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

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.

河蚬属（Corbicula）包含原产于亚洲、非洲及澳大利亚温带/热带区域的河口或淡水双壳类，该类群涵盖有性生殖物种与克隆（雄核发育）谱系两类。其中克隆谱系已在全球淡水生态系统中成为入侵类群，属于最为成功的水生入侵谱系之一。既往研究已记录4种入侵克隆谱系，分别为A型、B型、C型与Rlc型，其分布范围各有不同。其中A型（欧洲地区称R型）在全球均有分布；B型仅见于北美，主要分布于美国西部；C型（欧洲地区称S型）既存在于欧洲流域，也见于南美洲；Rlc型则仅在欧洲有记录。近期在新大陆伊利诺伊河（五大湖流域）报道了一种疑似第五种入侵形态——D型，该类群与A型、B型同域分布。初始研究显示，D型在贝壳形态学上具有独特性：拥有锈色放射纹，珍珠层呈白色且齿部为紫色。不过，基于标准分子标记（线粒体细胞色素c氧化酶亚基I与核核糖体28S RNA）的分析并未明确其遗传分化程度。为解决这一问题，本研究通过下一代双酶切限制性位点关联DNA测序技术获取了1699至30027个核基因组位点，开展系统基因组学分析。结果证实，D型确实是一种独立的新大陆入侵谱系，其种群基因组特征符合克隆性。在9项系统基因组学分析中，有7项将4种新大陆入侵河蚬谱系（A型、B型、C型与D型）归入同一个克隆类群，该类群与日本琵琶湖特有种沙当河蚬（C. sandai）互为姐妹群。克隆类群的分化时间估算为149万年（置信区间：±0.401~2.955百万年），而4种入侵谱系冠群分支的分化时间估算范围为0.27~0.44百万年。本研究未在受试种群的4种入侵谱系间发现核基因渐渗迹象。与之相反，6份沙当河蚬样本中有2份在Structure聚类分析中显示出与多种入侵克隆谱系的部分核基因组组分。本研究结果为该复杂类群中克隆性的起源与维持机制提供了新的认识。