Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas

Science Advances
Yibo HuFuwen Wei

Abstract

The red panda (Ailurus fulgens), an endangered Himalaya-endemic mammal, has been classified as two subspecies or even two species - the Himalayan red panda (A. fulgens) and the Chinese red panda (Ailurus styani) - based on differences in morphology and biogeography. However, this classification has remained controversial largely due to lack of genetic evidence, directly impairing scientific conservation management. Data from 65 whole genomes, 49 Y-chromosomes, and 49 mitochondrial genomes provide the first comprehensive genetic evidence for species divergence in red pandas, demonstrating substantial inter-species genetic divergence for all three markers and correcting species-distribution boundaries. Combined with morphological evidence, these data thus clearly define two phylogenetic species in red pandas. We also demonstrate different demographic trajectories in the two species: A. styani has experienced two population bottlenecks and one large population expansion over time, whereas A. fulgens has experienced three bottlenecks and one very small expansion, resulting in very low genetic diversity, high linkage disequilibrium, and high genetic load.

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Citations

Jul 4, 2020·Science China. Life Sciences·Guangping HuangFuwen Wei
Feb 17, 2021·Molecular Biology and Evolution·Ellie E ArmstrongUma Ramakrishnan
Apr 4, 2021·Animals : an Open Access Journal From MDPI·Damber BistaPeter John Murray
Apr 2, 2021·The Science of the Total Environment·Sikha KarkiTim Cadman

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Datasets Mentioned

BETA
AM711897

Methods Mentioned

BETA
PCA
Illumina sequencing
genotyping

Software Mentioned

DNASP
SAMtools
SIFT
TreeMix
PSMC
RAxML
ANNOVAR
BEAST
Burrows Alignment ( BWA )
vcftools

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