Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa
Open accessAbstract
Transcriptome-enabled phylogenetic analyses have dramatically improved our understanding of metazoan phylogeny in recent years, although several important questions remain. The branching order near the base of the tree is one such outstanding issue. To address this question we assemble a novel data set comprised of 1,080 orthologous loci derived from 36 publicly available genomes and dissect the phylogenetic signal present in each individual partition. The size of this data set allows for a closer look at the potential biases and sources of non-phylogenetic signal. We assessed a range of measures for each data partition including information content, saturation, rate of evolution, long-branch score, and taxon occupancy and explored how each of these characteristics impacts phylogeny estimation. We then used these data to prepare a reduced set of partitions that fit an optimal set of criteria and are amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. All of our analyses support Ctenophora as the sister lineage to other Metazoa, although support for this relationship varies among analyses. We find no support for the traditional view uniting the ctenophores and Cnidaria (jellies, anemones, corals, and kin). We also examine phylogenetic placement of myriapods (centipedes and millipedes) and find it more sensitive to the type of analysis and data used. Our study provides a workflow for minimizing systematic bias in whole genome-based phylogenetic analyses.
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Another recent study including only data from published whole-genome sequences (46) found support for Ctenophora-sister, but support for this hypothesis became insignificant when the data were analyzed under a biologically more realistic, site-heterogeneous model.
“Beyond our results, another recent study including only data from published whole-genome sequences (46) found support for Ctenophora-sister, but support for this hypothesis became insignificant when the data were analyzed under a biologically more realistic, site-heterogeneous model.”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [46]
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Experimental — accuracy not yet measuredThe study assessed robustness of age estimates by running analyses under autocorrelated and uncorrelated relaxed molecular-clock models, three fossil calibration sets, three root age priors (800, 1000, 1360 Ma), and three alternative placements of Ctenophora.
“In order to assess the robustness of our age estimates to a number of prior assumptions, we ran analyses under (1) an autocorrelated and an uncorrelated relaxed molecular-clock model – the former assuming that the rate of molecular evolution of a lineage is correlated with the rate of its mother lineage, the latter allowing completely independent rates from lineage to lineage; (2) three different”
From Dating early animal evolution using phylogenomic data (2017) · cites this paper as [23]
The Results and discussion section ('Different classes of genes tell similar stories'; page unavailable) evaluates three possible placements of Ctenophora, but as phylogenetic hypotheses, not assumptions for estimating ages. The Methods sections on evolutionary rates and Bayesian analyses (pages unavailable) describe branch-length comparisons and CAT-GTR analyses; our copy does not report the claimed relaxed-clock models, fossil calibration sets, root-age priors, or robustness tests of age estimates. (LLM, conf=0.83)
Experimental — accuracy not yet measuredIn previous studies, Porifera-sister tended to be better supported by smaller, manually curated phylogenomic datasets, whereas datasets with many more genes assembled by automated procedures tended to support Ctenophora-sister.
“In previous studies, the Porifera-sister hypothesis has tended to be better supported by smaller, manually constructed and curatedphylogenomicdatasets[1-3],whereasdatasetsfeaturing many more genes and assembled using entirely automated procedures have tended to support Ctenophora-sister (e.g., [5-10]).”
From A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals (2017) · cites this paper as [9]
Disagreement mainly hinges on contradictory placements of ctenophores and sponges: either Porifera-sister or Ctenophora-sister.
“Disagreement mainly hinges on the contradictory phylogenetic placements of ctenophores and sponges in different phylogenomic studies: either with sponges branching first (''Porifera-sister'') and ctenophores grouping with cnidarians and bilaterians (consistent with the classical view of a single origin of neurons in the eumetazoan stem lineage) [1-4, 12], or instead with ctenophores as the first”
From A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals (2017) · cites this paper as [9]
Experimental — accuracy not yet measuredAnalyses of large-scale molecular superalignments have failed thus far to provide a widely accepted consensus for the branching order among the five major animal lineages.
“Analyses of large-scale molecular superalignments assembled from genomic or transcriptomic data have failed thus far to provide a widely accepted consensus for the branching order among the five major animal lineages, i.e., sponges, placozoans, ctenophores, cnidarians, and bilaterians [1-12].”
From A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals (2017) · cites this paper as [9]
While strong support for Ctenophora-sister may be obtained from phylogenomic datasets, our analysis suggests these results are caused by undetected systematic bias.
“Thus, while strong support for Ctenophora-sister may be obtained from phylogenomic datasets (2 -6, 46, 55), our analysis suggests these results are caused by undetected systematic bias.”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [46]
Amino acid recoding has long been considered a powerful strategy to reduce compositional heterogeneity and saturation in the data.
“Amino acid recoding has long been considered as a powerful strategy to reduce compositional heterogeneity and saturation in the data [7, 13-15, 31-36]”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [35]
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References 73 · Cited by 172
Research works printed but not linked: 1
- [50]Hyman L The invertebrates. I. Protozoa through Coelenterata 1940 New York McGraw-Hill
- Authors
- Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C.
- Affiliations
- University of California, Davis (US)
- American Museum of Natural History (US)
- University of New Hampshire (US)
- Corresponding author
- Borowiec, Marek L.
- Plachetzki, David C.
- Venue
- BMC Genomics
- Publisher
- openRxiv
- Published
- 2015-01-16
- Volume
- 16
- Issue
- 1
- Pages
- 987-987
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC4657218
- OpenAlex
- W2176014258
- Cited by
- 172
- References
- 73
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 9 · 2023: 11 · 2022: 11 · 2021: 19 · 2020: 14 · 2019: 18 · 2018: 26 · 2017: 19 · 2016: 24 · 2015: 12
- FWCI
- 20.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Science Foundation (1402432)
- Life Sciences Research Foundation
- Directorate for Biological Sciences (DEB-1402432)
- University of California, Davis
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
- Keywords
- Ctenophora, animals, metazoan phylogeny, sponge phylogeny, long-branch attraction, phylogenetic signal, orthologous loci
- MeSH terms
- Animals, Humans, Phylogeny, Bias, Evolution, Molecular, Genomics, Ctenophora, Genetic Loci, Data Mining
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