Genomic Signatures of Sexual Conflict

Kasimatis, Katja R; Nelson, Thomas C.; Phillips, Patrick C.

doi:10.1093/jhered/esx080

Cited by 45 publications

(59 citation statements)

References 109 publications

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“…This bias in genetic variation suggests that there may be differential selection (intralocus sexual conflict) between males and females for autosomal or pseudoautosomal regions (segments of sex chromosomes that recombine) in the deacon rockfish genome. Adaptive genetic differences can occur between the sexes if males and females are placed under different selection pressures for traits such as reproduction and behavior (Bonduriansky & Chenoweth, ; Cox & Calsbeek, ; Kasimatis, Nelson, & Phillips, ). The genetic basis for such traits can be attributed to variation at a single locus (Bonduriansky & Chenoweth, ; Bonduriansky, Maklakov, Zajitschek, & Brooks, ; Cox & Calsbeek, ; Kasimatis et al, ; Mank, ; Parker & Partridge, ; Rowe, Chenoweth, & Agrawal, ), which can lead to high estimates of F ST (Flanagan & Jones, ; Lucotte, Laurent, Heyer, Ségurel, & Toupance, ), as observed in this study (Table C).…”

Section: Discussionmentioning

confidence: 99%

“…Adaptive genetic differences can occur between the sexes if males and females are placed under different selection pressures for traits such as reproduction and behavior (Bonduriansky & Chenoweth, ; Cox & Calsbeek, ; Kasimatis, Nelson, & Phillips, ). The genetic basis for such traits can be attributed to variation at a single locus (Bonduriansky & Chenoweth, ; Bonduriansky, Maklakov, Zajitschek, & Brooks, ; Cox & Calsbeek, ; Kasimatis et al, ; Mank, ; Parker & Partridge, ; Rowe, Chenoweth, & Agrawal, ), which can lead to high estimates of F ST (Flanagan & Jones, ; Lucotte, Laurent, Heyer, Ségurel, & Toupance, ), as observed in this study (Table C). A recent RAD sequencing study of gulf pipefish Syngnathus scovelli (Evermann & Kendall, 1896) found that males typically possessed the minor allele, whereas females had the major (Flanagan & Jones, ), which is the same pattern observed for most of the 92 deacon rockfish outlier loci in this study.…”

Section: Discussionmentioning

confidence: 99%

Section: Identity Of Outlier Locimentioning

confidence: 99%

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Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Vaux

Rasmuson

Kautzi

et al. 2019

Ecology and Evolution

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Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50‐km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Vaux

Rasmuson

Kautzi

et al. 2019

Ecology and Evolution

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show abstract

“…Our work in no way challenges the notion that SAS could be widespread across the genome. However, the above and previous (Kasimatis, Nelson, & Phillipps, 2017) theoretical considerations indicate that intersex differentiation maintained by continuous sexually antagonistic viability selection within a population should be subtle in magnitude.…”

Section: Analytical Implicationsmentioning

confidence: 90%

Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection?

et al. 2019

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Females and males within a species commonly have distinct reproductive roles, and the associated traits may be under perpetual divergent natural selection between the sexes if their sex‐specific control has not yet evolved. Here, we explore whether such sexually antagonistic selection can be detected based on the magnitude of differentiation between the sexes across genome‐wide genetic polymorphisms by whole‐genome sequencing of large pools of female and male threespine stickleback fish. We find numerous autosomal genome regions exhibiting intersex allele frequency differences beyond the range plausible under pure sampling stochasticity. Alternative sequence alignment strategies rule out that these high‐differentiation regions represent sex chromosome segments misassembled into the autosomes. Instead, comparing allele frequencies and sequence read depth between the sexes reveals that regions of high intersex differentiation arise because autosomal chromosome segments got copied into the male‐specific sex chromosome (Y), where they acquired new mutations. Because the Y chromosome is missing in the stickleback reference genome, sequence reads derived from DNA copies on the Y chromosome still align to the original homologous regions on the autosomes. We argue that this phenomenon hampers the identification of sexually antagonistic selection within a genome, and can lead to spurious conclusions from population genomic analyses when the underlying samples differ in sex ratios. Because the hemizygous sex chromosome sequence (Y or W) is not represented in most reference genomes, these problems may apply broadly.

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“…While the maintenance of polymorphism may have been a primary motivation for previous work, a goal of modern genomics is to use specific signals of genomic differentiation to identify the loci underlying sexually antagonistic genetic effects (Mank 2017a). Building on our previous work (Kasimatis et al 2017) allowed us to consider the expected degree of between-sex divergence both when an antagonistic polymorphism is maintained at equilibrium in the population, and when no such stable equilibrium exists, so one of the two alleles sweeps towards fixation to the detriment of one sex. Our model and accompanying simulations highlight several potential limitations of detecting sex-specific differentiation in empirical studies.…”

Section: Discussionmentioning

confidence: 99%

Limits to Genomic Divergence Under Sexually Antagonistic Selection

Kasimatis

Ralph

Phillips

2019

Preprint

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Since the autosomal genome is shared between the sexes, sex-specific fitness optima present an evolutionary challenge. While sexually antagonistic selection might favor different alleles within females and males, segregation randomly reassorts alleles at autosomal loci between sexes each generation. This process of homogenization during transmission thus prevents between-sex allelic divergence generated by sexually antagonistic selection from accumulating across multiple generations. However, recent empirical studies have reported high male-female F ST statistics. Here, we use a population genetic model to evaluate whether these observations could plausibly be produced by sexually antagonistic selection. To do this, we use both a single-locus model with nonrandom mate choice, and individual-based simulations to study the relationship between strength of selection, degree of between-sex divergence, and the associated genetic load. We show that selection must be exceptionally strong to create measurable divergence between the sexes and that the decrease in population fitness due to this process is correspondingly high. Individual-based simulations with selection genome-wide recapitulate these patterns and indicate that small sample sizes and sampling variance can easily generate substantial male-female divergence. We therefore conclude that caution should be taken when interpreting autosomal allelic differentiation between the sexes.Several different processes could in principle generate divergence (or apparent divergence) between the sexes. First, sex biases in chromosome segregation through associations with the sex determining region could distort allele frequencies between the sexes. Over time, this segregation distortion can contribute to the generation of neo-sex chromosomes (Jaenike 2003; Kozielska et al. 2010) -particularly heteromorphic sex chromosomes -leading to sex-specific differentiation in the trivial sense that the locus is completely absent in one sex. Second, gametic selection resulting in a sex-specific fertilization bias could also distort allele frequencies (Joseph and Kirkpatrick 2004). Both of these processes occur during the gametic phase of the lifecycle and have long been recognized for their potential ability to distort segregation ratios within the sexes (reviewed in Immler and Otto 2018). In contrast, sexually antagonistic viability selection that occurs post-fertilization is a fundamentally different mechanism because there is no direct co-segregation of sex with

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Genomic Signatures of Sexual Conflict

Cited by 45 publications

References 109 publications

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection?

Limits to Genomic Divergence Under Sexually Antagonistic Selection

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