# Hervé Philippe
Hervé Philippe is a molecular phylogeneticist who works on molecular evolution and the robustness of phylogenies; he held an appointment as Associate Professor in the Department of Biochemistry at the Centre Robert-Cedergren, Université de Montréal.[1](http://www.centrerc.umontreal.ca/HPhilippea.html) He is known for Nature papers on the origin of red algae and chloroplasts (2000), a non-hyperthermophilic ancestor for Bacteria (2002), and the deuterostome affinities of acoelomorph flatworms (2011), and for methodological work against long-branch attraction (tree-building error grouping fast-evolving lineages wrongly together) in tree reconstruction.[2](https://megasun.bch.umontreal.ca/Software/HPLab/HPpubli.html) He holds a Tier 2 Canada Research Chair in [Bioinformatics](https://www.edgepedia.org/bioinformatics) and Evolutionary Genomics, held since September 1, 2002.[3](https://biochimie.umontreal.ca/en/research/research-chairs/)
| Fact | Detail |
|---|---|
| Field | Molecular evolution; robustness of phylogenies; phylogenomics[1](http://www.centrerc.umontreal.ca/HPhilippea.html) |
| Position | Associate Professor, Department of Biochemistry, Centre Robert-Cedergren, Université de Montréal[1](http://www.centrerc.umontreal.ca/HPhilippea.html) |
| Chair | Canada Research Chair in Bioinformatics and Evolutionary Genomics, Tier 2, since September 1, 2002[3](https://biochimie.umontreal.ca/en/research/research-chairs/) |
| Signature work | "Acoelomorph flatworms are deuterostomes related to Xenoturbella", Nature 470:255–258, 2011[2](https://megasun.bch.umontreal.ca/Software/HPLab/HPpubli.html) |
| Other major papers | Red algae and chloroplast origins (Nature, 2000); non-hyperthermophilic ancestor for Bacteria (Nature, 2002); tunicates as closest relatives of vertebrates (Nature, 2006)[2](https://megasun.bch.umontreal.ca/Software/HPLab/HPpubli.html) |
| Current affiliation | CHANGE team, CNRS Station d'Écologie Théorique et Expérimentale, Moulis[4](https://sete-moulis-cnrs.fr/en/research/change-research/team/item/188-philippe-herve) |
| Programs led | Protist EST Program (PEP) and Organelle Genome Megasequencing Program (OGMP)[5](https://megasun.bch.umontreal.ca/) |
## Career and affiliations
His publication record places him at the Phylogénie et Evolution Moléculaires laboratory of Université Paris-Sud in Orsay in 2000, when the slow-fast method paper appeared in Proceedings of the Royal Society B.[6](https://royalsocietypublishing.org/doi/10.1098/rspb.2000.1130) By 2003 his address was the Canadian Institute for Advanced Research, Département de [Biochimie](https://www.edgepedia.org/biochimie), Université de Montréal, printed on his review of horizontal gene transfer in Current Opinion in [Microbiology](https://www.edgepedia.org/microbiology).[7](https://ic.unicamp.br/~meidanis/PUB/Mestrado/2006-Zupo/Philippe-Douady-CurrOpin-2003.pdf) According to the 2005 phylogenomics article in the [Annual Review of Ecology, Evolution, and Systematics](https://www.edgepedia.org/annual-review-of-ecology-evolution-and-systematics), of which he was an author, his affiliation was with the Canadian Institute for Advanced Research and the Université de Montréal.[8](https://www.annualreviews.org/content/journals/10.1146/annurev.ecolsys.35.112202.130205) The Canada Research Chair in Bioinformatics and Evolutionary Genomics, Tier 2, has been held in the Department of Biochemistry at Université de Montréal since September 1, 2002.[3](https://biochimie.umontreal.ca/en/research/research-chairs/)
At Montréal his laboratory led or co-led two large collaborative Canadian genomics programs: the Protist EST Program (PEP), in which eight Canadian research groups sequenced cDNA of protists to explore eukaryotic genome diversity, and the Organelle Genome Megasequencing Program (OGMP), a collaboration of seven groups determining complete organelle genomes.[5](https://megasun.bch.umontreal.ca/) The laboratory also built the GOBASE organelle genome database and the TBestDB database managing PEP data; GOBASE was defunct as of April 2017.[5](https://megasun.bch.umontreal.ca/) His present listed affiliation is the CHANGE team at the CNRS Station d'Écologie Théorique et Expérimentale at Moulis, with a CNRS contact address.[4](https://sete-moulis-cnrs.fr/en/research/change-research/team/item/188-philippe-herve)
