Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance

Abstract

The Neotropical region exhibits the greatest worldwide diversity and the diversification history of several clades is related to the puzzling geomorphologic and climatic history of this region. The freshwater Amazon ecoregion contains the main hydrographic basins of the Neotropical region that are highly dendritic and ecologically diverse. It contains a rich and endemic fish fauna, including one of its most iconic and economically important representatives, the bony‐tongue Arapaima gigas (Teleostei, Osteoglossiformes). Here, we evaluated the projected distribution of the genus in different historical periods (Present, Last Glacial Maximum, Last Interglacial Maximum and Near Future) and interpreted these results in light of the genomic diversity and modeled historical demography. For that, we combined species distribution models, population genetic analysis using SNPs and deep learning model selection. We analyzed a representative sample of the genus from the two basins where it naturally occurs, four localities in the Amazon (Am) and three in the Tocantins‐Araguaia (To‐Ar) basin, as well as individuals from three fish farms. We inferred a potentially smaller distribution in the glacial period, with a possible refuge in central Am. Our genetic data agrees with this result, suggesting a higher level of genetic diversity in the Am basin, compared to that observed in To‐Ar. Our deep learning model comparison indicated that the To‐Ar basin was colonized by the population from the Am basin. Considering a global warming scenario in the near future, A. gigas could reach an even larger range, especially if anthropogenic related dispersal occurs, potentially invading new areas and impacting their communities.

Coalescent‐based species delimitation meets deep learning: Insights from a highly fragmented cactus system

“…Simulations have shown that CNNs maximize the use of available information from the data and increase the capacity to distinguish divergent evolutionary histories, frequently overcoming the limitations of other traditional approaches (Flagel et al, 2019). Despite the recent use of CNNs in population genetics (Flagel et al, 2019;Sanchez et al, 2020) and phylogeography (Fonseca et al, 2021;Oliveira et al, 2020;Souza et al, 2019), this approach has not previously been tested in the context of species delimitation using genetic data.…”

Geography, climate and changes in host plants distribution explain patterns of genomic variation within the cactus moth

“…21 kya), we evaluated 15 environmental variables retrieved at 30 arc-sec (˜1 km) of resolution. Four bioclimatic variables (Bio 8, 9, 18 and 19) were discarded for having artificial breaks (Oliveira et al, 2020). Highly correlated variables (R >0.9) according to variance inflation factor criterion were excluded for downstream analyses resulting in a final dataset of 6 bioclimatic variables (Bio 2,3,5,13,14 and 15).…”

The Genetic Differentiation of Pyrrhulina (Teleostei, Characiformes) Species is Likely Influenced by Both Geographical Distribution and Chromosomal Rearrangements

“…The development and improvement of large-scale genotyping-by-sequencing (GBS) procedures allowed high-resolution analysis using Single Nucleotide Polymorphisms (SNPs) for genetic diversity studies in non-model organisms ( Steane et al, 2011 ; Yang et al, 2013 ; Sánchez-Sevilla et al, 2015 ; Alkimin et al, 2018 ; Souza et al, 2019 ; Oliveira et al, 2020 ; Sassi et al, 2021 ). Combining such genomic and cytogenetic data for pairs of species/populations in which there are variations related to geographic distribution, analysis of chromosomal rearrangements, and sex chromosome systems provide a critical tool to understanding the role of these events to generate biodiversity.…”