References
Amini, S., Pushkarev, D., Christiansen, L., Kostem, E., Royce, T., Turk, C., … others. (2014). Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.Nature Genetics , 46 (12), 1343–1349.
Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P. A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics , 17 (2), 81.
Angert, A. L., Bontrager, M. G., & Ågren, J. (2020). What Do We Really Know About Adaptation at Range Edges? Annual Review of Ecology, Evolution, and Systematics , 51 , 341–361.
Baker, H. G. (1965). Characteristics and modes of origin of weeds. In H. G. Baker & G. Stebbins (Eds.), The genetics of colonizing species: Proceedings of the First International Union of Biological Sciences Symposia on General Biology (pp. 147–172). ACADEMIC PRESS INC.
Baker, H., & Stebbins, G. (1965). The Genetics of Colonizing Species (1st ed.). New York: ACADEMIC PRESS INC.
Barrett, S. C. H. (2015). Foundations of invasion genetics: the Baker and Stebbins legacy. Molecular Ecology , 24 (9), 1927–1941.
Barton, N. H., & Etheridge, A. M. (2004). The effect of selection on genealogies. Genetics , 166 (2), 1115–1131.
Battey, C. J., Ralph, P. L., & Kern, A. D. (2020). Predicting geographic location from genetic variation with deep neural networks.ELife , 9 , e54507.
Bergland, A. O., Tobler, R., Gonzalez, J., Schmidt, P., & Petrov, D. (2016). Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. MOLECULAR ECOLOGY , 25 (5), 1157–1174. doi:10.1111/mec.13455
Bertolotti, A. C., Layer, R. M., Gundappa, M. K., Gallagher, M. D., Pehlivanoglu, E., Nome, T., … others. (2020). The structural variation landscape in 492 Atlantic salmon genomes. BioRxiv .
Bi, K., Linderoth, T., Singhal, S., Vanderpool, D., Patton, J. L., Nielsen, R., … Good, J. M. (2019). Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genetics , 15 (5), e1008119.
Bock, D. G., Caseys, C., Cousens, R. D., Hahn, M. A., Heredia, S. M., Hübner, S., … Rieseberg, L. H. (2015). What we still don’t know about invasion genetics. Molecular Ecology , 24 (9), 2277–2297.
Booker, T. R., Yeaman, S., & Whitlock, M. (2020). Variation in recombination rate affects detection of FST outliers under neutrality.BioRxiv .
Brandvain, Y., & Wright, S. I. (2016). The limits of natural selection in a nonequilibrium world. Trends in Genetics , 32 (4), 201–210.
Brown, A. M. V, Huynh, L. Y., Bolender, C. M., Nelson, K. G., & McCutcheon, J. P. (2014). Population genomics of a symbiont in the early stages of a pest invasion. MOLECULAR ECOLOGY , 23 (6, SI), 1516–1530. doi:10.1111/mec.12366
Browning, S. R., & Browning, B. L. (2007). Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics , 81 (5), 1084–1097.
Browning, S. R., & Browning, B. L. (2015). Accurate non-parametric estimation of recent effective population size from segments of identity by descent. The American Journal of Human Genetics , 97 (3), 404–418.
Buffalo, V., & Coop, G. (2020). Estimating the genome-wide contribution of selection to temporal allele frequency change. Proceedings of the National Academy of Sciences , 117 (34), 20672–20680. doi:10.1073/pnas.1919039117
Calfee, E., Agra, M. N., Palacio, M. A., Ramirez, S. R., & Coop, G. (2020). Selection and hybridization shaped the Africanized honey bee invasion of the Americas. BioRxiv .
Calfee, E., Agra, M. N., Palacio, M. A., Ramírez, S. R., & Coop, G. (2020). Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas. PLoS Genetics , 16 (10), e1009038.
Chan, A. H., Jenkins, P. A., & Song, Y. S. (2012). Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.PLoS Genetics , 8 (12), e1003090.
Choi, Y., Chan, A. P., Kirkness, E., Telenti, A., & Schork, N. J. (2018). Comparison of phasing strategies for whole human genomes.PLoS Genetics , 14 (4), e1007308.
