Table 1.
Alignment details.
Figure 1.
Phylogenetic Representativeness.
A, Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD) computed for the sample used for this study. AvTD is plotted on left axis: the circle represents the value obtained from the present sample, whereas continuous lines indicate the lower 95% confidence limit, the maximum value for that sample dimension (thick lines), and the mean AvTD (thin line). VarTD is plotted on the right axis: the diamond represents the value obtained from the present sample, whereas dotted lines indicate the minimum value for that sample dimension, the upper 95% confidence limit (thick lines), and the mean VarTD (thin line). B, shuffling test with 100 randomly shuffled master lists (see text for details). Mean VarTD (thin dotted lines), upper 95% VarTD confidence limit (upper thick dotted lines), lower 95% AvTD confidence limit (lower thick continue lines), and mean AvTD (thin continue lines) are shown as the 95% confidence intervals across the replicates. Axes, circle, and diamond as above.
Figure 2.
Uncorrected (“p-”) distances plotted on Maximum Likelihood distances to estimate saturation in our dataset for each of six partitions separately. See text for details on partition names. Units of x-axis in substitutions/position. Linear interpolation is also shown, whose details are listed in Table S1.
Figure 3.
Each analysis was performed on 1,000 random quartets; the left simplex shows point distribution; the central one the subdivision among the three corners; the right one the subdivision among Voronoi cells [96], [115]. A, Likelihood Mapping for the concatenated alignment without grouping. B, Likelihood Mapping for the concatenated alignment with Opponobranchia excluded and remaining taxa subdivided into Palaeoheterodonta (a), Anomalodesmata (b), Heterodonta (c), and Pteriomorphia (d). The three possible topologies are shown at vertices.
Figure 4.
Neighbornet network based on LogDet distances.
Figure 5.
Shown is p14 tree, computed partitioning our dataset into ribosomal and protein coding genes; these were analyzed using the M3 codon model (see text for details). Values at the nodes are Posterior Probabilities (PP); nodes were collapsed if PP<0.95. Color code as follows: violet, Opponobranchia; blue, Palaeoheterodonta; brown, Anomalodesmata; green, Heterodonta; red, Pteriomorphia. Astartoidea and Carditoidea, previously classified as heterodonts and included hereafter among pteriomorphians, are shown in orange and marked with asterisks.
Table 2.
Results of Akaike Information Criterion test.
Figure 6.
Bivalve major morphological characters.
Optimization of six major morphological characters on bivalve phylogeny as retrieved in this work. Each tree shows the parsimony reconstruction of ancestral state given the p14 topology and a matrix of morphological characters compiled following [13] and [19]; see text for more detail. A, gill grade; B, hinge; C, gill cilia; D, stomach type; E, labial palps; F, shell microstructure.
Figure 7.
Revision of bivalve phylogeny and systematics.
The evolutionary tree was sketched as outlined in this paper (see text for details). Superfamilial relationships are shown, with proposed ordinal classification; for anomalodesmatans, we used the nomenclature from Newell [13] and Vokes [63]. Color code as in Figure 5. Asterisks mark newly-proposed ordinal categories; Neoheterodontei sensu [31] and Amarsipobranchia (comprising subclasses Anomalodesmata, Heterodonta, and Pteriomorphia) are also shown.