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      RAD sequencing reveals genomewide divergence between independent invasions of the European green crab ( Carcinus maenas) in the Northwest Atlantic

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          Abstract

          Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab ( Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction‐site‐associated DNA sequencing‐derived SNPs to explore fine‐scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise F ST ~0.001 to 0.15) and spread across many loci, with a mean F ST ~0.052 and 52% of loci examined characterized by F ST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.

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          Evolutionary genetics of invasive species

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            Ecological and evolutionary consequences of coastal invasions

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              Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

              Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (maxcount = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms.
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                Author and article information

                Contributors
                nick.jeffery@dfo-mpo.gc.ca
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                14 March 2017
                April 2017
                : 7
                : 8 ( doiID: 10.1002/ece3.2017.7.issue-8 )
                : 2513-2524
                Affiliations
                [ 1 ] Northwest Atlantic Fisheries CentreFisheries and Oceans Canada St. John's NLCanada
                [ 2 ] Bedford Institute of OceanographyFisheries and Oceans Canada Dartmouth NSCanada
                [ 3 ] Ocean Sciences Center and Biology DepartmentMemorial University of Newfoundland St John's NLCanada
                [ 4 ] Aquatic Biotechnology LaboratoryBedford Institute of Oceanography Dartmouth Nova ScotiaCanada
                [ 5 ] Gulf Fisheries CentreFisheries and Oceans Canada Moncton New BrunswickCanada
                [ 6 ] Faculty of Computer ScienceDalhousie University Halifax Nova ScotiaCanada
                Author notes
                [*] [* ] Correspondence

                Nicholas W. Jeffery, Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, Canada.

                Email: nick.jeffery@ 123456dfo-mpo.gc.ca

                Author information
                http://orcid.org/0000-0003-4242-5712
                Article
                ECE32872
                10.1002/ece3.2872
                5395438
                28428843
                68056eb5-a4e0-474b-b060-e267404187e0
                © 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
                : 12 January 2017
                : 08 February 2017
                : 10 February 2017
                Page count
                Figures: 8, Tables: 3, Pages: 12, Words: 9620
                Funding
                Funded by: Natural Sciences and Engineering Research Council of Canada
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece32872
                April 2017
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.0.9 mode:remove_FC converted:18.04.2017

                Evolutionary Biology
                carcinus maenas,coi,european green crab,population structure,restriction‐site‐associated dna sequencing

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