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Phylogenomics Data Tweaks Tree of Life

NEW YORK (GenomeWeb News) – New phylogenomic research is shaking the tree of life, suggesting new relationships between creatures and challenging long-held assumptions about animals at its base.

An international team of researchers compared data from 150 genes for animals in almost 80 taxa, creating expressed sequence tags for dozens of animals for which genetic data was lacking. The findings, published in Nature’s advanced online edition yesterday, have led to a reorganization of some branches on the tree of life. Most notably, they indicate that comb jellyfish actually diverged earlier than the sponge, a seemingly less complicated organism.

“What is exciting is that this new information changes our basic understanding about the natural world — information found in basic biology books and natural history posters,” lead author Casey Dunn, who is currently an ecologist and evolutionary biologist at Brown University, said in a statement. “While the tree of life is far from complete after this study, it is clearer.”

Although researchers have been fiddling with the tree of life for almost 150 years, since Darwin’s The Origin of Species, there are still unanswered questions.

Genetic information has produced some revisions to the tree of life. Even so, the authors point out, genomic data or expressed sequence tag data has been unavailable for many species. And some previous analyses were based on small data sets or ribosomal proteins.

For this paper, the researchers focused on creatures belonging to some of the earliest tree of life branches such as mollusks, various worms, comb jellies, and centipedes. Dunn and his colleagues evaluated a matrix from 77 taxa and 150 genes using maximum likelihood and Bayesian analyses. They also analyzed a 64-taxon matrix that excluded so-called unstable taxa, which are only included in a particular clade part of the time.

To create these matrices, the team assembled cDNA libraries for 29 species for which genomic or EST data was unavailable. This expressed sequence tag data — representing nearly 40 million bases — was analyzed in conjunction with other available sequence data.

The results confirmed some previously divined relationships. But it challenges others. For example, the results cast doubt on the inclusion of millipedes and centipedes near insects. Instead, the authors suggest that they are more closely related to spiders.

The data also argues against sponges being the oldest living multicellular creature. Phylogenomic data suggests comb jellyfish, not sponges, should occupy that position. That was particularly surprising since comb jellyfish have specialized tissues while sponges do not.

“The placement of ctenophores (comb jellies) as the sister group to all other sampled metazoans is strongly supported in all our analyses,” the authors wrote. “If corroborated by further analyses, it would have major implications for early animal evolution, indicating either that sponges have been greatly simplified or that the complex morphology of ctenophores has arisen independently from that of metazoans.”

There are likely more changes in store for the tree of life, though, as researchers continue fleshing out phylogenomic relationships. “[T]hese new results show that these new genomic approaches will be able to resolve at least some problems that have been previously intractable,” Dunn said.

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