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      Molecular diversity of Pseudoscorpiones in southern High Appalachian leaf litter

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          Abstract

          The Pseudoscorpiones fauna of North America is diverse, but in regions like the southern Appalachian Mountains, they are still poorly documented with respect to their species diversity, distributions and ecology. Several families have been reported from these mountains and neighbouring areas. Here we analyse barcoding data of 136 specimens collected in leaf litter, most of them from high-elevation coniferous forest. We used ASAP as a species delimitation method to obtain an estimation of the number of species present in the region. For this and based on interspecific genetic distance values previously reported in Pseudoscorpions, we considered three different genetic Kimura two-parameter distance thresholds (3%/5%/8%), to produce more or less conservative estimates. These distance thresholds resulted in 64/47/27 distinct potential species representing the families Chthoniidae (33/22/12 species) and Neobisiidae (31/25/15) and at least six different genera within them. The diversity pattern seems to be affected by the Asheville Depression, a major biogeographic barrier in this area, with a higher diversity to the west of this geographic feature, particularly within the family Neobisiidae . The absence of representatives from other families amongst our studied samples may be explained by differences in their ecological requirements and occupation of different microhabitats.

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          A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

          Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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            W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

            This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
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              ASAP: assemble species by automatic partitioning

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                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2024
                11 January 2024
                : 12
                : e115928
                Affiliations
                [1 ] Clemson University, Clemson, United States of America Clemson University Clemson United States of America
                Author notes
                Corresponding authors: Ernesto Recuero ( ernestorecuerogil@ 123456gmail.com ), Michael S. Caterino ( mcateri@ 123456clemson.edu ).

                Academic editor: Jana Christophoryová

                Author information
                https://orcid.org/0000-0002-2597-5707
                Article
                115928 23857
                10.3897/BDJ.12.e115928
                10797626
                38249569
                a3494bba-4f18-4115-b087-639a9ed22756
                Ernesto Recuero, Michael S. Caterino

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 17 November 2023
                : 03 January 2024
                Page count
                Figures: 2, Tables: 0, References: 36
                Categories
                Research Article

                soil diversity,megabarcoding,species delimitation,asheville depression,arachnida,appalachia

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