Williams S T, Foster P G, Hughes C, Harper E M, Taylor J D, Littlewood D T J, Dyal P, Hopkins K P, Briscoe A G
Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
Mol Phylogenet Evol. 2017 May;110:60-72. doi: 10.1016/j.ympev.2017.03.004. Epub 2017 Mar 6.
Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent lineages were missing from these analyses and increased representation of these groups may yet improve resolution. Here, we add seven new sequences from the Anomalodesmata and one unidentified semelid species (Bryopa lata, Euciroa cf. queenslandica, Laternula elliptica, Laternula truncata, Lyonsia norwegica, Myadora brevis, Tropidomya abbreviata, "Abra" sp.). We show that relationships in a mitogenomic tree for the Class are improved by the addition of seven anomalodesmatans from this highly divergent clade, but are still not completely consistent with relationships recovered in studies of nuclear genes. We suggest that some anomalous relationships (for instance the non-monophyly of Bivalvia) may be partially explained by compositional heterogeneity in the mitogenome and suggest that the addition of more taxa may help resolve both this effect and possible instances of long branch attraction. We also identify several curious features about anomalodesmatan mitogenomes. For example, many protein-coding gene boundaries are poorly defined in marine bivalves, but particularly so in anomalodesmatans, primarily due to non-conserved boundary sequences. The use of transcriptomic and genomic data together enabled better definition of gene boundaries, the identification of possible pseudogenes and suggests that most genes are translated monocistronically, which contrasts with many other studies. We also identified a possible case of gene duplication of ND5 in Myadora brevis (Myochamidae). Mitogenome size in the Anomalodesmata ranges from very small compact molecules, with the smallest for Laternula elliptica (Laternulidae) only 14,622bp, to Bryopa lata (Clavagellidae) which is at least 31,969bp long and may be >40,000bp. Finally, sampled species show a high degree of sequence divergence and variable gene order, although intraspecific variation in Laternula elliptica is very low.
过去，双壳纲的有丝分裂基因组树一直存在问题，但这些分析遗漏了几个高度分化的谱系，增加这些类群的代表性可能会提高分辨率。在这里，我们添加了来自异齿亚纲的七个新序列和一个未鉴定的短齿蛤科物种（宽唇异齿蛤、昆士兰真异齿蛤、椭圆海螂、截形海螂、挪威小海螂、短肌蛤、短缩偏顶蛤、“阿布拉”属物种）。我们表明，通过添加来自这个高度分化分支的七个异齿亚纲物种，该纲有丝分裂基因组树中的关系得到了改善，但仍与核基因研究中恢复的关系不完全一致。我们认为，一些异常关系（例如双壳纲的非单系性）可能部分是由有丝分裂基因组中的组成异质性解释的，并表明添加更多分类单元可能有助于解决这种影响以及可能的长枝吸引情况。我们还确定了异齿亚纲有丝分裂基因组的几个奇特特征。例如，许多蛋白质编码基因的边界在海洋双壳类中定义不明确，但在异齿亚纲中尤其如此，主要是由于边界序列不保守。转录组和基因组数据的联合使用能够更好地定义基因边界，识别可能的假基因，并表明大多数基因是单顺反子翻译的，这与许多其他研究形成对比。我们还在短肌蛤（短肌蛤科）中发现了一个可能的ND5基因重复案例。异齿亚纲的有丝分裂基因组大小范围从非常小的紧凑分子，椭圆海螂（海螂科）最小，只有14,622bp，到宽唇异齿蛤（棒蛤科），至少长31,969bp，可能大于40,000bp。最后，尽管椭圆海螂的种内变异非常低，但采样物种显示出高度的序列分歧和可变的基因顺序。
