Assessing the root of bilaterian animals with scalable phylogenomic methods

By A. Hejnol, Matthias Obst, Alexandros Stamatakis, Michael Ott, G. Rouse, G. Edgecombe, P. Martinez, J. Baguñá, X. Bailly, U. Jondelius and 7 more. Proceedings of the Royal Society of London. Biological Sciences, 2009

749 citations recorded by the source corpus.

Subfields: Global and Planetary Change, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/42bbd01ef11a27598bfca4d491bb39026d2e6b20

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Citations in the corpus

OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, methodology): “The construction of large phylogenomic supermatrices, has been the method of choice for resolving the deepest nodes in the tree of life (Dunn et al., 2008; Egger et al., 2015; Fernández et al., 2014; Hejnol et al., 2009) .”
Animal biodiversity: An introduction to higher-level classification and taxonomic richness (2011, background): “Ctenophora was placed as sister group to the remaining animals (Porifera (Placozoa (Cnidaria, Bilateria))) in phylogenomic analyses by Dunn et al. (2008) and Hejnol et al. (2009).”
Animal biodiversity: An update of classification and diversity in 2013. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013) (2013, methodology): “Ctenophora was placed as sister group to the remaining animals (Porifera (Placozoa (Cnidaria, Bilateria))) in phylogenomic analyses by Dunn et al. (2008) and Hejnol et al. (2009); this was favoured over other hypotheses.”
Animal Phylogeny and Its Evolutionary Implications (2014, methodology): “…group to other animals Philippe et al. (2009) Placozoa Porifera Xenacoelomorpha Ambulacraria Xenacoelomorpha is sister group to other Bilateria Hejnol et al. (2009) Lophophorata, Lophotrochozoa Nesnidal et al. (2013) Kryptrochozoa, Brachiozoa Hejnol et al. (2009) Xenacoelomorpha is within…”
Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement (2012, result): “…although it has been shown, both with simulation and with empirical results, that missing data in and of themselves are not always problematic; instead, it is information content in the data at hand what really matters (Wiens, 2003; Goloboff et al ., 2009; Hejnol et al ., 2009; Wiens, 2009).”
Phylogeny and diversification of bryozoans (2015, background): “Although statistical support for the latter grouping tends to be poor (Hejnol et al. 2009), an analysis by Struck et al. (2014) in which terminals with a large proportion of missing data were excluded found strong support for this clade.”
Pitfalls in supermatrix phylogenomics (2017, neutral): “2008), as sister to all the remaining Bilateria (Hejnol et al. 2009) or within Deuterostomia (Philippe et al.”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, background): “It is worth mentioning that the monophyly of Porifera is not unequivocally accepted [28,46]; only the analysis of 30,000 positions with a rich taxon sampling and a complex model of evolution recovers it with significant statistical support [3].”
Morphology should not be forgotten in the era of genomics—a phylogenetic perspective (2015, background): “ (2008) published the 91 first comprehensive analysis of animal relationships using transcriptomics, soon expanded 92 to include a few additional missing species and key lineages like acoelomorphs and 93 placozoans (Hejnol et al., 2009).”
Higher-level metazoan relationships: recent progress and remaining questions (2011, methodology): “Acoelomorpha and Xenoturbella are a clade Hejnol et al. (2009) corroborated previous suggestions that the acoel and nemertodermatid flatworms form a clade, Acoelomorpha, that is sister group to all other bilaterian animals, the latter being united under the taxonomic name Nephrozoa in recognition…”
The Evolution of Brachiopoda (2016, background): “…have allowed this ﬁeld to take another major leap forward with technology that enables the rapid and relatively inexpensive reconstruction of evolutionary relationships among massive numbers of taxa using phylogenomic data (e.g., Hejnol et al. 2009, Nesnidal et al. 2013, Luo et al. 2015).”
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies (2014, neutral): “[11-24]).”
NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, background): “The classification of major metazoan lineages generally follows the broad consensus of recent phylogenomic studies (68–71) while taking a conservative approach to areas that remain contentious or unresolved (e.g. whether Xenacoelo-morpha is the sister group to all other Bilateria (72) or is a clade…”