Extensive, recent lntron gains in Daphnia populations

Wenli Li, Abraham E. Tucker, Way Sung, W. Kelley Thomas, Michael Lynch

Research output: Contribution to journalArticle

90 Citations (Scopus)

Abstract

Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a populationgenomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.

Original languageEnglish (US)
Pages (from-to)1260-1262
Number of pages3
JournalScience
Volume326
Issue number5957
DOIs
StatePublished - Nov 27 2009
Externally publishedYes

Fingerprint

Daphnia
Introns
Population
Genetic Drift
Population Genetics
Gene Frequency
Exons
Alleles
Genome
Genes

ASJC Scopus subject areas

  • General

Cite this

Li, W., Tucker, A. E., Sung, W., Kelley Thomas, W., & Lynch, M. (2009). Extensive, recent lntron gains in Daphnia populations. Science, 326(5957), 1260-1262. https://doi.org/10.1126/science.1179302

Extensive, recent lntron gains in Daphnia populations. / Li, Wenli; Tucker, Abraham E.; Sung, Way; Kelley Thomas, W.; Lynch, Michael.

In: Science, Vol. 326, No. 5957, 27.11.2009, p. 1260-1262.

Research output: Contribution to journalArticle

Li, W, Tucker, AE, Sung, W, Kelley Thomas, W & Lynch, M 2009, 'Extensive, recent lntron gains in Daphnia populations', Science, vol. 326, no. 5957, pp. 1260-1262. https://doi.org/10.1126/science.1179302
Li W, Tucker AE, Sung W, Kelley Thomas W, Lynch M. Extensive, recent lntron gains in Daphnia populations. Science. 2009 Nov 27;326(5957):1260-1262. https://doi.org/10.1126/science.1179302
Li, Wenli ; Tucker, Abraham E. ; Sung, Way ; Kelley Thomas, W. ; Lynch, Michael. / Extensive, recent lntron gains in Daphnia populations. In: Science. 2009 ; Vol. 326, No. 5957. pp. 1260-1262.
@article{969be39d16fa462ca814c5712e0f7bf7,
title = "Extensive, recent lntron gains in Daphnia populations",
abstract = "Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a populationgenomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.",
author = "Wenli Li and Tucker, {Abraham E.} and Way Sung and {Kelley Thomas}, W. and Michael Lynch",
year = "2009",
month = "11",
day = "27",
doi = "10.1126/science.1179302",
language = "English (US)",
volume = "326",
pages = "1260--1262",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "5957",

}

TY - JOUR

T1 - Extensive, recent lntron gains in Daphnia populations

AU - Li, Wenli

AU - Tucker, Abraham E.

AU - Sung, Way

AU - Kelley Thomas, W.

AU - Lynch, Michael

PY - 2009/11/27

Y1 - 2009/11/27

N2 - Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a populationgenomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.

AB - Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a populationgenomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.

UR - http://www.scopus.com/inward/record.url?scp=70849137211&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70849137211&partnerID=8YFLogxK

U2 - 10.1126/science.1179302

DO - 10.1126/science.1179302

M3 - Article

C2 - 19965475

AN - SCOPUS:70849137211

VL - 326

SP - 1260

EP - 1262

JO - Science

JF - Science

SN - 0036-8075

IS - 5957

ER -