Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis)

Jonathan J. FONG, Pi Peng LI, Bao Tian YANG, Zheng Yan ZHOU, Adam D. LEACHÉ, Mi-Sook MIN, Bruce WALDMAN

Research output: Journal PublicationsJournal Article (refereed)Researchpeer-review

3 Citations (Scopus)

Abstract

The Oriental fire-bellied toad (Bombina orientalis) is a commonly used study organism, but knowledge of its evolutionary history is incomplete. We analyze sequence data from four genetic markers (mtDNA genes encoding cytochrome c oxidase subunit I, cytochrome b, and 12S–16S rRNA; nuDNA gene encoding recombination activating gene 2) from 188 individuals across its range in Northeast Asia to elucidate phylogeographic patterns and to identify the historic events that shaped its evolutionary history. Although morphologically similar across its range, B. orientalis exhibits phylogeographic structure, which we infer was shaped by geologic, climatic, and anthropogenic events. Phylogenetic and divergence-dating analyses recover four genetically distinct groups of B. orientalis: Lineage 1—Shandong Province and Beijing (China); Lineage 2—Bukhan Mountain (Korea); Lineage 3—Russia, Northeast China, and northern South Korea; and Lineage 4—South Korea. Lineage 2 was previously unknown. Additionally, we discover an area of secondary contact on the Korean Peninsula, and infer a single dispersal event as the origin of the insular Jeju population. Skyline plots estimate different population histories for the four lineages: Lineages 1 and 2 experienced population decreases, Lineage 3 remained stable, while Lineage 4 experienced a sharp increase during the Holocene. The timing of the population expansion of Lineage 4 coincides with the advent of rice cultivation, which may have facilitated the increase in population size by providing additional breeding habitat.
Original languageEnglish
Pages (from-to)69-75
Number of pages7
JournalMolecular Phylogenetics and Evolution
Volume97
DOIs
Publication statusPublished - 1 Apr 2016
Externally publishedYes

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Geology
Genetic Structures
toad
toads
geology
demography
Human Activities
Anura
genetic structure
human activity
Demography
Korea
Korean Peninsula
cytochrome
gene
China
history
History
Population
Republic of Korea

Cite this

FONG, Jonathan J. ; LI, Pi Peng ; YANG, Bao Tian ; ZHOU, Zheng Yan ; LEACHÉ, Adam D. ; MIN, Mi-Sook ; WALDMAN, Bruce. / Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis). In: Molecular Phylogenetics and Evolution. 2016 ; Vol. 97. pp. 69-75.
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abstract = "The Oriental fire-bellied toad (Bombina orientalis) is a commonly used study organism, but knowledge of its evolutionary history is incomplete. We analyze sequence data from four genetic markers (mtDNA genes encoding cytochrome c oxidase subunit I, cytochrome b, and 12S–16S rRNA; nuDNA gene encoding recombination activating gene 2) from 188 individuals across its range in Northeast Asia to elucidate phylogeographic patterns and to identify the historic events that shaped its evolutionary history. Although morphologically similar across its range, B. orientalis exhibits phylogeographic structure, which we infer was shaped by geologic, climatic, and anthropogenic events. Phylogenetic and divergence-dating analyses recover four genetically distinct groups of B. orientalis: Lineage 1—Shandong Province and Beijing (China); Lineage 2—Bukhan Mountain (Korea); Lineage 3—Russia, Northeast China, and northern South Korea; and Lineage 4—South Korea. Lineage 2 was previously unknown. Additionally, we discover an area of secondary contact on the Korean Peninsula, and infer a single dispersal event as the origin of the insular Jeju population. Skyline plots estimate different population histories for the four lineages: Lineages 1 and 2 experienced population decreases, Lineage 3 remained stable, while Lineage 4 experienced a sharp increase during the Holocene. The timing of the population expansion of Lineage 4 coincides with the advent of rice cultivation, which may have facilitated the increase in population size by providing additional breeding habitat.",
author = "FONG, {Jonathan J.} and LI, {Pi Peng} and YANG, {Bao Tian} and ZHOU, {Zheng Yan} and LEACH{\'E}, {Adam D.} and Mi-Sook MIN and Bruce WALDMAN",
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Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis). / FONG, Jonathan J.; LI, Pi Peng; YANG, Bao Tian; ZHOU, Zheng Yan; LEACHÉ, Adam D.; MIN, Mi-Sook; WALDMAN, Bruce.

