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

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.

Phylogeography of Muller's termite frog suggests the vicariant role of the Central Brazilian Plateau

“…Presumably, the lack of habitat specificity in Dermatonotus allows higher gene flow, preventing local speciation, which is contrary to the pattern observed in Phyllopezus, which are highly associated to rock outcrops and Prado et al, 2012;Werneck et al, 2015). These were more pronounced in Caatinga biota, which shows synchronous expansions in response to climatic fluctuations across taxa (Gehara et al, 2017).…”

“…Other DOF taxa diverging in the Neogene also underwent demographic changes in Pleistocene (Magalhaes et al., ; Prado et al., ; Werneck et al., ). These were more pronounced in Caatinga biota, which shows synchronous expansions in response to climatic fluctuations across taxa (Gehara et al., ).…”

“…Although most phylogeographic studies in South America evoke the Pleistocene refuge hypothesis (Haffer, 1969) as the main driving force for speciation (Turchetto-Zolet, Pinheiro, Salgueiro, & Palma-Silva, 2013), Quaternary climatic fluctuations seem to have played a secondary role in the DOF, mainly influencing demographic changes of taxa through time (e.g. Gehara et al, 2017;Magalhaes et al, 2014;Prado et al, 2012;Werneck, Leite, Geurgas, & Rodrigues, 2015). Even in the face of those findings, the historical biogeography of the DOF is still poorly understood, especially because most studies have not tested diversification scenarios using model-based simulation approaches, and fewer still account for historical demographic changes.…”

Local adaptation in mainland anole lizards: Integrating population history and genome–environment associations

“…Genetic clustering analyses of A. ortonii and A. punctatus found that Atlantic Forest samples compose a distinct genetic group from Amazonian samples in both species, pointing to an important role of forest separation in promoting population genetic divergence. The idea of expansion of semi‐arid habitats in northeastern Brazil during the Quaternary, causing fragmentation of forest habitats, is supported by genetic studies of species from these dry regions (Gehara et al, ; Thomé et al, ). Former expansions of open and dry habitats may have favored speciation and further diversification of forest organisms, as supported by a pattern of sister relationships between species or clades that occur in Amazonia and the Atlantic Forest as seen in birds, snakes, and mammals (e.g., Costa, ; Batalha‐Filho et al, ; Dal‐Vechio, Prates, Grazziotin, Zaher, & Rodrigues, ).…”

An integrated model of population genetics and community ecology

“…Even the comparative phylogeographic models that globally operate at the assemblage level have yet to be grounded in ecological theory that can account for stochastic and deterministic forces underlying community assembly (Gehara et al, 2017;Prates et al, 2016). Fortunately, the community assembly models that generate expectations for temporally dynamic SADs (Missa, Dytham, & Morlon, 2016) and speciation/colonization rates (Rosindell & Harmon, 2013) could have an identifiable relationship with population genetic parameters like divergence times, admixture, expansion, colonization times and changes in effective population sizes.…”