## Representative work
**Acoelomorph flatworms and Xenoturbella.** His 2011 Nature paper, "Acoelomorph flatworms are deuterostomes related to Xenoturbella" (Nature 470:255–258), assembled three independent data sets, mitochondrial genes, a phylogenomic set of 38,330 amino-acid positions, and new microRNA complements, and showed that the position of [Acoelomorpha](https://www.edgepedia.org/acoelomorpha) is strongly affected by a long-branch attraction artifact.[9](https://pmc.ncbi.nlm.nih.gov/articles/PMC4025995/) When long-branch attraction was minimized, the analysis supported placing both acoelomorphs and Xenoturbella within the deuterostomes, as the sister group of the Ambulacraria, a clade the authors named Xenacoelomorpha.[9](https://pmc.ncbi.nlm.nih.gov/articles/PMC4025995/)
His publication list further records "The origin of red algae and the evolution of chloroplasts" (Nature 405:69–72, May 4, 2000), "Phylogeny: a non-hyperthermophilic ancestor for bacteria" (Nature 417:244, May 16, 2002), "Tunicates and not cephalochordates are the closest living relatives of vertebrates" (Nature 439:965–968, 2006), and "A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals" (Current Biology 27:958–967, 2017).[2](https://megasun.bch.umontreal.ca/Software/HPLab/HPpubli.html) The 2006 tunicate result is cited by a companion Nature study that placed Xenoturbella as the sister group of the two ambulacrarian phyla, bringing the number of living deuterostome phyla to four.[10](https://www.nature.com/articles/nature05241)
## Phylogenomic methods
**Against long-branch attraction.** The 2000 Proceedings of the Royal Society B paper showed that supposedly early-branching amitochondriate eukaryote lineages are, in terms of nucleotide substitution, fast-evolving ones misplaced at the base of the tree by a long-branch attraction artifact, using the slow-fast method of analyzing only slowly evolving positions; it argued that eukaryotic phylogeny is best summarized by a multifurcation, consistent with a "Big Bang" of eukaryotic lineages.[6](https://royalsocietypublishing.org/doi/10.1098/rspb.2000.1130) In prokaryotes, his 2003 review argued that the history of microorganisms cannot be represented by the phylogeny of the core genes alone, since horizontal gene transfer means a coherent phylogenetic pattern emerges from about a hundred genes but represents only a tiny fraction of the genome.[7](https://ic.unicamp.br/~meidanis/PUB/Mestrado/2006-Zupo/Philippe-Douady-CurrOpin-2003.pdf)
**Site-heterogeneous models.** The 2004 [Molecular Biology and Evolution](https://www.edgepedia.org/molecular-biology-and-evolution) paper "A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process" is described in a 2023 Nature Reviews Genetics review as a landmark study introducing site-heterogeneous models of sequence evolution.[11](https://preview-www.nature.com/articles/s41576-023-00620-x) His 2005 Annual Review phylogenomics article argued that failing to fully capture the process of sequence evolution in the underlying models leads to tree-reconstruction artifacts, with better models, improved taxon sampling, and exclusion of misleading data as remedies.[8](https://www.annualreviews.org/content/journals/10.1146/annurev.ecolsys.35.112202.130205) The 2011 PLOS Biology paper "Resolving difficult phylogenetic questions: why more sequences are not enough" demonstrated the point quantitatively: using the site-homogeneous WAG+F+Γ model instead of the site-heterogeneous CAT+Γ model made the fast-evolving ctenophores emerge at the base of all animals with 98% bootstrap support, exactly as expected for a long-branch attraction artifact due to model mis-specification.