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      From Gondwana to GAARlandia: Evolutionary history and biogeography of ogre-faced spiders (Deinopis)

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          ASTRAL: genome-scale coalescent-based species tree estimation

          Motivation: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees. Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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            Biogeographic areas and transition zones of Latin America and the Caribbean islands based on panbiogeographic and cladistic analyses of the entomofauna.

             Juan Morrone (2005)
            Track and cladistic biogeographic analyses based on insect taxa are used as a framework to interpret patterns of the Latin American and Caribbean entomofauna by identifying biogeographic areas on the basis of endemicity and arranging them hierarchically in a system of regions, subregions, dominions, and provinces. The Nearctic region, inhabited by Holarctic insect taxa, comprises five provinces: California, Baja California, Sonora, Mexican Plateau, and Tamaulipas. The Mexican transition zone comprises five provinces: Sierra Madre Occidental, Sierra Madre Oriental, Transmexican Volcanic Belt, Balsas Basin, and Sierra Madre del Sur. The Neotropical region, which harbors many insect taxa with close relatives in the tropical areas of the Old World, comprises four subregions: Caribbean, Amazonian, Chacoan, and Parana. The South American transition zone comprises five provinces: North Andean Paramo, Coastal Peruvian Desert, Puna, Atacama, Prepuna, and Monte. The Andean region, which harbors insect taxa with close relatives in the Austral continents, comprises three subregions: Central Chilean, Subantarctic, and Patagonian.
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              Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns.

              The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. We examined the relative roles played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1,393 terminals). Parsimony-based tree fitting in conjunction with permutation tests was used to examine to what extent Southern Hemisphere biogeographic patterns fit the breakup sequence of Gondwana and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana breakup: (Africa(New Zealand(southern South America, Australia))). Trans-Antarctic dispersal (Australia southern South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (southern South America(Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.
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                Author and article information

                Journal
                Journal of Biogeography
                J Biogeogr
                Wiley
                03050270
                November 2018
                November 2018
                September 25 2018
                : 45
                : 11
                : 2442-2457
                Affiliations
                [1 ]Department of Biology; University of Vermont; Burlington Vermont
                [2 ]Department of Biology; Lewis & Clark College; Portland Oregon
                [3 ]Department of Entomology and Nematology; University of California Davis; Davis California
                [4 ]Department of Entomology; National Museum of Natural History, Smithsonian Institution; Washington District of Columbia
                [5 ]Department of Terrestrial Zoology; Western Australian Museum; Welshpool DC WA Australia
                [6 ]Department of Biological Sciences; Auburn Museum of Natural History; Auburn Alabama
                [7 ]Evolutionary Zoology Laboratory; Institute of Biology, Scientific Research Centre, Slovenian Academy of Sciences and Arts; Ljubljana Slovenia
                [8 ]Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research; National Institute of Biology; Ljubljana Slovenia
                Article
                10.1111/jbi.13431
                © 2018

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