Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex

<p>Abstract</p> <p>Background</p> <p>Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. Sequence homogeneity of these copies depends on relative rates of mutation and recombination, including gene conversion and unequal crossing over, between misaligned copies. The internally repetitive intergenic spacer (IGS) is located between the genes for the 28S and 18S ribosomal RNAs. To identify patterns of recombination and/or homogenization within IGS repeat arrays, and to identify regions of the IGS that are under functional constraint, we analyzed 13 complete IGS sequences from 10 individuals representing four species in the <it>Daphnia pulex </it>complex.</p> <p>Results</p> <p>Gene conversion and unequal crossing over between misaligned IGS repeats generates variation in copy number between arrays, as has been observed in previous studies. Moreover, terminal repeats are rarely involved in these events. Despite the occurrence of recombination, orthologous repeats in different species are more similar to one another than are paralogous repeats within species that diverged less than 4 million years ago. Patterns consistent with concerted evolution of these repeats were observed between species that diverged 8-10 million years ago. Sequence homogeneity varies along the IGS; the most homogeneous regions are downstream of the 28S rRNA gene and in the region containing the core promoter. The inadvertent inclusion of interspecific hybrids in our analysis uncovered evidence of both inter- and intrachromosomal recombination in the nonrepetitive regions of the IGS.</p> <p>Conclusions</p> <p>Our analysis of variation in ribosomal IGS from <it>Daphnia </it>shows that levels of homogeneity within and between species result from the interaction between rates of recombination and selective constraint. Consequently, different regions of the IGS are on substantially different evolutionary trajectories.</p

Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia

<p>Abstract</p> <p>Background</p> <p>Despite their ubiquity and high diversity in eukaryotic genomes, DNA transposons are rarely encountered in ribosomal DNA (rDNA). In contrast, R-elements, a diverse group of non-LTR retrotransposons, specifically target rDNA. <it>Pokey </it>is a DNA transposon that targets a specific rDNA site, but also occurs in many other genomic locations, unlike R-elements. However, unlike most DNA transposons, <it>Pokey </it>has been a stable component of <it>Daphnia </it>genomes for over 100 million years. Here we use qPCR to estimate the number of 18S and 28S ribosomal RNA genes and <it>Pokey </it>elements in rDNA (r<it>Pokey</it>), as well as other genomic locations (g<it>Pokey</it>) in two species of <it>Daphnia</it>. Our goals are to estimate the correlation between (1) the number of 18S and 28S rRNA genes, (2) the number of 28S genes and r<it>Pokey</it>, and (3) the number of r<it>Pokey </it>and g<it>Pokey</it>. In addition, we ask whether <it>Pokey </it>number and distribution in both genomic compartments are affected by differences in life history between <it>D. pulex </it>and <it>D. pulicaria</it>.</p> <p>Results</p> <p>We found differences in 18S and 28S gene number within isolates that are too large to be explained by experimental variation. In general, <it>Pokey </it>number within isolates is modest (< 20), and most are g<it>Pokey</it>. There is no correlation between the number of rRNA genes and r<it>Pokey</it>, or between r<it>Pokey </it>and g<it>Pokey</it>. However, we identified three isolates with unusually high numbers of both r<it>Pokey </it>and g<it>Pokey</it>, which we infer is a consequence of recent transposition. We also detected other rDNA insertions (r<it>Inserts</it>) that could be degraded <it>Pokey </it>elements, R- elements or the divergent <it>Pokey</it>B lineage recently detected in the <it>Daphnia </it>genome sequence. Unlike r<it>Pokey</it>, r<it>Inserts </it>are positively correlated with rRNA genes, suggesting that they are amplified by the same mechanisms that amplify rDNA units even though r<it>Pokey </it>is not. Overall, <it>Pokey </it>frequency and distribution are similar in <it>D. pulex </it>and <it>D. pulicaria </it>suggesting that differences in life history have no impact on <it>Pokey</it>.</p> <p>Conclusions</p> <p>The possibility that many rDNA units do not contain a copy of both 18S and 28S genes suggests that rDNA is much more complicated than once thought, and warrants further study. In addition, the lack of correlation between r<it>Pokey</it>, g<it>Pokey </it>and rDNA unit numbers suggests that <it>Pokey </it>transposition rate is generally very low, and that recombination, in combination with natural selection, eliminates r<it>Pokey </it>much faster than g<it>Pokey</it>. Our results suggest that further research to determine the mechanisms by which <it>Pokey </it>has escaped complete inactivation by its host (the usual fate of DNA transposons), would provide important insights into transposon biology.</p

D- and L-lactate dehydrogenases during invertebrate evolution

Background: The L-lactate and D-lactate dehydrogenases, which are involved in the reduction of pyruvate to L(-)-lactate and D(+)-lactate, belong to evolutionarily unrelated enzyme families. The genes encoding L-LDH have been used as a model for gene duplication due to the multiple paralogs found in eubacteria, archaebacteria, and eukaryotes. Phylogenetic studies have suggested that several gene duplication events led to the main isozymes of this gene family in chordates, but little is known about the evolution of L-Ldh in invertebrates. While most invertebrates preferentially oxidize L-lactic acid, several species of mollusks, a few arthropods and polychaetes were found to have exclusively D-LDH enzymatic activity. Therefore, it has been suggested that L-LDH and DLDH are mutually exclusive. However, recent characterization of putative mammalian D-LDH with significant similarity to yeast proteins showing D-LDH activity suggests that at least mammals have the two naturally occurring forms of LDH specific to L- and D-lactate. This study describes the phylogenetic relationships of invertebrate L-LDH and D-LDH with special emphasis on crustaceans, and discusses gene duplication events during the evolution of L-Ldh. Results: Our phylogenetic analyses of L-LDH in vertebrates are consistent with the general view that the main isozymes (LDH-A, LDH-B and LDH-C) evolved through a series of gene duplications after the vertebrates diverged from tunicates. We report several gene duplication events in the crustacean, Daphnia pulex, and the leech, Helobdella robusta. Several amino acid sequences with strong similarity to putative mammalian D-LDH and to yeast DLD1 with D-LDH activity were found in both vertebrates and invertebrates. Conclusion: The presence of both L-Ldh and D-Ldh genes in several chordates and invertebrates suggests that the two enzymatic forms are not necessarily mutually exclusive. Although, the evolution of L-Ldh has been punctuated by multiple events of gene duplication in both vertebrates and invertebrates, a shared evolutionary history of this gene in the two groups is apparent. Moreover, the high degree of sequence similarity among D-LDH amino acid sequences suggests that they share a common evolutionary history

The functional significance of ribosomal (r)DNA variation: Impacts on the evolutionary ecology of organisms.

■ Abstract The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content

The functional significance of ribosomal (r)DNA variation: Impacts on the evolutionary ecology of organisms.

■ Abstract The multigene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content

Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex

Background: Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. Results: We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. Conclusions: Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive