Noninvasive Genotyping and Mendelian Analysis of Microsatellites in African Savannah Elephants

Submitted by Archiver on Mon, 15/10/2018 - 16:44
Abstract

We obtained fresh dung samples from 202 (133 mother-offspring pairs) savannah elephants (Loxodonta africana) in Samburu,
Kenya, and genotyped them at 20 microsatellite loci to assess genotyping success and errors. A total of 98.6% consensus
genotypes was successfully obtained, with allelic dropout and false allele rates at 1.6% (n 5 46) and 0.9% (n 5 37) of heterozygous
and total consensus genotypes, respectively, and an overall genotyping error rate of 2.5% based on repeat typing.
Mendelian analysis revealed consistent inheritance in all but 38 allelic pairs from mother-offspring, giving an average mismatch
error rate of 2.06%, a possible result of null alleles, mutations, genotyping errors, or inaccuracy in maternity assignment. We
detected no evidence for large allele dropout, stuttering, or scoring error in the dataset and significant Hardy-Weinberg deviations
at only two loci due to heterozygosity deficiency. Across loci, null allele frequencies were low (range: 0.000–0.042) and
below the 0.20 threshold that would significantly bias individual-based studies. The high genotyping success and low errors
observed in this study demonstrate reliability of the method employed and underscore the application of simple pedigrees in
noninvasive studies. Since none of the sires were included in this study, the error rates presented are just estimates.

Author

J. B. A. OKELLO, G. WITTEMYER, H. B. RASMUSSEN, I. DOUGLAS-HAMILTON, S. NYAKAANA,
P. ARCTANDER, AND H. R. SIEGISMUND

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