Disclosure Declaration
The authors confirm that there are no known conflicts of interest associated with this publication.
Baker, H. G. (1965). Characteristics and modes of origin of weeds. In H. G. Baker and G. L. Stebbins (eds.), Genetics of Colonizing species, p. 137-172. Academic Press, New York.
Benzie, J. A. (2005). Cladocera: the genus Daphnia (including Daphniopsis). Kenobi Productions & Backhuys Publishers, Ghent, Leiden, 376 pp.
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics , 30 , 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
Branford, S. N., & Duggan, I. C. (2017). Grass carp (Ctenopharyngodon idella ) translocations, including hitchhiker introductions, alter zooplankton communities in receiving ponds.Marine and Freshwater Research, 68 , 2216-2227. https://doi.org/10.1071/Mf17051
Burns, C. W. (2013). Predictors of invasion success by Daphniaspecies: influence of food, temperature and species identity.Biological Invasions, 15 , 859-869. https://doi.org/10.1007/s10530-012-0335-5
Burns, C. W., Duggan, I. C., Banks, J. C., & Hogg, I. D. (2017). A new, subalpine species of Daphnia (Cladocera, Anomopoda) in theD. carinata species complex, in the South Island, New Zealand.Hydrobiologia, 798 , 151–169. https://doi.org/10.1007/s10750-016-2702-1
Calabrese, C., Simone, D., Diroma, M. A., Santorsola, M., Gutta, C., Gasparre, G., . . . Attimonelli, M. (2014). MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.Bioinformatics, 30 , 3115-3117. https://doi.org/10.1093/bioinformatics/btu483
Černý, M., & Hebert, P.D. (1993). Genetic diversity and breeding system variation in Daphnia pulicaria from North American lakes.Heredity, 71 :497. http://doi.org/10.1038/hdy.1993.168.
Colbourne, J. K., Crease, T. J., Weider, L. J., Hebert, P. D. , Dufresne, F., & Hobaek, A. (1998). Phylogenetics and evolution of a circumarctic species complex (Cladocera: Daphnia pulex ).Biological Journal of the Linnean Society, 65 , 347-365.
https://doi.org/10.1111/j.1095-8312.1998.tb01146.x
Crease, T. J., & Lynch, M. (1991). Ribosomal DNA variation inDaphnia pulex . Molecular Biology and Evolution,8 , 620-640. https://doi.org/10.1093/oxfordjournals.molbev.a040682
Crease, T. J., Floyd, R., Cristescu, M. E., & Innes, D. (2011). Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex. BMC Evolutionary Biology, 11 , 212. https://doi.org/10.1186/1471-2148-11-212
Crease, T. J., Omilian, A. R., Costanzo, K. S., & Taylor, D. J. (2012). Transcontinental phylogeography of the Daphnia pulex species complex. PLoS One , 7 , e46620. https://doi.org/10.1371/journal.pone.0046620
Cristescu, M. E., Constantin, A., Bock, D. G., Caceres, C. E., & Crease, T. J. (2012). Speciation with gene flow and the genetics of habitat transitions. Molecular Ecology, 21 , 1411-1422. https://doi.org/10.1111/j.1365-294X.2011.05465.x
Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009). Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.Bioinformatics, 25 :3207-3212. https://doi.org/10.1093/bioinformatics/btp579
Duggan, I. C., & Pullan, S. G. (2017). Do freshwater aquaculture facilities provide an invasion risk for zooplankton hitchhikers?Biological Invasions, 19 , 307-314. https://doi.org/10.1007/s10530-016-1280-5
Duggan, I. C., Robinson, K. V., Burns, C. W., Banks, J. C., & Hogg, I. D. (2012). Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia ’pulex’ in New Zealand fresh waters. Aquatic Invasions, 7 , 585-590. https://doi.org/10.3391/ai.2012.7.4.015
Ebert, D. (2005). Ecology, epidemiology, and evolution of parasitism in Daphnia . National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD.
Felsenstein, J. (1993). PHYLIP (phylogeny inference package) . University of Washington, Seattle, WA.
