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Cited by 326

The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.

Estimating the tempo and mode of gene family evolution from comparative genomic data

Open access
Hahn, Matthew W., De Bie, Tijl, Stajich, Jason E., Nguyen, Chi, Cristianini, Nello·2005·Genome Research
DOI 10.1101/gr.3567505
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Abstract

Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.

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Metadata

Authors
Hahn, M. W., De Bie, T., Stajich, J. E., Nguyen, C., & Cristianini, N.
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2005-08
Volume
15
Issue
8
Pages
1153-1160
ISSN
1088-9051 (ISSN-L)
DOI
10.1101/gr.3567505
OpenAlex
W2103581172
Cited by
326
References
59
Type
posted content
Language
en
Open access
bronze

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CoChat. (2026). Citation check: Estimating the tempo and mode of gene family evolution from comparative genomic data. https://app.cochat.ai/papers/10.1101/gr.3567505
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Hahn, M. W., De Bie, T., Stajich, J. E., Nguyen, C., & Cristianini, N. (2005). Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Research. https://doi.org/10.1101/gr.3567505

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