The Determinants of Genetic Diversity in Butterflies
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ARTICLE https://doi.org/10.1038/s41467-019-11308-4 OPEN The determinants of genetic diversity in butterflies Alexander Mackintosh1, Dominik R. Laetsch 1, Alexander Hayward2, Brian Charlesworth1, Martin Waterfall1, Roger Vila3 & Konrad Lohse 1 Under the neutral theory, genetic diversity is expected to increase with population size. While comparative analyses have consistently failed to find strong relationships between census population size and genetic diversity, a recent study across animals identified a strong cor- relation between propagule size and genetic diversity, suggesting that r-strategists that 1234567890():,; produce many small offspring, have greater long-term population sizes. Here we compare genome-wide genetic diversity across 38 species of European butterflies (Papilionoidea), a group that shows little variation in reproductive strategy. We show that genetic diversity across butterflies varies over an order of magnitude and that this variation cannot be explained by differences in current abundance, propagule size, host or geographic range. Instead, neutral genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that genetic diversity is determined both by differences in long-term population size and the effect of selection on linked sites. 1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK. 2 Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK. 3 Institut de Biologia Evolutiva (CSIC Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, ESP-08003 Barcelona, Spain. Correspondence and requests for materials should be addressed to A.M. (email: [email protected])ortoK.L.(email:[email protected]) NATURE COMMUNICATIONS | (2019) 10:3466 | https://doi.org/10.1038/s41467-019-11308-4 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11308-4 he genetic diversity segregating within a species is a central taxa with similar life-history strategies. However, if robustness to quantity; it determines its evolutionary potential, and is, in fluctuations in population size is the ultimate determinant of T 5 — turn, the outcome of its selective and demographic past. genetic diversity—as Romiguier et al. argue one would expect Under the neutral theory1 genetic diversity is expected to be other life-history traits to correlate with genetic diversity. In proportional to the product of the effective population size, Ne, particular, more specialized species may be able to avoid extinc- μ2 μ and the per-generation mutation rate, (provided that Ne is tion in spite of small census sizes and thus have reduced long- sufficiently small that the infinite sites mutation model is term Ne. Alternatively, if the efficacy of selection determines applicable3). Given that census population size varies widely intraspecific genetic diversity then variation between species may across the tree of life, much of the variation in genetic diversity be best explained by differences in recombination rate and the between species should be due to differences in census size. density of selective targets in the genome. However, correlates of census size, such as geographic range, Here we address these questions using butterflies (Papilionoi- have repeatedly been found to be poor predictors of genetic dea) as a model system. Papilionoidea share a common ancestor diversity4–7. In addition, genetic diversity seems to vary ~119 million years ago (MYA)19, and are characterised as r- remarkably little overall, given the wide range of population sizes strategists given their short life span and high fecundity20, with seen in nature. Although the extremely narrow ranges of genetic little variation in reproductive strategy. Butterflies, in particular diversity reported by early comparative studies based on allo- European species on which we focus, are arguably the best studied zymes6 are partly explained by balancing selection8, diversity at group of insects. Thanks to centuries of study by scientists and nearly neutral sites is also restricted to a narrow range of two amateur naturalists together with numerous recording schemes, orders of magnitude4 (with some notable exceptions5,9). While butterfly taxonomy, geographic ranges and life-histories are the fact that there are only four alternative states for a nucleotide known in great detail. This offers a unique opportunity not only site implies a hard upper bound on the possible level of nucleotide to revisit potential correlates of genetic diversity that have proven site diversity (of 0.75 assuming no mutational bias)10, the levels of difficult to quantify across large taxonomic scales (e.g. geographic neutral genetic diversity seen in natural populations remain far range and abundance), but also test the effects of ecological traits. below this. In particular, while niche breadth is difficult to quantify across The observation that genetic diversity does not correlate with distantly related taxa and has not so far been considered in measures of census size, known as Lewontin’s paradox, has comparative analyses of genetic diversity, accurate data for the intrigued evolutionary biologists for nearly half a century. Pro- number of larval host plants (LHP) exist for European butterflies. posed solutions to the paradox are generally of two types: the first We estimated genetic diversity from de novo transcriptome fl proposes that there may be a negative relationship between Ne data for 38 butter y species (sampling two individuals from each, μ11 and , and the second seeks reasons why Ne shows such little Supplementary Data 1). For simplicity, the estimation of synon- 12 fi π variation between species . Given the lack of rm evidence for ymous diversity was restricted to fourfold degenerate sites ( 4D) large differences in mutation rate among species with different and non-synonymous diversity was estimated at zero-fold π levels of variability, recent comparative studies have focused on degenerate sites ( 0D), i.e. sites where any nucleotide change identifying factors that determine long-term Ne and hence genetic leads to an amino acid difference. While synonymous sites are diversity13. subject to codon usage bias21,22, they are not directly affected by One explanation for the narrow range of genetic diversity other forms of selection. Although selection intensities on codon observed in nature is that natural selection continuously removes usage and biased gene conversion at synonymous sites have been neutral diversity linked to either beneficial12 or deleterious little studied in Lepidoptera23, recent population genomic studies 14,15 fi variants . Because the ef cacy of selection depends on the of Drosophila species suggest that the product of Ne and selection product Nes, selection is expected to be more efficient and coefficients for such sites is generally of the order of 1 or less, so therefore remove more neutral linked sites in species with large that they can be treated as nearly neutral24. Our rationale for 16 Ne. Recently, Corbett-Detig et al. have shown that the pro- modelling π4D and π0D jointly was to better understand the nature portional reduction of neutral diversity due to selection at linked of the underlying forces at the population level: theory predicts sites does indeed correlate with measures of census size such as that any correlate of neutral genetic diversity (π4D) that increases geographic range and (negatively) with body size. While Corbett- Ne should correlate less strongly with diversity at non- 16 25 Detig et al. argue that this can explain “… why neutral diversity synonymous sites (π0D) . This is because any increase in diver- does not scale as expected with census size”, a reanalysis of their sity due to reduced genetic drift is counteracted by the removal of data17 concluded that the effect of selection on linked neutral diversity due to more efficient selection. In contrast, any trait that π diversity is too small to provide a general explanation for the affects non-synonymous genetic diversity ( 0D) via the absolute narrow range of genetic diversity seen in nature. strength of selection s should be more strongly correlated with π An alternative (but not mutually exclusive) explanation is that diversity at non-synonymous sites ( 0D) than synonymous sites fl π variation in genetic diversity is constrained by uctuations in ( 4D), which are only indirectly affected. long-term population size. This would imply that genetic diver- We investigate the relation between average nucleotide site sity should correlate with life-history traits that affect a species diversity26 and five ecological traits: census size (estimated as the susceptibility to environmental fluctuations. Romiguier et al.5 and product of abundance and geographic range), body size, voltin- Chen et al.18 have uncovered a striking negative correlation ism, egg volume (relative to body size) and LHP breadth (Source between propagule size and genetic diversity across the animal Data) using a generalized linear mixed model. In addition, we test kingdom: species that are short-lived and invest little into many whether genome size and recombination rate affect genetic offspring (r-strategists) tend to have higher genetic diversity than diversity. In the absence of detailed recombination maps, we use long-lived species with few offspring and large parental invest- the number of chromosomes as a proxy for the length of the ment (K-strategists).