Genome Evolution and Developmental Constraint in Caenorhabditis elegans

Castillo-Davis, Cristian I.; Hartl, Daniel L.

doi:10.1093/oxfordjournals.molbev.a004131

Cited by 69 publications

(52 citation statements)

References 20 publications

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“…For example, biased usage of alternative codons can be driven by natural selection, provided that effective population sizes are sufficiently large (N e ¼ $10 6 ) (Akashi 1999). Codon bias is strongly correlated among orthologous genes of C. elegans and C. briggsae (Cutter and Ward 2005) and the codon bias of genes in C. elegans has been shown to be associated with gene expression, which has been interpreted as evidence of selection for translational efficiency (Stenico et al 1994;Duret and Mouchiroud 1999;Duret 2000;Marais and Duret 2001;Castillo-Davis and Hartl 2002;. How could selection result in these genomic patterns in the context of such low N e ?…”

Section: Patterns Of Nucleotide Polymorphismmentioning

confidence: 99%

Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae

et al. 2006

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Caenorhabditis briggsae provides a natural comparison species for the model nematode C. elegans, given their similar morphology, life history, and hermaphroditic mode of reproduction. Despite C. briggsae boasting a published genome sequence and establishing Caenorhabditis as a model genus for genetics and development, little is known about genetic variation across the geographic range of this species. In this study, we greatly expand the collection of natural isolates and characterize patterns of nucleotide variation for six loci in 63 strains from three continents. The pattern of polymorphisms reveals differentiation between C. briggsae strains found in temperate localities in the northern hemisphere from those sampled near the Tropic of Cancer, with diversity within the tropical region comparable to what is found for C. elegans in Europe. As in C. elegans, linkage disequilibrium is pervasive, although recombination is evident among some variant sites, indicating that outcrossing has occurred at a low rate in the history of the sample. In contrast to C. elegans, temperate regions harbor extremely little variation, perhaps reflecting colonization and recent expansion of C. briggsae into northern latitudes. We discuss these findings in relation to their implications for selection, demographic history, and the persistence of self-fertilization.

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Section: Patterns Of Nucleotide Polymorphismmentioning

confidence: 99%

Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae

et al. 2006

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“…Third, duplicates may simply be older than orthologs, that is, they predate speciation and therefore have had more time to evolve amino-acid substitutions (d N ). Under the last scenario, synonymous substitutions (d S ) would be expected to increase over time at a similar rate as d N ; however, if paralogs are more highly expressed than orthologs, they may be subject to high codon bias (Duret and Mouchiroud 1999;Castillo-Davis and Hartl 2002), which may result in underestimates of the synonymous substitution rate (d S )-even when likelihood methods are used (Dunn et al 2001). We find, however, that orthologs are more highly expressed (Hill et al 2000) than paralogs (P Ӷ 10…”

Section: Accelerated Protein and Regulatory Evolution In Duplicated Gmentioning

confidence: 99%

cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes

Castillo-Davis¹,

Hartl²,

Achaz³

2004

Genome Res.

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The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray data and experimentally verified regulatory elements in different eukaryotic species. By comparing the genomes of Caenorhabditis elegans and C. briggsae, we found that protein and regulatory evolution is weakly coupled in orthologs but not paralogs, suggesting that selective pressure on gene expression and protein evolution is quite similar and persists for a significant amount of time following speciation but not gene duplication. Additionally, duplicates of both species exhibit a dramatic acceleration of both regulatory and protein evolution compared to orthologs, suggesting increased directional selection and/or relaxed selection on both gene expression patterns and protein function in duplicate genes.[Supplemental material is available online at www.genome.org.]The relative importance of coding sequence change versus regulatory sequence change in evolution has vexed evolutionary geneticists for over 50 years. Given recent genomic analyses showing the conservation of many proteins among distantly related taxa, it has been proposed that regulatory changes play a key role in generating the great morphological diversity present in multicellular species. However, little is known about the evolution of gene regulation or its relationship to protein evolution. Do highly conserved genes also show conserved expression patterns? Or can gene expression evolve independently from protein function? The former pattern is expected if strong stabilizing selection acts on genes as integrated units in which protein sequence and expression pattern are not dissociable. At the same time it has been argued that "developmental systems drift" may result in reorganization of regulatory systems as long as general developmental patterns are preserved (True and Haag 2001). If so, a high turnover of gene regulatory elements may uncouple cis-elementmediated gene expression and protein evolution.Differences in gene expression between species (or between duplicate genes) may entail changes in gene expression levels under the same conditions at the same developmental times, as well as gene expression changes in spatial, temporal, and environmental dimensions. Hereafter, we refer to the former changes as changes in expression magnitude and the latter as changes in relative expression. First attempts to find a correlation between the evolution of relative expression and protein evolution in yeast (using only duplicates) yielded contradictory results; one study argued that expression differences are not correlated with protein evolution (Wagner 2000), wher...

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“…There is some genetic evidence for developmental constraint against genetic perturbations. For example, genes vital for embryogenesis appear to evolve more slowly than those not vital for embryogenesis in C. elegans, based on genome-wide RNAi data (Castillo-Davis and Hartl 2003b), and there is a paucity of duplicate genes among genes expressed during early development (Castillo-Davis and Hartl 2002).…”

Section: Shared Constraints Across Phylamentioning

confidence: 99%

“…Because highly expressed genes may be subject to codon bias, particularly in nematodes (Duret and Mouchiroud 1999;Castillo-Davis and Hartl 2002), and may result in underestimates of the synonymous substitution rate even with likelihood methods (Dunn et al 2001), we used dN as the principal indicator of protein divergence to categorize fast and slow evolving orthologs. However, similar results were found using the ratio dN/ dS (data not shown).…”

Section: ‫02מ‬mentioning

confidence: 99%

The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint

Castillo-Davis¹,

Kondrashov²,

Hartl³

et al. 2004

Genome Res.

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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

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Genome Evolution and Developmental Constraint in Caenorhabditis elegans

Cited by 69 publications

References 20 publications

Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae

Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae

cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes

The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint

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