Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil

Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion–contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test...

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Vydáno v:Molecular ecology Ročník 26; číslo 18; s. 4756 - 4771
Hlavní autoři: Gehara, Marcelo, Garda, Adrian A., Werneck, Fernanda P., Oliveira, Eliana F., Fonseca, Emanuel M., Camurugi, Felipe, Magalhães, Felipe de M., Lanna, Flávia M., Sites, Jack W., Marques, Ricardo, Silveira‐Filho, Ricardo, São Pedro, Vinícius A., Colli, Guarino R., Costa, Gabriel C., Burbrink, Frank T.
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Blackwell Publishing Ltd 01.09.2017
Témata:
amphibians
Amphibians - classification
Animals
Aridity
Bayes Theorem
Bayesian analysis
Bayesian theory
Biota
Brazil
Caatinga
Climate
Communities
comparative phylogeography
Contraction
data collection
Data processing
Demographics
dry environmental conditions
Dry forests
Ecosystems
extinction
fauna
Forests
hABC
Mathematical models
Models, Genetic
Phylogeny
Phylogeography
Pleistocene
Population Dynamics
population expansion
Population growth
Quaternary
reptiles
Reptiles - classification
Seasonal variations
Species
Tropical forests
Brazil
hABC
population expansion
Caatinga
reptiles
amphibians
comparative phylogeography
ISSN:0962-1083, 1365-294X, 1365-294X
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Abstract Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion–contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single‐locus data, we can now perform large‐scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single‐locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric‐adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.
AbstractList Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.
Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion–contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation ( hABC ) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single‐locus data, we can now perform large‐scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single‐locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric‐adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.
Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion–contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single‐locus data, we can now perform large‐scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single‐locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric‐adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.
Author Camurugi, Felipe
Sites, Jack W.
São Pedro, Vinícius A.
Fonseca, Emanuel M.
Oliveira, Eliana F.
Silveira‐Filho, Ricardo
Costa, Gabriel C.
Garda, Adrian A.
Magalhães, Felipe de M.
Lanna, Flávia M.
Burbrink, Frank T.
Colli, Guarino R.
Gehara, Marcelo
Werneck, Fernanda P.
Marques, Ricardo
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  organization: American Museum of Natural History
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  givenname: Adrian A.
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  organization: Universidade Federal do Rio Grande do Norte
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  organization: Instituto Nacional de Pesquisas da Amazônia (INPA)
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  surname: Oliveira
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  organization: Universidade Federal do Mato Grosso do Sul
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  surname: Fonseca
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  organization: Universidade Federal do Rio Grande do Norte
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  organization: Universidade Federal da Paraíba
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  surname: Magalhães
  fullname: Magalhães, Felipe de M.
  organization: Universidade Federal da Paraíba
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  givenname: Flávia M.
  surname: Lanna
  fullname: Lanna, Flávia M.
  organization: Universidade Federal do Rio Grande do Norte
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  givenname: Jack W.
  surname: Sites
  fullname: Sites, Jack W.
  organization: Brigham Young University
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  givenname: Ricardo
  surname: Marques
  fullname: Marques, Ricardo
  organization: Universidade Federal da Paraíba
– sequence: 11
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  surname: Silveira‐Filho
  fullname: Silveira‐Filho, Ricardo
  organization: Universidade Federal da Paraíba
– sequence: 12
  givenname: Vinícius A.
  surname: São Pedro
  fullname: São Pedro, Vinícius A.
  organization: Universidade Federal de São Carlos
– sequence: 13
  givenname: Guarino R.
  surname: Colli
  fullname: Colli, Guarino R.
  organization: Universidade de Brasília
– sequence: 14
  givenname: Gabriel C.
  surname: Costa
  fullname: Costa, Gabriel C.
  organization: Auburn University at Montgomery
– sequence: 15
  givenname: Frank T.
  surname: Burbrink
  fullname: Burbrink, Frank T.
  organization: American Museum of Natural History
BackLink https://www.ncbi.nlm.nih.gov/pubmed/28734050$$D View this record in MEDLINE/PubMed
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ISSN 0962-1083
1365-294X
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Issue 18
Keywords hABC
population expansion
Caatinga
reptiles
amphibians
comparative phylogeography
Language English
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http://onlinelibrary.wiley.com/termsAndConditions#vor
2017 John Wiley & Sons Ltd.
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PublicationTitle Molecular ecology
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Snippet Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion–contraction dynamics of...
Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of...
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StartPage 4756
SubjectTerms amphibians
Amphibians - classification
Animals
Aridity
Bayes Theorem
Bayesian analysis
Bayesian theory
Biota
Brazil
Caatinga
Climate
Communities
comparative phylogeography
Contraction
data collection
Data processing
Demographics
dry environmental conditions
Dry forests
Ecosystems
extinction
fauna
Forests
hABC
Mathematical models
Models, Genetic
Phylogeny
Phylogeography
Pleistocene
Population Dynamics
population expansion
Population growth
Quaternary
reptiles
Reptiles - classification
Seasonal variations
Species
Tropical forests
Title Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fmec.14239
https://www.ncbi.nlm.nih.gov/pubmed/28734050
https://www.proquest.com/docview/1942571632
https://www.proquest.com/docview/1922509028
https://www.proquest.com/docview/2010208250
Volume 26
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