Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiian Drosophila yolk protein gene Yp2

Kin F. Ho, Elysse M. Craddock, Fabio Piano, Michael P. Kambysellis

Research output: Contribution to journalArticle

Abstract

Nucleotide sequence analysis has demonstrated that interspecific size variation in the YP2 yolk protein among Hawaiian Drosophila is due to in- frame insertions and deletions in two repetitive segments of the coding region of the Yp2 gene. Sequence comparisons of the complex repetitive region close to the 5' end of this gene across 34 endemic Hawaiian taxa revealed five length morphs, spanning a length difference of 21 nucleotides (nt). A phylogenetic character reconstruction of the length mutations on an independently derived molecular phylogeny showed clade-specific length variants arising from six ancient events: two identical insertions of 6 nt, and four deletions, one of 6 nt, one of 12 nt, and two identical but independent deletions of 15 nt. These mutations can be attributed to replication slippage with nontandem trinucleotide repeats playing a major role in the slipped-strand mispairing. Geographic analysis suggests that the 15 nt deletion which distinguishes the planitibia subgroup from the cyrtoloma subgroup occurred on Oahu about 3 million years ago. The homoplasies observed caution against relying too heavily on nucleotide insertions/deletions for phylogenetic inference. In contrast to the extensive repeat polymorphisms within other Drosophila and the human species, the more complex 5' Yp2 repetitive region analyzed here appears to lack polymorphism among Hawaiian Drosophila, perhaps due to founder effects, low population sizes, and hitchhiking effects of selection on the immediately adjacent 5' region.

Original languageEnglish (US)
Pages (from-to)116-124
Number of pages9
JournalJournal of Molecular Evolution
Volume43
Issue number2
StatePublished - 1996

Fingerprint

Drosophila Proteins
Egg Proteins
yolk proteins
Nucleic Acid Repetitive Sequences
mutation
Drosophila
polymorphism
Nucleotides
Genes
nucleotides
phylogenetics
DNA
founder effect
Mutation
protein
gene
phylogeny
population size
genes
Polymorphism

Keywords

  • Founder effects
  • Genetic hitchhiking
  • Hawaiian Drosophila
  • Nucleotide insertions/deletions
  • Nucleotide length mutations
  • Replication slippage
  • Trinucleotide repeats
  • Yolk protein genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)
  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Genetics
  • Molecular Biology
  • Genetics(clinical)

Cite this

Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiian Drosophila yolk protein gene Yp2. / Ho, Kin F.; Craddock, Elysse M.; Piano, Fabio; Kambysellis, Michael P.

In: Journal of Molecular Evolution, Vol. 43, No. 2, 1996, p. 116-124.

Research output: Contribution to journalArticle

@article{2746fe25bc1d4658a1cb477a5c10fac6,
title = "Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiian Drosophila yolk protein gene Yp2",
abstract = "Nucleotide sequence analysis has demonstrated that interspecific size variation in the YP2 yolk protein among Hawaiian Drosophila is due to in- frame insertions and deletions in two repetitive segments of the coding region of the Yp2 gene. Sequence comparisons of the complex repetitive region close to the 5' end of this gene across 34 endemic Hawaiian taxa revealed five length morphs, spanning a length difference of 21 nucleotides (nt). A phylogenetic character reconstruction of the length mutations on an independently derived molecular phylogeny showed clade-specific length variants arising from six ancient events: two identical insertions of 6 nt, and four deletions, one of 6 nt, one of 12 nt, and two identical but independent deletions of 15 nt. These mutations can be attributed to replication slippage with nontandem trinucleotide repeats playing a major role in the slipped-strand mispairing. Geographic analysis suggests that the 15 nt deletion which distinguishes the planitibia subgroup from the cyrtoloma subgroup occurred on Oahu about 3 million years ago. The homoplasies observed caution against relying too heavily on nucleotide insertions/deletions for phylogenetic inference. In contrast to the extensive repeat polymorphisms within other Drosophila and the human species, the more complex 5' Yp2 repetitive region analyzed here appears to lack polymorphism among Hawaiian Drosophila, perhaps due to founder effects, low population sizes, and hitchhiking effects of selection on the immediately adjacent 5' region.",
keywords = "Founder effects, Genetic hitchhiking, Hawaiian Drosophila, Nucleotide insertions/deletions, Nucleotide length mutations, Replication slippage, Trinucleotide repeats, Yolk protein genes",
author = "Ho, {Kin F.} and Craddock, {Elysse M.} and Fabio Piano and Kambysellis, {Michael P.}",
year = "1996",
language = "English (US)",
volume = "43",
pages = "116--124",
journal = "Journal of Molecular Evolution",
issn = "0022-2844",
publisher = "Springer New York",
number = "2",