Chown, S. L., Hodgins, K. A., Griffin, P. C., Oakeshott, J. G., Byrne, M., & Hoffmann, A. A. (2015). Biological invasions, climate change and genomics. EVOLUTIONARY APPLICATIONS , 8 (1), 23–46. doi:10.1111/eva.12234
Clavero, M., Brotons, L., Pons, P., & Sol, D. (2009). Prominent role of invasive species in avian biodiversity loss. Biological Conservation , 142 (10), 2043–2049.
Clavero, M., & García-Berthou, E. (2005). Invasive species are a leading cause of animal extinctions. Trends in Ecology & Evolution , 20 (3), 110.
Comeault, A. A., Wang, J., Tittes, S., Isbell, K., Ingley, S., Hurlbert, A. H., & Matute, D. R. (2020). Genetic Diversity and Thermal Performance in Invasive and Native Populations of African Fig Flies.MOLECULAR BIOLOGY AND EVOLUTION , 37 (7), 1893–1906. doi:10.1093/molbev/msaa050
Cristescu, M. E. (2015). Genetic reconstructions of invasion history.MOLECULAR ECOLOGY , 24 (9, SI), 2212–2225. doi:10.1111/mec.13117
Currat, M., Excoffier, L., Maddison, W., Otto, S. P., Ray, N., Whitlock, M. C., & Yeaman, S. (2006). Comment on” Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens” and” Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans”.Science , 313 (5784), 172.
DeGiorgio, M., Huber, C. D., Hubisz, M. J., Hellmann, I., & Nielsen, R. (2016). SweepFinder2: increased sensitivity, robustness and flexibility.Bioinformatics , 32 (12), 1895–1897.
Demené, A., Legrand, L., Gouzy, J., Debuchy, R., Saint-Jean, G., Fabreguettes, O., & Dutech, C. (2019). Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe. FUNGAL GENETICS AND BIOLOGY , 130 , 122–133. doi:10.1016/j.fgb.2019.06.002
Dennenmoser, S., Sedlazeck, F. J., Iwaszkiewicz, E., Li, X.-Y., Altmueller, J., & Nolte, A. W. (2017). Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. MOLECULAR ECOLOGY , 26 (18), 4712–4724. doi:10.1111/mec.14134
Dennenmoser, S., Sedlazeck, F. J., Schatz, M. C., Altmueller, J., Zytnicki, M., & Nolte, A. W. (2019). Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. MOLECULAR ECOLOGY , 28 (6, SI), 1491–1505. doi:10.1111/mec.14969
Depaulis, F., Mousset, S., & Veuille, M. (2003). Power of neutrality tests to detect bottlenecks and hitchhiking. Journal of Molecular Evolution , 57 (1), S190–S200.
Deschamps, S., Llaca, V., & May, G. D. (2012). Genotyping-by-sequencing in plants. Biology , 1 (3), 460–483.
Ding, J., Mack, R. N., Lu, P., Ren, M., & Huang, H. (2008). China’s booming economy is sparking and accelerating biological invasions.Bioscience , 58 (4), 317–324.
Duranton, M., Bonhomme, F., & Gagnaire, P.-A. (2019). The spatial scale of dispersal revealed by admixture tracts. Evolutionary Applications , 12 (9), 1743–1756.
Edmonds, C. A., Lillie, A. S., & Cavalli-Sforza, L. L. (2004). Mutations arising in the wave front of an expanding population.Proceedings of the National Academy of Sciences , 101 (4), 975–979.
Estoup, A., & Guillemaud, T. (2010). Reconstructing routes of invasion using genetic data: why, how and so what? Molecular Ecology ,19 (19), 4113–4130.
Estoup, A., Ravigné, V., Hufbauer, R., Vitalis, R., Gautier, M., & Facon, B. (2016). Is there a genetic paradox of biological invasion?Annual Review of Ecology, Evolution, and Systematics , 47 , 51–72.
Excoffier, L., & Ray, N. (2008). Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology & Evolution , 23 (7), 347–351.
Flagel, L., Brandvain, Y., & Schrider, D. R. (2019). The unreasonable effectiveness of convolutional neural networks in population genetic inference. Molecular Biology and Evolution , 36 (2), 220–238.
Foll, M., Gaggiotti, O. E., Daub, J. T., Vatsiou, A., & Excoffier, L. (2014). Widespread signals of convergent adaptation to high altitude in Asia and America. The American Journal of Human Genetics ,95 (4), 394–407.
