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      DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity

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          Abstract

          In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I ( COI) gene from all morphospecies of reef brittle stars collected during a large‐scale biodiversity survey in the southwestern Indian Ocean ( SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005–0.064) and mean interspecific genetic distances within genera (0.056–0.316) were concordant with previous echinoderm studies. This study revealed that brittle‐star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo‐West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.

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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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            Comparative phylogeography of the ocean planet.

            Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
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              Mass extinction in poorly known taxa.

              Since the 1980s, many have suggested we are in the midst of a massive extinction crisis, yet only 799 (0.04%) of the 1.9 million known recent species are recorded as extinct, questioning the reality of the crisis. This low figure is due to the fact that the status of very few invertebrates, which represent the bulk of biodiversity, have been evaluated. Here we show, based on extrapolation from a random sample of land snail species via two independent approaches, that we may already have lost 7% (130,000 extinctions) of the species on Earth. However, this loss is masked by the emphasis on terrestrial vertebrates, the target of most conservation actions. Projections of species extinction rates are controversial because invertebrates are essentially excluded from these scenarios. Invertebrates can and must be assessed if we are to obtain a more realistic picture of the sixth extinction crisis.
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                Author and article information

                Contributors
                eboissin@gmail.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                19 November 2017
                December 2017
                : 7
                : 24 ( doiID: 10.1002/ece3.2017.7.issue-24 )
                : 11197-11203
                Affiliations
                [ 1 ] PSL Research University: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan Perpignan Cedex France
                [ 2 ] Laboratoire d'Excellence “CORAIL” Papetoai Moorea French Polynesia
                [ 3 ] Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
                [ 4 ] Florida Museum of Natural History Gainesville FL USA
                [ 5 ] UMR ENTROPIE UR‐IRD‐CNRS Université de La Réunion Sainte‐ClotildeLa Réunion France
                Author notes
                [*] [* ] Correspondence

                Emilie Boissin, PSL Research University: EPHE‐UPVD‐CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.

                Email: eboissin@ 123456gmail.com

                Author information
                http://orcid.org/0000-0002-4110-790X
                Article
                ECE33554
                10.1002/ece3.3554
                5743570
                32243c58-ca88-46f2-a916-0f1b50e03d03
                © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                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.

                History
                : 04 August 2017
                : 26 September 2017
                : 28 September 2017
                Page count
                Figures: 2, Tables: 1, Pages: 7, Words: 5276
                Funding
                Funded by: Agence Nationale de la Recherche
                Award ID: ANR‐06‐BDIV‐002 (BIOTAS)
                Funded by: FP7 People: Marie‐Curie Actions
                Award ID: MC‐CIG‐618480
                Award ID: ANR‐06‐BDIV‐002
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece33554
                December 2017
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.2.8 mode:remove_FC converted:26.12.2017

                Evolutionary Biology
                cryptic species,diversification,invertebrates,peripheral areas,species delineation

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