---
OA_embargo: 6 months
OA_place: publisher
OA_type: hybrid
_id: '6658'
abstract:
- lang: eng
text: 'New genes are a major source of novelties, and a disproportionate amount
of them are known to show testis expression in later phases of male gametogenesis
in different groups such as mammals and plants. Here, we propose that this enhanced
expression is a consequence of haploid selection during the latter stages of male
gametogenesis. Because emerging adaptive mutations will be fixed faster if their
phenotypes are expressed by haploid rather than diploid genotypes, new genes with
advantageous functions arising during this unique stage of development have a
better chance to become fixed. To test this hypothesis, expression levels of genes
of differing evolutionary age were examined at various stages of Drosophila spermatogenesis.
We found, consistent with a model based on haploid selection, that new Drosophila
genes are both expressed in later haploid phases of spermatogenesis and harbor
a significant enrichment of adaptive mutations. Additionally, the observed overexpression
of new genes in the latter phases of spermatogenesis was limited to the autosomes.
Because all male cells exhibit hemizygous expression for X-linked genes (and therefore
effectively haploid), there is no expectation that selection acting on late spermatogenesis
will have a different effect on X-linked genes in comparison to initial diploid
phases. Together, our proposed hypothesis and the analyzed data suggest that natural
selection in haploid cells elucidates several aspects of the origin of new genes
by explaining the general prevalence of their testis expression, and a parsimonious
solution for new alleles to avoid being lost by genetic drift or pseudogenization. '
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Raices, Julia
id: 3EE67F22-F248-11E8-B48F-1D18A9856A87
last_name: Raices
- first_name: Paulo
full_name: Otto, Paulo
last_name: Otto
- first_name: Maria
full_name: Vibranovski, Maria
last_name: Vibranovski
citation:
ama: Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline
expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118
apa: Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives
new gene male germline expression. Genome Research. Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/gr.238824.118
chicago: Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives
New Gene Male Germline Expression.” Genome Research. Cold Spring Harbor
Laboratory Press, 2019. https://doi.org/10.1101/gr.238824.118.
ieee: J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene
male germline expression,” Genome Research, vol. 29, no. 7. Cold Spring
Harbor Laboratory Press, pp. 1115–1122, 2019.
ista: Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male
germline expression. Genome Research. 29(7), 1115–1122.
mla: Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.”
Genome Research, vol. 29, no. 7, Cold Spring Harbor Laboratory Press, 2019,
pp. 1115–22, doi:10.1101/gr.238824.118.
short: J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.
date_created: 2019-07-21T21:59:15Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2025-05-20T06:25:39Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1101/gr.238824.118
external_id:
isi:
- '000473730600007'
file:
- access_level: open_access
checksum: 4636f03a6750f90b88bf2bc3eb9d71ae
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-24T08:05:56Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6670'
file_name: 2019_GenomeResearch_Raices.pdf
file_size: 2319022
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
fulldoi: https://doi.org/10.1101/gr.238824.118
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1115-1122
publication: Genome Research
publication_identifier:
eissn:
- ' 1549-5469'
issn:
- 1088-9051
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Haploid selection drives new gene male germline expression
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
OA_type: closed access
_id: '902'
abstract:
- lang: eng
text: 'We compare the functional spectrum of protein evolution in two separate animal
lineages with respect to two hypotheses: (1) rates of divergence are distributed
similarly among functional classes within both lineages, indicating that selective
pressure on the proteome is largely independent of organismic-level biological
requirements; and (2) rates of divergence are distributed differently among functional
classes within each lineage, indicating species-specific selective regimes impact
genome-wide substitutional patterns. Integrating comparative genome sequence with
data from tissue-specific expressed-sequence-tag (EST) libraries and detailed
database annotations, we find a functional genomic signature of rapid evolution
and selective constraint shared between mammalian and nematode lineages despite
their extensive morphological and ecological differences and distant common ancestry.
In both phyla, we find evidence of accelerated evolution among components of molecular
systems involved in coevolutionary change. In mammals, lineage-specific fast evolving
genes include those involved in reproduction, immunity, and possibly, maternal-fetal
conflict. Likelihood ratio tests provide evidence for positive selection in these
rapidly evolving functional categories in mammals. In contrast, slowly evolving
genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla
are involved in core molecular processes such as transcription, translation, and
protein transport. Thus, strong purifying selection appears to act on the same
core cellular processes in both mammalian and nematode lineages, whereas positive
and/or relaxed selection acts on different biological processes in each lineage.'
acknowledgement: "We thank all members of the Hartl lab for their friendly support
and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and
the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein
for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center
for Genomics Research at Harvard University and Gordon Kindl- mann at the University
of Utah Scientific Computing and Imag- ing Institute for computational resources.
R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences
and Engineering Research Council of Canada.\r\nThe publication costs of this article
were defrayed in part by payment of page charges. This article must therefore be
hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate
this fact."
article_processing_charge: No
article_type: original
author:
- first_name: Cristian
full_name: Castillo Davis, Cristian
last_name: Castillo Davis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Daniel
full_name: Hartl, Daniel
last_name: Hartl
- first_name: Rob
full_name: Kulathinal, Rob
last_name: Kulathinal
citation:
ama: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic
distribution of protein divergence in two animal phyla: Coevolution, genomic conflict,
and constraint. Genome Research. 2004;14(5):802-811. doi:10.1101/gr.2195604'
apa: 'Castillo Davis, C., Kondrashov, F., Hartl, D., & Kulathinal, R. (2004).
The functional genomic distribution of protein divergence in two animal phyla:
Coevolution, genomic conflict, and constraint. Genome Research. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gr.2195604'
chicago: 'Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal.
“The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla:
Coevolution, Genomic Conflict, and Constraint.” Genome Research. Cold Spring
Harbor Laboratory Press, 2004. https://doi.org/10.1101/gr.2195604.'
ieee: 'C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional
genomic distribution of protein divergence in two animal phyla: Coevolution, genomic
conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring
Harbor Laboratory Press, pp. 802–811, 2004.'
ista: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional
genomic distribution of protein divergence in two animal phyla: Coevolution, genomic
conflict, and constraint. Genome Research. 14(5), 802–811.'
mla: 'Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein
Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.”
Genome Research, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004,
pp. 802–11, doi:10.1101/gr.2195604.'
short: C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research
14 (2004) 802–811.
date_created: 2018-12-11T11:49:06Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2026-09-30T13:33:40Z
day: '01'
doi: 10.1101/gr.2195604
extern: '1'
external_id:
pmid:
- '15123580'
fulldoi: https://doi.org/10.1101/gr.2195604
intvolume: ' 14'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 802 - 811
pmid: 1
publication: Genome Research
publication_identifier:
eissn:
- 1549-5469
issn:
- 1088-9051
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '6750'
status: public
title: 'The functional genomic distribution of protein divergence in two animal phyla:
Coevolution, genomic conflict, and constraint'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14
year: '2004'
...