This month, we published two papers in PloS Biology on the genetic architecture of speciation in Heliconius butterflies, among the best-known study systems in speciation research. Both papers represent the culmination of many years of work, but at first glance they appear to come to contradictory conclusions. In this piece we discuss why this is the case, and show how it relates to a broader debate about the importance of major loci versus polygenic effects in evolution.
In fact, from the start our two papers approach the same system from different directions. In the first paper, by Merrill et al., we focus on the fact that two closely-related species that co-occur in Panama (Heliconius melpomeneand H. cydno) have evolved strong assortative mating behaviour: they really do not like to hybridize, and much prefer to mate with their own kind. This paper asked about the gene(s) underlying divergence in these preference behaviours, which would inform us about a key step in the evolution of distinct species from a common ancestor.
In contrast, in the second paper by Martin et al., we start from the knowledge that these two species are capable of producing fertile male hybrids, and that their genomes carry the signatures of extensive genetic mixing, or ‘admixture’. While hybridisation is rare (on a per-individual basis) very occasional inter-species mating is enough to scramble the genomes of two species, if it occurs over millions of generations. The second paper therefore addresses how natural selection is acting against the hybrids and their offspring, which carry different combinations of genes from both species. This selection acts to keep the species distinct despite the potential to become genetically mixed.
The main finding of the Merrill et al paper is that just three genetic loci control a large proportion of the differences in mating preference between the species. Remarkably, one of these loci controls both the colour of the butterfly wings andpreference for that colour (though this does not necessarily imply that the same genes are involved). The discovery that changes in a complex behaviour can arise through changes at just a few loci seems surprising, and has important implications for speciation. A new species can arise much more readily if natural selection can act on a few genes of large effect, rather than many loci of small effect. This genetic system that we have discovered should therefore make speciation easier.
By contrast, Martin et al show that the landscape of admixture between these species is consistent with a highly ‘polygenic’ barrier, in which the species boundary is maintained by natural selection acting at multitudes of ‘barrier loci’ across the genome, suggesting a minor contribution of any given locus. This joins a number of studies showing similar trends in both plants and animals. So how do we reconcile these findings? Is speciation more dependent on a few major effect loci that prevent hybridisation, or many small effect loci that lead to the elimination of hybrids?
We think there is less of a paradox here than first appears, and that the papers are more complementary than contradictory. This is because the papers not only consider different components of speciation (pre-mating versus post-mating isolation), but also use different strategies (trait-focused versus genome-focused approaches).
Most speciation events probably involve both pre-mating and post-mating isolating mechanisms: those that limit the production of hybrids as well as those that reduce the survival and reproductive output of any hybrids that are produced. It is perhaps unsurprising that by dissecting these different levels at which isolating mechanisms act, we find different genetic architectures.
The two studies also used entirely different methodologies, designed to detect different things. The approach of Merrill et al., called QTL mapping, is classed as ‘forward genetics’, which starts with a trait of interest and identifies the loci that are associated with that trait. While there almost certainly are some smaller-effect loci that also contribute to the mate preference differences between the species, the QTL mapping approach was only ever likely to find the large-effect ones. Without accurately scoring the phenotypes of an extremely large number of individuals, which is normally very difficult to achieve in behavioural studies, quantitative genetic analyses are unlikely to detect any but the largest effect loci.
Martin et al. used a ‘reverse-genetics’ approach, which starts by identifying signatures of selection in the genome, naive to the trait that is being selected. We searched for variation in the extent of admixture across the genome, as a proxy for the strength of selection against individuals carrying foreign DNA at any genomic locus (i.e. the ‘species barrier’). We found that the species barrier strength is strongly predicted by the recombination rate – the rate at which chromosomes are shuffled in the production of gametes each generation. Increased recombination reduces the extent to which selection acting at a given locus will affect neighbouring parts of the genome. The observed correlation between recombination and admixture can only be explained if manybarrier loci are sprinkled throughout the genome – apparently in contradiction to the fewloci of large effect detected by Merril et al.,.
However, this genome-wide pattern does not preclude the existence of a few barrier loci with a disproportionately large effect, and indeed some genomic regions are particularly resistant to admixture, including the ‘Z’ sex chromosome. This chromosome is known to harbour loci that contribute to hybrid sterility between the species. We know that natural selection also acts strongly against hybrids with mixed wing patterns, because the hybrid pattern is not recognised by predators as a warning that these butterflies are distasteful and should be avoided. But we also know that there are many other ecological differences between these species, including habitat and host plant preferences, so it is unsurprising that very many loci experience some selection (albeit weak in many cases) against foreign DNA.
One striking finding is that the large effect behaviour loci identified by Merrill et al. did not stand out as particularly strong localised species barriers in the genome scan. This may partly be explained by resolution: QTL mapping only provides an approximate location for the functional locus, so it is difficult to be sure where precisely to expect to see reduced admixture. But another factor is that these loci, although important for speciation, might not act as localised barrier loci. A locus that affects hybrid fitness will tend to show reduced admixture, but that is not necessarily the case for a locus that affects whether hybrids are produced in the first place. An assortative mating locus that prevents production of F1 hybrids could be important for speciation but its impact on the pattern of admixture will depend on what happens in later generation hybrids.
Finally, one mechanism by which assortative mating may arise is termed ‘reinforcement’, where selection favours traits that reduce the chance of producing unfit (and costly) hybrids. This relies on an association between the genes under selection for hybrid fitness and those that promote assortative mating (like behavioural preferences). In other words, alleles underlying divergent mating behaviours may not themselves be under direct selection, but may rely on finding themselves in butterflies with the matching species specific traits. Whether we expect genome scans to detect loci under this type of indirect selection remains unclear. This is an area that could provide a focus for future theoretical studies.
In summary, we have found evidence both for a highly polygenic architecture, but also loci with major effects on species boundaries. An appealing story would be that early stages of speciation are characterised by ecological selection acting on a few loci of major effect, but that later stages involve accumulation of differences at many traits that are more polygenic – however we cannot distinguish the time course of speciation from these studies that represent a snapshot of a single species pair. There are also implications here for future speciation studies. The genome scan approach will not necessarily find loci with a large effect on species barriers, even where they exist. Even if no major ‘islands’ of reduced admixture are found, this does not preclude large-effect loci influencing specific traits. As is so often the case in biology, the reality does not fit any single narrative.
This post was written by Chris Jiggins, Simon Martin and Richard Merrill