The genomic footprint of sexual selection

By R. Axel W. Wiberg

This week my co-authors and I published our paper in Evolution Letters. This study was many years in the making and as well as providing insights into the role of sexual selection in evolution, it is a show-case of the power of long-term experiments, experimental evolution, and comparative genomics.

The project started many years ago. In 2002, Rhonda Snook, who is now Professor at Stockholm University and was then at the University of Sheffield, set up an ambitious experiment. She was interested in understanding the role of sexual selection, the process produced by the competition of individuals over reproductive resources and mating opportunities, in driving the evolution of traits and producing differences between populations. To directly investigate this, she set up an experimental evolution study which manipulated the sexual selection environment. The general approach involves setting up different “environments” and then letting populations adapt to these environments and evolve over many generations. The evolutionary response can then be studied by comparing the organisms from the different treatments. In one treatment, elevated promiscuity, individual females were kept in a tube with six males for mating, while in another treatment, enforced monogamy, a female was kept with only a single male. The main difference between the treatments was therefore the level of competition among males for the reproductive resources of the female, generating strong sexual selection in the elevated promiscuity treatment, and abolishing it in the enforced monogamy treatment. The same treatments were applied every generation, using the offspring from the previous generation, with 1 generation being ~30 days. Each treatment was replicated 4 times so that maintaining each generation involved ~2000 flies that had to be fed, moved around, and maintained every month. 

This experiment was kept going for many generations, and rounds of funding, with several studies investigating evolutionary changes to males and females these altered mating systems had produced. Below is a timeline of these studies spanning a total of nearly 20 years and counting. This most recent publication in Evolution Letters is the green dot.

In 2013, I started my PhD studies under the supervision of Professor Mike Ritchie at the University of St Andrews. Mike had, at that time, already collaborated with Rhonda for some time on several experiments with these experimentally evolved flies. By now the “genomics revolution” was in full-swing and whole-genome sequencing was all the rage. After finding phenotypic responses such as changes to courtship song characteristics, and more harmful males with higher courting rates in the elevated promiscuity treatment, time had come to characterise the genetic changes between the E and M treatments. By now these flies had been evolving for ~160 generations (11-12 years). For context and to give a sense of the relative timescales, humans are thought to have a generation time of ~30 years (the time it takes, on average, for a human to grow, develop into an adult, and produce new offspring). With that generation time, 160 generations are equivalent to 4,800 years, which would mean a start of the experiment in ~2800 BCE, around the time that the construction of the pyramids of Egypt began.

An important context for this work is that researchers have been very interested in the role that sexual selection plays in evolution, especially it’s role in shaping genetic variation. Studies comparing the genomes of different populations or species often find differences at genes that have an important role in mating behaviours, female preferences, and male signalling. These give a tantalising hint that sexual selection is indeed an important component of population divergence and speciation, processes at the core of evolution. However, because there are so many other differences between populations and species, for example ecology, it’s very difficult to infer that a particular change was driven by selection in the context of mating (i.e. by sexual selection). Experimental evolution offers an elegant solution to this problem. Because we can set up the experiment in the lab, we can control all other variables and only change the mating system or the level of sexual selection. We can then attribute genetic changes between the treatments to the variable we have changed (the level of sexual selection).

We already knew that there were differences between the elevated promiscuity and enforced monogamy lines in gene expression but what was not known is whether there were any alleles or genetic markers that had changed in frequency between the elevated promiscuity and enforced monogamy populations. So my task became to extract DNA from samples of flies from each replicate, get the genomes sequenced, and then compare the genomes of the lines to identify genetic differences between the treatments.

The problem of identifying genetic changes at the whole-genome scale, led me to an unexpected detour evaluating different statistical approaches and to eventually propose some improvements in a separate paper in Methods in Ecology and Evolution. In the current Evolution Letters paper we show that there have indeed been many genetic changes between the two treatments, and that there are more differences between them than expected by random fluctuations in allele frequencies alone. We also show that these changes occur in quite distinct clusters in the genome (see, for example, (1) in figure 2 below). We were also able to show that, in many cases, the regions of the genome within these clusters show reduced genetic variation within the either the elevated promiscuity or enforced monogamy treatments (see for example (2) in the figure 2 below), which are characteristic signals of selection. These regions also contain several interesting genes that are known to be involved in mating behaviours and other traits related to reproduction. Genes that stand out include seminal fluid proteins that are passed to females during mating and have a variety of effects on the physiology of mated females, making them very good candidates for sexual selection. Finally, the changes between the elevated promiscuity and enforced monogamy lines are over-represented on the X-chromosome, which is thought to be a “hot-spot” for genes under sexual selection.

In summary, this paper is an important contribution to the field of evolutionary biology. We are able to isolate the process of sexual selection from other factors and investigate direct changes in response to this process. This has been a challenge in comparisons to natural systems where populations and species often vary in many different aspects. Fully understanding the consequences of the genetic changes in these experimentally evolved populations will require more work but we are super excited to have taken one more step in understanding the role of sexual selection as an evolutionary force.

My co-authors in on this paper were Paris Veltsos, Rhonda Snook, and Mike Ritchie. The original article is freely available to read and download from Evolution Letters.