Coalescent simulations indicate that the São Francisco River is a biogeographic barrier for six vertebrates in a seasonally dry South American forest

Abstract

The riverine barrier hypothesis has been extensively explored in Neotropical rainforests, while its importance in drier regions such as the Caatinga, a seasonally dry tropical forest in northeastern Brazil, has only recently received more attention. The Caatinga is bisected by the São Francisco River (SFR), which has long been suggested to be an important biogeographic feature in the region. However, recent studies have found mixed support for the role of the SFR as a hard barrier, most of them relying on the presence or absence of genetic breaks congruent with its course. Here, we used published multilocus and next-generation data from six vertebrate species to test the SFR’s strength as a barrier. Using model-based approaches (approximate Bayesian computation and supervised machine learning), we tested demographic models incorporating full, intermediate, and zero migration across the SFR, estimating divergence times and migration rates for each species. We found support for the SFR’s role as a barrier, allowing gene flow for some species. Estimated divergence times varied among species but are limited to the late Pleistocene, coherent with one of several proposed paleocourse changes in the river’s geological history. Contrary to the mixed results of previous studies, our study supports the SFR as an important phylogeographic barrier across different taxonomic groups, driving diversification in the Caatinga.

Geoclimatic drivers of diversification in the largest arid and semi‐arid environment of the Neotropics: Perspectives from phylogeography

“…Few studies used model‐ or simulation‐based tools to unambiguously identify SFR‐based vicariance (Almeida et al., 2020; Bruschi et al., 2019). However, some model‐based studies recovered shallow structure with ongoing gene flow across the SFR (Coelho, Guillory, & Gehara, 2022; Oliveira, Martinez, et al., 2018; Thomé, Carstens, Rodrigues, Alexandrino, & Haddad, 2021) or negligible structure/high gene flow across the SFR (Miranda et al., 2016; Oliveira et al., 2015; Thomé, Carstens, Rodrigues, Galetti Jr, et al., 2021).…”

“…The remaining SFRH studies focus on animals, and over half of those on reptiles and amphibians, which commonly show strong to mixed effects of the SFR (Figure 2b), especially arid‐adapted or fossorial species that may have lower vagility than less specialized taxa. In most species, the SFR is likely to act as a soft barrier that permits some gene flow while leading to weakly structured lineages on either bank (Coelho, Guillory, & Gehara, 2022; Fegies et al., 2021; Oliveira, Martinez, et al., 2018; Werneck et al., 2015), especially if the SFR has fluctuated in width and the steepness of its banks (i.e. its strength as a barrier) over time.…”

“…Sister relationships between disjunct species in isolated SDTF nuclei • Pleistocene divergence times • Model support for divergence w/o migration, with ↓ N e at time of divergence • Resistance across intervening non-SDTF habitats predicts genetic distance • Pleistocene ↓ N e in non-SDTF populations (see FCH• Model support for divergence w/o migration, and with ↓ N e at the time of divergence, then recent ↑ N e (see • Potential admixture/hybridization after population expansion SFRH • Model support for divergence (migration determines 'hardness' of barrier) (seeCoelho, Camurugi, et al, 2022;Coelho, Guillory, & Gehara, 2022) • Divergence times concordant with paleocourse change • Temporal concordance in divergence times of co-distributed species • Resistance across SFR predicts genetic distance CBPH • Model support for divergence (migration determines 'hardness' of barrier) (see Oliveira, Gehara, et al, 2018) • Elevational resistance predicts genetic distance MMIH • ↑ elevation areas predict ↑ genetic diversity (see Brusquetti et al, 2018) • Miocene divergence times • Support for out-of-refuge models with range expansion to ↓ elevation areasfor a richer understanding of their effect on genetic diversity. The most recently published phylogeography article on the SFRH, for instance, still cites geological literature from 25 years ago (Oliveira-Silva et al, 2023).…”

Integrative methods reveal multiple drivers of diversification in rice paddy snakes

“…Coalescent models can incorporate multilocus or genomic datasets and can be fine-tuned to test phylogeographic hypotheses with large sample sizes. Obtaining accurate divergence dates is critical for downstream studies that aim to identify the causal factors of population splits and speciation, especially at potential biogeographic barriers 20 . Herein, we examine whether rice paddy snake diversification coincides with the rise of the Khorat Plateau and test for differences in each species’ environmental niche.…”

Integrative Methods Reveal Multiple Drivers of Diversification in Rice Paddy Snakes

“…Coalescent models can incorporate multilocus or genomic datasets and can be ne-tuned to test speci c phylogeographic hypotheses with large sample sizes. Obtaining accurate divergence dates is critical for downstream studies that aim to identify the causal factors of population splits and speciation, especially at potential biogeographic barriers [20] . Herein, we examine whether rice paddy snake diversi cation coincides with the rise of the Khorat Plateau and also test for differences in each species' environmental niche.…”