Figure A.1 Mtcytb Maximum Likelihood (ML) Tree for 31Lamellibrachiawith a Fragment Size

Figure A.1 mtCYTB maximum likelihood (ML) tree for 31Lamellibrachiawith a fragment size of 380bp.All Lamellibrachiasequences are new and Escarpia laminata is the outgroup taxon. GenBank accession numbers follow the species name. Bootstrap support (1000 replicates, Tamura-Nei model) is located either above or below the node. Scale is measured as number of substitutions per nucleotide site.

Figure A.2 HbB2i maximum likelihood (ML) tree for 30Lamellibrachiawith a fragment size of 668bp. All Lamellibrachiasequences are newly isolated and Escarpia laminata is the outgroup taxon. GenBank accession numbers follow the species name. Bootstrap support (1000 replicates, Tamura-Nei model) is located either above or below the node. Two haplotypes for four heterozygous individuals are denoted by (A) and (B); addition of these haplotypes result in 34 sequences present for analysis. Scale is measured as number of substitutions per nucleotide site.

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Table A.1Average between group pairwise distances(p) between Lamellibrachiaand Escarpia (outgroup) for mitochondrial Cytochrome B (CYTB) and Hemoglobin subunit B2 intron (HbB2i). Analyses were conducted using the p-distance modelat 1000 bootstrap replicatesimplemented in MEGA 5.05 (Tamura et al., 2011). P distances shown below the diagonal andstandard error estimates are shown above the diagonal.

Table A.2 Primers used in this study

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Table A.3 Summarystatistics forTajima’s D test of neutrality organized by gene and species. S is number of sites with substitutions; Pi is the mean number of pairwise differences. Distance method used is pairwise difference withno Gamma correction and indels not taken into account.

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Table A.4Null allele frequencies for all loci usedin three Lamellibrachia taxafrom the Gulf of Mexico. NA refers to the number of alleles, NFrefers to thenull allele frequency and SE refers to the standard error. The Individual Inbreeding Model (IIM) was implemented in INEst v1.0 (Chybicki and Burczyk, 2009)

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Table A.5 Pairwise genetic differentiation matrix between the Lamellibrachia species that are significantly different at p = 0.001.FST values (below diagonal) and Jost’s D (above diagonal)were calculated in GenoDive (Meirmans and Hedrick, 2011). FST measures the differences in the numbers of heterozygotes between subpopulations, while Jost’s D quantifies genetic diversity in terms of effective number of alleles (Jost, 2008, Ryman and Leimar, 2009). Calculations of both metrics show similar patterns of differentiation between groups.

Table A. 6Lamellibrachia individuals used in the present study collected from sitesbelow 1000m in the Gulf of Mexico. Only a single aggregation of vestimentiferans was collected during each dive. In some cases both taxa were collected from the same aggregation.

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