Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 101 (6), 1622-5

Divergent Gene Copies in the Asexual Class Bdelloidea (Rotifera) Separated Before the Bdelloid Radiation or Within Bdelloid Families

Affiliations

Divergent Gene Copies in the Asexual Class Bdelloidea (Rotifera) Separated Before the Bdelloid Radiation or Within Bdelloid Families

David B Mark Welch et al. Proc Natl Acad Sci U S A.

Abstract

Rotifers of the asexual class Bdelloidea are unusual in possessing two or more divergent copies of every gene that has been examined. Phylogenetic analysis of the heat-shock gene hsp82 and the TATA-box-binding protein gene tbp in multiple bdelloid species suggested that for each gene, each copy belonged to one of two lineages that began to diverge before the bdelloid radiation. Such gene trees are consistent with the two lineages having descended from former alleles that began to diverge after meiotic segregation ceased or from subgenomes of an alloploid ancestor of the bdelloids. However, the original analyses of bdelloid gene-copy divergence used only a single outgroup species and were based on parsimony and neighbor joining. We have now used maximum likelihood and Bayesian inference methods and, for hsp82, multiple outgroups in an attempt to produce more robust gene trees. Here we report that the available data do not unambiguously discriminate between gene trees that root the origin of hsp82 and tbp copy divergence before the bdelloid radiation and those which indicate that the gene copies began to diverge within bdelloid families. The remarkable presence of multiple diverged gene copies in individual genomes is nevertheless consistent with the loss of sex in an ancient ancestor of bdelloids.

Figures

Fig. 1.
Fig. 1.
Three gene trees of hsp82 in Rotifera. Monogononts, acanthocephalans, and the seisonid are described in ref. ; bdelloids and the notation of bdelloid gene copies are described in ref. . (A) The tree presented in ref. . Branch lengths are proportional to the number of changes by maximum parsimony, with support for clades shown as a percent of 1,000 bootstrap replicates by maximum parsimony (above) and neighbor joining of a Kimura two-parameter distance matrix (below).(B) The tree found by a heuristic ML search using a nucleotide model of all positions. Branch lengths are proportional to the inferred number of substitutions, with support for clades shown as percent of bootstrap support (above) and posterior probability (below). Support for Philodinidae ranged from 71% to 76% of bootstrap replicates and from 91% to 97% posterior probability using various models of nucleotide substitution; the same rooting of bdelloid sequences is obtained when only codon third positions are used. (C) The tree found by a heuristic ML search using a nucleotide model of codon first and second positions. Branch lengths are proportional to the inferred number of substitutions, with support for clades shown as percent of bootstrap support (above) and posterior probability (below). The same rooting of bdelloid sequences is found when a codon-based model is used with ML.
Fig. 2.
Fig. 2.
Phylogenetic analyses of tbp. Numbers are percentage support of bootstrap replicates under nucleotide models of all positions, codon first and second positions only, and under a codon model, respectively (above the line), and of posterior probability with separate models for codon first and second positions, codon third positions, and introns (below the line). (Scale bar, changes per nucleotide according to ML using all positions.)

Comment in

  • Bdelloid rotifers revisited.
    Birky CW Jr. Birky CW Jr. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2651-2. doi: 10.1073/pnas.0308453101. Epub 2004 Feb 23. Proc Natl Acad Sci U S A. 2004. PMID: 14981265 Free PMC article. No abstract available.

Similar articles

See all similar articles

Cited by 14 articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback