Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations

Gui Lian Sheng, Nikolas Basler, Xue Ping Ji, Johanna L.A. Paijmans, Federica Alberti, Michaela Preick, Stefanie Hartmann, Michael V. Westbury, Jun Xia Yuan, Nina G. Jablonski, Georgios Xenikoudakis, Xin Dong Hou, Bo Xiao, Jian Hui Liu, Michael Hofreiter, Xu Long Lai, Axel Barlow

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions. Sheng et al. present the first nuclear paleogenome of the giant panda, one of the most iconic mammalian species. Their results elucidate the population history of this species during the Holocene and show that although some genetic diversity was lost, parts of the genome of extinct populations survive in the extant panda gene pool.

Original languageEnglish (US)
Pages (from-to)1695-1700.e6
JournalCurrent Biology
Volume29
Issue number10
DOIs
StatePublished - May 20 2019

Fingerprint

Ursidae
Ailuropoda melanoleuca
Genes
Population
China
Genome
Biodiversity
genetic variation
genome
Tibet
Gene Pool
Gene Flow

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Sheng, G. L., Basler, N., Ji, X. P., Paijmans, J. L. A., Alberti, F., Preick, M., ... Barlow, A. (2019). Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. Current Biology, 29(10), 1695-1700.e6. https://doi.org/10.1016/j.cub.2019.04.021
Sheng, Gui Lian ; Basler, Nikolas ; Ji, Xue Ping ; Paijmans, Johanna L.A. ; Alberti, Federica ; Preick, Michaela ; Hartmann, Stefanie ; Westbury, Michael V. ; Yuan, Jun Xia ; Jablonski, Nina G. ; Xenikoudakis, Georgios ; Hou, Xin Dong ; Xiao, Bo ; Liu, Jian Hui ; Hofreiter, Michael ; Lai, Xu Long ; Barlow, Axel. / Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. In: Current Biology. 2019 ; Vol. 29, No. 10. pp. 1695-1700.e6.
@article{a0829fda7e474ea9b4422ace56dd4d2a,
title = "Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations",
abstract = "Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions. Sheng et al. present the first nuclear paleogenome of the giant panda, one of the most iconic mammalian species. Their results elucidate the population history of this species during the Holocene and show that although some genetic diversity was lost, parts of the genome of extinct populations survive in the extant panda gene pool.",
author = "Sheng, {Gui Lian} and Nikolas Basler and Ji, {Xue Ping} and Paijmans, {Johanna L.A.} and Federica Alberti and Michaela Preick and Stefanie Hartmann and Westbury, {Michael V.} and Yuan, {Jun Xia} and Jablonski, {Nina G.} and Georgios Xenikoudakis and Hou, {Xin Dong} and Bo Xiao and Liu, {Jian Hui} and Michael Hofreiter and Lai, {Xu Long} and Axel Barlow",
year = "2019",
month = "5",
day = "20",
doi = "10.1016/j.cub.2019.04.021",
language = "English (US)",
volume = "29",
pages = "1695--1700.e6",
journal = "Current Biology",
issn = "0960-9822",
publisher = "Cell Press",
number = "10",

}

Sheng, GL, Basler, N, Ji, XP, Paijmans, JLA, Alberti, F, Preick, M, Hartmann, S, Westbury, MV, Yuan, JX, Jablonski, NG, Xenikoudakis, G, Hou, XD, Xiao, B, Liu, JH, Hofreiter, M, Lai, XL & Barlow, A 2019, 'Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations', Current Biology, vol. 29, no. 10, pp. 1695-1700.e6. https://doi.org/10.1016/j.cub.2019.04.021

Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. / Sheng, Gui Lian; Basler, Nikolas; Ji, Xue Ping; Paijmans, Johanna L.A.; Alberti, Federica; Preick, Michaela; Hartmann, Stefanie; Westbury, Michael V.; Yuan, Jun Xia; Jablonski, Nina G.; Xenikoudakis, Georgios; Hou, Xin Dong; Xiao, Bo; Liu, Jian Hui; Hofreiter, Michael; Lai, Xu Long; Barlow, Axel.

In: Current Biology, Vol. 29, No. 10, 20.05.2019, p. 1695-1700.e6.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations

AU - Sheng, Gui Lian

AU - Basler, Nikolas

AU - Ji, Xue Ping

AU - Paijmans, Johanna L.A.

AU - Alberti, Federica

AU - Preick, Michaela

AU - Hartmann, Stefanie

AU - Westbury, Michael V.

AU - Yuan, Jun Xia

AU - Jablonski, Nina G.

AU - Xenikoudakis, Georgios

AU - Hou, Xin Dong

AU - Xiao, Bo

AU - Liu, Jian Hui

AU - Hofreiter, Michael

AU - Lai, Xu Long

AU - Barlow, Axel

PY - 2019/5/20

Y1 - 2019/5/20

N2 - Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions. Sheng et al. present the first nuclear paleogenome of the giant panda, one of the most iconic mammalian species. Their results elucidate the population history of this species during the Holocene and show that although some genetic diversity was lost, parts of the genome of extinct populations survive in the extant panda gene pool.

AB - Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions. Sheng et al. present the first nuclear paleogenome of the giant panda, one of the most iconic mammalian species. Their results elucidate the population history of this species during the Holocene and show that although some genetic diversity was lost, parts of the genome of extinct populations survive in the extant panda gene pool.

UR - http://www.scopus.com/inward/record.url?scp=85065664618&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85065664618&partnerID=8YFLogxK

U2 - 10.1016/j.cub.2019.04.021

DO - 10.1016/j.cub.2019.04.021

M3 - Article

C2 - 31080081

AN - SCOPUS:85065664618

VL - 29

SP - 1695-1700.e6

JO - Current Biology

JF - Current Biology

SN - 0960-9822

IS - 10

ER -

Sheng GL, Basler N, Ji XP, Paijmans JLA, Alberti F, Preick M et al. Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. Current Biology. 2019 May 20;29(10):1695-1700.e6. https://doi.org/10.1016/j.cub.2019.04.021