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1. Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks ( Quercus section Cerris )

   https://doi.org/10.1093/aob/mcad032  

   Denk, Thomas ; Grimm, Guido W. ; Hipp, Andrew L. ; Bouchal, Johannes M. ; Schulze, Ernst-Detlef ; Simeone, Marco C. ( February 2023 , Annals of Botany)

   Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex, the holly oaks.

   We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D-statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth–death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches.

   East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process.

   Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections.

    

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2. Ecological and Phenotypic Diversification after a Continental Invasion in Neotropical Freshwater Stingrays

   https://doi.org/10.1093/icb/icac019  

   Kolmann, M A ; Marques, F P ; Weaver, J C ; Dean, M N ; Fontenelle, J P ; Lovejoy, N R ( April 2022 , Integrative and Comparative Biology)

   Abstract Habitat transitions are key potential explanations for why some lineages have diversified and others have not—from Anolis lizards to Darwin's finches. The ecological ramifications of marine-to-freshwater transitions for fishes suggest evolutionary contingency: some lineages maintain their ancestral niches in novel habitats (niche conservatism), whereas others alter their ecological role. However, few studies have considered phenotypic, ecological, and lineage diversification concurrently to explore this issue. Here, we investigated the macroevolutionary history of the taxonomically and ecologically diverse Neotropical freshwater river rays (subfamily Potamotrygoninae), which invaded and diversified in the Amazon and other South American rivers during the late Oligocene to early Miocene. We generated a time-calibrated, multi-gene phylogeny for Potamotrygoninae and reconstructed evolutionary patterns of diet specialization. We measured functional morphological traits relevant for feeding and used comparative phylogenetic methods to examine how feeding morphology diversified over time. Potamotrygonine trophic and phenotypic diversity are evenly partitioned (non-overlapping) among internal clades for most of their history, until 20–16 mya, when more recent diversification suggests increasing overlap among phenotypes. Specialized piscivores (Heliotrygon and Paratrygon) evolved early in the history of freshwater stingrays, while later trophic specialization (molluscivory, insectivory, and crustacivory) evolved in the genus Potamotrygon. Potamotrygonins demonstrate ecological niche lability in diets and feeding apparatus; however, diversification has mostly been a gradual process through time. We suggest that competition is unlikely to have limited the potamotrygonine invasion and diversification in South America. 

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3. Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

   https://doi.org/10.1111/mec.15534  

   Buainain, Nelson ; Canton, Roberta ; Zuquim, Gabriela ; Tuomisto, Hanna ; Hrbek, Tomas ; Sato, Hiromitsu ; Ribas, Camila C. ( July 2020 , Molecular Ecology)

   Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally‐dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.

    

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4. Integrating historical biogeography and environmental niche evolution to understand the geographic distribution of Datureae

   https://doi.org/10.1002/ajb2.1281  

   Dupin, Julia ; Smith, Stacey D. ( May 2019 , American Journal of Botany)

   The distributions of plant clades are shaped by abiotic and biotic factors as well as historical aspects such as center of origin. Dispersals between distant areas may lead to niche evolution when lineages are established in new environments. Alternatively, dispersing lineages may exhibit niche conservatism, moving between areas with similar environmental conditions. Here we test these contrasting hypotheses in the Datureae clade (Solanaceae).

   We used maximum likelihood methods to estimate the ancestral range of Datureae along with the history of biogeographic events. We then characterized the niche of each taxon using climatic and soil variables and tested for shifts in environmental niche optima. Finally, we examined how these shifts relate to the niche breadth of taxa and clades within Datureae and the degree of overlap between them.

   Datureae originated in the Andes and subsequently expanded its range to North America and non‐Andean regions of South America. The ancestral niche, and that of mostDaturaandTrompettiaspecies, is dry, whileBrugmansiaspecies likely shifted toward a more mesic environment. Nonetheless, most Datureae present moderate to high overlap in niche breadth today.

   The expansion of Datureae into North America was associated with niche conservatism, with dispersal into similarly dry areas as occupied by the ancestral lineage. Subsequent niche evolution, including the apparent shift to a mesic niche inBrugmansia, diversified the range of habitats occupied by species in the tribe Datureae but also led to significant niche overlap among the three genera.

    

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5. Biogeography of the neotropical freshwater stingrays (Myliobatiformes: Potamotrygoninae) reveals effects of continent‐scale paleogeographic change and drainage evolution

   https://doi.org/10.1111/jbi.14086  

   Fontenelle, João Pedro ; Portella Luna Marques, Fernando ; Kolmann, Matthew A. ; Lovejoy, Nathan R. ; Floeter, ed., Sergio ( March 2021 , Journal of Biogeography)

   Paleogeographic changes have had profound effects on the evolution and diversity of the Neotropical biota. However, the influence of marine incursions on the origin, diversification, and distribution of fishes is still incompletely understood. We investigate the biogeographical and chronological patterns of diversification for the marine‐derived Neotropical freshwater stingrays (subfamily Potamotrygoninae) at a continental scale.

   Neotropics, South America.

   Neotropical freshwater stingrays. Subfamily Potamotrygoninae (Myliobatiformes: Chondrichthyes).

   We generated a time‐calibrated phylogeny for 35 of the 38 valid species of Neotropical freshwater stingrays, from most of the major river basins of South America, using four genes. We used BEAST2 to determine the chronology of population and species divergence events, and “BioGeoBEARS” to infer historical biogeographic patterns.

   The Potamotrygoninae originated during the early/middle Miocene in the upper Amazon region. We recover clades associated with particular geographic areas and detect a recurrent pattern of upper Amazon clades sister to clades in adjacent basins. The timing of dispersals from the upper Amazon to adjacent areas corresponds with the end of the Pebas wetlands. Lower Amazon and Shield associated taxa are relatively young.

   We propose that the origin of the Neotropical freshwater stingrays is related to marine incursions that occurred during the Oligocene/Miocene. Subsequent diversification of Potamotrygoninae occurred in the Pebas wetland system in the upper Amazon with colonization of adjacent basins. These movements were generally unidirectional, with few lineages returning to the upper Amazon, and we speculate that ecological factors drove this pattern. We observed a burst of potamotrygonine diversification 5 Ma that appears to be related to the modern channelization of the Amazon Basin.

    

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