Downloaded by guest on September 30, 2021 www.pnas.org/cgi/doi/10.1073/pnas.1800334115 a Bunnefeld community Lynsey ecological diverse a history of complex the reveal data Whole-genome pce,eooia tigadnurlpoesshv osuch interacting population no discordant in have very expansion processes histories. accommodate can neutral range and and concor- of requirement fitting a direction ecological predicts and species, codispersal component While origin across community. history dant a population in pre- in species contrasting variation make random for also or dictions models fitting alternative ecological These with no assembly. associated species, are component processes our among such to interactions coadaptation central coevolutionary sustained allows and is interactions codispersal species applies while with because models associated evolve, traits these neutral how of ecologically of understanding and that Which random values (5). entirely trait process an be sorting community on Alternatively, could local coevolution? based assembly by the communities shaped been involving into not 4), have pools a (2, through species fitting repeatedly of ecological arise main- of communities are similar process them among do interactions Or side ecological tained? that distributions such their commu- side expanding original by species single of component a sets with of such nity, expansion How by similar interac- (2). 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Graham , | alwasps gall | a,3 n ordLohse Konrad and , ulse nieJn 6 2018. 26, June online Published 1073/pnas.1800334115/-/DCSupplemental. at online information supporting contains article This 3 2 1 eoeasmle r eoie nteEA(ceso nos. (accession ENA the in BunnefeldEtAL deposited Archive are ERP109243 Nucleotide European assemblies the in Genome under deposited been no. (accession have distributed (ENA) reads Raw is deposition: Data article Editorial BY-NC-ND). the (CC 4.0 access by License invited NonCommercial-NoDerivatives editor open guest a This is C.M. Submission. Direct PNAS Board. a is article K.L. This interest. and of conflict L.B. no paper. declare tools; the authors wrote reagents/analytic The K.L. new and per- G.N.S., contributed K.L. L.B., and and K.L. data; G.N.S., and analyzed J.H., L.B., J.H. research; research; designed formed K.L. and G.N.S., contributions: Author a-soitdiscs opiighrioosisc ot and hosts insect herbivorous comprising insects, oak-associated 1 (Fig. tracking (13). play host obli- at delayed the be mutualism, also despite pollination may this that, of suggesting tree nature populations, Joshua gate moth between yucca divergence asynchronous and for evi- exists Indeed, the understood. dence or little coadaptations remains fitting represent ecological these of (10– which results to interactions extent trophic in the structure parasitoids but that 12), and traits herbivores show Both systems 9). such (8, enemies set consistent parasitoid a of by attacked the commonly is which are by in herbivores fitting trees, widespread exemplified temperate with ecological are associated communities These or insect rich mechanism. codispersal assembly either com- plausible which guilds in a between for found interactions is species, specific diversity of less terrestrial involved by of dominated lineages much munities of the However, coevolution of 7). both codiversification (6, show and special- commonly traits and these associated plants and between pollinators, those ist as such associations, species ...adKL otiue qal oti work. this to equally contributed K.L. and [email protected]. Email: addressed. be should correspondence whom work. To this to equally contributed J.H. and L.B. httgte opie5%o l nmlspecies. animal all of 50% comprise groups together trophic that herbi- two enemies—the insect natural Palearctic parasitoid and and Western vores of data of history community genomic assembly multispecies novo the a de infer use to approaches we likelihood-based Here, space time. over through system both a associations and species in of is coevolution inference for This requires potential and interrupted? the are assessing interactions to central that such distributions. interactions, separately, ecological current prey,or preserving how occupy together, their disperse to is and they spread Do question (predators parasites) key species and linked A hosts trophically assemble. of they sets is how little about but common, known are communities biological Widespread Significance eew sesteeiec o oratraiemodels alternative four for evidence the assess we Here obligate in expected are histories population Concordant .Pto n ahmtc oecnb on at found be can code Mathematica and Python ). nteasml fa xmlrcmuiyof community exemplar an of assembly the in A–D) 2018 b ilgcl&EvrnetlSine,Uiest fStirling, of University Sciences, Environmental & Biological ERP023079 . a,3 n h hr edAcie(ceso no. 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ECOLOGY Fig. 1. Population histories under alternative hypotheses of community assembly. (A) Under strict codispersal species disperse between refugia together from a shared origin and their population histories show the same topology and timing of population splits. (B) Host tracking predicts that hosts and parasitoids share a common geographic origin, but allows parasitoids to follow after their hosts. Host tracking is significant ecologically because hosts can achieve a measure of enemy-free space (20) which decouples coevolutionary interactions between trophic levels. Enemy escape has been seen over ecological timescales (21, 22), but has rarely been studied in the context of population histories (20). (C) Ecological fitting results in the same set of interacting species in each refuge, but allows highly discordant patterns of range expansion from different origins. (D) Under an ecological and biogeographic null model, expansion times are random draws from a single community-wide distribution. Shown is a six-species community with two parasitoids (orange) and one gall wasp host (brown) expanding out of the east and two parasitoids (gray) and one gall wasp (blue) expanding out of the west. Split times (T1 and T2) are drawn randomly from an exponential distribution. (E) The demographic history of each species is captured by a seven-parameter model. We assume a separate population size (Ne) for each refugial population (three parameters). In this example, NE < NW < NC (shown by width of bars and where NE is the Ne for the eastern refugium, and so on) and an instantaneous admixture event (shown by a horizontal arrow) at Tadm transfers a fraction f of the central population into the east. The ancestral populations always share an Ne with one of their descendant populations. Here, Anc1 shares an Ne with the central population and Anc2 shares an Ne with the eastern population. (F) Exemplar members of the oak gall community. Galls induced by the four oak gall wasp species (Bottom) are attacked by a range of parasitoid wasps (Top). Natural enemies from Top Left to Top Right: Torymus auratus, Synergus umbraculus, Eurytoma brunniventris, and Ormyrus nitidulus. (S. umbraculus is an inquiline oak gall wasp that inhabits galls induced by other oak gall wasps; for brevity we group it with parasitoid species hereafter). Galls from Bottom Left to Bottom Right: Andricus grossulariae, Neuroterus quercusbaccarum, Biorhiza pallida, and Pseudoneuroterus saliens. [Scale bars: 1 mm (Top row) and 1 cm (Bottom row).]

parasitoid and inquiline natural enemies (Fig. 1 legend). These Western Palearctic from Iberia to Iran. Associated parasitoids models include strict codispersal (simultaneous range expansion), attack only cynipid galls, making this system ecologically closed host tracking (parasitoids’ pursuit of their hosts), and ecological and hence suitable for analysis in isolation (8). Single-species fitting (local recruitment of parasitoids from alternative hosts), analyses of community members (15–18) have found westward each of which makes contrasting predictions for spatial patterns of declines in genetic diversity that support expansion into Europe genetic variation within and among species. We also evaluate the from Western Asia, an “out of the East” pattern that is concor- support for an alternative null model of assembly under ecologi- dant with inferred divergence of Western Palearctic gall wasp cal neutrality in which a species’ history is a random draw from a lineages in Western Asia 5–7 Mya (19). However, the extent to community-wide distribution regardless of its trophic interactions which this is true of the whole community, and particularly the with other community members (5, 14). parasitoids, remains unclear (20). Our exemplar community comprises oak cynipid gall wasp her- We test the predictions of each model of community assembly bivores and their chalcid parasitoid wasp natural enemies, which using whole-genome sequence (WGS) data for 13 species (4 gall form a set of interacting species whose distributions span the wasp herbivores and 9 parasitoids) of the oak gall community,

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ECOLOGY Table 1. Maximum composite-likelihood estimates (MCLE) of demographic parameters and population topologies under the best supported model for each species

Species binomial Species code Anc1 Anc2 Topology NW NC NE Tadm T1 T2 f So → Si Parasitoids Cecidostiba fungosa Cfun West West East 22.9 367.5 25.0 142** 142 622 0.79 W → E Eupelmus annulatus Eann East West West 15.5 82.1 40.4 0 41 131 0.03 – Eurytoma brunniventris Ebru Centre Centre East 1162 47.5 116.3 0* 72 1051 0.91 W → E Megastigmus dorsalis Mdor Centre East East 2.5 34.3 11.4 0* 8 90 0.39 C → E Megastigmus stigmatizans Msti – West Polytomy 6.4 1.0 0.4 – 37 37 – – Ormyrus nitidulus Onit Centre Centre East 3.6 17.9 10.6 24 24 113 0 – Ormyrus pomaceus Opom East East West 18.0 71.3 30.3 53 102 217 0.06 – Synergus umbraculus Sumb Centre West West 8.7 13.4 19.8 38** 41 309 0.54 C → W Torymus auratus Taur – East Polytomy 1050 20.9 41.7 – 80 80 – – Gall wasp hosts Andricus grossulariae Agro Centre East East 1.0 1.9 13.9 14 35 45 0.09 E → W Biorhiza pallida Bpal East West West 13.0 20.0 65.0 0* 19 135 0.12 W → E Neuroterus quercusbaccarum Neuqba Centre East East 10.3 20.7 12.2 153** 154 1175 0.34 C → E Pseudoneuroterus saliens Neusal Centre Centre East 2.4 35.7 11.0 60 66 474 0.05 –

4 Divergence (T1, T2) and admixture times (Tadm) are given in thousands of years (ky), and effective population sizes (NW , NC , NE) are ×10 individuals. Anc1 and Anc2 indicate which current population size is shared with the younger and older ancestral populations, respectively (Fig. 1E). For Tadm, * indicates that the 95% confidence interval (CI) of the estimate for this parameter includes zero, while ** indicates that the 95% CI overlaps the 95% CI for T1. So → Si indicates the source and sink population for the admixture event, where the 95% CI for f was found to not overlap zero.

M. stigmatizans (Table 1). Given that a large number of species edge of the generation times of each species (which we have; have nonoverlapping confidence intervals (computed using a full Materials and Methods and ref. 20) and (ii) an equal mutation parametric bootstrap; Materials and Methods) for this split, we rate across species (which seems reasonable) (see SI Appendix, can confidently reject assembly via strict codispersal (Fig. 2). Table S3 for uncalibrated parameter estimates for the top three Irrespective of whether we consider all species jointly or only best-supported models for each species). those with a putative eastern origin, the deepest population split (T2) is not consistently older in gall wasp hosts than in their Testing Ecologically Neutral Assembly. Our rejection of the codis- parasitoid enemies (Fig. 2), arguing against both delayed host persal and delayed host tracking models raises the question of tracking and widespread enemy escape. We stress that our com- whether the observed variation in species’ demographic histo- parison of population divergence times across species does not ries is nonetheless structured or whether it is compatible with rely on any absolute calibration but assumes only (i) knowl- a neutral model of community assembly. We address the first

Msti l Mdorl l l Taur l Onit l l Eann l l Opom l l Sumb ll l Cfun l l Ebrul l l

Bpall l l Agro l l l Neusal l l Neuqba ll l 0 50 100 150 500 1000 Time (kyrs)

Fig. 2. Community-wide patterns of range expansion across the Western Palearctic. Estimates for nine parasitoids and four gall wasp host species are shown at Top and Bottom, respectively (for species abbreviations see Table 1). Divergence times are shown in green and comprise a point estimate flanked by 95% CIs. The arrow on the older divergence time for each species shows the direction of range expansion; e.g., a right-pointing arrow indicates expansion from west to east. Note that the arrow is absent for Msti and Taur because their histories are unresolved polytomies and hence nondirectional. Where supported in the best model, admixture times are shown in black. The arrow gives the direction of admixture, again comprising a point estimate flanked by 95% CIs. CIs are arbitrary for the three species with admixture estimated at the present day. Orange vertical bars indicate interglacials. The best-fitting community-wide mixture distribution (Materials and Methods) of divergence and admixture times is shown in gray. Note that the x axis on the right-hand side is compressed relative to that on the left. Point estimates and 95% CIs are tabulated in SI Appendix, Table S6.

E6510 | www.pnas.org/cgi/doi/10.1073/pnas.1800334115 Bunnefeld et al. 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Coincide the Pulses Expansion Community-Wide (T ture others all of independently diverged each (∆ that species seven and auratus (T. dorsalis times indistin- divergence with species similar of guishably clusters support three contained marginal codivergence the of of grid discretized for a (T species (using each codivergence in split Considering oldest to community. the required this only of are history events demographic divergence the many explain how asking by question ruby(4,tesmls clgclynurlmdlwould model neutral ecologically simplest the (14), Arguably whether is question meaningful, more argue we and second, A lnL T 1 .brunniventris E. 2 − ; 1 = adm t8 kya, 82 at .Tems asmnosmodel parsimonious most The Methods). and Materials f ]. epciey (see respectively) , . siae.Teifrneo omnt-ieparam- community-wide of inference The estimates. ) df, 3 8, T aaeesand parameters adm h omnt-iemdso iegneand divergence of modes community-wide The uemsannulatus Eupelmus p n h letslt(T split oldest the and ) 0 = and .308; .quercusbaccarum N. aeil n Methods and Materials al S4). 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N. PNAS u nigta pce differ species that finding Our | o.115 vol. | .grossulariae, A. o 28 no. | E6511

ECOLOGY studies of genetic diversity (26, 34) have ignored demography, Info 2). Finally, our parametric bootstrap replicates which were comparing species with respect to their demographic histories simulated with recombination show that recombination (which makes it possible (at least in principle) to test for assembly rules. may differ between species) had minimal effects on model and For example, if ecological fitting plays an important role in com- parameter estimates. munity assembly, more generalist and/or widespread parasitoids should have older histories than specialists. We do indeed find Implications for Comparative Phylogeography. Previous compara- that T2 and ancestral Ne are positively correlated with both host tive studies have been unable to build such a nuanced picture range and abundance, which is compatible with this idea (SI of community assembly in this or any other system due to limita- Appendix, Fig. S2). However, confirming this relationship will tions in both available data and analytical approaches (20, 47, 48) require larger samples of species. [although new methods have begun to emerge (49, 50); see ref. 13 for an early successful example]. In particular, we conducted Eastern Origins and Westerly Winds. A majority of members of the a previous analysis of the oak gall wasp community based solely oak gall community have an eastern origin, a pattern that is com- on mitochondrial data sampled for the same set of refugia and patible with the east to west declines in genetic diversity found an overlapping set of taxa. In contrast to the present study, this by previous studies of this community (16, 17, 31) and West- previous analysis had very limited power to resolve even simple ern Palearctic taxa more generally (35, 36). It also matches the demographic histories with or without gene flow (20). inferred origin of gall wasp lineages now found across the West- We now have both the inference tools and the data neces- ern Palearctic ca. 10 Mya in Anatolia/Iran (19). The longitudinal sary to resolve divergence and admixture relationships among colonization history of deciduous oaks in the Western Palearc- multiple populations and across many trophically linked species. tic is currently too poorly resolved to know whether gall wasps Given the resolution of WGS data, it becomes hard to justify tracked their oak hosts westward into Europe (37, 38). While the logic of testing for strict codivergence (51), if this implies only a few species in the oak gall community show evidence for identical divergence times across species. Three recent com- admixture, it is intriguing that our inference of admixture is (i) parative phylogeographic analyses, each based on thousands of most substantial in the three species with the oldest histories, ddRAD loci, avoided using approaches that test for strict codi- N. quercusbaccarum, Cecidostiba fungosa, and E. brunniventris vergence, but instead compared parameter estimates post hoc (Table 1), and (ii) directed predominantly from the west into the among species (52–54). For example, Oswald et al. (53) found east, that is, in the opposite direction of population divergence. that six pairs of codistributed birds shared the same mode of We conducted a simple simulation study to confirm that this divergence (isolation with asymmetric migration) but diverged directional signal is not an artifact of our modeling approach; i.e., asynchronously. Our approach replaces informal post hoc com- admixture back into the source population is not easier to detect parisons with a formal comparative framework that both incor- than in the reverse direction (Materials and Methods). Inference porates uncertainty in species-specific parameter estimates and of gene flow between refugia is compatible with the documented characterizes community-wide distributions of divergence times. range expansion by both gall wasps and associated parasitoids over similar spatial scales (17, 39) and the ability of gall wasps to Outlook. Being able to efficiently reconstruct intraspecific his- reach offshore islands (40). Given that both chalcid parasitoids tories from genome-scale data across multiple species means and cynipids have been observed in aerial samples taken 200 m that one can infer the tempo and mode of community assembly from the ground (41) and the prevailing winds in the Western across space and through time. The composite-likelihood frame- Palearctic are from the west, it seems plausible that gene flow work we use applies to a wide range of demographic histories into the east is simply easier and therefore more likely than in (31, 55) and, as we have shown here, lends itself to compar- the reverse direction. ative analyses. Given sufficient replication in terms of species, such analyses open the door to answering a range of fundamental Limitations and Potential Confounding Factors. While the demo- questions in evolution and ecology. For example, an interesting graphic models we consider are necessarily simplifications of avenue of future research will be to explicitly include selec- the truth, they capture key population-level processes that have tion in comparative analyses. In particular, it will be fascinating been largely ignored by previous comparative analyses. First, to ask whether and how range shifts and admixture events are many comparative phylogeographic studies have focused on accompanied by selection on genes that may be involved in host– divergence between only pairs of populations (20, 42). Second, parasitoid interactions. It will soon be possible to use WGS data analyses of divergence and admixture between multiple popula- to compare not only the demographic histories of interacting tions have, for the sake of tractability, often assumed equal Ne species but also the signatures of selective sweeps and their tar- among populations (43, 44) which can bias estimates of diver- gets in the genome. In practice, such more detailed comparisons gence and admixture. Our finding that Ne varies by up to two will require both further work on inference methods and more orders of magnitude among populations within species (Table 1) complete datasets, including more contiguous (and functionally highlights the importance of modeling Ne parameters explicitly annotated) reference genomes and larger samples of individuals (45, 46). While this study’s reanalysis of B. pallida inferred little and taxa. admixture when accounting for Ne differences between refugia, a previous analysis based on a single sample per population (43) Materials and Methods suggested substantial gene flow from east to west under a model Samples and Sequencing. in which ancestral Ne was fixed across all populations. Sample processing. We generated WGS data for three species of oak To make robust inferences about community assembly, it is gall wasp hosts, eight parasitoids, and one inquiline. We also reana- imperative to minimize biases that might affect comparability lyzed WGS data generated for a pilot study for B. pallida, another gall among species. We have sequenced species to the same cover- wasp species (43) (ENA Sequence Read Archive: http://www.ebi.ac.uk/ena/ age whenever possible and have used the same bioinformatic data/view/ERP002280). For each species we sampled a minimum of two pipeline and comparable block lengths (in terms of diversity) for male individuals from each of three refugial populations spanning the Western Palearctic: Iberia (west), the Balkans (center), and Iran (east) (SI all species. To test whether selective constraint is likely to differ Appendix, Table S2). Only a single eastern sample was available for two drastically among species or trophic levels (which could lead to species, Ormyrus pomaceus and B. pallida, and a single western sample for systematic biases in demographic estimates), we compared diver- S. umbraculus. sity across all sites to that at synonymous coding sites and found DNA was extracted from (haploid) male individuals, using the Qiagen no difference between hosts and parasitoids (SI Appendix, Suppl. DNeasy kit. Nextera libraries were generated for each individual specimen

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ECOLOGY weights of the lowest weighted component of the previous distribution. Mike Hickerson for discussions throughout the project and to Ally Phillimore We identified the most parsimonious model as the simplest model (i.e., for a critical manuscript review. We are grateful to Rob Ness for advice on with the fewest parameters) which did not give a significant reduction the bioinformatics; to Pablo Fuentes-Utrilla, Gyorgy˝ Csoka,´ George Melika, in lnL. The python scripts and Mathematica notebooks are available at and Majide Tavakoli for contributing specimens; to Richard R. Askew for https://github.com/KLohse/BunnefeldEtAL 2018. help with identification; and to William Walton for collating the ecologi- cal data. This work was supported by a standard grant from the Natural ACKNOWLEDGMENTS. We thank Richard Harrison, James Nicholls, Sarah Environmental Research Council (NERC) United Kingdom (to G.N.S. and White, and Lisa Cooper for help in the laboratory and Edinburgh Genomics K.L.) (NE/J010499/1). K.L. is supported by a NERC Independent Research for sequencing. We give many thanks to Stuart Baird, Alex Hayward, and fellowship (NE/L011522/1).

1. Vellend M (2010) Conceptual synthesis in community ecology. Q Rev Biol 85:183–206. 36. Duvaux L, Belkhir K, Boulesteix M, Boursot P (2011) Isolation and gene flow: Inferring 2. Janzen DH (1985) On ecological fitting. Oikos 45:308–310. the speciation history of European house mice. Mol Ecol 20:5248–5264. 3. Ricklefs RE (2015) Intrinsic dynamics of the regional community. Ecol Lett 18:497–503. 37. Petit RJ, et al. (2002) Chloroplast DNA variation in European white oaks: Phylogeog- 4. Agosta SJ, Klemens JA (2008) Ecological fitting by phenotypically flexible genotypes: raphy and patterns of diversity based on data from over 2600 populations. For Ecol Implications for species associations, community assembly and evolution. Ecol Lett Manag 156:5–26. 11:1123–1134. 38. Atkinson R, Rokas A, Stone G (2007) Longitudinal patterns in species richness and 5. Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography, genetic diversity in European oaks and oak gallwasps. Phylogeography in Southern Princeton Monographs in Population Biology (Princeton Univ Press, Princeton). European Refugia, ed Weiss S (Springer, Dordrecht, The Netherlands), pp 127–154. 6. Jousselin E, Rasplus JY, Kjellberg F (2003) Convergence and coevolution in a 39. Stone GN, Sunnucks P (1993) Genetic consequences of an invasion through a mutualism: Evidence from a molecular phylogeny of ficus. Evolution 57:1255–1269. patchy environment–The cynipid gallwasp Andricus quercuscalicis (Hymenoptera: 7. Mueller UG, Rehner SA, Schultz TR (1998) The evolution of agriculture in ants. Science Cynipidae). Mol Ecol 2:251–268. 281:2034–2038. 40. Walker P, Leather SR, Crawley MJ (2002) Differential rates of invasion in three related 8. Stone GN, Schonrogge¨ K, Atkinson RJ, Bellido D, Pujade-Villar J (2002) The population alien oak gall wasps (cynipidae: Hymenoptera). Divers Distrib 8:335–349. biology of oak gall waps (hymenoptera: Cynipidae). Annu Rev Entomol 47:633–668. 41. Chapman J, Reynolds D, Smith A, Smith E, Woiwod I (2004) An aerial netting study of 9. Leppanen¨ SA, Altenhofer E, Liston AD, Nyman T (2013) Ecological versus phyloge- insects migrating at high altitude over England. Bull Entomol Res 94:123–136. netic determinants of trophic associations in a plant-leafminer-parasitoid food web. 42. Hickerson MJ, Stahl EA, Lessios HA, Crandall K (2006) Test for simultaneous divergence Evolution 67:1493–1502. using approximate Bayesian computation. Evolution 60:2435–2453. 10. Bailey R, et al. (2009) Host niches and defensive extended phenotypes structure 43. Hearn J, et al. (2014) Likelihood-based inference of population history from parasitoid wasp communities. PLoS Biol 7:e1000179. low-coverage de novo genome assemblies. Mol Ecol 23:198–211. 11. Askew RR (1980) The diversity of insect communities in leaf mines and plant galls. J 44. Yu Y, Dong J, Liu KJ, Nakhleh L (2014) Maximum likelihood inference of reticulate Anim Ecol 49:145–152. evolutionary histories. Proc Natl Acad Sci USA 111:16448–16453. 12. Stireman JO, Singer MS (2003) Determinants of parasitoid-host associations: Insights 45. Marko PB, Hart MW (2011) The complex analytical landscape of gene flow inference. from a natural tachinid-lepidopteran community. Ecology 84:296–310. Trends Ecol Evol 26:448–456. 13. Smith CI, Godsoe WKW, Tank S, Yoder JB, Pellmyr O (2008) Distinguishing coevolution 46. Hung CM, Drovetski SV, Zink RM (2017) The roles of ecology, behaviour and effective from covariance in an obligate pollination mutualism: Asynchronous divergence in population size in the evolution of a community. Mol Ecol 26:3775–3784. Joshua tree and its pollinators. Evolution 62:2676–2687. 47. Sutton TL, Riegler M, Cook JM (2016) One step ahead: A parasitoid disperses farther 14. Rosindell J, Hubbell SP, Etienne RS (2011) The unified neutral theory of biodiversity and forms a wider geographic population than its fig wasp host. Mol Ecol 25:882–894. and biogeography at age ten. Trends Ecol Evol 26:340–348. 48. Esp´ındola A, Carstens BC, Alvarez N (2014) Comparative phylogeography of mutual- 15. Lohse K, Sharanowski B, Stone GN (2010) Quantifying the population history of the ists and the effect of the host on the genetic structure of its partners. Biol J Linn Soc oak gall parasitoid Cecidostiba fungosa. Evolution 58:439–442. 113:1021–1035. 16. Stone GN, et al. (2007) The phylogeographical clade trade: Tracing the impact 49. Beeravolu Reddy C, Hickerson MJ, Frantz LAF, Lohse K (2017) Blockwise site fre- of human-mediated dispersal on the colonization of northern Europe by the oak quency spectra for inferring complex population histories and recombination. gallwasp Andricus kollari. Mol Ecol 16:2768–2781. bioRxiv:077958. Preprint, posted September 25, 2017. 17. Hayward A, Stone GN (2006) Comparative phylogeography across two trophic lev- 50. Xue AT, Hickerson MJ (2015) The aggregate site frequency spectrum for comparative els: The oak gall wasp Andricus kollari and its chalcid parasitoid Megastigmus population genomic inference. Mol Ecol 24:6223–6240. stigmatizans. Mol Ecol 15:479–489. 51. Papadopoulou A, Knowles LL (2016) Toward a paradigm shift in compara- 18. Nicholls JA, et al. (2010) Concordant phylogeography and cryptic speciation in two tive phylogeography driven by trait-based hypotheses. Proc Natl Acad Sci USA western Palaearctic oak gall parasitoid species complexes. Mol Ecol 19:592–609. 113:8018–8024. 19. Stone GN, et al. (2009) Extreme host plant conservatism during at least 20 million 52. Satler JD, Carstens BC (2017) Do ecological communities disperse across biogeo- years of host plant pursuit by oak gallwasps. Evolution 63:854–869. graphic barriers as a unit? Mol Ecol 26:3533–3545. 20. Stone GN, et al. (2012) Reconstructing community assembly in time and space reveals 53. Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT (2017) Isolation with asym- enemy escape in a western palaearctic insect community. Curr Biol 22:531–537. metric gene flow during the nonsynchronous divergence of dry forest birds. Mol Ecol 21. Prior KM, Hellmann JJ (2013) Does enemy loss cause release? A biogeographical 26:1386–1400. comparison of parasitoid effects on an introduced insect. Ecology 94:1015–1024. 54. Rougemont Q, et al. (2017) Inferring the demographic history underlying parallel 22. Vosteen I, Gershenzon J, Kunert G (2016) Enemy-free space promotes maintenance of genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Mol host races in an aphid species. Oecologia 181:659–672. Ecol 26:142–162. 23. Lohse K, Chmelik M, Martin SH, Barton NH (2016) Efficient strategies for calculating 55. Bunnefeld L, Frantz LAF, Lohse K (2015) Inferring bottlenecks from genome-wide blockwise likelihoods under the coalescent. Genetics 202:775–786. samples of short sequence blocks. Genetics 201:1157–1169. 24. Lohse K, Harrison RJ, Barton NH (2011) A general method for calculating likelihoods 56. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina under the coalescent process. Genetics 58:977–987. sequence data. Bioinformatics 30:2114–2120. 25. Romiguier J, et al. (2014) Comparative population genomics in animals uncovers the 57. Martin M (2011) Cutadapt removes adapter sequences from high-throughput determinants of genetic diversity. Nature 515:261–263. sequencing reads. EMBnet J 17:10. 26. Leffler EM, et al. (2012) Revisiting an old riddle: What determines genetic diversity 58. Andrews S (2010) FastQC: A quality control application for high throughput levels within species? PLoS Biol 10:1–9. sequence data. Available at www.bioinformatics.babraham.ac.uk/projects/fastqc. 27. Thompson J (2005) The Geographic Mosaic of Coevolution (Univ of Chicago Press, Accessed December 12, 2013. Chicago). 59. Bankevich A, et al. (2012) SPAdes: A new genome assembly algorithm and its 28. Hoberg EP, Brooks DR (2008) A macroevolutionary mosaic: Episodic host-switching, applications to single-cell sequencing. J Comput Biol 19:455–477. geographical colonization and diversification in complex host–parasite systems. J 60. Zimin AV, et al. (2013) The MaSuRCA genome assembler. Bioinformatics 29:2669– Biogeogr 35:1533–1550. 2677. 29. Keightley PD, et al. (2009) Analysis of the genome sequences of three Drosophila 61. Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in melanogaster spontaneous mutation accumulation lines. Genome Res 19:1195– large genomes. Bioinformatics 21:i351–i358. 1201. 62. Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements 30. Stone GN, van der Ham RWJM, Brewer JG (2008) Fossil oak galls preserve ancient in genomic sequences. Curr Protoc Bioinformatics Chap 4:Unit 4.10. multitrophic interactions. Proc R Soc B Biol Sci 275:2213–2219. 63. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein 31. Lohse K, Barton NH, Melika N, Stone GN (2012) A likelihood-based comparison of database search programs. Nucleic Acids Res 25:3389–3402. population histories in a parasitoid guild. Mol Ecol 49:832–842. 64. Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M (2013) Blobology: Exploring 32. Ricklefs RE (2008) Disintegration of the ecological community. Am Nat 172:741–750. raw genome data for contaminants, symbionts and parasites using taxon-annotated 33. Askew RR (1961) On the biology of the inhabitants of oak galls of Cynipidae gc-coverage plots. Front Genet 4:237. (Hymenoptera) in Britain. Trans Soc Br Entomol 14:237–258. 65. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler 34. Corbett-Detig RB, Hartl DL, Sackton TB (2015) Natural selection constrains neutral transform. Bioinformatics 25:1754–1760. diversity across a wide range of species. PLoS Biol 13:1–25. 66. Auwera GAVD, et al. (2013) From FastQ data to high confidence variant calls: 35. Koch MA, et al. (2006) Three times out of Asia minor: The phylogeography of Arabis The genome analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43: alpina l. (Brassicaceae). Mol Ecol 15:825–839. 11.10.1–11.10.33.

E6514 | www.pnas.org/cgi/doi/10.1073/pnas.1800334115 Bunnefeld et al. Downloaded by guest on September 30, 2021 Downloaded by guest on September 30, 2021 9 ot J ikno-ebt 21)Ifrneo eeflwi h rcs of process the in flow gene of Inference (2017) and H analyzing for Wilkinson-Herbots package RJ, software A Costa Phylonet: 69. (2008) L Nakhleh D, Ruths C, Than 68. (2017) I Research Wolfram 67. unfl tal. et Bunnefeld pcain nefiin aiu-ieiodmto o h isolation-with-initial- the for method model. maximum-likelihood migration efficient An speciation: relationships. evolutionary reticulate reconstructing IL). Champaign, Genetics 205:1597–1618. ahmtc,Vrin11.1.1.0 Version Mathematica, M Bioinformatics BMC WlrmRsac,Inc., Research, (Wolfram 9:322. 2 elhrJ teig M cenG(06 fcetcaecn simulation coalescent Efficient (2016) G McVean from AM, mixtures and Etheridge splits population J, of Kelleher Inference 72. (2012) JK Pritchard JK, data. genomic Pickrell using flow gene 71. with speciation of test ratio likelihood A (2010) Z Yang 70. n eelgclaayi o ag apesizes. sample large for analysis 1–22. genealogical and data. frequency allele genome-wide Evol Biol Genome 2:200–211. LSGenet PLoS PNAS 8:1–17. | o.115 vol. LSCmu Biol Comput PLoS | o 28 no. | E6515 12:

ECOLOGY