TY - JOUR
T1 - Comparative and predictive phylogeography in the South American diagonal of open formations
T2 - Unravelling the biological and environmental influences on multitaxon demography
AU - Bonatelli, Isabel A.S.
AU - Gehara, Marcelo
AU - Carstens, Bryan C.
AU - Colli, Guarino R.
AU - Moraes, Evandro M.
N1 - Funding Information:
This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001 to I.A.S.B., by the São Paulo Research Foundation (FAPESP, grant 2018‐03428‐5) and National Council for Scientific and Technological Development (CNPq, grant 03940/2019‐0) to E.M.M. G.R.C. thanks Coordenação de Apoio à Formação de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Apoio à Pesquisa do Distrito Federal (FAPDF), and USAID's PEER programme under cooperative agreement AID‐OAA‐A‐11‐00012 for financial support.
Funding Information:
This study was financed in part by the Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior ? Brasil (CAPES) ? Finance Code 001 to I.A.S.B., by the S?o Paulo Research Foundation (FAPESP, grant 2018-03428-5) and National Council for Scientific and Technological Development (CNPq, grant 03940/2019-0) to E.M.M. G.R.C. thanks Coordena??o de Apoio ? Forma??o de Pessoal de N?vel Superior (CAPES), Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq), Funda??o de Apoio ? Pesquisa do Distrito Federal (FAPDF), and USAID's PEER programme under cooperative agreement AID-OAA-A-11-00012 for financial support. Monique Romeiro Brito and Fl?via M?l Lanna helped with RF analysis and shared R scripts. Marcos Dantas-Queiroz shared R scripts. Danilo Trabuco do Amaral helped with phylogenetic analysis and provided bioinformatic assistance. Fernando de Faria Franco and Cynthia Prado shared information about their taxa of study. Fernando de Faria Franco provided valuable comments that helped improve the manuscript. We also thank six anonymous referees for valuable comments on the manuscript.
Publisher Copyright:
© 2021 John Wiley & Sons Ltd.
PY - 2022/1
Y1 - 2022/1
N2 - Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.
AB - Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.
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U2 - 10.1111/mec.16210
DO - 10.1111/mec.16210
M3 - Article
C2 - 34614269
AN - SCOPUS:85117250357
VL - 31
SP - 331
EP - 342
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 1
ER -