}

TY - JOUR

T1 - Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiian Drosophila yolk protein gene Yp2

AU - Ho, Kin F.

AU - Craddock, Elysse M.

AU - Piano, Fabio

AU - Kambysellis, Michael P.

PY - 1996

Y1 - 1996

N2 - Nucleotide sequence analysis has demonstrated that interspecific size variation in the YP2 yolk protein among Hawaiian Drosophila is due to in- frame insertions and deletions in two repetitive segments of the coding region of the Yp2 gene. Sequence comparisons of the complex repetitive region close to the 5' end of this gene across 34 endemic Hawaiian taxa revealed five length morphs, spanning a length difference of 21 nucleotides (nt). A phylogenetic character reconstruction of the length mutations on an independently derived molecular phylogeny showed clade-specific length variants arising from six ancient events: two identical insertions of 6 nt, and four deletions, one of 6 nt, one of 12 nt, and two identical but independent deletions of 15 nt. These mutations can be attributed to replication slippage with nontandem trinucleotide repeats playing a major role in the slipped-strand mispairing. Geographic analysis suggests that the 15 nt deletion which distinguishes the planitibia subgroup from the cyrtoloma subgroup occurred on Oahu about 3 million years ago. The homoplasies observed caution against relying too heavily on nucleotide insertions/deletions for phylogenetic inference. In contrast to the extensive repeat polymorphisms within other Drosophila and the human species, the more complex 5' Yp2 repetitive region analyzed here appears to lack polymorphism among Hawaiian Drosophila, perhaps due to founder effects, low population sizes, and hitchhiking effects of selection on the immediately adjacent 5' region.

AB - Nucleotide sequence analysis has demonstrated that interspecific size variation in the YP2 yolk protein among Hawaiian Drosophila is due to in- frame insertions and deletions in two repetitive segments of the coding region of the Yp2 gene. Sequence comparisons of the complex repetitive region close to the 5' end of this gene across 34 endemic Hawaiian taxa revealed five length morphs, spanning a length difference of 21 nucleotides (nt). A phylogenetic character reconstruction of the length mutations on an independently derived molecular phylogeny showed clade-specific length variants arising from six ancient events: two identical insertions of 6 nt, and four deletions, one of 6 nt, one of 12 nt, and two identical but independent deletions of 15 nt. These mutations can be attributed to replication slippage with nontandem trinucleotide repeats playing a major role in the slipped-strand mispairing. Geographic analysis suggests that the 15 nt deletion which distinguishes the planitibia subgroup from the cyrtoloma subgroup occurred on Oahu about 3 million years ago. The homoplasies observed caution against relying too heavily on nucleotide insertions/deletions for phylogenetic inference. In contrast to the extensive repeat polymorphisms within other Drosophila and the human species, the more complex 5' Yp2 repetitive region analyzed here appears to lack polymorphism among Hawaiian Drosophila, perhaps due to founder effects, low population sizes, and hitchhiking effects of selection on the immediately adjacent 5' region.

KW - Founder effects

KW - Genetic hitchhiking

KW - Hawaiian Drosophila

KW - Nucleotide insertions/deletions

KW - Nucleotide length mutations

KW - Replication slippage

KW - Trinucleotide repeats

KW - Yolk protein genes

UR - http://www.scopus.com/inward/record.url?scp=0029761646&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0029761646&partnerID=8YFLogxK

M3 - Article

C2 - 8660436

AN - SCOPUS:0029761646

VL - 43

SP - 116

EP - 124

JO - Journal of Molecular Evolution

JF - Journal of Molecular Evolution

SN - 0022-2844

IS - 2

ER -