Fontaine, M. C., Labbe, F., Dussert, Y., Deliere, L., Richart-Cervera, S., Giraud, T., & Delmotte, F. (2020). Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola. BioRxiv . doi:https://doi.org/10.1101/2020.09.22
Foutel-Rodier, F., & Etheridge, A. M. (2020). The spatial Muller’s ratchet: surfing of deleterious mutations during range expansion.Theoretical Population Biology , 135 , 19–31.
Fumagalli, M. (2013). Assessing the effect of sequencing depth and sample size in population genetics inferences. PLoS One ,8 (11), e79667.
Gattepaille, L. M., Jakobsson, M., & Blum, M. G. B. (2013). Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity , 110 (5), 409–419.
Gibson, M. J. S., de Lourdes Torres, M., Brandvain, Y., & Moyle, L. C. (2020). Reconstructing the history and biological consequences of a plant invasion on the Galápagos islands. BioRxiv . doi:https://doi.org/10.1101/2020.09.26.313627;
Gower, G. R., Picazo, P. I., Fumagalli, M., & Racimo, F. (2020). Detecting adaptive introgression in human evolution using convolutional neural networks. BioRxiv . doi:https://doi.org/10.1101/2020.09.18.301069
Grabenstein, K. C., & Taylor, S. A. (2018). Breaking barriers: causes, consequences, and experimental utility of human-mediated hybridization.Trends in Ecology & Evolution , 33 (3), 198–212.
Guillot, G., Jónsson, H., Hinge, A., Manchih, N., & Orlando, L. (2016). Accurate continuous geographic assignment from low-to high-density SNP data. Bioinformatics , 32 (7), 1106–1108.
Hahn, M. W. (2019). Molecular population genetics . Sinauer Associates New York.
Hallatschek, O., Hersen, P., Ramanathan, S., & Nelson, D. R. (2007). Genetic drift at expanding frontiers promotes gene segregation.Proceedings of the National Academy of Sciences , 104 (50), 19926–19930.
Hallatschek, O., & Nelson, D. R. (2008). Gene surfing in expanding populations. Theoretical Population Biology , 73 (1), 158–170.
Haller, B. C., Galloway, J., Kelleher, J., Messer, P. W., & Ralph, P. L. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources , 19 (2), 552–566.
Haller, B. C., & Messer, P. W. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher model. Molecular Biology and Evolution , 36 (3), 632–637.
Hamelin, R. C., & Roe, A. D. (2020). Genomic biosurveillance of forest invasive alien enemies: A story written in code. EVOLUTIONARY APPLICATIONS , 13 (1, SI), 95–115. doi:10.1111/eva.12853
Harris, K., & Nielsen, R. (2013). Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet , 9 (6), e1003521.
Haygood, R., Ives, A. R., & Andow, D. A. (2003). Consequences of recurrent gene flow from crops to wild relatives. Proceedings of the Royal Society of London. Series B: Biological Sciences ,270 (1527), 1879–1886.
Hegarty, M. J. (2012). Invasion of the hybrids. MOLECULAR ECOLOGY , 21 (19), 4669–4671. doi:10.1111/j.1365-294X.2012.05720.x
Hessenauer, P., Fijarczyk, A., Martin, H., Prunier, J., Charron, G., Chapuis, J., … Landry, C. R. (2020). Hybridization and introgression drive genome evolution of Dutch elm disease pathogens.NATURE ECOLOGY & EVOLUTION , 4 (4), 626–638. doi:10.1038/s41559-020-1133-6
Hivert, V., Leblois, R., Petit, E. J., Gautier, M., & Vitalis, R. (2018). Measuring genetic differentiation from pool-seq data.Genetics , 210 (1), 315–330.
Hosokawa, T., Kikuchi, Y., Nikoh, N., Shimada, M., & Fukatsu, T. (2006). Strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria. PLoS Biol , 4 (10), e337.
Hovick, S. M., & Whitney, K. D. (2014). Hybridisation is associated with increased fecundity and size in invasive taxa: meta-analytic support for the hybridisation-invasion hypothesis. Ecology Letters , 17 (11), 1464–1477.
