Ancient Phylogenetic Relationships
Abstract
Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.
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Misalignments as well as varying evolutionary rates and compositional biases between distinct lineages can adversely impact the recovered phylogenetic tree and result in incorrect topologies.
“Second, although this is true for any phylogenetic analysis, misalignments as well as varying evolutionary rates and compositional biases between distinct lineages can adversely impact the recovered phylogenetic tree and result in incorrect topologies (Felsenstein 1981;Gribaldo and Philippe 2002;Heaps et al. 2014).”
From The Emergence of Life (2019) · cites this paper as Gribaldo and Philippe 2002
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- Authors
- Gribaldo, S., & Philippe, H.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Venue
- Theoretical Population Biology
- Publisher
- Elsevier BV
- Published
- 2002-06
- Volume
- 61
- Issue
- 4
- Pages
- 391-408
- ISSN
- 0040-5809 (ISSN-L)
- OpenAlex
- W2001721767
- Cited by
- 314
- References
- 8
- Citations by year
- 2024: 6 · 2023: 19 · 2022: 4 · 2021: 1 · 2020: 32 · 2019: 4 · 2018: 3 · 2017: 4 · 2016: 5 · 2015: 9 · 2014: 16 · 2013: 7 · 2012: 7
- FWCI
- 10.06
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Theoretical Population Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- deep phylogeny, long-branch attraction, compositional bias, horizontal gene transfer, recombination, universal tree of life, hyperthermophilic bacteria, eukaryotic phylogeny, prokaryotic phylogeny
- MeSH terms
- Amino Acid Sequence, Animals, Humans, Molecular Sequence Data, Phylogeny, Sequence Homology, Amino Acid
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