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The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species’ range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity.

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Aim The Neotropical Dry Diagonal (DD) is a corridor of distinct dry environments in central South America. The main hypotheses suggest that these environments may have expanded during the glacial cycles together with a retraction of rainforests, and then shrank when the climate became wetter and warmer. However, few studies have explicitly tested the hypotheses on DD evolution. We conducted a phylogeographical study on Nephila sexpunctata, a spider endemic to Neotropical dry habitats, to enrich the understanding of DD evolutionary history. Location South‐western portion of the DD (Cerrado and Chaco). Methods We sequenced two mitochondrial regions and one nuclear DNA region of 65 individuals from 10 locations across the species’ range. We conducted analyses of genetic structure, variability, demography and inferred divergence times. We used an ecological niche modelling framework to generate hypotheses on the species’ distribution along the last glacial cycle and a model‐based approach to test the demographical scenarios that might explain the genetic patterns. Results Both markers presented low genetic diversity. Mitochondrial markers had high genetic structure, with specific geographical lineages within each biome, while the nuclear marker presented low genetic structure. Phylogeographical and demographical events encompass the last glacial cycle, with a strong post‐Last Glacial Maximum (LGM) population and spatial expansion. Model testing corroborated the recent demographical expansion of N. sexpunctata. Main Conclusions Our data suggest that Quaternary climate cycles, when moist forests periodically expanded towards the dry vegetation, influenced the diversification of DD organisms by promoting demographical events. These events might explain the genetic structure observed in N. sexpunctata; differently from what was expected by the Pleistocene refugia model, some DD species may have experienced post‐LGM expansion. Climate and geological events have both affected DD‐endemic organisms’ diversification.

Aim Amazonia and Atlantic Rain Forests share a common biogeographical origin and have an interconnected history that includes the drier biomes between them. It is not clear if the establishment of the South American Dry Diagonal promoted isolation between these forests or if connections between them have occurred after this event. We sought to investigate biotic diversification and geographical evolution in these biomes with a phylogeographical study of Nephila clavipes, a rain forest dwelling spider. Location South America. Methods We collected 320 individuals from 49 sites and sequenced one mitochondrial and two nuclear DNA regions. We analysed the genetic diversity, structure and demography, did phylogenetic inferences, estimated divergence times, inferred ancestral areas and applied a model‐based approach to test competitive hypotheses on the species’ evolution. Results An ancient split, coincident with the Central Cordillera final uplift, segregated a Trans‐Andean Colombian lineage from the others. Four lineages occur in Brazil, with a Pleistocene divergence: one in Amazonia, one in the northern and southern Atlantic Forest and two associated with the Dry Diagonal, but also reaching the Southern Atlantic Forest and Amazonia. The biogeographical analysis indicated that some lineages have expanded their ranges along the Pleistocene. Main conclusions Pleistocene connections of Amazonia and Atlantic rain forests through the central part of the Cerrado were supported. No phylogeographical break was detected along the Atlantic Forest. Geological and climatic events contributed to lineage diversification in N. clavipes. Studying widely distributed species is primary in unveiling evolutionary patterns in highly complex regions.

Historical processes that have interrupted gene flow between distinct evolutionary lineages have played a fundamental role in the evolution of the enormous diversity of species found in the Neotropical region. Numerous studies have discussed the role of geographic barriers and Pleistocene forest refugia in the diversification of the region’s biodiversity. In the present study, we investigated the relative contribution of these different factors to the evolutionary history of Pithecopus nordestinus , a Neotropical tree frog, which is amply distributed in the Brazilian Atlantic Forest and adjacent areas of the Caatinga biome. We used an extensive sample and multilocus DNA sequences to provide an overview of the intraspecific genetic diversity of P. nordestinus , characterize historical diversification patterns, and identify possible phylogenetic splits. We tested different scenarios of diversification based on Pleistocene Refugia and river barrier models using approximate Bayesian computation (ABC) and ecological niche modeling (ENM). The phylogenetic approach indicate the occurrence of processes of phylogeographic divergence in both time and space, related to historical shifts in the course of the São Francisco River during Plio-Pleistocene period, resulting in two principal, highly divergent clades. The ABC model provided strong statistical support for this scenario, confirming the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus . We believe that the climatic changes that occurred during the Pleistocene also played a secondary role in the genetic signatures identified, reinforcing the divergence of populations isolated by physical barriers. These findings reinforce the conclusion that the two models of diversification (geographic barriers and refugia) are not mutually exclusive in the Neotropical domain but may interact extensively during the diversification of species on a regional scale.