Elevated levels of expression associated with regions of the<i>Drosophila</i>genome that lack crossing over

Haddrill, Penelope R.; Waldron, Fergal M; Charlesworth, Brian

doi:10.1098/rsbl.2008.0376

Cited by 30 publications

(37 citation statements)

References 30 publications

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“…This prediction is supported by data from sex chromosomes (Berlin and Ellegren 2006;Wykoff et al 2002), mitochondrial genomes (Nachman et al 1994(Nachman et al , 1996Rand and Kann 1996) and Drosophila genomic regions with different recombination rates (Haddrill et al 2007). There is evidence of homologous recombination in DNA viruses (Thiry et al 2004;Wilkinson and Weller 2003) and in both positive strand (Agol 2006;Lukashev 2005;Twiddy and Holmes 2003;Worobey and Holmes 1999) and negative-strand (Hughes 2007;Kukkonen et al 2005;Spann et al 2003) ssRNA viruses.…”

Section: Discussionsupporting

confidence: 60%

More effective purifying selection on RNA viruses than in DNA viruses

Hughes

2007

Gene

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Analysis of the pattern of nucleotide diversity in 222 independent viral sequence datasets showed the prevalence of purifying selection. In spite of the higher mutation rate of RNA viruses, our analyses revealed stronger evidence of the action of purifying selection in RNA viruses than in DNA viruses. The ratio of nonsynonymous to synonymous nucleotide diversity was significantly lower in RNA viruses than in DNA viruses, indicating that nonsynonymous mutations have been removed at a greater rate (relative to the mutation rate) in the former than in the latter. Moreover, statistics that measure the occurrence of rare polymorphisms revealed significantly a greater excess of rare nonsynonymous polymorphisms in RNA viruses than in DNA viruses but no difference with respect to synonymous polymorphisms. Since rare nonsynonymous polymorphisms are likely to be undergoing the effects of purifying selection acting to eliminate them, this result implies a stronger signature of ongoing purifying selection in RNA viruses than in DNA viruses. Across datasets from both DNA viruses and RNA viruses, we found a negatively allometric relationship between nonsynonymous and synonymous nucleotide diversity; in other words, nonsynonymous nucleotide diversity increased with synonymous nucleotide diversity at a less than linear rate. These findings are most easily explained by the occurrence of slightly deleterious mutations. The fact that the negative allometry was more pronounced in RNA viruses than in DNA viruses provided additional evidence that purifying selection is more effective in the former than in the latter.

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Section: Discussionsupporting

confidence: 60%

More effective purifying selection on RNA viruses than in DNA viruses

Hughes

2007

Gene

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“…More recent studies have confirmed the main observation of reduced selection at synonymous sites in regions with strongly reduced rates of recombination, even after correcting for possible nonselective influences on nucleotide composition (Kliman and Hey, 1993a;Comeron et al, 1999;Zurovcova and Eanes, 1999;Comeron and Kreitman, 2002;Hey and Kliman, 2002;Marais and Piganeau, 2002;Marais et al, 2003;Haddrill et al, 2007). It should be noted however that the relationship between codon bias and recombination rate in Drosophila could also be influenced by nonselective factors.…”

Section: Direct and Indirect Evidence Of Hr In Eukaryotesmentioning

confidence: 77%

“…Analyses of rates of protein evolution between Drosophila species show that genes located in genomic regions with strongly reduced recombination have an excess of fixed deleterious mutations and a deficit of fixed advantageous mutations compared to highly recombining genomic regions (Hilton et al, 1994;Takano, 1998;Comeron and Kreitman, 2000;Betancourt and Presgraves, 2002;Zhang and Parsch, 2005;Haddrill et al, 2007). Also, the study of recent nonrecombining chromosomes (for example, neo-Y chromosome in Drosophila miranda) reveals an equivalent pattern with reduced effectiveness of selection (Bachtrog and Charlesworth, 2002;Bachtrog, 2003).…”

Section: Direct and Indirect Evidence Of Hr In Eukaryotesmentioning

confidence: 99%

The Hill–Robertson effect: evolutionary consequences of weak selection and linkage in finite populations

2007

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The 'Hill-Robertson (HR) effect' describes that linkage between sites under selection will reduce the overall effectiveness of selection in finite populations. Here we discuss the major concepts associated with the HR effect and present results of computer simulations focusing on the linkage effects generated by multiple sites under weak selection. Most models of linkage and selection forecast differences in effectiveness of selection between chromosomes or chromosomal regions involving a number of genes. The abundance and physical clustering of weakly selected mutations across genomes, however, justify the investigation of HR effects at a very local level and we pay particular attention to linkage effects among selected sites of the same gene. Overall, HR effects caused by weakly selected mutations predict differences in effectiveness of selection between genes that differ in exon-intron structures and across genes. Under this scenario, introns might play an advantageous role reducing intragenic HR effects. Finally, we summarize observations that are consistent with local HR effects in Drosophila, discuss potential consequences on population genetic studies and suggest future lines of research.

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“…In species with a smaller N e , selection plays a less important role, causing slightly deleterious mutations to be fixed at an elevated rate. The same pattern is repeated across genomic regions with smaller N e , such as regions with low recombination, in which linkage between weakly selected loci reduces the effectiveness of selection (Haddrill et al, 2007;Presgraves, 2005). Conversely, temporally increased substitution rates have also been found in lineages that had undergone population size expansions, due to the fixation of slightly advantageous back-mutations (Charlesworth and Eyre-Walker, 2007).…”

Section: The Molecular Clock Age Estimates and The Fossil Recordmentioning

confidence: 83%

A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences

Poortvliet

Olsen

Croll

et al. 2015

Molecular Phylogenetics and Evolution

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a b s t r a c tManta and devil rays are an iconic group of globally distributed pelagic filter feeders, yet their evolutionary history remains enigmatic. We employed next generation sequencing of mitogenomes for nine of the 11 recognized species and two outgroups; as well as additional Sanger sequencing of two mitochondrial and two nuclear genes in an extended taxon sampling set. Analysis of the mitogenome coding regions in a Maximum Likelihood and Bayesian framework provided a well-resolved phylogeny. The deepest divergences distinguished three clades with high support, one containing Manta birostris, Manta alfredi, Mobula tarapacana, Mobula japanica and Mobula mobular; one containing Mobula kuhlii, Mobula eregoodootenkee and Mobula thurstoni; and one containing Mobula munkiana, Mobula hypostoma and Mobula rochebrunei. Mobula remains paraphyletic with the inclusion of Manta, a result that is in agreement with previous studies based on molecular and morphological data. A fossil-calibrated Bayesian random local clock analysis suggests that mobulids diverged from Rhinoptera around 30 Mya. Subsequent divergences are characterized by long internodes followed by short bursts of speciation extending from an initial episode of divergence in the Early and Middle Miocene (19-17 Mya) to a second episode during the Pliocene and Pleistocene (3.6 Mya -recent). Estimates of divergence dates overlap significantly with periods of global warming, during which upwelling intensity -and related high primary productivity in upwelling regions -decreased markedly. These periods are hypothesized to have led to fragmentation and isolation of feeding regions leading to possible regional extinctions, as well as the promotion of allopatric speciation. The closely shared evolutionary history of mobulids in combination with ongoing threats from fisheries and climate change effects on upwelling and food supply, reinforces the case for greater protection of this charismatic family of pelagic filter feeders.

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Elevated levels of expression associated with regions of theDrosophilagenome that lack crossing over

Cited by 30 publications

References 30 publications

More effective purifying selection on RNA viruses than in DNA viruses

More effective purifying selection on RNA viruses than in DNA viruses

The Hill–Robertson effect: evolutionary consequences of weak selection and linkage in finite populations

A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences

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