneious, jModelTest, Structure Harvester
Applications Phylogenetics, Population genetic analysis
Organisms Homo sapiens, Loxodonta cyclotis