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Abstract
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
Highlights
For over a decade, molecular phylogeneticists have enjoyed the use of automated methods to use shotgun DNA sequencing data to decipher the deepest relationships in the animal tree of life [1,2]
This paradigm has continued the disruptive tradition of molecular phylogenetics, allowing the placement of taxa whose morphology and embryology have proven uninformative or misleading in this regard, and demonstrating that early animal evolution resulted in considerably more flexibility in phenotypic evolution than initially expected [3,4,5]
Highly parallel short-read sequencing has essentially overtaken Sanger and competing second-generation sequencing technologies, there is still a dearth of genomic data from several phyla (e.g. Bryozoa, Loricifera, Kinorhyncha and Nematomorpha), and it has been a decade since the last major synoptic attempt to infer the relationships among all animal groups [2], despite exemplary recent analyses focused on specific clades [17,18]
Summary
Molecular phylogeneticists have enjoyed the use of automated methods to use shotgun DNA sequencing data to decipher the deepest relationships in the animal tree of life [1,2]. Highly parallel short-read sequencing has essentially overtaken Sanger and competing second-generation sequencing technologies, there is still a dearth of genomic data from several phyla (e.g. Bryozoa, Loricifera, Kinorhyncha and Nematomorpha), and it has been a decade since the last major synoptic attempt to infer the relationships among all animal groups [2], despite exemplary recent analyses focused on specific clades [17,18]. It seems there has not yet been an attempt to investigate the animal tree of life using genome-scale data from representatives of all metazoan phyla. Collating a mixture of published ( prior to 2018) and new transcriptome and genome data sequenced largely with Illumina technology, and employing numerous strategies to control the influence of systematic error [19] and to build both general and taxonspecific matrices from a single orthology assignment, we empirically review the signals for and robustness of most animal clades recognized in the recent era
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