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Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets.

ABSTRACT: There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].

SUBMITTER: Neumann JS

PROVIDER: S-EPMC7875439 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets.

Neumann Johannes S JS Desalle Rob R Narechania Apurva A Schierwater Bernd B Tessler Michael M

Systematic biology 20210201 2

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 c ...[more]

PMID: 32462193

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Project description:The construction of morphological character matrices is central to paleontological systematic study, which extracts paleontological information from fossils. Although the word information has been repeatedly mentioned in a wide array of paleontological systematic studies, its meaning has rarely been clarified nor specifically defined. It is important, however, to establish a standard to measure paleontological information because fossils are hardly complete, rendering the recognition of homologous and homoplastic structures difficult. Here, based on information theory, we show the deep connections between paleontological systematic study and communication system engineering. Information is defined as the decrease of uncertainty and it is the information in morphological characters that allows distinguishing operational taxonomic units (OTUs) and reconstructing evolutionary history. We propose that concepts in communication system engineering such as source coding and channel coding, correspond to the construction of diagnostic features and the entire character matrices in paleontological studies. The two coding strategies should be distinguished following typical communication system engineering, because they serve dual purposes. With character matrices from six different vertebrate groups, we analyzed their information properties including source entropy, mutual information, and channel capacity. Estimation of channel capacity shows character saturation of all matrices in transmitting paleontological information, indicating that, due to the presence of noise, oversampling characters not only increases the burden in character scoring, but also may decrease quality of matrices. We further test the use of information entropy, which measures how informative a variable is, as a character weighting criterion in parsimony-based systematic studies. The results show high consistency with existing knowledge with both good resolution and interpretability.

Dataset Information

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets.

Publications

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets.

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