Molecular Systematics Of Veneridae (Bivalvia, Mollusca)

The Veneridae (Rafinesque,1815), known as venus clams, is the most richly speciosefamily of heterodont bivalve mollusks. This family includes more than800extant speciesgrouped into about14subfamilies. Many species of Veneridae are economically importantand ecologically crucial due to their huge abundance in benthic environments. However,Because of great diversity and the lack of systematic studies, venus clams have a confusingtaxonomic history and their relationships remain poorly understood. Besides, due toparallelism of interspecific morphological variability and pronounced intraspecificecophenotypes, the intra-and interspecific phenotypic variability of many venerids areindistinct or even overlapping. Therefore, species boundaries of these clams are difficult oreven impossible to define accurately based solely on morphological features.Molecular systematics is considered a robust test of evolutionary relationships recentlyand there have been a number of attempts to address venerid systematics using molecular data.Nevertheless, most of those efforts only included few venerid species and only used a singlemarker. Therefore, there are many pending problems about venerid systematics, from speciesto family level, to resolve. To further resolve the problems about evolutionary relationshipsand taxonomic system of the family Veneridae, especially within Chinese venerid fauna, anupdated molecular systematics of venus clams is presented herein.First, DNA sequence information from fragments of two mitochondrial genes (COI and16S) and one nuclear protein-coding gene (H3) for135taxa (128venerids, five nonveneridveneroids and two other outgroups) were used to reconstruct the phylogenetic relationships ofvenus clams. The best-fit model of nucleotide substitution models were tested in jModeltestand MrModeltest. Phylogenetic analyses were inferred using maximum parsimony, maximumlikelihood and Bayesian approaches. According to the molecular results, Taxa of thetraditional family Veneridae divided into two major clades and is not recovered asmonophyletic. Besides, most of the nominal subfamilies and genera formed para-polyphyleticclades. The classification of taxa along the coast China are revised based on theirphylogenetic position. The synonymization of chionine genus Placamen with Clausinella isrejected. Chionine subgenera Anomalodiscus and Cryptonema are given full generic rankagain and incorporated into Venerinae and Tapetinae, respectively. The results also evidence that the synonymization of the genus Tigammona and Periglypta is inappropriate.Second, a total of315specimens of around60venerid species sampled along the coastof China were used to explore species diversity under DNA barcoding approach. Geneticdistances were calculated using the Kimura2-parameter model in MEGA, and then COIsequences were grouped into provisional clusters as MOTUs in TaxonDNA. Aneighbor-joining tree was reconstructed for the complete dataset and to infer the systematicrelationships among species of certain groups more effectively, the maximum likelihoodapproach was applied using PhyML. Nearly all individuals identified to species level based onmorphological traits possessed distinct barcode clusters, except for the specimens of onespecies pair, Phacosoma biscoticum and P. fibulum. Among the26individuals that were notassigned binomial names a priori, twelve respectively nested within a species genealogy. Theremaining individuals formed five monophyletic clusters that potentially represent speciesnew to science or at least unreported in China. Five putative hidden species were alsouncovered. The present study shows that DNA barcoding is effective in species delimitationand can aid taxonomists by indicating useful diagnostic morphological traits, informingneedful revision, and flagging unseen species.Finally, subgenus Protapes in seas of the south China were used as a case study toillustrate how multi-locus genes and increasing samples confirm the species status of crypticspecies uncovered in barcoding study and how these evidences provide us more insights. Sixgene sequences COI,16S, H3,18S,28S, and ITS1were used herein. Barcodes were groupedinto provisional clusters as MOTUs. These MOTUs were treated as potential species andthese species candidates were tested iteratively in both distance-based and phylogeny-basedapproaches. The results showed that the two species candidates within Paphia (Protapes)gallus uncovered in barcoding study are real biological species, and two hidden species existwithin P.(P.) sinuosa. In addition, the clade of P.(P.) sinuosa complex occupied the basalposition in the phylogenetic trees, indicating this lineage is more ancient than P.(P.) galluscomplex. The results double the number of Protapes living species in the western Pacific,suggesting we might have only scratched the surface of Protapes biodiversity in this region.The present study shows that the approach, combining DNA barcoding with subsequentmultiple-line analyses, is effective in biodiversity exploration.