Klopfstein, S., Currat, M., & Excoffier, L. (2006). The fate of mutations surfing on the wave of a range expansion. Molecular Biology and Evolution , 23 (3), 482–490.
Kolar, C. S., & Lodge, D. M. (2001). Progress in invasion biology: predicting invaders. Trends in Ecology & Evolution ,16 (4), 199–204.
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: analysis of next generation sequencing data. BMC Bioinformatics ,15 (1), 356.
Laster, M. L., & Sheng, C. F. (1995). Search for hybrid sterility for Helicoverpa zea in crosses between the North American H. zea and H. armigera (Lepidoptera: Noctuidae) from China. Journal of Economic Entomology , 88 (5), 1288–1291.
Lee, C. E. (2002). Evolutionary genetics of invasive species.Trends in Ecology & Evolution , 17 (8), 386–391.
Lee, C. E., & Gelembiuk, G. W. (2008). Evolutionary origins of invasive populations. Evolutionary Applications , 1 (3), 427–448.
Lee, Y., Schmidt, H., Collier, T. C., Conner, W. R., Hanemaaijer, M. J., Slatkin, M., … Cornel, A. J. (2019). Genome-wide divergence among invasive populations of Aedes aegypti in California. BMC GENOMICS , 20 . doi:10.1186/s12864-019-5586-4
Leitwein, M., Duranton, M., Rougemont, Q., Gagnaire, P.-A., & Bernatchez, L. (2020). Using haplotype information for conservation genomics. Trends in Ecology & Evolution , 35 (3), 245–258.
Lodge, D. M. (1993). Species invasions and deletions: community effects and responses to climate and habitat change. In Species invasions and deletions: community effects and responses to climate and habitat change. (pp. 367–387). Sinauer Associates Inc.
Lombaert, E., Guillemaud, T., Cornuet, J.-M., Malausa, T., Facon, B., & Estoup, A. (2010). Bridgehead effect in the worldwide invasion of the biocontrol harlequin ladybird. PloS One , 5 (3), e9743.
Long, A., Liti, G., Luptak, A., & Tenaillon, O. (2015). Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nature Reviews Genetics , 16 (10), 567–582.
Lou, R. N., Jacobs, A., Wilder, A., & Therkildsen, N. O. (2020). A beginner’s guide to low-coverage whole genome sequencing for population genomics. Authorea Preprints .
Luqman, H., Widmer, A., Fior, S., & Wegmann, D. (2020). Identifying loci under selection via explicit demographic models. BioRxiv . doi:https://doi.org/10.1101/2020.07.20.211581
Lutgen, D., Ritter, R., Olsen, R.-A., Schielzeth, H., Gruselius, J., Ewels, P. A., … others. (2020). Linked-read sequencing enables haplotype-resolved resequencing at population scale. BioRxiv .
Malinsky, M. (2019). Dsuite-fast D-statistics and related admixture evidence from VCF files. MOLECULAR ECOLOGY RESOURCES . doi:10.1111/1755-0998.13265
Mallet, J. (2005). Hybridization as an invasion of the genome.Trends in Ecology & Evolution , 20 (5), 229–237. doi:http://dx.doi.org/10.1016/j.tree.2005.02.010
Marques, D. A., Meier, J. I., & Seehausen, O. (2019). A combinatorial view on speciation and adaptive radiation. Trends in Ecology & Evolution .
Maxwell, S. L., Fuller, R. A., Brooks, T. M., & Watson, J. E. M. (2016). Biodiversity: The ravages of guns, nets and bulldozers.Nature News , 536 (7615), 143.
McCartney, M. A., Mallez, S., & Gohl, D. M. (2019). Genome projects in invasion biology. Conservation Genetics , 1–22.
McFarlane, S. E., & Pemberton, J. M. (2019). Detecting the true extent of introgression during anthropogenic hybridization. Trends in Ecology & Evolution , 34 (4), 315–326.
McGaughran, A. (2020). Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?BMC Genomics , 21 (1), 1–10.
McVean, G. A. T., & Cardin, N. J. (2005). Approximating the coalescent with recombination. Philosophical Transactions of the Royal Society B: Biological Sciences , 360 (1459), 1387–1393.
Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … others. (2020). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. BioRxiv .
