Ancestral Reconstruction: Theory and Practice

Groussin, Mathieu; Daubin, Vincent; Gouy, Manolo; Tannier, Éric

doi:10.1016/b978-0-12-800049-6.00166-9

Cited by 4 publications

(1 citation statement)

References 85 publications

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“…It can be applied to sequences (DNA, RNA or protein), as well as to morphological characters. It has been widely used to understand the history of gain and loss of gene families over long time scales, and to produce hypotheses on how these gains and losses may have influenced the evolutionary trajectories of extant organisms (Groussin et al, 2016). The power of this technique has allowed it to play a crucial role in diverse topics from tick evolution (Mans et al, 2016) to flower morphology and pollination (Pérez et al, 2006) to the unicellular-to-multicellular transition (Ros-Rocher et al, 2021) and many others (Harms & Thornton, 2010) (Kohn et al, 2006) (Sverdlov et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Dollo parsimony overestimates ancestral gene content reconstructions

Gàlvez-Morante,

Guéguen,

Natsidis

et al. 2023

Preprint

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Ancestral reconstruction is a widely-used technique that has been applied to understand the history of gain and loss of gene families over evolutionary time scales, and to produce hypotheses on how these gains and losses may have influenced the evolutionary trajectories of extant organisms.Ancestral gene content can be reconstructed via different phylogenetic methods, such as maximum likelihood or Bayesian inference, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character can only be gained once in evolutionary history. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence (including random sequence similarity and parallel gene gains), non-orthologous homology or lateral gene transfer. The aim of this study is to test Dollo parsimony’s suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach which allows a gene family to be gained more than once within a tree.In order to test our hypothesis, we first compared the performance of the two approaches on a series of artificial datasets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, which were more pronounced at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.

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Section: Introductionmentioning

confidence: 99%

Dollo parsimony overestimates ancestral gene content reconstructions

Gàlvez-Morante,

Guéguen,

Natsidis

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders

Cribbie,

Doerr,

Chauve

2024

Methods in Molecular Biology

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Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions

Gàlvez-Morante,

Guéguen,

Natsidis

et al. 2024

Genome Biology and Evolution

View full text Add to dashboard Cite

Ancestral reconstruction is a widely-used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach which allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial datasets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.

show abstract

Ancestral Reconstruction: Theory and Practice

Cited by 4 publications

References 85 publications

Dollo parsimony overestimates ancestral gene content reconstructions

Dollo parsimony overestimates ancestral gene content reconstructions

AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders

Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions

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