Molecular Population Genetics of Male Accessory Gland Proteins in Drosophila

Begun, David J.; Whitley, Penn; Todd, Bridget L.; Waldrip-Dail, Heidi M.; Clark, Andrew G.

doi:10.1093/genetics/156.4.1879

Cited by 169 publications

(16 citation statements)

References 54 publications

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“…Here, polyspermy (the fertilization of a single egg by multiple sperm) drives coevolution between sperm and egg recognition proteins with signatures of escalatory (Clark et al 2009) and chase-away Red Queen dynamics (Levitan 2006;Manier and Palumbi 2008;Pujolar and Pogson 2011;Sunday and Hart 2013). Elevated rates of evolution in seminal fluid proteins from Drosophila provide another example in which the rate of divergence of fertilization success-related proteins suggests a role in sexual conflict (Begun et al 2000;Wolfner 2002;Wagstaff 2005). These studies exemplify some of the most powerful information we have on the Red Queen Hypothesis on a macroevolutionary scale.…”

Section: Genomics Of Sexual Conflict: Selection Toward Multiple and M...mentioning

confidence: 99%

Genomic Signatures of Sexual Conflict

Kasimatis

Nelson

Phillips

2017

Journal of Heredity

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Sexual conflict is a specific class of intergenomic conflict that describes the reciprocal sex-specific fitness costs generated by antagonistic reproductive interactions. The potential for sexual conflict is an inherent property of having a shared genome between the sexes and, therefore, is an extreme form of an environment-dependent fitness effect. In this way, many of the predictions from environment-dependent selection can be used to formulate expected patterns of genome evolution under sexual conflict. However, the pleiotropic and transmission constraints inherent to having alleles move across sex-specific backgrounds from generation to generation further modulate the anticipated signatures of selection. We outline methods for detecting candidate sexual conflict loci both across and within populations. Additionally, we consider the ability of genome scans to identify sexually antagonistic loci by modeling allele frequency changes within males and females due to a single generation of selection. In particular, we highlight the need to integrate genotype, phenotype, and functional information to truly distinguish sexual conflict from other forms of sexual differentiation.

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Section: Genomics Of Sexual Conflict: Selection Toward Multiple and M...mentioning

confidence: 99%

Genomic Signatures of Sexual Conflict

Kasimatis

Nelson

Phillips

2017

Journal of Heredity

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“…For example, house-keeping genes are expected to show lower rates of adaptive fixation than nonhouse-keeping genes ( Hurst and Smith 1999 ), whereas genes involved in coevolutionary arms races are notorious for their accelerated rates of adaptive fixation. For example, male–female conflict over optimal investment and male–male competition to fertilize eggs are thought to have led to the high rates of evolution seen in the gamete recognition and fertilization proteins of many species and in some of the accessory proteins of Drosophila ( Begun et al 2000 ; Swanson et al 2003 ; Kern et al 2004 ; Pröschel et al 2006 a; Haerty et al 2007 ; Vacquier and Swanson 2011 ). Conflict between genomic components that can “cheat” Mendelian inheritance, either through biased transmission (such as segregation and sex-ratio distorters) or through over-replication (such as endogenous retroviruses and transposable elements) also appear to drive high rates of adaptive protein fixation ( Presgraves 2007 ; Rowley et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical ParthenogenDaphnia magna

Fields

McTaggart

Reisser

et al. 2022

Molecular Biology and Evolution

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Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared to Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.

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“…Acp62F, protects sperm in the female reproductive tract from protease attack (Lung et al, 2002) and contributes to the up-regulation of genes involved in egg production and muscle development (Avila et al, 2011). We also note that Acp62F has been identified as a potential candidate for balancing selection in D. simulans (Begun et al, 2000).…”

Section: Soft Sweeps Dominate Local Adaptation In D Serratamentioning

confidence: 68%

Direct and indirect impacts of positive selection on genomic variation in Drosophila serrata

Wang

Allen

Reddiex

et al. 2022

Preprint

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Understanding the extent to which microevolutionary adaptation relies on novel beneficial mutations, as opposed to previously neutral standing genetic variation, is an important goal of evolutionary genetics. Progress towards this goal has been enhanced during the genomic era through the study of selective sweeps. Selective sweeps fall into two categories: hard sweeps via new mutations and soft sweeps via pre-existing mutations. However, data are currently lacking on the relative frequency of these two types of selective sweep. In this study, we examined 110 whole genome sequences from Drosophila serrata sampled from eastern Australia and searched for hard and soft sweeps using a deep learning algorithm (diploS/HIC). Analyses revealed that approximately 15% of the D. serrata genome was directly impacted by soft sweeps, and that 46% of the genome was indirectly influenced via linkage to these soft sweeps. In contrast, hard sweep signatures were very rare, only accounting for 0.1% of the scanned genome. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under frequent selection due to evolutionary arms races (e.g. immunity and sperm competition) were detected. Within soft sweep regions and those flanking them, there was an over-representation of SNPs with predicted deleterious effects, suggesting positive selection drags deleterious variants to higher frequency due to their linkage with beneficial loci. This study provides insight into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.

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Molecular Population Genetics of Male Accessory Gland Proteins in Drosophila

Cited by 169 publications

References 54 publications

Genomic Signatures of Sexual Conflict

Genomic Signatures of Sexual Conflict

Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical ParthenogenDaphnia magna

Direct and indirect impacts of positive selection on genomic variation in Drosophila serrata

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