DOI: 10.5061/dryad.4395r55
title: Data from: Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

description: The genus Corbicula consists of estuarine or freshwater clams native to
 temperate/tropical regions of Asia, Africa, and Australia that
 collectively encompass both sexual species and clonal (androgenetic)
 lineages. The latter have become globally invasive in freshwater systems
 and they represent some of the most successful aquatic invasive lineages.
 Previous studies have documented four invasive clonal lineages, Forms A,
 B, C, and Rlc, with varying known distributions. Form A (R in Europe)
 occurs globally, Form B is found solely in North America, mainly the
 western United States, Form C (S in Europe) occurs both in European
 watersheds and in South America, and Rlc is known from Europe. A putative
 fifth invasive morph, Form D, was recently described in the New World from
 the Illinois River (Great Lakes watershed), where it occurs in sympatry
 with Forms A and B. An initial study showed Form D to be conchologically
 distinct: possessing rust-colored rays and white nacre with purple teeth.
 However, its genetic distinctiveness using standard molecular markers
 (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S
 RNA) was ambiguous. To resolve this issue, we performed a phylogenomic
 analysis using 1,699-30,027 nuclear genomic loci collected via the next
 generation double digested restriction-site associated DNA sequencing
 method. Our results confirmed Form D to be a distinct invasive New World
 lineage with a population genomic profile consistent with clonality. A
 majority (7/9) of the phylogenomic analyses recovered the four New World
 invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal
 clade, sister to the non-clonal Lake Biwa (Japan) endemic, C. sandai. The
 age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–
 2.955 my) whereas the estimated ages of the four invasive lineage crown
 clades ranged from 0.27-0.44 my. We recovered no evidence of nuclear
 genomic admixture among the four invasive lineages in our study
 populations. In contrast, 2/6 C. sandai individuals displayed partial
 nuclear genomic Structure assignments with multiple invasive clonal
 lineages. These results provide new insights into the origin and
 maintenance of clonality in this complex system.
description: ipyrad Parameter
 filesFile includes the ipyrad
 parameter specifications used to process the Illumina sequencing reads of
 Corbicula individuals for the 85, 90, and 95% similarity thresholds and
 across 75, 50, and 25% taxon coverages.Haponski-OFoighil-Corbicula-ipyrad-parameter-files.zipRAxML matricesFile contains the data matrices used to construct the phylogenomic trees in RAxML. Files are labeled with their corresponding similarity threshold (85, 90, or 95%) and taxon coverage (25, 50, or 75%). We also include the matrices used to re-run (rr) analyses where individuals were dropped (id). See Results section for further details.Haponski-OFoighil-Corbicula-RAxML-matrices.zipMrBayes matrixFile contains the data matrix used to construct the Bayesian phylogenomic tree in MrBayes for the 90% similarity threshold with 75% of taxa included.Haponski-OFoighil-Corbicula-MrBayes-matrix.zipmPTP AnalysisFile contains the 90% similarity threshold with 75% taxon coverage .fasta alignment file and the maximum likelihood tree from RAxML used to construct the mPTP tree.Haponski-OFoighil-Corbicula-mPTP.zipBEAST input90% similarity threshold with 75% taxon coverage .nex data matrix used to estimate Corbicula lineage divergence times in BEAST.Haponski-OFoighil-corbicula-90-75-sSNP-BEAST-input.nexStructure matricesFile contains all Structure input files for analyses across 34 Corbicula individuals, each of the invasive Forms, and for C. sandai. Files were created using the 90% similarity threshold including 75% of individuals dataset.Haponski-OFoighil-Corbicula-Structure-matrices.zipDAPC inputGenepop formatted file of the 90% similarity threshold with 75% of taxa used as input to the Discriminant analysis of Principal Components (DAPC).cor-90-75-AATTC-sSNP-genepop.genSingle SNP VCF file90% similarity threshold with 75% of individuals single SNP (sSNP) file used to generate the input matrices for Structure, BEAST, and DAPC.cor-90-75-AATTC-sSNP.vcf