Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data

Abstract

Cryptic species have been increasingly revealed in the marine realm through an analytical approach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes and morphology). Illustrations of cryptic taxa improve our understanding of species diversity and evolutionary histories within marine animals. The pen shell Atrina pectinata is known to exhibit extensive morphological variations that may harbour cryptic diversity. In this study, we investigated A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial (cytochrome c oxidase subunit I, mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well as morphology. Phylogenetic analyses of mtCOI 'DNA barcoding gene' sequences resolved six divergent lineages with intralineage divergences between 0.4% and 0.8%. Interlineage sequence differences ranged from 4.3% to 22.0%, suggesting that six candidate cryptic species are present. The nrITS gene revealed five deep lineages with Kimura 2-parameter distances of 3.7-30.3%. The five nuclear lineages generally corresponded to mtCOI lineages 1-4 and (5+6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences of significant variance were found within an individual, clearly implying recent hybridization events between/among the evolutionary lineages, which contributed to cytonuclear discordance. Morphologically, five morphotypes matched the five genetic lineages, although the intermediates may well blur the boundaries of different morphotypes. This study demonstrates the importance of combining multiple lines of evidence to explore species cryptic diversity and past evolutionary histories.

Causations of phylogeographic barrier of some rocky shore species along the Chinese coastline

“…We combined new sequences with previously published sequences from the Chinese coast to construct a database of mitochondrial and nuclear DNA from four species, including three rocky-shore species (limpet Siphonaria japonica , limpet C. toreuma [20], macroalga S. horneri [36]) and one muddy-shore species (bivalve Atrina pectinata [37]). These species possess different habitat preferences, reproductive seasons and breeding modes (See Table 1, [37–40]), which provide insights into the responses of intertidal and subtidal species to multi-factors.…”

Survival time of juvenile pen shell Atrina pectinata (Bivalvia: Pinnidae) in hyposaline water

“…The orthodox species name at present for these pen shells is unclear owing to the taxonomic confusion of Atrina (Lemer et al 2014). Yet, these pen shells all have been confirmed to be identical to ''Atrina pectinata Lineage 2'' (sensu Liu et al 2011) by the analyses of the mtDNA COI region (Hashimoto, personal data). Therefore, we provisionally call our material ''Atrina pectinata Lineage 2'' or ''Atrina pectinata''.…”

Mitochondrial phylogeography of a surf clam Mactra veneriformis in the East China Sea: Genetic homogeneity across two biogeographic boundaries

“…Mutation rates used in former molluscan studies, ranging from 0.35 to 1.2% per million years (myr À1 ), were usually estimated from deep splits of interspecific phylogeny (e.g. Hellberg and Vacquier, 1999;Marko, 2002;Lessios, 2008;Liu et al, 2011b). This approach however was recently questioned because more evidence showed that transient mutations accumulated in populations more quickly than that fixed in phylogenetic divergences, known as the 'time-dependent mutation rate' hypothesis (Ho et al, 2005).…”

“…Marine species, especially coastal invertebrates experiencing a direct loss of habitat, were forced to migrate into the basin (Liu et al, 2007;Ni et al, 2012). Different populations got chances to mix together and formed a panmictic population there (Liu et al, 2011b). After the LGM, the survived biota might migrate out and quickly repopulate along the coastline following the flooding (Liu et al, 2007).…”