DeepgenomicdivergenceandphenotypicadmixtureofthetreefrogDendropsophuselegans

Phylogeography and Population genetics in South America

Scripts and input files for the analyses used in the manuscript submitted at the Frontiers in Ecology and Evolution:

PIRANI, R. M., TONINI, J. F. R., THOMAZ, A. T., NAPOLI, M., KNOWLES, L. L., WERNECK, F. P. Deep genomic divergence and phenotypic admixture of the treefrog Dendropsophus elegans (Hylidae: Amphibia) coincide with riverine boundaries at Brazilian Atlantic Forest. Frontiers Ecology and Evolution. 2022; (10) 1-15.

Input files for the analyses presented in the manuscript.

1. Individuals reconstruction and relationship

. D.elegans.nex: SVDQuartets Nexus individuals input file

1. Individuals reconstruction and relationship

. RAxMLbipartitions.Deleganstree: RaxML individuals file

1. Population genetic structure

. North14ind5001snp.ustr: STRUCTURE input file within the North population

. South11ind5001snp.ustr: STRUCTURE input file within the South population

. Total29ind5001snp.ustr: STRUCTURE input file total species

1. Estimation of geographic barriers and gene flow

. params-chain.ini: contains the parameters for each run

. Deleg_transpose.coord: contains the samples localities

. Deleg_transpose.diffs: contains the observed genetic dissimilarities

. Deleg_transpose.outer: contains the estimated polygon around the species distribution

1. Demographic migration model for Dendropsophus elegans populations

. doceMMSFS.obs: site frequency spectrum (SFS) for the minor allele for each population sample for the Doce River

. doce_M.est: prior and rules for the migration model for the Doce River

. doce_M.tpl: estimated parameters for the Doce River

. guacuMMSFS.obs: site frequency spectrum (SFS) for the minor allele for each population sample for the Paraguau River

. guacu_M.est: prior and rules for the migration model for the Paraguau River

. guacu_M.tpl: estimated parameters for the Paraguau River

. paraMMSFS.obs: site frequency spectrum (SFS) for the minor allele for each population sample for the Paraba do Sul River

. para_M.est: prior and rules for the migration model for the Paraba do Sul River

. para_M.tpl: estimated parameters for the Paraba do Sul River

. ribeiraMMSFS.obs: site frequency spectrum (SFS) for the minor allele for each population sample for the Ribeira do Iguape River

. ribeira_M.est: prior and rules for the migration model for the Ribeira do Iguape River

. ribeira_M.tpl: estimated parameters for the Ribeira do Iguape River

1. Species range expansion after the Last Glacial Maximum (LGM)

. subdata2_North.nex: input files used to calculate the North population expansion implemented by X-Origin R script for Dendropsophus elegans species.

. subdata2_South.nex: input files used to calculate the South population expansion implemented by X-Origin R script for Dendropsophus elegans species.