Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis

Abstract

The phylogenetic relationship of living Thai Donacidae was herein studied. Two methodologies, geometric morphometrics (GM) and genetic analysis of COI sequences, were combined and applied to identify the valid taxa and explain biodiversity and the distribution pattern in this family. A total of 587 living specimens were tested to analyze the shape and size patterns by Elliptic Fourier Analysis (EFA). Shell identification and GenBank sequences were added to construct the phylogenetic relationship and haplotype network. Centroid size was used to identify the specimens to the subgenus level. Donax (Hecuba) scortum, was easily distinguished from other species by Principal Component analysis (PCA) of shell size and shape. Donax (Dentilatona) incarnatus and Donax (Deltachion) semisulcatus semisulcatus were identified using Canonical Variates Analysis (CVA). Pairwise comparison of EFA was used for species level recognition, particularly shape overlap was observed for medium and small shell size. Based on genetic distance and haplotype network of COI sequences, Donax (Latona) faba and D. (Latona) solidus could be grouped in the same clade. Intraspecific and interspecific genetic data variation of some common species in different geographical localities of Thailand was observed. Three distribution patterns of Donax species were observed along the two-marine system of Thailand.

Keywords: Bivalve; COI; Donax; Elliptic Fourier shape analysis; Thailand.

Fig. 1.

The relative distribution (%) of eight Donax species along the coastline show the sampling location and the distribution pattern.

Fig. 2.

60 Outline digitized landmarks along the inner edge of left valve. Scale bar = 5 mm.

Fig. 3.

Box-plot Mean and SE of Size Frequency, Kruskal-Wallis test, non-parametric ANOVA, of eight Donacid valid species. 1: Donax (Latona) cuneatus; 2: D. (Latona) solidus; 3: D. (Latona) faba; 4: D. (Dentilatona) incarnatus; 5: D. (Deltachion) spinosus; 6: D. (Deltachion) bruneirufi; 7: D. (Deltachion) semisulcatus semisulcatus; 8: D. (Hecuba) scortum. Double asterisks (**) highly significant at p ≤ 0.01. In square box means centroid size in group is not significantly different at p > 0.05 under Mann-Whitney pairwise comparisons.

Fig. 4.

Mean outline shape constructed from 10 harmonics of elliptic Fourier analysis of eight Donax species from Thai waters: Donax (Latona) cuneatus (A), D. (Latona) solidus (B), D. (Latona) faba (C), D. (Deltachion) spinosus (D), D. (Dentilatona) incarnatus (E), D. (Deltachion) bruneirufi (F), D. (Deltachion) semisulcatus semisulcatus (G) and D. (Hecuba) scortum (H).

Fig. 5.

Plot graph of PCA scores of EF coefficient, circle represent 95 percent confidence ellipses.

Fig. 6.

Scatterplot of shape, represent by PC I score (y-axis) per centroid size (x-axis) of eight Donax species.

Fig. 7.

CVA of EFA coefficients and mean shape outline from seven species under same group. Within each species, the specimen is enclosed by a convex hull polygon. Separation on the first two canonical analysis axes.

Fig. 8.

CVA of EFA coefficients and mean shape outline from three overlapping species from subgenus Latona, large size species group. Within each species, the specimens are enclosed by a convex hull polygon.

Fig. 9.

Frequency distribution of Discriminant analysis of subgenus Latona by two population comparison. Donax (Latona) faba and D. (Latona) solidus (A); D. (Latona) faba and D. (Latona) cuneatus (B); D. (Latona) solidus and D. (Latona) cuneatus (C).

Fig. 10.

CVA of EFA coefficients and mean shape outline from three overlapping species of subgenus Deltachion, small size group. Within each species, the specimen is enclosed by a convex hull polygon.

Fig. 11.

Frequency distribution of Discriminant analysis of two overlapping populations, Donax (Deltachion) bruneirufi (grey) and D. (Deltachion) spinosus (white).

Fig. 12.

Outline overlain, size-normalized average outline of each two species in discriminant analysis; Donax (Latona) solidus (white) and D. (Latona) cuneatus (grey) (A); D. (Latona) solidus (white) and D. (Latona) faba (grey area) (B); D. (Latona) cuneatus (white area) and Donax (Latona) faba (grey area) (C); D. (Deltachion) bruneirufi (white) and D. (Deltachion) spinosus (grey) (D). Arrows highlight distinct position from overlain shape of white area species extend from grey area species.

Fig. 13.

Phylogenetic analysis based on genetic sequence derived from cytochrome oxidase I (COI) gene of Donax spp. and other related species using the maximum likelihood (ML) method. The bootstrap values were calculated with 1000 replicates.

Fig. 14.

The haplotype network analysis of six species based on COI sequences were constructed in shell morphology picture. Scale in 1 to 10 samples of available localities. The nucleotide diversity was calculated at 0.117006 and Number of segregating sites at 215. Number in parenthesis represents nucleotide substitution difference (A); Colour illustrations of collected Thai Donax species for molecular analysis of cytochrome c oxidase subunit I. Scale bar: B = 1 cm.