Statistical tests for detecting gene conversion.

Sawyer, Stanley

doi:10.1093/oxfordjournals.molbev.a040567

Cited by 444 publications

(254 citation statements)

References 12 publications

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“…Using the ORF-centered 4 Kb-long gene pieces (tentatively including 5′-promoter and 3′-untranslated contexts) extracted from the NCBI genome database (http://www.ncbi.nlm.nih.gov/genome/), we analyzed gene conversion among porcine type I IFN sequences. Gene conversion was analyzed with GENECONV software using the default setting to compute both the Sim P-value (estimated based on permutation) and the Bonferroni-corrected (BC) KA (BLAST-like) P-value [25]. Table 2 lists pairs of porcine type I IFN gene sequences that had one or both P-values less than 0.05, thus indicating significant potential for gene conversion within the comparative gene domains, including tentative regulatory sequences at 5′- and 3′-termini as well as the coding ORFs.…”

Section: Resultsmentioning

confidence: 99%

“…Gene conversion was analyzed with GENECONV [25] the default setting. Both the Sim P-value based on permutation and Bonferroni-corrected (BC) KA (BLAST-like) P-values were used to estimate gene conversion among compared homologues.…”

Section: Resultsmentioning

confidence: 99%

“…A dN:dS ratio greater than 1 indicates a positive selection implying rapid changes in amino acids to accommodate an emerging novel function; whereas, a ratio less than 1 implies a purifying selection that results in no amino acid change [7], [25], [27]. We computed dN:dS values of porcine type I IFNs using two different algorithms, as shown in Figure 3 and Table 3 [25], [27]. Purifying selection, which related to pairwise comparisons of multi-gene subfamilies of porcine IFN-α, IFN-ω, and particularly IFN-δ, was significantly (p<0.05) detected.…”

Section: Resultsmentioning

confidence: 99%

“…Gene conversion was analyzed with GENECONV [25] at the default setting. The program identifies highly similar sequence subsets within aligned sequences and determines their statistical significance by computing a global P-value and a local P-value.…”

Section: Methodsmentioning

confidence: 99%

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Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity

2014

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Type I interferons (IFNs), key antiviral cytokines, evolve to adapt with ever-changing viral threats during vertebrate speciation. Due to novel pathogenic pressure associated with Suidae speciation and domestication, porcine IFNs evolutionarily engender both molecular and functional diversification, which have not been well addressed in pigs, an important livestock species and animal model for biomedical sciences. Annotation of current swine genome assembly Sscrofa10.2 reveals 57 functional genes and 16 pseudogenes of type I IFNs. Subfamilies of multiple IFNA, IFNW and porcine-specific IFND genes are separated into four clusters with ∼60 kb intervals within the IFNB/IFNE bordered region in SSC1, and each cluster contains mingled subtypes of IFNA, IFNW and IFND. Further curation of the 57 functional IFN genes indicates that they include 18 potential artifactual duplicates. We performed phylogenetic construction as well as analyses of gene duplication/conversion and natural selection and showed that porcine type I IFN genes have been undergoing active diversification through both gene duplication and conversion. Extensive analyses of the non-coding sequences proximal to all IFN coding regions identified several genomic repetitive elements significantly associated with different IFN subtypes. Family-wide studies further revealed their molecular diversity with respect to differential expression and restrictive activity on the resurgence of a porcine endogenous retrovirus. Based on predicted 3-D structures of representative animal IFNs and inferred activity, we categorized the general functional propensity underlying the structure-activity relationship. Evidence indicates gene expansion of porcine type I IFNs. Genomic repetitive elements that associated with IFN subtypes may serve as molecular signatures of respective IFN subtypes and genomic mechanisms to mediate IFN gene evolution and expression. In summary, the porcine type I IFN profile has been phylogenetically defined family-wide and linked to diverse expression and antiviral activity, which is important information for further biological studies across the porcine type I IFN family.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity

2014

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“…grimshawi were obtained from their unpublished, publicly available genomes (http://rana.lbl.gov/drosophila/). GENECONV was used to test for gene conversion between paralogs, using the method of Sawyer [61]. Phylogenetic reconstruction of multigene families was implemented in Mr. Bayes v3.0b4.…”

Section: Methodsmentioning

confidence: 99%

Gene Duplication and Adaptive Evolution of Digestive Proteases in Drosophila arizonae Female Reproductive Tracts

2007

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It frequently has been postulated that intersexual coevolution between the male ejaculate and the female reproductive tract is a driving force in the rapid evolution of reproductive proteins. The dearth of research on female tracts, however, presents a major obstacle to empirical tests of this hypothesis. Here, we employ a comparative EST approach to identify 241 candidate female reproductive proteins in Drosophila arizonae, a repleta group species in which physiological ejaculate–female coevolution has been documented. Thirty-one of these proteins exhibit elevated amino acid substitution rates, making them candidates for molecular coevolution with the male ejaculate. Strikingly, we also discovered 12 unique digestive proteases whose expression is specific to the D. arizonae lower female reproductive tract. These enzymes belong to classes most commonly found in the gastrointestinal tracts of a diverse array of organisms. We show that these proteases are associated with recent, lineage-specific gene duplications in the Drosophila repleta species group, and exhibit strong signatures of positive selection. Observation of adaptive evolution in several female reproductive tract proteins indicates they are active players in the evolution of reproductive tract interactions. Additionally, pervasive gene duplication, adaptive evolution, and rapid acquisition of a novel digestive function by the female reproductive tract points to a novel coevolutionary mechanism of ejaculate–female interaction.

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Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

Winternitz

Wares

2013

Ecology and Evolution

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Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC.

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Statistical tests for detecting gene conversion.

Cited by 444 publications

References 12 publications

Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity

Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity

Gene Duplication and Adaptive Evolution of Digestive Proteases in Drosophila arizonae Female Reproductive Tracts

Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

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