In: Molecular Phylogenetics and Evolution, Vol. 97, 01.04.2016, p. 69-75.

Research output: Journal PublicationsJournal Article (refereed)Researchpeer-review

TY - JOUR

T1 - Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis)

AU - FONG, Jonathan J.

AU - LI, Pi Peng

AU - YANG, Bao Tian

AU - ZHOU, Zheng Yan

AU - LEACHÉ, Adam D.

AU - MIN, Mi-Sook

AU - WALDMAN, Bruce

PY - 2016/4/1

Y1 - 2016/4/1

N2 - The Oriental fire-bellied toad (Bombina orientalis) is a commonly used study organism, but knowledge of its evolutionary history is incomplete. We analyze sequence data from four genetic markers (mtDNA genes encoding cytochrome c oxidase subunit I, cytochrome b, and 12S–16S rRNA; nuDNA gene encoding recombination activating gene 2) from 188 individuals across its range in Northeast Asia to elucidate phylogeographic patterns and to identify the historic events that shaped its evolutionary history. Although morphologically similar across its range, B. orientalis exhibits phylogeographic structure, which we infer was shaped by geologic, climatic, and anthropogenic events. Phylogenetic and divergence-dating analyses recover four genetically distinct groups of B. orientalis: Lineage 1—Shandong Province and Beijing (China); Lineage 2—Bukhan Mountain (Korea); Lineage 3—Russia, Northeast China, and northern South Korea; and Lineage 4—South Korea. Lineage 2 was previously unknown. Additionally, we discover an area of secondary contact on the Korean Peninsula, and infer a single dispersal event as the origin of the insular Jeju population. Skyline plots estimate different population histories for the four lineages: Lineages 1 and 2 experienced population decreases, Lineage 3 remained stable, while Lineage 4 experienced a sharp increase during the Holocene. The timing of the population expansion of Lineage 4 coincides with the advent of rice cultivation, which may have facilitated the increase in population size by providing additional breeding habitat.

AB - The Oriental fire-bellied toad (Bombina orientalis) is a commonly used study organism, but knowledge of its evolutionary history is incomplete. We analyze sequence data from four genetic markers (mtDNA genes encoding cytochrome c oxidase subunit I, cytochrome b, and 12S–16S rRNA; nuDNA gene encoding recombination activating gene 2) from 188 individuals across its range in Northeast Asia to elucidate phylogeographic patterns and to identify the historic events that shaped its evolutionary history. Although morphologically similar across its range, B. orientalis exhibits phylogeographic structure, which we infer was shaped by geologic, climatic, and anthropogenic events. Phylogenetic and divergence-dating analyses recover four genetically distinct groups of B. orientalis: Lineage 1—Shandong Province and Beijing (China); Lineage 2—Bukhan Mountain (Korea); Lineage 3—Russia, Northeast China, and northern South Korea; and Lineage 4—South Korea. Lineage 2 was previously unknown. Additionally, we discover an area of secondary contact on the Korean Peninsula, and infer a single dispersal event as the origin of the insular Jeju population. Skyline plots estimate different population histories for the four lineages: Lineages 1 and 2 experienced population decreases, Lineage 3 remained stable, while Lineage 4 experienced a sharp increase during the Holocene. The timing of the population expansion of Lineage 4 coincides with the advent of rice cultivation, which may have facilitated the increase in population size by providing additional breeding habitat.

UR - http://commons.ln.edu.hk/sw_master/5115

U2 - 10.1016/j.ympev.2015.12.019

DO - 10.1016/j.ympev.2015.12.019

M3 - Journal Article (refereed)

VL - 97

SP - 69

EP - 75

JO - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

SN - 1055-7903

ER -