Gutekunst, J., Andriantsoa, R., Falckenhayn, C., Hanna, K., Stein, W., Rasamy, J., & Lyko, F. (2018). Clonal genome evolution and rapid invasive spread of the marbled crayfish. Nature Ecology & Evolution , 2 :567-573. http://doi.org/10.1038/s41559-018-0467-9
Hebert, P. D. (1978). The population bilogy of Daphnia(Crustacea, Daphnidae). Biological Reviews, 53 , 387-426. https://doi.org/10.1111/j.1469-185X.1978.tb00860.x
Hebert, P. D., & Crease, T. J. (1980). Clonal coexistence inDaphnia pulex (Leydig): another planktonic paradox.Science, 207 , 1363-1365. https://doi.org/10.1126/science.207.4437.1363
Hebert, P.D., & Crease, T. J. (1983). Clonal diversity in populations of Daphnia pulex reproducing by obligate parthenogenesis.Heredity 51 :353.
http://doi.org/doi:10.1038/hdy.1983.40.
Hebert, P. D., Beaton, M. J., Schwartz, S. S., & Stanton, D. J. (1989). Polyphyletic origins of asexuality in Daphnia pulex . I. Breeding-system variation and levels of clonal diversity.Evolution, 43 , 1004-1015. https://doi.org/10.1111/j.1558-5646.1989.tb02546.x
Hebert, P. D., Schwartz, S. S., Ward, R. D., & Finston, T. L. (1993). Macrogeographic patterns of breeding system diversity in theDaphnia pulex group. I. Breeding systems of Canadian populations.Heredity , 70 , 148. https://doi.org/10.1038/hdy.1993.24
Heier, C. R., & Dudycha, J. L. (2009). Ecological speciation in a cyclic parthenogen: Sexual capability of experimental hybrids betweenDaphnia pulex and Daphnia pulicaria . Limnology and Oceanography, 54 , 492-502. https://doi.org/10.4319/lo.2009.54.2.0492
Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2017). UFBoot2: improving the ultrafast bootstrap approximation.Molecular Biology and Evolution, 35 , 518-522. https://doi.org/10.1093/molbev/msx281
Innes, D. J., & Hebert, P. D. (1988). The origin and genetic basis of obligate parthenogenesis in Daphnia pulex . Evolution,42 , 1024-1035. https://doi.org/10.2307/2408918
Keith, N., Tucker, A. E., Jackson, C. E., Sung, W., Lucas Lledo, J. I., Schrider, D. R., . . . Lynch, M. (2016). High mutational rates of large-scale duplication and deletion in Daphnia pulex .Genome Research, 26 , 60-69. https://doi.org/10.1101/gr.191338.115
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets.Molecular Biology and Evolution, 33 , 1870-1874. https://doi.org/10.1093/molbev/msx281
Larsson, P. (1991). Intraspecific variability in response to stimuli for male and ephippia formation in Daphnia pulex . In Biology of Cladocera (pp. 281-290): Springer.
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25 , 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., . . . Durbin, R. (2009). The sequence alignment/map format and SAMtools.Bioinformatics, 25 , 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
Loytynoja, A. (2014). Phylogeny-aware alignment with PRANK.Methods in Molecular Biology, 1079 , 155-170. https://doi.org/10.1007/978-1-62703-646-7_10
Lynch, M. (1984). Destabilizing hybridization, general-purpose genotypes and geographic parthenogenesis. The Quarterly Review of Biology ,59 , 257-290.
https://doi.org/10.1086/413902
Lynch, M., Burger, R., Butcher, D., & Gabriel, W. (1993). The mutational meltdown in asexual populations. Journal of Heredity,84 , 339-344. https://doi.org/10.1093/oxfordjournals.jhered.a111354
Lynch, M., Seyfert, A., Eads, B., & Williams, E. (2008). Localization of the genetic determinants of meiosis suppression in Daphnia pulex . Genetics , 180 , 317–327.
