Empirical threshold values for quantitative trait mapping.

The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the accuracy of mapping multiple QTLs by using genetic markers are much increased by employing multiple QTL models instead of the single QTL models (and no QTL models) used in interval mapping. However, the computational work involved with multiple QTL models is considerable when the number of QTLs is large. In this paper it is proposed to combine multiple linear regression methods with conventional interval mapping. This is achieved by fitting one QTL at a time in a given interval and simultaneously using (part of) the markers as cofactors to eliminate the effects of additional QTLs. It is shown that the proposed method combines the easy computation of the single QTL interval mapping method with much of the efficiency and accuracy of multiple QTL models.

Interval Mapping of Multiple Quantitative Trait Loci

In two papers published at about the same time almost thirty years ago, Frank (Evolution, 45, 1991a, 262) and Hurst and Pomiankowski (Genetics, 128, 1991, 841) independently suggested that divergence of meiotic drive systems-comprising genes that cheat meiosis and genes that suppress this cheating-might provide a general explanation for Haldane's rule and the large X-effect in interspecific hybrids. Although at the time, the idea was met with skepticism and a conspicuous absence of empirical support, the tide has since turned. Some of the clearest mechanistic explanations we have for hybrid male sterility involve meiotic drive systems, and several other cases of hybrid sterility are suggestive of a role for meiotic drive. In this article, I review these ideas and their descendants and catalog the current evidence for the meiotic drive model of speciation. In addition, I suggest that meiotic drive is not the only intragenomic conflict to involve the X chromosome and contribute to hybrid incompatibility. Sexually and parentally antagonistic selection pressures can also pit the X chromosome and autosomes against each other. The resulting intragenomic conflicts should lead to co-evolution within populations and divergence between them, thus increasing the likelihood of incompatibilities in hybrids. I provide a sketch of these ideas and interpret some empirical patterns in the light of these additional X-autosome conflicts.

Selfish X chromosomes and speciation.

In many species females have been shown to preferentially mate with males that exhibit the most elaborate sexual ornaments. The handicap hypothesis is a major theory proposed to explain the evolution of such exaggerated traits. It postulates that the ornament is costly and handicaps the bearer such that only high quality males are able to produce the most exaggerated ornamentation. In this thesis I examined questions about male ornament evolution and the handicap hypothesis in the stalk-eyed fly, Teleopsis dalmanni. I examined how meiotic drive, a selfish genetic element that produces female-biased broods, associated with male eyespan (the sexually selected trait in T. dalmanni) in natural populations. I demonstrated a link between meiotic drive and ornament size, whereby small eyespan males were more likely to carry the meiotic drive X chromosome. I then examined how meiotic drive affected the condition-dependent expression of male eyespan. I found that although the mean eyespan of meiotic drive males was smaller, the overall degree of condition dependence was unaffected. Next, I explicitly tested whether there was empirical evidence for the handicap hypothesis in T. dalmanni. In wild populations, I found that under high experimental stress, survival was strongly correlated with male eyespan. In contrast, there was no relationship between eyespan and survival when flies were under low experimental stress. These results provide strong support for the handicap hypothesis. Laboratory experiments yielded similar results. I then explored how environmental quality influenced key components of sexual selection (lek structure and behaviour). I found that under low environmental quality, mean and variance in harem size and the strength of mate choice declined, suggesting reduced sexual selection in poor environments. Finally, I describe for the first time the existence of male mate choice in T. dalmanni, a species that had previously been invoked to exemplify a traditional model of female choice.

What drives sexual selection? : meiotic drive, stress and mate choice in stalk-eyed flies

Some stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we produce a chromosome-level genome assembly of the stalk-eyed fly, T. dalmanni, to elucidate the pattern of genomic divergence associated with the presence of drive elements. We find evidence for multiple nested inversions along the sex ratio haplotype and widespread differentiation and divergence between the inversion types along the entire X chromosome. In addition, the genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally active TE families that have produced new insertions. Moreover, we find that many TE families are expressed at a significantly higher level in SR male testis, suggesting a molecular connection between these two types of selfish genetic elements in this species. We identify T. dalmanni orthologs of genes involved in genome defense via the piRNA pathway, including core members maelstrom, piwi and Argonaute3, that are diverging in sequence, expression or copy number between the SR and standard (ST) chromosomes, and likely influence TE regulation in flies carrying a sex ratio X chromosome.

/pdf/transposable-element-control-disrupted-by-meiotic-drive-in-a-3ouoe6gj3x.pdf

Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome

We use three allopatric populations of the stalk-eyed fly Teleopsis dalmanni from Southeast Asia to test two predictions made by the sex chromosome drive hypothesis for Haldane’s rule. The first is that modifiers that suppress or enhance drive should evolve rapidly and independently in isolated populations. The second is that drive loci or modifiers should also cause sterility in hybrid males. We tested these predictions by assaying the fertility of 2066 males derived from backcross experiments involving two pairs of populations and found that the proportion of mated males that fail to produce any offspring ranged from 38 to 60% among crosses with some males producing strongly female-biased or male-biased sex ratios. After genotyping each male at 25–28 genetic markers we found quantitative trait loci (QTL) that jointly influence male sterility, sperm length, and biased progeny sex ratios in each pair of populations, but almost no shared QTL between population crosses. We also discovered that the extant X SR chromosome has no effect on sex ratio or sterility in these backcross males. Whether shared QTL are caused by linkage or pleiotropy requires additional study. Nevertheless, these results indicate the presence of a “cryptic” drive system that is currently masked by suppressing elements that are associated with sterility and sperm length within but not between populations and, therefore, must have evolved since the populations became isolated, i.e. , in

https://www.genetics.org/content/genetics/198/3/1167.full.pdf

Haldane’s Rule Is Linked to Extraordinary Sex Ratios and Sperm Length in Stalk-Eyed Flies

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Haldane’s Rule Is Linked to Extraordinary Sex Ratios and Sperm Length in Stalk-Eyed Flies