[12](https://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1000602) The same paper states that site-heterogeneous models fit phylogenomic datasets better and reduce sensitivity to such artifacts.[12](https://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1000602)
## Recent developments
The xenacoelomorph question he opened in 2011 has continued to move. His team page lists a 2019 Current Biology paper, "Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria" (29:1818–1826), and a 2021 [Science Advances](https://www.edgepedia.org/science-advances) paper, "Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria" (7(12):eabe2741), on which he is a co-author.[4](https://sete-moulis-cnrs.fr/en/research/change-research/team/item/188-philippe-herve) A 2024 study went further, arguing that the subphylum Acoelomorpha is itself a long-branch attraction artifact obscuring a clade of Xenoturbella and Acoela, which it names Xenacoela, and that Xenacoelomorpha is not the sister group to all other bilaterians.[13](https://pmc.ncbi.nlm.nih.gov/articles/PMC11407873/)
His recent output has also moved toward ciliate genomics: the team page lists a 2022 Trends in Microbiology review on phenotypic plasticity through disposable genetic adaptation in ciliates (30(2):120–130) and two 2024 papers on [Tetrahymena](https://www.edgepedia.org/tetrahymena) thermophila, one on its macronuclear genomic landscape in Microbial Genomics (10:001175) and one on copper and thermal stress response in Environmental Microbiology Reports.[4](https://sete-moulis-cnrs.fr/en/research/change-research/team/item/188-philippe-herve) His current CNRS affiliation is the SETE Moulis CHANGE team.[4](https://sete-moulis-cnrs.fr/en/research/change-research/team/item/188-philippe-herve)
## References
1. Hervé Philippe, Ph.D., Centre Robert-Cedergren, Université de Montréal. http://www.centrerc.umontreal.ca/HPhilippea.html
2. HP publications (Hervé Philippe laboratory publication list). https://megasun.bch.umontreal.ca/Software/HPLab/HPpubli.html
3. Research Chairs, Département de biochimie et médecine moléculaire, Université de Montréal. https://biochimie.umontreal.ca/en/research/research-chairs/
4. CHANGE, PHILIPPE Hervé, CNRS SETE Moulis. https://sete-moulis-cnrs.fr/en/research/change-research/team/item/188-philippe-herve
5. Evolutionary & Integrative Genomics, Université de Montréal laboratory site. https://megasun.bch.umontreal.ca/
6. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proceedings of the Royal Society B, 2000. https://royalsocietypublishing.org/doi/10.1098/rspb.2000.1130
7. Horizontal gene transfer and phylogenetics. Current Opinion in Microbiology, 2003. https://ic.unicamp.br/~meidanis/PUB/Mestrado/2006-Zupo/Philippe-Douady-CurrOpin-2003.pdf
8. Phylogenomics. Annual Review of Ecology, Evolution, and Systematics, 2005. https://www.annualreviews.org/content/journals/10.1146/annurev.ecolsys.35.112202.130205
9. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 2011. https://pmc.ncbi.nlm.nih.gov/articles/PMC4025995/
10. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature, 2006. https://www.nature.com/articles/nature05241
11. Incongruence in the phylogenomics era. Nature Reviews Genetics, 2023. https://preview-www.nature.com/articles/s41576-023-00620-x
12. Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. PLOS Biology, 2011. https://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1000602
13. Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida, 2024. https://pmc.ncbi.nlm.nih.gov/articles/PMC11407873/
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*Topic: Encyclopedia › Life and health › Life and health scientists › Ecologists and evolutionary biologists › Molecular evolution and phylogenetics*
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