Testing for genetic evidence of Population expansion and contraction: An empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model

Jay F. Storz, Mark A. Beaumont

Research output: Contribution to journalArticle

242 Citations (Scopus)

Abstract

The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an exemplary species pair to use for such tests. The purpose of this study was to test alternative hypotheses about historical patterns of demographic expansion and contraction in C. sphinx and C. brachyotis using a coalescent-based analysis of microsatellite variation. Specifically, we used a hierarchical Bayesian model based on Markov chain Monte Carlo simulations to estimate the posterior distribution of genealogical and demographic parameters. The results revealed strong evidence for population contraction in both species. Evidence for a population contraction in C. brachyotis was expected on the basis of biogeographic considerations. However, similar evidence for population contraction in C. sphinx does not support the hypothesis that this species underwent a pronounced range expansion during the late Quaternary. Genetic evidence for population decline may reflect the consequences of habitat destruction on a more recent time scale.

Original languageEnglish (US)
Pages (from-to)154-166
Number of pages13
JournalEvolution
Volume56
Issue number1
DOIs
StatePublished - Jan 1 2002

Fingerprint

Population Genetics
Genetic Testing
empirical analysis
Sphinx
Microsatellite Repeats
contraction
demographic statistics
Demography
microsatellite repeats
DNA
Chiroptera
testing
Cynopterus
Population
Genealogy and Heraldry
Pteropodidae
Markov Chains
Ice
Population Dynamics
tropical rain forests

Keywords

  • Bats
  • Bayesian inference
  • Coalescent
  • Cynopterus
  • Demographic history
  • Markov chain Monte Carlo
  • Microsatellite DNA
  • Population bottleneck
  • Zoogeography

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Agricultural and Biological Sciences(all)

Cite this

@article{327b14bd5c8d476ea0b7691fc98a4016,
title = "Testing for genetic evidence of Population expansion and contraction: An empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model",
abstract = "The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an exemplary species pair to use for such tests. The purpose of this study was to test alternative hypotheses about historical patterns of demographic expansion and contraction in C. sphinx and C. brachyotis using a coalescent-based analysis of microsatellite variation. Specifically, we used a hierarchical Bayesian model based on Markov chain Monte Carlo simulations to estimate the posterior distribution of genealogical and demographic parameters. The results revealed strong evidence for population contraction in both species. Evidence for a population contraction in C. brachyotis was expected on the basis of biogeographic considerations. However, similar evidence for population contraction in C. sphinx does not support the hypothesis that this species underwent a pronounced range expansion during the late Quaternary. Genetic evidence for population decline may reflect the consequences of habitat destruction on a more recent time scale.",
keywords = "Bats, Bayesian inference, Coalescent, Cynopterus, Demographic history, Markov chain Monte Carlo, Microsatellite DNA, Population bottleneck, Zoogeography",
author = "Storz, {Jay F.} and Beaumont, {Mark A.}",
year = "2002",
month = "1",
day = "1",
doi = "10.1111/j.0014-3820.2002.tb00857.x",
language = "English (US)",
volume = "56",
pages = "154--166",
journal = "Evolution; international journal of organic evolution",
issn = "0014-3820",
publisher = "Society for the Study of Evolution",
number = "1",

}

TY - JOUR

T1 - Testing for genetic evidence of Population expansion and contraction

T2 - An empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model

AU - Storz, Jay F.

AU - Beaumont, Mark A.

PY - 2002/1/1

Y1 - 2002/1/1

N2 - The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an exemplary species pair to use for such tests. The purpose of this study was to test alternative hypotheses about historical patterns of demographic expansion and contraction in C. sphinx and C. brachyotis using a coalescent-based analysis of microsatellite variation. Specifically, we used a hierarchical Bayesian model based on Markov chain Monte Carlo simulations to estimate the posterior distribution of genealogical and demographic parameters. The results revealed strong evidence for population contraction in both species. Evidence for a population contraction in C. brachyotis was expected on the basis of biogeographic considerations. However, similar evidence for population contraction in C. sphinx does not support the hypothesis that this species underwent a pronounced range expansion during the late Quaternary. Genetic evidence for population decline may reflect the consequences of habitat destruction on a more recent time scale.

AB - The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an exemplary species pair to use for such tests. The purpose of this study was to test alternative hypotheses about historical patterns of demographic expansion and contraction in C. sphinx and C. brachyotis using a coalescent-based analysis of microsatellite variation. Specifically, we used a hierarchical Bayesian model based on Markov chain Monte Carlo simulations to estimate the posterior distribution of genealogical and demographic parameters. The results revealed strong evidence for population contraction in both species. Evidence for a population contraction in C. brachyotis was expected on the basis of biogeographic considerations. However, similar evidence for population contraction in C. sphinx does not support the hypothesis that this species underwent a pronounced range expansion during the late Quaternary. Genetic evidence for population decline may reflect the consequences of habitat destruction on a more recent time scale.

KW - Bats

KW - Bayesian inference

KW - Coalescent

KW - Cynopterus

KW - Demographic history

KW - Markov chain Monte Carlo

KW - Microsatellite DNA

KW - Population bottleneck

KW - Zoogeography

UR - http://www.scopus.com/inward/record.url?scp=0036006020&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036006020&partnerID=8YFLogxK

U2 - 10.1111/j.0014-3820.2002.tb00857.x

DO - 10.1111/j.0014-3820.2002.tb00857.x

M3 - Article

C2 - 11913661

AN - SCOPUS:0036006020

VL - 56

SP - 154

EP - 166

JO - Evolution; international journal of organic evolution

JF - Evolution; international journal of organic evolution

SN - 0014-3820

IS - 1

ER -