Adrian A Davin
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Explore the profile of Adrian A Davin including associated specialties, affiliations and a list of published articles.
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10
Citations
308
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Recent Articles
1.
Williams T, Davin A, Szantho L, Stamatakis A, Wahl N, Woodcroft B, et al.
ISME J
. 2024 Jul;
18(1.
PMID: 39001714
In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species...
2.
Mahendrarajah T, Moody E, Schrempf D, Szantho L, Dombrowski N, Davin A, et al.
Nat Commun
. 2023 Nov;
14(1):7456.
PMID: 37978174
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated...
3.
Williams T, Davin A, Morel B, Szantho L, Spang A, Stamatakis A, et al.
Genome Biol Evol
. 2023 Jul;
15(7).
PMID: 37463417
ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on...
4.
Harris B, Sheridan P, Davin A, Gubry-Rangin C, Szollosi G, Williams T
Methods Mol Biol
. 2022 Sep;
2569:189-211.
PMID: 36083449
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the...
5.
Davin A, Schrempf D, Williams T, Hugenholtz P, Szollosi G
Methods Mol Biol
. 2022 Sep;
2569:75-94.
PMID: 36083444
Many organisms are able to incorporate exogenous DNA into their genomes. This process, called lateral gene transfer (LGT), has the potential to benefit the recipient organism by providing useful coding...
6.
Rinke C, Chuvochina M, Mussig A, Chaumeil P, Davin A, Waite D, et al.
Nat Microbiol
. 2021 Jun;
6(7):946-959.
PMID: 34155373
The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the...
7.
Coleman G, Davin A, Mahendrarajah T, Szantho L, Spang A, Hugenholtz P, et al.
Science
. 2021 May;
372(6542).
PMID: 33958449
A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the...
8.
Davin A, Tricou T, Tannier E, de Vienne D, Szollosi G
Bioinformatics
. 2019 Oct;
36(4):1286-1288.
PMID: 31566657
Summary: Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct...
9.
Duchemin W, Gence G, Arigon Chifolleau A, Arvestad L, Bansal M, Berry V, et al.
Bioinformatics
. 2018 May;
34(21):3646-3652.
PMID: 29762653
Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc.-along with a mapping onto a species tree....
10.
Davin A, Tannier E, Williams T, Boussau B, Daubin V, Szollosi G
Nat Ecol Evol
. 2018 Apr;
2(5):904-909.
PMID: 29610471
Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show...