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      Genetic structure and distribution of Parisotoma notabilis (Collembola) in Europe: Cryptic diversity, split of lineages and colonization patterns

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          Abstract

          Climatic and biome changes of the past million years influenced the population structure and genetic diversity of soil-living arthropods in Europe. However, their effects on the genetic structure of widespread and abundant soil animal species such as the Collembola Parisotoma notabilis remain virtually unknown. This generalist and parthenogenetic species is an early colonizer of disturbed habitats and often occurs in human modified environments. To investigate ancient climatic influence and recent distributions on the genetic structure of P. notabilis we analyzed populations on a pan-European scale using three genetic markers differing in substitution rates. The results showed that P. notabilis comprises several genetic lineages with distinct distribution ranges that diverged in the Miocene. Genetic distances of COI between lineages ranged between 15% and 18% and molecular clock estimates suggest Late Miocene divergences considering the standard arthropod rate of 2.3% per my. Compared to other soil-living arthropods like oribatid mites, European lineages of P. notabilis are rather young and genetically uniform. The close association with anthropogenic habitats presumably contributed to rapid spread in Europe.

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          Most cited references18

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          TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

          Summary: TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). Methods available include model selection and phylogenetic tree estimation using the Bayesian inference and maximum likelihood (ML) approaches, in addition to recombination detection methods. The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from ML co-estimation of the tree and the substitution model. Phylogenetic software available includes PhyML, RAxML and MrBayes. Availability: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris. Contact: iain.milne@scri.ac.uk
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            Sequence-based species delimitation for the DNA taxonomy of undescribed insects.

            Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
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              Speciation, hybrid zones and phylogeography - or seeing genes in space and time.

              G Hewitt (2001)
              The origins and development of the study of speciation, hybrid zones and phylogeography are outlined using evolutionary iconography. This traces the ideas in this field from Lamarck and Darwin through to the present as represented in diagrams and figures. A 'tree of trees' summarizes this growth and current vitality. The new facility to use various DNA sequences from nuclear, mitochondrial and chloroplast genomes to determine genetic variation throughout a species range is examined particularly. There is great genomic subdivision across species distributions, which can be interpreted in the light of the recent demonstrations of severe palaeoclimatic oscillations. Refugia and postglacial colonization routes are proposed for several organisms across Europe. The role of geography in speciation through the Pleistocene is considered. These emerging principles and analyses are applied to data available on a variety of organisms in other regions of the world, such as the Arctic, North America and the Tropics, and including the progress of Homo sapiens through the last ice age. Some suggestions are made for future research directions.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 February 2017
                2017
                : 12
                : 2
                : e0170909
                Affiliations
                [001]Georg August University Göttingen, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
                Nanjing Agricultural University, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: SS IS.

                • Data curation: HvS.

                • Formal analysis: HvS IS.

                • Funding acquisition: SS IS.

                • Investigation: HvS.

                • Methodology: HvS IS.

                • Project administration: IS.

                • Resources: HvS SS IS.

                • Software: HvS.

                • Supervision: SS IS.

                • Validation: HvS SS IS.

                • Visualization: HvS.

                • Writing – original draft: HvS.

                • Writing – review & editing: SS IS.

                Article
                PONE-D-16-28838
                10.1371/journal.pone.0170909
                5295681
                28170395
                5c6091a0-b339-4d81-8f2a-42b8a6b8bab3
                © 2017 von Saltzwedel et al

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

                History
                : 21 July 2016
                : 12 January 2017
                Page count
                Figures: 2, Tables: 4, Pages: 15
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: SCHE 376/13-1 u. 13-2
                Award Recipient :
                This study was funded by the Deutsche Forschungsgemeinschaft (SCHE 376/13-1 u. 13-2).
                Categories
                Research Article
                Biology and Life Sciences
                Paleontology
                Paleogenetics
                Earth Sciences
                Paleontology
                Paleogenetics
                People and Places
                Geographical Locations
                Europe
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
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