Relaxation of Selective Constraint on the Ultra-Large Mitochondrial Genomes of Arcidae (Mollusca: Bivalvia)

The mitochondrial genomes(mitogenomes)are purportedly under selection for smaller size to improve their replica-tion and translation efficiency.However,the mitogenomes of Arcidae species are larger than those of other bivalves,and are among the largest metazoan mitogenomes reported to date.In order to explore the differences of base composition and selective constraints between the large and small mitogenomes,we compared the mitogenomes of 9 large arcid mitogenomes and 77 small bivalves mitogenomes.Base composition analyses indicated that Arcidae mitogenomes have significantly greater GC skews in both their whole genomes and coding sequences.This result suggests that the replication of the large mitogenomes in Arcidae may be slower than those in other bivalves,exposing the parental strand to deamination for a longer time.Selection pressure analyses showed that the mitochondrial protein-coding genes of Arcidae species have significantly higher Ka/Ks ratios than other bivalves,suggesting that they have accumulated more nonsynonymous nucleotide substitutions.Seven protein-coding genes(atp6,cox1-3,nad1,nad4 and nad5)show significant difference for Ka/Ks ratios between the Arcidae and non-Arcidae groups.However,these divergences are not observed in the nuclear gene within histone H3.From these observations,we concluded that the large mitoge-nomes of Arcidae species experienced more relaxed selective constraints.As some Arcidae species are more tolerant to hypoxia that can lead to low metabolic rate,the relaxed selective constraints of mitogenomes may be energy-related.This study provides new insights into the evolution of Arcidae mitogenomes.

Population dynamics and condition index of natural stock of blood cockle,Tegillarca granosa(Mollusca,Bivalvia,Arcidae)in the Marudu Bay,Malaysia

The population parameters of blood cockles,Tegillarca granosa in the intertidal zone of Marudu Bay,Sabah,Malaysia were investigated based on monthly length-weight frequency data(July 2017 to June 2018).A total of 279 cockle individuals with shell length and weight ranging from 27.7 mm to 82.2 mm and 13.11 g to 192.7 g were subjected to analysis.T.granosa in Marudu Bay showed a consistent moderately high condition index 4.98±0.86 throughout the year.The exponent b of the length-weight relationship was 2.6 demonstrating negative allometric growth.The estimated asymptotic length(L_(∞)),growth coefficient(K)and growth performance(Ф)of the T.granosa population in Marudu Bay were estimated at 86.68 mm,0.98 a^(-1) and 3.87,respectively.The observed maximum shell length was 82.55 mm and the predicted maximum shell length was 84.44 mm with estimated maximum life span(t_(max))of 3.06 years.The estimated mean lengths at the end of 2,4,6,8,10 and 12 months of age were 21.31 mm,31.16 mm,39.53 mm,46.63 mm,52.67 mm and 57.79 mm.Total,natural,and fishing mortalities were estimated at 2.39 a^(-1),1.32 a^(-1) and 1.07 a^(-1).The exploitation level(E)was 0.45.Results of the current study also demonstrated that T.granosa in the Marudu Bay has two major recruitment peaks;one in March and another in October.The exploitation level revealed that natural stock of T.granosa in the Marudu Bay was approaching the maximum exploitation level.If such trend continues or demand for T.granosa is increasing,coupled with no effective fisheries management in place,possibility of the T.granosa population in the Marudu Bay to collapse is likely to elevate.

Mitochondrial DNA Markers for PCR-Based Phylogenetic Analysis of Ark Shells

Arcidae species are commercially important bivalves in Japan and are commonly referred to as bloody ark due to their red blood. They have thick shells with distinct radiating ribs, and the numbers of these ribs are important morphological features for species discrimination. However, some Arcidae species are morphologically indistinguishable, with a similar number of the ribs in adults and deficient rib formation, particularly among juveniles. Thus, we developed a reliable molecular marker to genetically discriminate between 7 Arcidae species belonging to Scapharca, Anadara, and Tegillarca based on species-specific polymorphic segments of mitochondrial DNA. PCR amplification of partial COI, 16S rRNA, 12S rRNA, and Cyt b genes was performed on 7 species using 8 primer sets. Only the set of Scapharca-specific forward primer and universal reverse primer for the partial COI gene successfully yielded single PCR products from all 7 species examined. Thus, nucleotide sequences of 481 bp portion of these PCR products were determined, and the degrees of nucleotide substitutions ranged from 0.4% between S. broughtonii and T. granosa to 20.2% between S. satowi and A. antiquata. In addition, a phylogenetic tree showed significant differences between 7 species, with higher bootstrap support than 69.