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      Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

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          Abstract

          Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are “evolutionary dead‐ends.” This implies that cave‐adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave‐dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave‐dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave‐dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a “dead‐end” for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.

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          Most cited references 58

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          TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

          We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.
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            Dispersal in Freshwater Invertebrates

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              Model inadequacy and mistaken inferences of trait-dependent speciation.

              Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models-have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are inferred to have statistically significant associations with speciation rate. We first demonstrate this unfortunate effect for a known model assumption violation: shifts in speciation rate associated with a character not included in the model. We further show that for many empirical phylogenies, characters simulated in the absence of state-dependent diversification exhibit an even higher Type I error rate, indicating that the method is susceptible to additional, unknown model inadequacies. For traits that evolve slowly, the root cause appears to be a statistical framework that does not require replicated shifts in character state and diversification. However, spurious associations between character state and speciation rate arise even for traits that lack phylogenetic signal, suggesting that phylogenetic pseudoreplication alone cannot fully explain the problem. The surprising severity of this phenomenon suggests that many trait-diversification relationships reported in the literature may not be real. More generally, we highlight the need for diagnosing and understanding the consequences of model inadequacy in phylogenetic comparative methods.
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                Author and article information

                Contributors
                dbstern@gwmail.gwu.edu
                Journal
                Evolution
                Evolution
                10.1111/(ISSN)1558-5646
                EVO
                Evolution; International Journal of Organic Evolution
                John Wiley and Sons Inc. (Hoboken )
                0014-3820
                1558-5646
                20 September 2017
                October 2017
                : 71
                : 10 ( doiID: 10.1111/evo.2017.71.issue-10 )
                : 2522-2532
                Affiliations
                [ 1 ] Computational Biology Institute The George Washington University Ashburn Virginia 20147
                [ 2 ] Department of Biology University of Florida Gainesville Florida
                [ 3 ] Licenciatura en Ciencia Forense, Facultad de Medicina Universidad Nacional Autónoma de México México
                [ 4 ] Lab. Biología Evolutiva y Genética de Poblaciones Universidad de Quintana Roo Cozumel México
                [ 5 ] Department of Biological Sciences Florida International University North Miami Florida 33181
                [ 6 ] Section of Invertebrate Zoology Carnegie Museum of Natural History Pittsburgh Pennsylvania 15213‐4080
                [ 7 ] Department of Invertebrate Zoology, U.S. National Museum of Natural History Smithsonian Institution Washington District of Columbia 20013
                Article
                EVO13326
                10.1111/evo.13326
                5656817
                28804900
                © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 3, Tables: 1, Pages: 11, Words: 7737
                Product
                Funding
                Funded by: Division of Environmental Biology
                Award ID: 1301820
                Award ID: 1601631
                Funded by: Florida Fish and Wildlife Conservation Commission
                Award ID: NG07‐104
                Funded by: US National Science Foundation
                Categories
                Brief Communication
                Brief Communications
                Custom metadata
                2.0
                evo13326
                October 2017
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.2.1 mode:remove_FC converted:26.10.2017

                Evolutionary Biology

                crayfish, caves, diversification, extinction, habitat, range size, synthesis

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