Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

Abstract

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, Corbicula 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 to 0.44 my. We recovered very little 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.

Keywords: Clonal; Corbicula; Form D; Genomics; Invasive; Lineage; ddRADseq.

Figure 1. Photographic plate of the four invasive New World Corbicula Forms (A) A, (B) B, (C) C, and (D) D and the sexually reproducing (E) Lake Biwa endemic C. sandai and (F) estuarine C. japonica specimens genotyped in this study.

Photos of Forms A, B, and D were taken by M. Jared Thomas and Danielle Ruffatto and Form C, C. sandai, and C. japonica by Taehwan Lee.

Figure 2. Map showing sampling locations for (A) invasive New World Corbicula Forms A, B, C, and D and (B) the sexually reproducing Lake Biwa endemic C. sandai and estuarine C. japonica specimens.

See Table S1 for sampling location details and number of individuals per site. Map was created using ArcMap v10.6.1 (Esri, Redlands, CA, USA).

Figure 3. Maximum likelihood phylogenomic tree depicting relationships among the four invasive New World Corbicula forms and the sexually reproducing C. sandai for the 2,245 locus 90% similarity threshold clustering across 75% of individuals.

Tree was rooted with two individuals of C. japonica. Values on tree nodes indicate maximum likelihood bootstrap/posterior probability supports/speciation event supports from mPTP/BEAST age estimates. * Denotes bootstrap and posterior probability supports of 100% and 1.00, respectively. Photos of Forms A, B, and D were taken by M. Jared Thomas and Danielle Ruffatto and Form C, C. sandai, and C. japonica by Taehwan Lee.

Figure 4. Structure bar graphs showing the most likely assignment of the 34 Corbicula individuals for (A) K = 2 and (B) K = 5, (C) Form A, (D) Form B, (E) Form C, (F) Form D, and (G) C. sandai based on ∆K (see Fig. S4).

Structure analyses used a single SNP per locus (totaling 2,175 SNPs) for each individual and each vertical bar represents an individual clam. Labels on Structure graphs indicate the sampling locations for each individual (see Table S1). In (B) * indicates Form C individual COR3–6 from Iguazu Falls. Photos of Forms A, B, and D were taken by M. Jared Thomas and Danielle Ruffatto and Form C, C. sandai, and C. japonica by Taehwan Lee.

Figure 5. Results from the discriminant analysis of principal components (DAPC; Jombart, Devillard & Balloux, 2010) for the four invasive Corbicula forms and the sexually reproducing C. sandai.

Individuals are represented as dots with 95% confidence intervals surrounding them. Clusters are color coded to match those recovered by the Structure analyses (Fig. 4).

Figure 6. Boxplots showing diversity values for each of the invasive New World Corbicula forms and C. sandai.

(A) Observed and (B) expected heterozygosity and (C) the inbreeding coefficient (F_IS). Lowercase letters above the boxes indicate results from the Tukey’s test.