The Mitochondrial Genome of Phoronis architecta—Comparisons Demonstrate that Phoronids Are Lophotrochozoan Protostomes

Abstract

The proper reconstruction of the relationships among the animal phyla is central to interpreting patterns of animal evolution from the genomic level to the morphological level. This is true not only of the more speciose phyla but also of smaller groups. We report here the nearly complete DNA sequence of the mitochondrial genome of the phoronid Phoronis architecta, which has a gene arrangement remarkably similar to that of a protostome animal, the chiton Katharina tunicata. Evolutionary analysis of both gene arrangements and inferred amino acid sequences of these taxa, along with those of three brachiopods and other diverse animals, strongly supports the hypothesis that lophophorates are part of the large group that includes mollusks and annelids-i.e., the Lophotrochozoa-and solidly refutes the alternative of their being deuterostomes.

The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes

“…4) that robustly supports the Chaetognatha, represented here by P. gotoi, as the sister group to the protostomes included in this study. This result corroborates that of Nielsen et al (2) although their analysis placed the phoronids and brachiopods as deuterostomes, an untenable position given the results of independent molecular data sets (32,33). The shortest alternative tree that does not include a monophyletic grouping of protostomes and chaetognaths requires 32 extra steps and is rejected by the Templeton test (12) in favor of the shortest tree uniting the groups (n ϭ 116, z ϭ Ϫ2.9711, P ϭ 0.003).…”

Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

“…In contrast, a sister-group relationship of phoronids with inarticulate (linguliform) brachiopods was supported by the first analysis based on directly determined sequences from more than one specimen of each taxon (Cohen and Gawthrop 1996), and by a later analysis that included a freshly determined sequence from P. ijimai (Cohen 2000). The molecular affinity of both phoronids and brachiopods with protostomes has been less controversial, being supported by all SSU rDNA evidence and by additional molecular data from mitochondrial sequences and from other nuclear genes (Cohen et al 1998a;de Rosa et al 1999;Cohen 2000;Helfenbein 2000;Saito et al 2000;Helfenbein and Boore 2003;Ruiz-Trillo et al 2004). Although the (phoronid+brachiopod) clade has been questioned (Peterson and Eernisse 2001), existing evidence from SSU sequences supports the following conclusions: (1) both brachiopods and phoronids belong among the protostomes, their closest affinity being with molluscs and annelids; (2) no well-supported sistergroup relationship links brachiopods and phoronids with any other phylum; (3) brachiopods and phoronids form a generally well-supported clade, within which (4) a clade of (phoronids+inarticulate brachiopods) is moderately well supported; and (5) there is weak evidence for phoronids being the sister-group of craniiform inarticulate brachiopods.…”

The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)

“…However, these features vary sufficiently among lineages to provide useful characters for phylogenetic reconstruction. Such genome-level characters have proven to be especially robust indicators of evolutionary relatedness due to their complexity and low frequency of reversal (Helfenbein and Boore, 2004).…”