Mérel, V., Gibert, P., Buch, I., Rada, V. R., Estoup, A., Gautier, M., … Vieira, C. (2020). The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. BioRxiv . doi:https://doi.org/10.1101/2020.11.06.370932
Moorjani, P., Sankararaman, S., Fu, Q., Przeworski, M., Patterson, N., & Reich, D. (2016). A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proceedings of the National Academy of Sciences ,113 (20), 5652–5657.
Muirhead, J. R., Minton, M. S., Miller, W. A., & Ruiz, G. M. (2015). Projected effects of the Panama Canal expansion on shipping traffic and biological invasions. Diversity and Distributions , 21 (1), 75–87.
Nielsen, R., Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G., & Bustamante, C. (2005). Genomic scans for selective sweeps using SNP data. Genome Research , 15 (11), 1566–1575.
Oerke, E. C. (2006). Crop losses to pests. The Journal of Agricultural Science , 144 , 31.
Olazcuaga, L., Loiseau, A., Parrinello, H., Paris, M., Fraimout, A., Guedot, C., … others. (2020). A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure.Molecular Biology and Evolution .
Otte, K. A., & Schlötterer, C. (2020). Detecting selected haplotype blocks in evolve and resequence experiments. Molecular Ecology Resources .
Patton, A. H., Margres, M. J., Stahlke, A. R., Hendricks, S., Lewallen, K., Hamede, R. K., … others. (2019). Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian Devils. Molecular Biology and Evolution ,36 (12), 2906–2921.
Paulose, J., & Hallatschek, O. (2020). The impact of long-range dispersal on gene surfing. Proceedings of the National Academy of Sciences , 117 (14), 7584–7593.
Peischl, S., Dupanloup, I., Kirkpatrick, M., & Excoffier, L. (2013). On the accumulation of deleterious mutations during range expansions.Molecular Ecology , 22 (24), 5972–5982.
Peischl, S., & Excoffier, L. (2015). Expansion load: recessive mutations and the role of standing genetic variation. Molecular Ecology , 24 (9), 2084–2094.
Peischl, S., & Gilbert, K. J. (2020). Evolution of dispersal can rescue populations from expansion load. The American Naturalist ,195 (2), 349–360.
Popovic, I., Matias, A. M. A., Bierne, N., & Riginos, C. (2020). Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia.EVOLUTIONARY APPLICATIONS , 13 (3, SI). doi:10.1111/eva.12857
Prentis, P. J., Wilson, J. R. U., Dormontt, E. E., Richardson, D. M., & Lowe, A. J. (2008). Adaptive evolution in invasive species. TRENDS IN PLANT SCIENCE , 13 (6), 288–294. doi:10.1016/j.tplants.2008.03.004
Puckett, E. E., Magnussen, E., Khlyap, L. A., Strand, T. M., Lundkvist, A., & Munshi-South, J. (2020). Genomic analyses reveal three independent introductions of the invasive brown rat (Rattus norvegicus) to the Faroe Islands. HEREDITY , 124 (1), 15–27. doi:10.1038/s41437-019-0255-6
Quilodrán, C. S., Tsoupas, A., & Currat, M. (2020). The Spatial Signature of Introgression After a Biological Invasion With Hybridization. Frontiers in Ecology and Evolution , 8 , 321.
Rhee, J.-K., Li, H., Joung, J.-G., Hwang, K.-B., Zhang, B.-T., & Shin, S.-Y. (2016). Survey of computational haplotype determination methods for single individual. Genes & Genomics , 38 (1), 1–12.
Ricciardi, A. (2007). Are modern biological invasions an unprecedented form of global change? Conservation Biology , 21 (2), 329–336.
Rieseberg, L. H., Raymond, O., Rosenthal, D. M., Lai, Z., Livingstone, K., Nakazato, T., … Lexer, C. (2003). Major ecological transitions in wild sunflowers facilitated by hybridization.Science , 301 (5637), 1211–1216.
Rieseberg, L. H., Wood, T. E., & Baack, E. J. (2006). The nature of plant species. Nature , 440 (7083), 524.
