---
_id: '871'
abstract:
- lang: eng
text: 'BACKGROUND: Gene duplications have a major role in the evolution of new biological
functions. Theoretical studies often assume that a duplication per se is selectively
neutral and that, following a duplication, one of the gene copies is freed from
purifying (stabilizing) selection, which creates the potential for evolution of
a new function. RESULTS: In search of systematic evidence of accelerated evolution
after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic
genomes to compare the mode and strength of selection acting on recently duplicated
genes (paralogs) and on similarly diverged, unduplicated orthologous genes in
different species. We find that the ratio of nonsynonymous to synonymous substitutions
(Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve
at similar rates, without significant asymmetry, indicating that both paralogs
produced by a duplication are subject to purifying selection. This selection is,
however, substantially weaker than the purifying selection affecting unduplicated
orthologs that have diverged to the same extent as the analyzed paralogs. Most
of the recently duplicated genes appear to be involved in various forms of environmental
response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS:
The results of this analysis indicate that recently duplicated paralogs evolve
faster than orthologs with the same level of divergence and similar functions,
but apparently do not experience a phase of neutral evolution. We hypothesize
that gene duplications that persist in an evolving lineage are beneficial from
the time of their origin, due primarily to a protein dosage effect in response
to variable environmental conditions; duplications are likely to give rise to
new functions at a later phase of their evolution once a higher level of divergence
is reached.'
acknowledgement: We are grateful to A.S. Kondrashov for numerous helpful suggestions,
to I. King Jordan, M.A. Roytberg, J.L. Spouge and D.A. Kondrashov for useful discussions
and to A.S. Kondrashov, I. King Jordan and D.J. Lipman for critical reading of the
manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Kondrashov F, Rogozin I, Wolf Y, Koonin E. Selection in the evolution of gene
duplications . Genome Biology. 2002;3(2). doi:10.1186/gb-2002-3-2-research0008
apa: Kondrashov, F., Rogozin, I., Wolf, Y., & Koonin, E. (2002). Selection in
the evolution of gene duplications . Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2002-3-2-research0008
chicago: Kondrashov, Fyodor, Igor Rogozin, Yuri Wolf, and Eugene Koonin. “Selection
in the Evolution of Gene Duplications .” Genome Biology. BioMed Central,
2002. https://doi.org/10.1186/gb-2002-3-2-research0008.
ieee: F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution
of gene duplications ,” Genome Biology, vol. 3, no. 2. BioMed Central,
2002.
ista: Kondrashov F, Rogozin I, Wolf Y, Koonin E. 2002. Selection in the evolution
of gene duplications . Genome Biology. 3(2).
mla: Kondrashov, Fyodor, et al. “Selection in the Evolution of Gene Duplications
.” Genome Biology, vol. 3, no. 2, BioMed Central, 2002, doi:10.1186/gb-2002-3-2-research0008.
short: F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
date_created: 2018-12-11T11:48:57Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-26T11:48:27Z
day: '01'
doi: 10.1186/gb-2002-3-2-research0008
extern: '1'
external_id:
pmid:
- '11864370'
intvolume: ' 3'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC65685/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1465-6906
publication_status: published
publisher: BioMed Central
publist_id: '6781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Selection in the evolution of gene duplications '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 3
year: '2002'
...
---
_id: '888'
abstract:
- lang: eng
text: 'BACKGROUND: Detection of changes in a protein''s evolutionary rate may reveal
cases of change in that protein''s function. We developed and implemented a simple
relative rates test in an attempt to assess the rate constancy of protein evolution
and to detect cases of functional diversification between orthologous proteins.
The test was performed on clusters of orthologous protein sequences from complete
bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae),
complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and
partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid
sequence evolution rates are significantly correlated on different branches of
phylogenetic trees representing the great majority of analyzed orthologous protein
sets from all three domains of life. However, approximately 1% of the proteins
from each group of species deviates from this pattern and instead shows variation
that is consistent with an acceleration of the rate of amino-acid substitution,
which may be due to functional diversification. Most of the putative functionally
diversified proteins from all three species groups are predicted to function at
the periphery of the cells and mediate their interaction with the environment.
CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the
three species groups analyzed here. Deviations from this rate constancy are probably
due to changes in selective constraints associated with diversification between
orthologs. Functional diversification between orthologs is thought to be a relatively
rare event. However, the resolution afforded by the test designed specifically
for genomic-scale datasets allowed us to identify numerous cases of possible functional
diversification between orthologous proteins.'
acknowledgement: We thank Alexey Kondrashov for many helpful discussions and constructive
criticisms, Charles DeLisi, David Landsman, Detlef Leipe, Wojciech Makalowski and
Itai Yanai for critical reading of the manuscript and constructive comments and
L. Aravind for advice on protein function prediction. The release of the unpublished
P. furiosus genome sequence by the Utah Genome Center at the University of Utah
is acknowledged and appreciated.
article_number: research0053.1
article_processing_charge: No
article_type: original
author:
- first_name: Ingo
full_name: Jordan, Ingo
last_name: Jordan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Roman
full_name: Tatusov, Roman
last_name: Tatusov
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. Constant relative
rate of protein evolution and detection of functional diversification among bacterial,
archaeal and eukaryotic proteins . Genome Biology. 2001;2(12). doi:10.1186/gb-2001-2-12-research0053
apa: Jordan, I., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y., & Koonin,
E. (2001). Constant relative rate of protein evolution and detection of functional
diversification among bacterial, archaeal and eukaryotic proteins . Genome
Biology. BioMed Central. https://doi.org/10.1186/gb-2001-2-12-research0053
chicago: Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf,
and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection
of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins
.” Genome Biology. BioMed Central, 2001. https://doi.org/10.1186/gb-2001-2-12-research0053.
ieee: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin,
“Constant relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol.
2, no. 12. BioMed Central, 2001.
ista: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant
relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12), research0053.1.
mla: Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection
of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins
.” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001,
doi:10.1186/gb-2001-2-12-research0053.
short: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome
Biology 2 (2001).
date_created: 2018-12-11T11:49:02Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-05-31T12:15:37Z
day: '01'
doi: 10.1186/gb-2001-2-12-research0053
extern: '1'
external_id:
pmid:
- '11790256'
intvolume: ' 2'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64838/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1465-6906
publication_status: published
publisher: BioMed Central
publist_id: '6758'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Constant relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2
year: '2001'
...