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Identification of conservation priority units in the Asian elephant, Elephas maximus

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Abstract

Conservation biologists often deal with species that have small, fragmented populations throughout their range, making it necessary to prioritize populations for management. Genetics provides tools to assist with prioritization according to the levels and distribution of genetic diversity and evolutionary distinctiveness. Many studies have used nuclear microsatellite loci to measure genetic diversity in disparate populations and mitochondrial DNA to assess genetic distinctiveness. However, comparing metrics based on microsatellite genotypes ascertained in different laboratories is complicated by the selection of different loci with distinct nucleotide repeat motifs. This issue may be resolved by comparing metrics to a well-characterized reference population with shared microsatellite markers. The Asian elephant, Elephas maximus, is an endangered species with 50–60% of populations in India and Sri Lanka, and small, fragmented populations throughout southeast and insular Asia. We assessed range-wide genetic diversity of the Asian elephant by directly comparing allelic diversity and heterozygosity estimates from 35 populations, overcoming marker selection bias by calibrating metrics to a large population on the Nakai Plateau, Lao PDR, genotyped at 25 loci. We coupled these results with mtDNA analysis to evaluate genetic distinctiveness and identify potential conservation management units. We found the greatest diversity in the populations of southeast Asia and the greatest genetic distinctiveness among the subspecies designations, particularly Borneo and Sumatra, and other southeast Asian populations. The populations of southeast Asia, albeit small, fragmented, and at high risk of extirpation, contain valuable diversity and distinctiveness and are thus of high priority for the preservation of the Asian elephant.

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Data availability

Data from the yardstick population (Nakai Plateau, 25 microsatellite loci) and the R code used to calculate the diversity ratios have been deposited in DRYAD: https://doi.org/10.5061/dryad.vdncjsz11. Genetic diversity data from populations used for comparison to the yardstick population are provided in Table 1. Accession numbers for all mtDNA sequences used in the evolutionary distinctiveness analyses are shown in Supplementary Table 2.

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Acknowledgements

We are grateful to the Lao Ministry of Agriculture and Forestry’s Department of Forestry, the Government of Lao PDR’s Provincial and District Agriculture and Forestry Offices (PAFO and DAFO) and the Nam Theun 2 Power Company Ltd. (NTPC) for their assistance with the survey of the Nakai Plateau area. This work would not have been possible without the wildlife survey guides, technicians, and administrative support from the Nam Theun 2 Watershed Management and Protection Authority (WMPA).

Funding

This research was funded by the American Philosophical Society Lewis and Clark Field Grant and the TransWorld Airline Scholarship fund. KB was funded by a National Science Foundation Graduate Research Fellowship. This is KBS contribution number 2355.

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KB designed the study and carried out the labwork, initial data analyses and writing of the first draft of the manuscript. JG and LLS conducted data analyses, data interpretation and contributed substantially to the writing of the final draft of the manuscript. LSE administered the project and contributed to the writing of the final draft of the manuscript. All authors reviewed and approved the final version of the manuscript.

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Correspondence to Lori S. Eggert.

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Budd, K., Gunn, J.C., Sullivan, L.L. et al. Identification of conservation priority units in the Asian elephant, Elephas maximus. Conserv Genet 24, 827–837 (2023). https://doi.org/10.1007/s10592-023-01542-1

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