Rispe, C., Legeai, F., Nabity, P. D., Fernandez, R., Arora, A. K., Baa-Puyoulet, P., … Tagu, D. (2020). The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC BIOLOGY , 18 (1). doi:10.1186/s12915-020-00820-5
Rius, M., Bourne, S., Hornsby, H. G., & Chapman, M. A. (2015). Applications of next-generation sequencing to the study of biological invasions. CURRENT ZOOLOGY , 61 (3), 488+. doi:10.1093/czoolo/61.3.488
Rose, N. H., Sylla, M., Badolo, A., Lutomiah, J., Ayala, D., Aribodor, O. B., … McBride, C. S. (2020). Climate and Urbanization Drive Mosquito Preference for Humans. Current Biology , 30 (18), 3570–3579.e6. doi:https://doi.org/10.1016/j.cub.2020.06.092
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., … others. (2002). Detecting recent positive selection in the human genome from haplotype structure.Nature , 419 (6909), 832–837.
Sakai, A. K., Allendorf, F. W., Holt, J. S., Lodge, D. M., Molofsky, J., With, K. A., … others. (2001). The population biology of invasive species. Annual Review of Ecology and Systematics , 32 (1), 305–332.
Sardain, A., Sardain, E., & Leung, B. (2019). Global forecasts of shipping traffic and biological invasions to 2050. Nat Sustain 2: 274–282.
Schirmer, M., D’Amore, R., Ijaz, U. Z., Hall, N., & Quince, C. (2016). Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics , 17 (1), 125.
Schlötterer, C., Kofler, R., Versace, E., Tobler, R., & Franssen, S. U. (2015). Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity , 114 (5), 431–440.
Schmidt, T. L., Swan, T., Chung, J., Karl, S., Demok, S., Yang, Q., … Hoffmann, A. A. (2020). Spatial population genomics of a recent mosquito invasion. BioRxiv . doi:10.1101/2020.11.30.405191
Schrider, D. R., & Kern, A. D. (2018). Supervised machine learning for population genetics: a new paradigm. Trends in Genetics ,34 (4), 301–312.
Seebens, H., Essl, F., Dawson, W., Fuentes, N., Moser, D., Pergl, J., … others. (2015). Global trade will accelerate plant invasions in emerging economies under climate change. Global Change Biology ,21 (11), 4128–4140.
Seixas, F. A., Boursot, P., & Melo-Ferreira, J. (2018). The genomic impact of historical hybridization with massive mitochondria DNA introgression. GENOME BIOLOGY , 19 . doi:10.1186/s13059-018-1471-8
Setter, D., Mousset, S., Cheng, X., Nielsen, R., DeGiorgio, M., & Hermisson, J. (2020). VolcanoFinder: genomic scans for adaptive introgression. PLoS Genetics , 16 (6), e1008867.
Shchur, V., Svedberg, J., Medina, P., Corbett-Detig, R., & Nielsen, R. (2020). On the distribution of tract lengths during adaptive introgression. G3: Genes, Genomes, Genetics , 10 (10), 3663–3673.
Shine, R., Brown, G. P., & Phillips, B. L. (2011). An evolutionary process that assembles phenotypes through space rather than through time. Proceedings of the National Academy of Sciences ,108 (14), 5708–5711.
Siewert, K. M., & Voight, B. F. (2020). BetaScan2: Standardized statistics to detect balancing selection utilizing substitution data.Genome Biology and Evolution , 12 (2), 3873–3877.
Smith, A. L., Hodkinson, T. R., Villellas, J., Catford, J. A., Csergo, A. M., Blomberg, S. P., … Buckley, Y. M. (2020). Global gene flow releases invasive plants from environmental constraints on genetic diversity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 117 (8), 4218–4227. doi:10.1073/pnas.1915848117
Smith, C. C. R., & Flaxman, S. M. (2020). Leveraging whole genome sequencing data for demographic inference with approximate bayesian computation. Molecular Ecology Resources , 20 (1), 125–139.
Stajich, J. E., & Hahn, M. W. (2005). Disentangling the effects of demography and selection in human history. Molecular Biology and Evolution , 22 (1), 63–73.
