Ancient DNA from giant panda (Ailuropoda melanoleuca) of south-western China reveals genetic diversity loss during the holocene

Gui Lian Sheng, Axel Barlow, Alan Cooper, Xin Dong Hou, Xue Ping Ji, Nina G. Jablonski, Bo Jian Zhong, Hong Liu, Lawrence J. Flynn, Jun Xia Yuan, Li Rui Wang, Nikolas Basler, Michael V. Westbury, Michael Hofreiter, Xu Long Lai

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

Original languageEnglish (US)
Article number198
JournalGenes
Volume9
Issue number4
DOIs
StatePublished - Apr 1 2018

Fingerprint

Ursidae
China
Population
Haplotypes
Ecosystem
Mitochondrial Genome
Far East
Population Density
Ancient DNA
Mitochondrial DNA
Siblings
Demography
DNA

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Sheng, Gui Lian ; Barlow, Axel ; Cooper, Alan ; Hou, Xin Dong ; Ji, Xue Ping ; Jablonski, Nina G. ; Zhong, Bo Jian ; Liu, Hong ; Flynn, Lawrence J. ; Yuan, Jun Xia ; Wang, Li Rui ; Basler, Nikolas ; Westbury, Michael V. ; Hofreiter, Michael ; Lai, Xu Long. / Ancient DNA from giant panda (Ailuropoda melanoleuca) of south-western China reveals genetic diversity loss during the holocene. In: Genes. 2018 ; Vol. 9, No. 4.
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title = "Ancient DNA from giant panda (Ailuropoda melanoleuca) of south-western China reveals genetic diversity loss during the holocene",
abstract = "The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.",
author = "Sheng, {Gui Lian} and Axel Barlow and Alan Cooper and Hou, {Xin Dong} and Ji, {Xue Ping} and Jablonski, {Nina G.} and Zhong, {Bo Jian} and Hong Liu and Flynn, {Lawrence J.} and Yuan, {Jun Xia} and Wang, {Li Rui} and Nikolas Basler and Westbury, {Michael V.} and Michael Hofreiter and Lai, {Xu Long}",
year = "2018",
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doi = "10.3390/genes9040198",
language = "English (US)",
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Sheng, GL, Barlow, A, Cooper, A, Hou, XD, Ji, XP, Jablonski, NG, Zhong, BJ, Liu, H, Flynn, LJ, Yuan, JX, Wang, LR, Basler, N, Westbury, MV, Hofreiter, M & Lai, XL 2018, 'Ancient DNA from giant panda (Ailuropoda melanoleuca) of south-western China reveals genetic diversity loss during the holocene', Genes, vol. 9, no. 4, 198. https://doi.org/10.3390/genes9040198

Ancient DNA from giant panda (Ailuropoda melanoleuca) of south-western China reveals genetic diversity loss during the holocene. / Sheng, Gui Lian; Barlow, Axel; Cooper, Alan; Hou, Xin Dong; Ji, Xue Ping; Jablonski, Nina G.; Zhong, Bo Jian; Liu, Hong; Flynn, Lawrence J.; Yuan, Jun Xia; Wang, Li Rui; Basler, Nikolas; Westbury, Michael V.; Hofreiter, Michael; Lai, Xu Long.

In: Genes, Vol. 9, No. 4, 198, 01.04.2018.

Research output: Contribution to journalArticle

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AU - Sheng, Gui Lian

AU - Barlow, Axel

AU - Cooper, Alan

AU - Hou, Xin Dong

AU - Ji, Xue Ping

AU - Jablonski, Nina G.

AU - Zhong, Bo Jian

AU - Liu, Hong

AU - Flynn, Lawrence J.

AU - Yuan, Jun Xia

AU - Wang, Li Rui

AU - Basler, Nikolas

AU - Westbury, Michael V.

AU - Hofreiter, Michael

AU - Lai, Xu Long

PY - 2018/4/1

Y1 - 2018/4/1

N2 - The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

AB - The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

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