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Historical genetic diversity and population structure of wild red pandas (Ailurus fulgens) in Nepal

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Abstract

Red pandas (Ailurus fulgens) are taxonomically unique mammals in the order Carnivora that evolved to an arboreal and herbivorous existence in the mountainous regions of south east-central Asia. Now endangered, they have a precarious future in nature due to ever-changing environmental conditions and increasing anthropogenic threats. This study reports on an early mitochondrial DNA survey successfully accomplished by fecal sampling of 68 (minimum) wild red pandas in three regional populations of Nepal at the western end of their range. From 383 bp of control region sequences, our study identified 17 haplotypes, relatively high haplotype diversity (Hd = 0.83) but low nucleotide diversity (π = 0.010) overall with both measures decreasing from east to west, a comparatively close phylogenetic relationship between mtDNA-defined subspecies, differentiation of one population, and the discovery of a haplotype in two samples that belongs to the purported subspecies previously recorded only from the eastern end of their range. We argue for caution in elevating taxonomic rank without incorporating other species-defining criteria, suggest reconsidering subspecies’ boundaries and investigating hybridization in the contact zone, provide some evolutionary hypotheses for the genetic distribution exposed, propose specific applications for conservation management, and stress inclusion of nuclear markers to complement future research. This study presents valuable information on red panda population genetics from the western end of their range in Nepal, essential for recovery programs like the IUCN Green Status of Species, to establish an historical baseline for future genetic monitoring and decision-making in the conservation of a rare but iconic endangered species.

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Availability of data and material

All sequences used in this study are available from GenBank as follows – outgroup taxa: Mydaus marchei AY587074, Mephitis mephitis AY587106, Mephitis mephitis AY587094, Mephitis macroura AY5871051, Spilogale putorius AY587075, Spilogale gracilis AY587078, Conepatus leuconotus AY587093, Conepatus chinga AY159818, Procyon lotor AB297804; all SSP red panda (Ailurus fulgens) and otter (Lontra canadensis) outgroup haplotype sequences from Dueck (2021) used in this study: SSP-1f = MT513939, SSP-2f = MT513940, SSP-3f = MT513941, SSP-4 s = MT513942, SSP-5 s = MT513943, SSP-6 s = MT513944, SSP-7 s = MT513945, SSP-8f = MT513946, SSP-9 s = MT513947, SSP-10 s = MT513948, SSP-11 s = MT513949; otter-b = MT513950; all haplotype sequences newly identified in this study from wild red pandas (A. fulgens) in Nepal: WRP-Af = OK381584, WRP-Bf = OK381585, WRP-Cs = OK381586, WRP-Df = OK381587, WRP-Ef = OK381588, WRP-Ff = OK381589, WRP-Gf = OK381590, WRP-Hf = OK381591, WRP-Jf = OK381592, WRP-Nf = OK381593, WRP-Pf = OK381594, WRP-Qf = OK381595, WRP-Rf = OK381596, WRP-Sf = OK381597; NCBI Reference Sequence for A. f. styani = NC009691 (Yonezawa et al. 2007).

Code availability

Not applicable.

Notes

  1. A current update indicates that red pandas may have already been extirpated in Manang since they have not been documented there recently (Bista et al. 2017).

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Acknowledgements

We thank the Government of Nepal’s Department of National Parks and Wildlife Conservation for research and export permits. We are indebted to Kathryn “Katie” Copenhaver for her excellent work and diligence in processing the samples. We thank Travis Glenn for SREL lab support and guidance, as well as Cris Hagen and Mandy Schable for sequencing assistance and Jennifer Dever for primer development. We also thank Miles Roberts from the Smithsonian Institution; Ray Guries from the University of Wisconsin; and in Nepal – Pralad Yonzon, Brian Williams, Pasang Sherpa, and Ganga Jung Gurung. We appreciate analysis support from Chris Wilson, Rodney Honeycutt, Deniz Aygoren, and Dean Williams, and editing by Dean Williams, Ken Cameron, Lori Eggert, and Jason Kilgore. Financial assistance was supplied by the Smithsonian Institution and Loucks Distinguished Fellowship Award to E.S., National Science Foundation Grant #DBI-0139572 to K. Copenhaver for a summer REU (Research Experience for Undergraduates) fellowship; living expenses provided to L.D. during manuscript preparation by the L.E. and M.J. Kinker Trust, and Financial Assistance Award #DE-FC09-96SR18-546 from the U.S. Department of Energy to the University of Georgia’s Savannah River Ecology Laboratory. L.D. wishes to recognize the contribution to geographical knowledge of Nepal made by her cousin Austin Hasel who, in 1963-65 as forestry advisor to Nepal for the U.S. Agency for International Development, was instrumental in the production of the first topographical maps for the entire country, critical for this study.

Funding

Financial assistance was supplied by: Smithsonian Institution and Loucks Distinguished Fellowship Award to E. Steffens; National Science Foundation Grant #DBI-0139572 for a summer R.E.U. fellowship to K.A. Copenhaver; and Financial Assistance Award #DE-FC09-96SR18-546 from the U.S. Department of Energy to the University of Georgia’s Savannah River Ecology Laboratory. No outside funding was received to assist with the preparation of this manuscript.

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Authors and Affiliations

  1. Savannah River Ecology Laboratory, Aiken, SC, 29802, USA

    Lucy A. Dueck

  2. Athens, TX, 75752, USA

    Lucy A. Dueck

  3. University of Wisconsin, Madison, WI, 53706, USA

    Erik A. Steffens

  4. Vashon, WA, 98070, USA

    Erik A. Steffens

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  1. Lucy A. Dueck
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Both authors contributed to the study concept and design. E.S. suggested the project, collected the samples, and edited and approved the manuscript. L.D. oversaw the project and laboratory analysis, performed the data analyses, and wrote the manuscript.

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Correspondence to Lucy A. Dueck.

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Dueck, L.A., Steffens, E.A. Historical genetic diversity and population structure of wild red pandas (Ailurus fulgens) in Nepal. Mamm Biol 102, 1723–1741 (2022). https://doi.org/10.1007/s42991-022-00272-0

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