Stern, D. Ben, & Lee, C. E. (2020). Evolutionary origins of genomic adaptations in an invasive copepod. NATURE ECOLOGY & EVOLUTION ,4 (8), 1084–1094. doi:10.1038/s41559-020-1201-y
Svedberg, J., Shchur, V., Reinman, S., Nielsen, R., & Corbett-Detig, R. (2020). Inferring Adaptive Introgression Using Hidden Markov Models.BioRxiv . doi:https://doi.org/10.1101/2020.08.02.232934;
Tay, W. T., & Gordon, K. H. J. (2019). Going global - genomic insights into insect invasions. CURRENT OPINION IN INSECT SCIENCE ,31 , 123–130. doi:10.1016/j.cois.2018.12.002
Tay, W. T., Rane, R., Padovan, A., Walsh, T., Elfekih, S., Downes, S., … others. (2020). Global FAW population genomic signature supports complex introduction events across the Old World.BioRxiv . doi:https://doi.org/10.1101/2020.06.12.147660
Todesco, M., Pascual, M. A., Owens, G. L., Ostevik, K. L., Moyers, B. T., Hübner, S., … others. (2016). Hybridization and extinction.Evolutionary Applications , 9 (7), 892–908.
Travis, J. M. J., Münkemüller, T., Burton, O. J., Best, A., Dytham, C., & Johst, K. (2007). Deleterious mutations can surf to high densities on the wave front of an expanding population. Molecular Biology and Evolution , 24 (10), 2334–2343.
Valencia-Montoya, W. A., Elfekih, S., North, H. L., Meier, J. I., Warren, I. A., Tay, W. T., … Jiggins, C. D. (2020). Adaptive introgression across semipermeable species boundaries between local Helicoverpa zea and invasive Helicoverpa armigera moths. Molecular Biology and Evolution . doi:10.1093/molbev/msaa108
Vallejo-Marin, M., & Hiscock, S. J. (2016). Hybridization and hybrid speciation under global change. NEW PHYTOLOGIST , 211 (4), 1170–1187. doi:10.1111/nph.14004
Viard, F., Riginos, C., & Bierne, N. (2020). Anthropogenic hybridization at sea: three evolutionary questions relevant to invasive species management. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES , 375 (1806, SI). doi:10.1098/rstb.2019.0547
Wang, J., Gaughan, S., Lamer, J. T., Deng, C., Hu, W., Wachholtz, M., … Lu, G. (2020). Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin. EVOLUTIONARY APPLICATIONS ,13 (2), 263–277. doi:10.1111/eva.12863
Wei, S.-J., Zhou, Y., Fan, X.-L., Hoffmann, A. A., Cao, L.-J., Chen, X.-X., & Xu, Z.-F. (2017). Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host. ECOLOGY AND EVOLUTION , 7 (14), 5400–5409. doi:10.1002/ece3.3097
Welles, S. R., & Dlugosch, K. M. (2018). Population genomics of colonization and invasion. In Population genomics (pp. 655–683). Springer.
Wu, N., Zhang, S., Li, X., Cao, Y., Liu, X., Wang, Q., … Zhan, S. (2019). Fall webworm genomes yield insights into rapid adaptation of invasive species. NATURE ECOLOGY & EVOLUTION , 3 (1), 105–115. doi:10.1038/s41559-018-0746-5
Yainna, S., Tay, W. T., Fiteni, E., Legeai, F., Clamens, A.-L., Gimenez, S., … others. (2020). Genomic balancing selection is key to the invasive success of the fall armyworm. BioRxiv . doi:https://doi.org/10.1101/2020.06.17.154880
Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., … others. (2010). Sequencing of 50 human exomes reveals adaptation to high altitude. Science , 329 (5987), 75–78.
Yoshida, K., Miyagi, R., Mori, S., Takahashi, A., Makino, T., Toyoda, A., … Kitano, J. (2016). Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback. ECOLOGY AND EVOLUTION , 6 (7), 2190–2204. doi:10.1002/ece3.2047
You, M., Ke, F., You, S., Wu, Z., Liu, Q., He, W., … others. (2020). Variation among 532 genomes unveils the origin and evolutionary history of a global insect herbivore. Nature Communications ,11 (1), 1–8.
Yuan, Z., Huang, W., Liu, S., Xu, P., Dunham, R., & Liu, Z. (2018). Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially markovian coalescent approach. GENETICA ,146 (2), 235–241. doi:10.1007/s10709-017-0006-7