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1. Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): Implications for the evolution of Amazonian landscapes during the Quaternary

   https://doi.org/10.1111/jbi.13169  

   Ribas, Camila C. ; Aleixo, Alexandre ; Gubili, Chrysoula ; d'Horta, Fernando M. ; Brumfield, Robb T. ; Cracraft, Joel ( January 2018 , Journal of Biogeography)

   To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genusRhegmatorhinaat multiple taxonomic and temporal scales.

   Amazonia.

   Antbirds (Thamnophilidae).

   We sequenced four mtDNAand nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow.

   Dense sampling throughout the distribution ofRhegmatorhinarevealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNAlineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity.

   Based on broad‐scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first, mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long‐standing question of identifying the main drivers of Amazonian diversification.

    

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2. Vegetation response to climatic changes in western Amazonia over the last 7,600 years

   https://doi.org/10.1111/jbi.13704  

   Nascimento, Majoi N. ; Martins, Gabriel S. ; Cordeiro, Renato C. ; Turcq, Bruno ; Moreira, Luciane S. ; Bush, Mark B. ( September 2019 , Journal of Biogeography)

   Ongoing and future anthropogenic climate change poses one of the greatest threats to biodiversity, affecting species distributions and ecological interactions. In the Amazon, climatic changes are expected to induce warming, disrupt precipitation patterns and of particular concern, to increase the intensity and frequency of droughts. Yet the response of ecosystems to intense warm, dry events is not well understood. In the Andes the mid‐Holocene dry event (MHDE),c. 9,000 to 4,000 years ago, was the warmest and driest period of the last 100,000 years which coincided with changes in evaporation and precipitation that caused lake levels to drop over most of tropical South America. This event probably approximates our near‐climatic future, and a critical question is:How much did vegetation change in response to this forcing?

   Lake Pata, Brazilian Western Amazonia.

   Terrestrial and aquatic plants.

   We used pollen, charcoal, total organic carbon (TOC), total nitrogen (TN), δ¹³C and δ¹⁵N data from a new high‐resolution core that spans the lastc. 7,600 years history of Lake Pata.

   We found that in the wettest section of Amazonia changes associated with the MHDE were detected in the geochemistry analysis but that vegetation changed very little in response to drought during the Holocene. This is the first high‐resolution core without apparent hiatuses that spans most of the Holocene (last 7,600 cal yrbp) from Lake Pata, Brazil. Changes in the organic geochemistry of sediments indicated that between c. 6,500 and 3,600 cal yrbplake levels dropped. Vegetation, however, showed little change as near‐modern forests were seen throughout the record, evidencing the substantial resilience of this system. Only a few species replacements and minor fluctuations in abundance were observed in the pollen record.

   The mid‐Holocene warming and reduced precipitation had a limited impact on western Amazonian forests. We attribute much of the resilience to a lack of fire in this system, and that if human‐set fires were to be introduced, the forest destruction from that cause would override that induced by climate alone.

    

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3. Varied diversification patterns and distinct demographic trajectories in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley

   https://doi.org/10.1111/mec.16417  

   Manthey, Joseph D. ; Bourgeois, Yann ; Meheretu, Yonas ; Boissinot, Stéphane ( March 2022 , Molecular Ecology)

   Taxon‐specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth's template and species‐specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole‐genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.

    

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4. Biogeographic reconstruction of the migratory Neotropical fish family Prochilodontidae (Teleostei: Characiformes)

   https://doi.org/10.1111/zsc.12531  

   Frable, Benjamin W. ; Melo, Bruno F. ; Fontenelle, João P. ; Oliveira, Claudio ; Sidlauskas, Brian L. ( March 2022 , Zoologica Scripta)

   Geographically, widespread Neotropical fish lineages offer opportunities to reconstruct historical biogeography patterns and infer processes leading to modern ichthyological diversity and distribution. The characiform family Prochilodontidae is well suited for such reconstruction because their migrations limit population substructure within river systems. Therefore, their biogeographic history should match closely the history of connectivity among Neotropical river basins. Here, we combine a time‐calibrated phylogeny with biogeographic model testing to recover the history of this family's diversification. Results support the Miocene rise of the Andean Eastern Cordillera as a dispersal barrier, but also indicate a much earlier Eocene origin of the trans‐Andean genusIchthyoelephas. Despite the early origin of the family and its three constituent genera, most prochilodontid lineages originated during the Miocene in Greater Amazonia, likely due to drainage reorganizations caused by Andean uplift. Subsequent speciation appears linked to interbasin exchanges and expansions of Amazonian lineages into Brazilian coastal systems. The modern richness ofProchilodusin easterly drainages appears to be relatively young, with onlyProchilodus vimboideslikely reaching that region prior to the late Miocene. The rise of the Vaupes Arch coincides with two splits between Orinocoan and Amazonian lineagescirca9 million years ago (Ma). However, two instances of later dispersal between these drainages reveal the permeability of the Vaupes Arch, suggesting that it may promote periodic speciation. This study illustrates how model‐based biogeographic studies of widespread groups can reconstruct historic paths of dispersal and help reveal how landscape evolution promoted modern diversity patterns.

    

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5. Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake

   https://doi.org/10.1111/jbi.14709  

   Jones, II, Leonard N. ; Leaché, Adam D. ; Burbrink, Frank T. ( August 2023 , Journal of Biogeography)

   Current distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences or spatiotemporal differences. In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA.

   North America.

   Common gartersnake,Thamnophis sirtalis.

   We evaluate the effects of major river basins and the forest‐grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure and demographic analyses of single nucleotide polymorphism data and address range expansion history with ecological niche modelling using locality and historic climate data.

   We identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex‐linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA.

   Our results provide strong evidence for a Pliocene origin forT. sirtalisin central‐southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate‐mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.

    

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