https://doi:10.1534/genetics.107.084657
Lynch, M., Gutenkunst, R., Ackerman, M., Spitze, K., Ye, Z., Maruki, T., & Jia, Z. (2017). Population genomics of Daphnia pulex .Genetics, 206 , 315-332. https://doi.org/10.1534/genetics.116.190611
Markova, S., Dufresne, F., Manca, M., & Kotlik, P. (2013). Mitochondrial capture misleads about ecological speciation in theDaphnia pulex complex. PLos One, 8 , e69497. https://doi.org/10.1371/journal.pone.0069497
Mergeay, J., Verschuren, D., & De Meester, L. (2006). Invasion of an asexual American water flea clone throughout Africa and rapid displacement of a native sibling species. Proceedings of the Royal Society B: Biological Sciences, 273 , 2839-2844. https://doi.org/10.1098/rspb.2006.3661
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution,32 , 268-274. https://doi.org/10.1093/molbev/msu300
Omilian, A. R., & Lynch, M. (2009). Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics,182 , 325-336. https://doi.org/10.1534/genetics.108.099549
Paland, S., Colbourne, J. K., & Lynch, M. (2005). Evolutionary history of contagious asexuality in Daphnia pulex . Evolution,59 , 800-813.
https://doi.org/10.1111/j.0014-3820.2005.tb01754.x
Parker, E. D., Selander, R. K., Hudson, R. O., Lester, L. J. (1977). Genetic diversity in colonizing parthenogenetic cockroaches. Evolution,  31 : 836–842. https://doi.org/10.2307/2407445
So, M., Ohtsuki, H., Makino, W., Ishida, S., Kumagai, H., Yamaki, K. G., & Urabe, J. (2015). Invasion and molecular evolution of Daphnia pulex in Japan. Limnology and Oceanography, 60 , 1129-1138. https://doi.org/10.1002/lno.10087
Stevenson, K. R., Coolon, J. D., & Wittkopp, P. J. (2013). Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome. BMC Genomics, 14 , 536. https://doi.org/10.1186/1471-2164-14-536
Tucker, A. E., Ackerman, M. S., Eads, B. D., Xu, S., & Lynch, M. (2013). Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex . Proceedings of the National Academy of Sciences, 110 , 15740-15745. https://doi.org/10.1073/pnas.1313388110
Vergilino, R., Markova, S., Ventura, M., Manca, M., & Dufresne, F. (2011). Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers. Molecular Ecology, 20 , 1191-1207. https://doi.org/10.1111/j.1365-294X.2011.05004.x
Wilmshurst, J. M., Anderson, A. J., Higham, T. F., & Worthy, T. H. (2008) Dating the late prehistoric dispersal of Polynesians to New Zealand using the commensal Pacific rat. Proceedings of the National Academy of Sciences of the United States of America,105 :7676-7680. https://doi.org/10.1073/pnas.0801507105.
Wu, T. D., & Watanabe, C. K. (2005). GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics,21 , 1859-1875. https://doi.org/10.1093/bioinformatics/bti310
Xu, S., Schaack, S., Seyfert, A., Choi, E., Lynch, M., & Cristescu, M. E. (2012). High mutation rates in the mitochondrial genomes ofDaphnia pulex . Molecular Biology and Evolution,29 , 763-769. https://doi.org/10.1093/molbev/msr243
Xu, S., Innes, D. J., Lynch, M., & Cristescu, M. E. (2013). The role of hybridization in the origin and spread of asexuality in Daphnia .Molecular Ecology , 22 , 4549-4561. https://doi.org/10.1111/mec.12407
Xu, S., Spitze, K., Ackerman, M. S., Ye, Z., Bright, L., Keith, N., . . . Lynch, M. (2015). Hybridization and the origin of contagious asexuality in Daphnia pulex . Molecular Biology and Evolution, 32 , 3215-3225. https://doi.org/10.1093/molbev/msv190
Ye, Z., Molinier, C., Zhao, C., Haag, C. R., & Lynch, M. (2019). Genetic control of male production in Daphnia pulex .Proceedings of the National Academy of Sciences of the United States of America, 116 , 15602-15609. https://doi.org/10.1073/pnas.1903553116
Data accession
NZ population data for this study were deposited to NCBI under BioProject ID PRJNA573527.
D. pulex/D. pulicaria genomic data can be accessed at BioProject ID PRJNA573529 and accession numbers SAMN03964756-SAMN03964769 (Xu et al. 2015), and the D. obtusa genomic sequences used in this study can be accessed at NCBI under accession number SAMN12816670. TheD. pulex genome assembly PA42 v4.1 is available at GenBank under accession GCA_900092285.2 (Ye et al. unpublished) and the corresponding annotation file is provided in File S1.