Bayesian Phylogenetic Analysis Supports Monophyly of Ambulacraria and of Cyclostomes

Abstract

Vertebrates are part of the phylum Chordata, itself part of a three-phylum group known as the deuterostomes. Despite extensive phylogenetic analysis of the deuterostome animals, several unresolved relationships remain. These include the relationship between the three deuterostome phyla (chordates, echinoderms and hemichordates), and the monophyletic or paraphyletic origin of the cyclostomes (hagfish and lampreys). Using robust Bayesian statistical analysis of 18S ribosomal DNA, mitochondrial genes and nuclear protein-coding DNA, we find strong support for a hemichordate-echinoderm clade, and for monophyly of the cyclostomes.

Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii

“…1b) (Furlong & Holland, 2002;Kuraku et al, 1999;Mallatt & Sullivan, 1998;Stock & Whitt, 1992), with few dissenting voices (Gürsoy et al, 2000;Rasmussen et al, 1998). Hence, in this paper we interpret our data in the light of either possible phylogenetic hypothesis.…”

“…Molecular phylogenies tend to support the monophyletic status of a hagfish/lamprey clade (Forey & Janvier, 1993;Delabre et al, 2002;Furlong & Holland, 2002;Takezaki et al, 2003), however. Either phylogenetic hypothesis together with the Quartet Mapping data and the previously published results for lamprey (Fried et al, 2003) have two implications.…”

Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes

“…The fact that model-based analyses of molecular data sets support cyclostome monophyly (Fig. 5A, Furlong and Holland, 2002;Delsuc et al, 2006;Mallatt and Winchell, 2007), and cyclostome monophyly is supported with high bootstrap pseudoreplicate scores or significant Bayesian posterior probabilities in these molecular phylogenies is not evidence that these data sets are immune to systematic error. The suspicions of a long-branch bias affecting the analysis of craniate relationships using the available molecular data extend beyond the obvious long terminal branches in the phylogeny (Fig.…”

“…Molecular phylogenetic investigations of crainiate relationships were initiated in the early 1990s, and essentially all published analyses using DNA or amino acid sequences have resulted in a monophyletic Cyclostomata with high bootstrap and significant Bayesian posterior support. The types of genes used to investigate cyclostome phylogeny have included nuclear-encoded rRNA genes (Stock and Whitt, '92;Lipscomb et al, '98;Mallatt and Sullivan, '98;Mallatt et al, 2001;Mallatt and Winchell, 2007), DNA sequences from single copy nuclear genes (Kuraku et al, '99;Furlong and Holland, 2002), hemoglobin amino acid sequences (Lanfranchi et al,'94), concatenated amino acid sequences from singe copy nuclear genes (Hedges, 2001;Takezaki et al, 2003;Blair and Hedges, 2005;Delsuc et al, 2006;Kuraku and Kuratani, 2006;Yu et al, 2008), and whole mtDNA genomes (Delarbre et al, 2002).…”

Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish Scyliorhinus canicula defines ancient and derived roles for fox genes in vertebrate development

“…These studies show that the two vertebrate Fox clusters arose by means of en bloc duplication from a single cluster and that this duplication occurred after the divergence of vertebrates and amphioxus, but before the radiation of osteichthyes. Two further vertebrate lineages diverged between these two nodes; the agnathans (lampreys and hagfish) and the chondrichthyes (sharks, rays, and relatives; Furlong and Holland, 2002). The timing of cluster duplication relative to the divergence of these lineages is currently unknown.…”