Genomic data from the Brazilian sibilator frog reveal contrasting pleistocene dynamics and regionalism in two South American dry biomes

Author(s)

Thome, Maria Tereza C. ^{[1, 2, 3]} ; Carstens, Bryan C. ^[1] ; Rodrigues, Miguel T. ^[4] ; Alexandrino, Joao ^[5] ; Haddad, Celio F. B. ^{[2, 3]}

Affiliation

^[1] Ohio State Univ, Dept Evolut Ecol & Organismal Biol, Columbus, OH 43210 - USA

^[2] Univ Estadual Paulista, Inst Biociencias, Dept Biodiversidade, Campus Rio Claro, Av 24A 1515, BR-13506900 Rio Claro, SP - Brazil

^[3] Univ Estadual Paulista, Inst Biociencias, Ctr Aquicultura, Campus Rio Claro, Av 24A 1515, BR-13506900 Rio Claro, SP - Brazil

^[4] Univ Sao Paulo, Inst Biociencias, Dept Zool, Sao Paulo, SP - Brazil

^[5] Univ Fed Sao Paulo, Dept Ecol & Biol Evolut, Inst Ciencias Ambientais Quim & Farmaceut, Diadema, SP - Brazil

• Document type: Journal article
• Source: Journal of Biogeography; v. 48, n. 5 FEB 2021.
• Web of Science Citations: 0

Abstract

Aim: Knowledge about the Neotropical dry formations, particularly the Caatinga, remains rudimentary compared to other biotas in the region. Here we address several biogeographical hypotheses by combining intense geographical and genomic sampling obtained for the Brazilian sibilator frog. We specifically test predictions related to the putative roles of past climate shifts (Pleistocene and Holocene) and local geographical barriers (past and current courses of the Sao Francisco River, SFR) in causing population differentiation in this species. Location: Caatinga and eastern Cerrado. Taxon: Brazilian sibilator frog Leptodactylus troglodytes. Methods: We sequenced up to similar to 15,000 single nucleotide polymorphisms for 159 samples from 61 locations. We inferred genetic structure using spatial clustering and examined population sizes through time. We estimated the relationship among populations using phylogenetic reconstruction, estimated historical distributions with ecological niche modelling and inferred demographic history under isolation-with-migration models. Results: Genetic diversity in L. troglodytes corresponds to biome boundaries, with one population in the Cerrado and two populations in the Caatinga, separated by the SFR. Demographic model selection indicates the Caatinga populations expanded since the end of the Pleistocene while the Cerrado population declined. Within the Caatinga, population expansion began earlier and was more extreme in the north. A continuous stability area maintained the two Caatinga populations, which share a common origin and began diverging in the mid-Pleistocene, first with symmetric gene flow and later under pronounced migration from the north. Main conclusions: We could not reject a role of past climate change in causing diversification of relictual populations in the Cerrado, but we found no evidence of multiple refuges or long-term isolation within the Caatinga. Instead, diversification in this biome appears to be caused by the SFR acting as a `soft barrier' that constrains migration over an extended period of time. (AU)

• FAPESP's process: 13/09088-8 - The history of the Caatinga: exploring phylogeographic patterns and evolutionary processes in three amphibians with next-generation sequencing data
• Grantee: Maria Tereza Chiarioni Thomé
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 11/50146-6 - Comparative phylogeography, phylogeny, paleoclimate modeling, and taxonomy of neotropical reptiles and amphibians
• Grantee: Miguel Trefaut Urbano Rodrigues
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants
• FAPESP's process: 11/51392-0 - History of Caatinga: comparative phylogeography of amphibians facing a xeric biome
• Grantee: Maria Tereza Chiarioni Thomé
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 18/03428-5 - Dimensions US-BIOTA-Sao Paulo: traits as predictors of adaptive diversification along the Brazilian Dry Diagonal
• Grantee: Vera Nisaka Solferini
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants
• FAPESP's process: 13/50741-7 - Diversity and conservation of Brazilian amphibians
• Grantee: Célio Fernando Baptista Haddad
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants