ABSTRACT The three-spined stickleback (_Gasterosteus aculeatus_) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to

freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine

ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined

stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern

freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated

linkage disequilibrium associated with marine–freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in

isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine–freshwater

differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range. Access through your institution Buy or subscribe This is a

preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value

online-access subscription $32.99 / 30 days cancel any time Learn more Subscribe to this journal Receive 12 digital issues and online access to articles $119.00 per year only $9.92 per issue

Learn more Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL

ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS INTERCONTINENTAL GENOMIC PARALLELISM IN

MULTIPLE THREE-SPINED STICKLEBACK ADAPTIVE RADIATIONS Article 30 November 2020 GENOMIC DATA AND MULTI-SPECIES DEMOGRAPHIC MODELLING UNCOVER PAST HYBRIDIZATION BETWEEN CURRENTLY ALLOPATRIC

FRESHWATER SPECIES Article 30 August 2021 FINE-SCALE CONTEMPORARY RECOMBINATION VARIATION AND ITS FITNESS CONSEQUENCES IN ADAPTIVELY DIVERGING STICKLEBACK FISH Article Open access 05 June

2024 DATA AVAILABILITY The RAD-seq data have been uploaded to the GenBank under accession numbers SAMN14078677 to SAMN14078738 (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA605695).

Previously published sequencing data are retrieved from studies specified in Supplementary Table 1. CODE AVAILABILITY The scripts used for analysing empirical data (genotype likelihood

estimation, filtering, LDna) and simulated data are available in DRYAD repository: https://doi.org/10.5061/dryad.b2rbnzsb1. CHANGE HISTORY * _ 22 APRIL 2021 A Correction to this paper has

been published: https://doi.org/10.1038/s41559-021-01447-7 _ REFERENCES * Schluter, D. & Conte, G. L. Genetics and ecological speciation. _Proc. Natl Acad. Sci. USA_ 106, 9955–9962

(2009). Article  CAS  PubMed  PubMed Central  Google Scholar  * Arendt, J. & Reznick, D. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?

_Trends Ecol. Evol._ 23, 26–32 (2008). Article  PubMed  Google Scholar  * DeFaveri, J., Shikano, T., Shimada, Y., Goto, A. & Merila, J. Global analysis of genes involved in freshwater

adaptation in threespine sticklebacks (_Gasterosteus aculeatus_). _Evolution_ 65, 1800–1807 (2011). Article  PubMed  Google Scholar  * Stern, D. L. The genetic causes of convergent

evolution. _Nat. Rev. Genet._ 14, 751–764 (2013). Article  CAS  PubMed  Google Scholar  * Bell, M. A. & Foster, S. A. _The Evolutionary Biology of the Threespine Stickleback_ (Oxford

Univ. Press, 1994). * Gibson, G. The synthesis and evolution of a supermodel. _Science_ 307, 1890–1891 (2005). Article  CAS  PubMed  Google Scholar  * Hendry, A. P., Peichel, C. L.,

Matthews, B., Boughman, J. W. & Nosil, P. Stickleback research: the now and the next. _Evol. Ecol. Res._ 15, 111–141 (2013). Google Scholar  * Lescak, E. A. et al. Evolution of

stickleback in 50 years on earthquake-uplifted islands. _Proc. Natl Acad. Sci. USA_ 112, E7204–E7212 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  * Östlund-Nilsson, S.,

Mayer, I. & Huntingford, F. A. _Biology of the Three-spined Stickleback_ (CRC Press, 2006). * McKinnon, J. S. & Rundle, H. D. Speciation in nature: the threespine stickleback model

systems. _Trends Ecol. Evol._ 17, 480–488 (2002). Article  Google Scholar  * Jones, F. C. et al. The genomic basis of adaptive evolution in threespine sticklebacks. _Nature_ 484, 55–61

(2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ferchaud, A. L. & Hansen, M. M. The impact of selection, gene flow and demographic history on heterogeneous genomic

divergence: three-spine sticklebacks in divergent environments. _Mol. Ecol._ 25, 238–259 (2016). Article  CAS  PubMed  Google Scholar  * Hohenlohe, P. A. et al. Population genomics of

parallel adaptation in threespine stickleback using sequenced RAD tags. _PLoS Genet._ 6, e1000862 (2010). Article  PubMed  PubMed Central  CAS  Google Scholar  * Hohenlohe, P. A. &

Magalhaes, I. S. in _Population Genomics_ (eds Oleksiak, M. F. & Rajora, O.P.) 249–276 (Springer, 2020). * Liu, S., Ferchaud, A. L., Gronkjaer, P., Nygaard, R. & Hansen, M. M.

Genomic parallelism and lack thereof in contrasting systems of three-spined sticklebacks. _Mol. Ecol._ 27, 4725–4743 (2018). Article  PubMed  Google Scholar  * Pujolar, J. M., Ferchaud, A.

L., Bekkevold, D. & Hansen, M. M. Non-parallel divergence across freshwater and marine three-spined stickleback _Gasterosteus aculeatus_ populations. _J. Fish Biol._ 91, 175–194 (2017).

Article  CAS  PubMed  Google Scholar  * Terekhanova, N. V., Barmintseva, A. E., Kondrashov, A. S., Bazykin, G. A. & Mugue, N. S. Architecture of parallel adaptation in ten lacustrine

threespine stickleback populations from the White Sea area. _Genome Biol. Evol._ 11, 2605–2618 (2019). Article  PubMed  PubMed Central  Google Scholar  * Terekhanova, N. V. et al. Fast

evolution from precast bricks: genomics of young freshwater populations of threespine stickleback _Gasterosteus aculeatus_. _PLoS Genet._ 10, e1004696 (2014). Article  PubMed  PubMed Central

  CAS  Google Scholar  * Chan, Y. F. et al. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. _Science_ 327, 302–305 (2010). Article  CAS 

PubMed  Google Scholar  * Colosimo, P. F. et al. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. _Science_ 307, 1928–1933 (2005). Article  CAS 

PubMed  Google Scholar  * Nelson, T. C. & Cresko, W. A. Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations. _Evol. Lett._ 2, 9–21 (2018).

Article  PubMed  PubMed Central  Google Scholar  * Kemppainen, P. et al. Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and

geographic structure. _Mol. Ecol. Resour._ 15, 1031–1045 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  * Betancur, R. R., Orti, G. & Pyron, R. A. Fossil-based comparative

analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes. _Ecol. Lett._ 18, 441–450 (2015). Article  Google Scholar  * Matschiner, M., Hanel, R. & Salzburger,

W. On the origin and trigger of the notothenioid adaptive radiation. _PLoS ONE_ 6, e18911 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Meynard, C. N., Mouillot, D.,

Mouquet, N. & Douzery, E. J. A phylogenetic perspective on the evolution of Mediterranean teleost fishes. _PLoS ONE_ 7, e36443 (2012). Article  CAS  PubMed  PubMed Central  Google

Scholar  * Sanciangco, M. D., Carpenter, K. E. & Betancur, R. R. Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae). _Mol. Phylogenet. Evol._ 94,

565–576 (2016). Article  PubMed  Google Scholar  * Fang, B., Merila, J., Matschiner, M. & Momigliano, P. Estimating uncertainty in divergence times among three-spined stickleback clades

using the multispecies coalescent. _Mol. Phylogenet. Evol._ 142, 106646 (2020). Article  PubMed  Google Scholar  * Fang, B., Merila, J., Ribeiro, F., Alexandre, C. M. & Momigliano, P.

Worldwide phylogeny of three-spined sticklebacks. _Mol. Phylogenet. Evol._ 127, 613–625 (2018). Article  PubMed  Google Scholar  * Orti, G., Bell, M. A., Reimchen, T. E. & Meyer, A.

Global survey of mitochondrial DNA sequences in the threespine stickleback: evidence for recent migrations. _Evolution_ 48, 608–622 (1994). Article  PubMed  Google Scholar  * Halliburton, R.

& Halliburton, R. _Introduction to Population Genetics_ (Pearson/Prentice Hall, 2004). * Hyten, D. L. et al. Impacts of genetic bottlenecks on soybean genome diversity. _Proc. Natl

Acad. Sci. USA_ 103, 16666–16671 (2006). Article  CAS  PubMed  PubMed Central  Google Scholar  * Johannesson, K. et al. Repeated evolution of reproductive isolation in a marine snail:

unveiling mechanisms of speciation. _Philos. Trans. R. Soc. Lond. B_ 365, 1735–1747 (2010). Article  Google Scholar  * Kemppainen, P., Lindskog, T., Butlin, R. & Johannesson, K. Intron

sequences of arginine kinase in an intertidal snail suggest an ecotype-specific selective sweep and a gene duplication. _Heredity_ 106, 808–816 (2011). Article  CAS  PubMed  Google Scholar 

* Roesti, M., Gavrilets, S., Hendry, A. P., Salzburger, W. & Berner, D. The genomic signature of parallel adaptation from shared genetic variation. _Mol. Ecol._ 23, 3944–3956 (2014).

Article  PubMed  PubMed Central  Google Scholar  * Varadharajan, S. et al. A high-quality assembly of the nine-spined stickleback (_Pungitius pungitius_) genome. _Genome Biol. Evol_. 11,

3291–3308 (2019). * Feder, J. L. & Nosil, P. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. _Evolution_ 64, 1729–1747 (2010). Article

  PubMed  Google Scholar  * Ramachandran, S. et al. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.

_Proc. Natl Acad. Sci. USA_ 102, 15942–15947 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bierne, N., Gagnaire, P. A. & David, P. The geography of introgression in a

patchy environment and the thorn in the side of ecological speciation. _Curr. Zool._ 59, 72–86 (2013). Article  Google Scholar  * Baker, V. R. & Bunker, R. C. Cataclysmic Late

Pleistocene flooding from glacial Lake Missoula—a review. _Quat. Sci. Rev._ 4, 1–41 (1985). Article  Google Scholar  * Bretz, J. H. The Lake Missoula floods and the channeled scabland. _J.

Geol._ 77, 505–543 (1969). Article  Google Scholar  * Oviatt, C. G. Chronology of Lake Bonneville, 30,000 to 10,000 yr BP. _Quat. Sci. Rev._ 110, 166–171 (2015). Article  Google Scholar  *

Upham, W. _The Glacial Lake Agassiz_ Vol. 25 (US Government Printing Office, 1896). * Hohenlohe, P. A., Bassham, S., Currey, M. & Cresko, W. A. Extensive linkage disequilibrium and

parallel adaptive divergence across threespine stickleback genomes. _Philos. Trans. R. Soc. Lond. B_ 367, 395–408 (2012). Article  CAS  Google Scholar  * Bolnick, D. I., Barrett, R. D. H.,

Oke, K. B., Rennison, D. J. & Stuart, Y. E. (Non)parallel evolution. _Annu. Rev. Ecol. Evol. Syst._ 49, 303–330 (2018). Article  Google Scholar  * Roda, F., Walter, G. M., Nipper, R.

& Ortiz-Barrientos, D. Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. _Mol. Ecol._ 26, 3687–3699 (2017). Article  CAS  PubMed  Google Scholar

  * Barghi, N. et al. Genetic redundancy fuels polygenic adaptation in _Drosophila_. _PLoS Biol._ 17, e3000128 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Kautt, A. F.,

Elmer, K. R. & Meyer, A. Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid

fishes. _Mol. Ecol._ 21, 4770–4786 (2012). Article  PubMed  Google Scholar  * Le Moan, A., Gagnaire, P. A. & Bonhomme, F. Parallel genetic divergence among coastal–marine ecotype pairs

of European anchovy explained by differential introgression after secondary contact. _Mol. Ecol._ 25, 3187–3202 (2016). Article  PubMed  CAS  Google Scholar  * Westram, A. et al. Do the same

genes underlie parallel phenotypic divergence in different _Littorina saxatilis_ populations? _Mol. Ecol._ 23, 4603–4616 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Morales, H. E. et al. Genomic architecture of parallel ecological divergence: beyond a single environmental contrast. _Sci. Adv._ 5, eaav9963 (2019). Article  PubMed  PubMed Central  Google

Scholar  * Roesti, M., Kueng, B., Moser, D. & Berner, D. The genomics of ecological vicariance in threespine stickleback fish. _Nat. Commun._ 6, 8767 (2015). Article  CAS  PubMed  Google

Scholar  * Twyford, A. D. & Friedman, J. Adaptive divergence in the monkey flower _Mimulus guttatus_ is maintained by a chromosomal inversion. _Evolution_ 69, 1476–1486 (2015). Article

  PubMed  PubMed Central  Google Scholar  * Faria, R. et al. Multiple chromosomal rearrangements in a hybrid zone between _Littorina saxatilis_ ecotypes. _Mol. Ecol._ 28, 1375–1393 (2018).

Article  CAS  Google Scholar  * Westram, A. M. et al. Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. _Evol. Lett._ 2, 297–309 (2018).

Article  PubMed  PubMed Central  Google Scholar  * Paccard, A. et al. Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake

versus stream habitats. _J. Hered._ 111, 43–56 (2020). CAS  PubMed  Google Scholar  * Conte, G. L. et al. Extent of QTL reuse during repeated phenotypic divergence of sympatric threespine

stickleback. _Genetics_ 201, 1189–1200 (2015). Article  PubMed  PubMed Central  CAS  Google Scholar  * Conte, G. L., Arnegard, M. E., Peichel, C. L. & Schluter, D. The probability of

genetic parallelism and convergence in natural populations. _Proc. Biol. Sci._ 279, 5039–5047 (2012). PubMed  PubMed Central  Google Scholar  * Hubbard, T. et al. Ensembl 2005. _Nucleic

Acids Res._ 33, D447–D453 (2005). Article  CAS  PubMed  Google Scholar  * Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. _Bioinformatics_ 25,

1754–1760 (2009). CAS  PubMed  PubMed Central  Google Scholar  * Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: an analysis tool set for population

genomics. _Mol. Ecol._ 22, 3124–3140 (2013). Article  PubMed  PubMed Central  Google Scholar  * Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and

population genetical parameter estimation from sequencing data. _Bioinformatics_ 27, 2987–2993 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Korneliussen, T. S.,

Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. _BMC Bioinform._ 15, 356 (2014). Article  Google Scholar  * Kitano, J. et al. A role for a neo-sex

chromosome in stickleback speciation. _Nature_ 461, 1079–1083 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  * Natri, H. M., Shikano, T. & Merilä, J. Progressive

recombination suppression and differentiation in recently evolved neo-sex chromosomes. _Mol. Biol. Evol._ 30, 1131–1144 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Hedrick, P. W. Sex: differences in mutation, recombination, selection, gene flow, and genetic drift. _Evolution_ 61, 2750–2771 (2007). Article  PubMed  Google Scholar  * Schaffner, S. F. The

X chromosome in population genetics. _Nat. Rev. Genet._ 5, 43–51 (2004). Article  CAS  PubMed  Google Scholar  * Li, Z., Kemppainen, P., Rastas, P. & Merila, J. Linkage disequilibrium

clustering-based approach for association mapping with tightly linked genomewide data. _Mol. Ecol. Resour._ 18, 809–824 (2018). Article  CAS  PubMed  Google Scholar  * Fox, E. A., Wright, A.

E., Fumagalli, M. & Vieira, F. G. ngsLD: evaluating linkage disequilibrium using genotype likelihoods. _Bioinformatics_ 35, 3855–3856 (2019). Article  CAS  PubMed  Google Scholar  *

Roesti, M., Moser, D. & Berner, D. Recombination in the threespine stickleback genome—patterns and consequences. _Mol. Ecol._ 22, 3014–3027 (2013). Article  CAS  PubMed  Google Scholar 

* Matthey‐Doret, R. & Whitlock, M. C. Background selection and FST: consequences for detecting local adaptation. _Mol. Ecol._ 28, 3902–3914 (2019). Article  PubMed  CAS  Google Scholar 

* Stankowski, S. et al. Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. _PLoS Biol._ 17, e3000391 (2019). Article  PubMed  PubMed Central

  CAS  Google Scholar  * Neuenschwander, S., Hospital, F., Guillaume, F. & Goudet, J. quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic

architecture in a dynamic metapopulation. _Bioinformatics_ 24, 1552–1553 (2008). Article  CAS  PubMed  Google Scholar  * Hu, A. et al. Influence of Bering Strait flow and North Atlantic

circulation on glacial sea-level changes. _Nat. Geosci._ 3, 118–121 (2010). Article  CAS  Google Scholar  * Meiri, M. et al. Faunal record identifies Bering isthmus conditions as constraint

to end-Pleistocene migration to the New World. _Proc. Biol. Sci._ 281, 20132167 (2014). PubMed  PubMed Central  Google Scholar  * Zheng, X. et al. A high-performance computing toolset for

relatedness and principal component analysis of SNP data. _Bioinformatics_ 28, 3326–3328 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS We

are grateful to the following people who helped in obtaining the samples used in this study: J. DeFaveri, A. Adill, W. Aguirre, T. Bakker, A. Bell, M. Bell, B. Borg, F. Franzén, A. Goto, A.

Hendry, G. Herczeg, F. von Hippel, A. Hirvonen, J. Hämäläinen, M. Kaukoranta, A. Kijewska, D. Kingsley, Y. Kosaka, L. Kvarnemo, D. Lajus, T. Leinonen, A. Levsen, S. McCairns, A. Millet, J.

Morozinska, C. Munk, H. Mäkinen, A. Nolte, K. Østbye, W. Pekkola, J. Pokela, M. Ravinet, K. Räsänen, D. Schluter, M. Seymor, T. Shikano, P. Sjöstrand, G. Staines, B. Stelbrink, I. Syvänperä,

A. Vasemägi, M. Webster, J. Willacker, H. Winkler and L. Zaveik. Our research was supported by Academy of Finland grant nos. 250435, 263722, 265211 and 1307943 to J.M. and grant no. 316294

to P.M., the Finnish Cultural Foundation grant no. 00190489 to P.K. and the Chinese Scholarship Council grant no. 201606270188 to B.F. We thank J. DeFaveri for feedback and linguistic

corrections. AUTHOR INFORMATION Author notes * These authors contributed equally: Bohao Fang, Petri Kemppainen. AUTHORS AND AFFILIATIONS * Ecological Genetics Research Unit, Organismal and

Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland Bohao Fang, Petri Kemppainen, Paolo Momigliano, Xueyun

Feng & Juha Merilä Authors * Bohao Fang View author publications You can also search for this author inPubMed Google Scholar * Petri Kemppainen View author publications You can also

search for this author inPubMed Google Scholar * Paolo Momigliano View author publications You can also search for this author inPubMed Google Scholar * Xueyun Feng View author publications

You can also search for this author inPubMed Google Scholar * Juha Merilä View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS P.K. and J.M.

conceived the concept of the study, with contributions from P.M. and B.F. B.F. and P.K. carried out analyses with significant contributions from P.M. P.K. and B.F. led the writing, with

significant contributions from P.M. and J.M. X.F. contributed to LiftOver analysis. B.F. visualized the data. All authors accepted the final version of this manuscript. CORRESPONDING AUTHORS

Correspondence to Bohao Fang or Petri Kemppainen. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature

remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EXTENDED DATA EXTENDED DATA FIG. 1 VISUALIZATION OF ALL LD-CLUSTERS IDENTIFIED BY

LDNA. In each panel, I) the top and II) middle plots represent the marine–freshwater differentiation (_F_ST) of the clustered loci of the individuals in the Atlantic and Eastern Pacific,

respectively. III) The bottom left plot shows population differentiation based on loci in each LD-cluster (principal component analysis; PCA). Only one chromosome is presented on the x axis

when the clustered loci were located on a single chromosome. IV) The bottom right plot depicts the number of in-group samples (as positive value) and the remaining samples (as negative

value). Global samples from various regions are shown in different colours; freshwater ecotypes are indicated by light-colour and marine ecotype by dark-colour. The same colour scheme was

used in the PCA. The p-values were obtained from permutation tests of cluster separation (Supplementary Information 1). EXTENDED DATA FIG. 2 ABILITY OF LDNA TO RECOVER MARINE–FRESHWATER

DIFFERENTIATED REGIONS FROM JONES ET AL.11. Jones et al.11 identified 812 regions showing parallel marine–freshwater differentiation in the Eastern Pacific (“_i-_regions”) and 81 regions

showing global parallelism (“_m-f_ regions”). (A) The proportions of _m-f_ and _i-_regions that were correctly recovered by LDna (red; at least one SNP from 29 LD-clusters mapped to these

regions), the proportion or regions for which we had data but LDna analyses failed to recover (cyan), and regions for which we had no genetic data (blue). (B) Number of high LD-SNPs

(produced by the first LDna-filtering step) and raw SNPs (bottom row) in regions that were and were not recovered by LDna and (C) size of the regions that were and were not recovered by LDna

(on _log__10_ scale). (D) _F_ST from raw SNPs located within regions that were and were not recovered by LDna. Overall, _m-f_ regions and _i-_ regions that were not recovered by LDna were

generally smaller, contained fewer SNPs (that is had lower sequencing coverage) and exhibited lower _F_ST than the regions correctly recovered by LDna. EXTENDED DATA FIG. 3 GENOME-WIDE

MARINE–FRESHWATER DIFFERENTIATION (_F_ST) IN THE ATLANTIC, EASTERN PACIFIC AND WESTERN PACIFIC OCEANS. (A–C) SNP-based _F_ST of the individuals in the Atlantic (ATL), Eastern Pacific (EP)

and Western Pacific (WP), respectively. Ecotype pairs follow the main analyses (Extended Data Table 2). (D) Window-based _F_ST (win-size=100 kb) between EP freshwater samples (n = 13) and EP

marine samples (n = 4). (E) Window-based _F_ST between EP freshwater samples (n = 13) and all Pacific marine samples (n = 13). (D, E) are significantly correlated (_r_ = 0.904, p < 

0.0001). (F, G) SNP-based EP genetic parallelism (LD-clusters 2, 21, 29) for the same ecotype comparison as (D, E), respectively. Loci from LD-clusters involved in genetic parallelism are

colour-coded for all panels (refer to main Fig. 2). EXTENDED DATA FIG. 4 PCA PLOT OF LDNA CLUSTERS WITH POPULATION IDENTIFICATION. See Supplementary Table 1 for population identifiers.

EXTENDED DATA FIG. 5 POPULATION DIVERSITY AND ISOLATION-BY-DISTANCE (IBD) IN MARINE THREE-SPINED STICKLEBACK POPULATIONS. (A) Boxplots of individual heterozygosity (proportion heterozygous

positions per individual) of marine individuals in different geographical regions (EP = Eastern Pacific, WP = Western Pacific and ATL = Atlantic; GLM, _F_2,64 = 43.05, _P_ < 0.001). (B)

Boxplots of individual heterozygosity of LD-cluster 2 in different geographical regions (GLM, _F_2,64 = 91.9, _P_ < 0.001). (C) IBD between marine populations. Note that the different

scales of empirical and simulated heterozygosity in (A, B) are not relevant. This is because in the simulations of all allele frequencies started from 0.5 and while a burn in of 10k

generations was appropriate for loci linked to QTL, neutral loci would have required four times more generations to reach equilibrium (see Supplementary Information 3). However, the trends

in terms of loss of heterozygosity away from the ancestral Eastern Pacific marine populations is still informative and consistent with the empirical data. EXTENDED DATA FIG. 6 MERCATOR

PROJECTION OF GLOBAL THREE-SPINED STICKLEBACK POPULATIONS USED IN THE STUDY. 166 three-spined stickleback individuals from 63 localities were used, including 119 freshwater individuals and

47 marine individuals. For a complete list of samples, see Supplementary Table 1. EXTENDED DATA FIG. 7 SUMMARY OF ALL LD-CLUSTERS. Shaded rows (LD-clusters) contribute to genetic parallelism

of regional or trans-oceanic freshwater populations. EXTENDED DATA FIG. 8 SAMPLING SCHEMES FOR _F_ST ANALYSES. The table specifies sampling schemes used for _F_ST analyses and figures.

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary notes 1–5, references, Figs. 1–3 and Table 1. REPORTING SUMMARY RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS

ARTICLE CITE THIS ARTICLE Fang, B., Kemppainen, P., Momigliano, P. _et al._ On the causes of geographically heterogeneous parallel evolution in sticklebacks. _Nat Ecol Evol_ 4, 1105–1115

(2020). https://doi.org/10.1038/s41559-020-1222-6 Download citation * Received: 01 April 2019 * Accepted: 14 May 2020 * Published: 22 June 2020 * Issue Date: 01 August 2020 * DOI:

https://doi.org/10.1038/s41559-020-1222-6 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not

currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative