References
Agapow, P.-M., & Burt, A. (2001). Indices of multilocus linkage
disequilibrium. Molecular Ecology Notes, 1 (1-2), 101–102. doi:
10.1046/j.1471-8278.2000.00014.x.
Ali, S., Gladieux, P., Rahman, H., Saqib, M. S., Fiaz, M., Ahmad, H., .
. . de Vallavieille-Pope, C. (2014). Inferring the contribution of
sexual reproduction, migration and off-season survival to the temporal
maintenance of microbial populations: A case study on the wheat fungal
pathogen Puccinia striiformisf.sp.tritici . Molecular
Ecology, 23 (3), 603–617. doi: 10.1111/mec.12629.
Ali, S., Soubeyrand, S., Gladieux, P., Giraud, T., Leconte, M., Gautier,
A., . . . Enjalbert, J. (2016). Cloncase: Estimation of sex frequency
and effective population size by clonemate resampling in partially
clonal organisms. Molecular Ecology Resources, 16 (4), 845–861.
doi: 10.1111/1755-0998.12511.
Arnaud-Haond, S., Alberto, F., Teixeira, S., Procaccini, G., Serrão, E.
A., & Duarte, C. M. (2005). Assessing genetic diversity in clonal
organisms: Low diversity or low resolution? Combining power and cost
efficiency in selecting markers. Journal of Heredity, 96 (4),
434–440. doi: 10.1093/jhered/esi043.
Arnaud-Haond, S., Duarte, C. M., Alberto, F., & Serrão, E. A. (2007).
Standardizing methods to address clonality in population studies.Molecular Ecology, 16 (24), 5115–5139. doi:
10.1111/j.1365-294x.2007.03535.x.
Arnaud-Haond, S., Stoeckel, S., & Bailleul, D. (2019). New insights
into the population genetics of partially clonal organisms: When
seagrass data meet theoretical expectations. arXiv:1902.10240v6.
Avise, J., & Nicholson, T. (2008). Clonality: The genetics,
ecology, and evolution of sexual abstinence in vertebrate animals . New
York, NY: Oxford University Press.
Avise, J. C. (2015). Evolutionary perspectives on clonal reproduction in
vertebrate animals. Proceedings of the National Academy of
Sciences of the United States of America, 112 (29), 8867–8873. doi:
10.1073/pnas.1501820112.
Ayala, F. J. (1998). Is sex better? Parasites say ”no”.Proceedings of the National Academy of Sciences of the United
States of America, 95 (7), 3346–3348. doi: 10.1073/pnas.95.7.3346.
Bailleul, D., Stoeckel, S., & Arnaud-Haond, S. (2016). RClone: A
package to identify multi locus clonal lineages and handle clonal data
sets inr. Methods in Ecology and Evolution, 7 (8), 966–970. doi:
10.1111/2041-210x.12550.
Balloux, F., Lehmann, L., & de Meeus, T. (2003). The population
genetics of clonal and partially clonal diploids. Genetics,
164 (4), 1635–1644.
Barrett, S. C. (2016). Invasion genetics: The baker and stebbins
legacy . Chicester, West Sussex: John Wiley & Sons.
Barrett, S. C. H. (2015). Foundations of invasion genetics: The Baker
and Stebbins legacy. Molecular Ecology, 24 (9), 1927–1941. doi:
10.1111/mec.13014.
Becheler, R., Masson, J.-P., Arnaud-Haond, S., Halkett, F., Mariette,
S., Guillemin, M.-L., . . . Stoeckel, S. (2017). ClonEstiMate, a
Bayesian method for quantifying rates of clonality of populations
genotyped at two-time steps. Molecular Ecology Resources, 17 (6),
e251–e267. doi: 10.1111/1755-0998.12698.
Berg, L. M., & Lascoux, M. (2000). Neutral genetic differentiation in
an island model with cyclical parthenogenesis. Journal of
Evolutionary Biology, 13 (3), 488–494. doi:
10.1046/j.1420-9101.2000.00185.x.
Bibr, C. (2017). Julie Sondra Decker, the invisible orientation: An
introduction to asexuality. Sexualities, 21 (5-6), 840–842. doi:
10.1177/1363460717724156.
De Meeûs, T., Lehmann, L., & Balloux, F. (2006). Molecular epidemiology
of clonal diploids: A quick overview and a short DIY (do it yourself)
notice. Infection, Genetics and Evolution, 6 (2), 163–170. doi:
10.1016/j.meegid.2005.02.004.
De Meeûs, T., Prugnolle, F., & Agnew, P. (2007). Asexual reproduction:
Genetics and evolutionary aspects. Cellular and Molecular Life
Sciences, 64 (11), 1355–1372. doi: 10.1007/s00018-007-6515-2.
Decker, J. S. (2015). The invisible orientation: An introduction
to asexuality . New York, NY: Skyhorse Publishing.
Dia, A., Guillou, L., Mauger, S., Bigeard, E., Marie, D., Valero, M., &
Destombe, C. (2014). Spatiotemporal changes in the genetic diversity of
harmful algal blooms caused by the toxic dinoflagellateAlexandrium minutum . Molecular Ecology, 23 (3), 549–560.
doi: 10.1111/mec.12617.
Dorken, M. E., & Eckert, C. G. (2001). Severely reduced sexual
reproduction in northern populations of a clonal plant,Decodonverticillatus (Lythraceae). Journal of Ecology,
89 (3), 339–350. doi: 10.1046/j.1365-2745.2001.00558.x.
Douhovnikoff, V., & Dodd, R. S. (2003). Intra-clonal variation and a
similarity threshold for identification of clones: Application toSalix exigua using AFLP molecular markers. Theoretical and
Applied Genetics, 106 (7), 1307–1315. doi: 10.1007/s00122-003-1200-9.
Eckert, C. G. (2002). The loss of
sex in clonal plants. In J. F. Stuefer, B. Erschbamer, H. Huber, &
J.-I. Suzuki (Eds.), Ecology and evolutionary biology of clonal
plants: Proceedings of clone-2000. An International workshop held in
Obergurgl, Austria, 20–25 August 2000 (pp. 279–298).
Dordrecht, Netherlands: Springer.
Evans, S. M., Sinclair, E. A., Poore, A. G. B., Steinberg, P. D.,
Kendrick, G. A., & Vergés, A. (2014). Genetic diversity in threatenedPosidonia australis seagrass meadows. Conservation
Genetics, 15 (3), 717–728. doi: 10.1007/s10592-014-0573-4.
Fehrer, J. (2010). Unraveling the mysteries of reproduction.Heredity, 104 (5), 421–422. doi: 10.1038/hdy.2010.12.
Gilabert, A., Dedryver, C. A., Stoeckel, S., Plantegenest, M., & Simon,
J. C. (2015). Longitudinal clines in the frequency distribution of
‘super-clones’ in an aphid crop pest. Bulletin of Entomological
Research, 105 (6), 694–703. doi: 10.1017/s0007485315000619.
Gorospe, K. D., Donahue, M. J., & Karl, S. A. (2015). The importance of
sampling design: Spatial patterns and clonality in estimating the
genetic diversity of coral reefs. Marine Biology, 162 (5),
917–928. doi: 10.1007/s00227-015-2634-8.
Halkett, F., Kindlmann, P., Plantegenest, M., Sunnucks, P., & Simon, J.
C. (2006). Temporal differentiation and spatial coexistence of sexual
and facultative asexual lineages of an aphid species at mating sites.Journal of Evolutionary Biology, 19 (3), 809–815. doi:
10.1111/j.1420-9101.2005.01055.x.
Halkett, F., Simon, J., & Balloux, F. (2005). Tackling the population
genetics of clonal and partially clonal organisms. Trends in
Ecology & Evolution, 20 (4), 194–201. doi: 10.1016/j.tree.2005.01.001.
Hand, D. J., & Yu, K. (2001). Idiot’s bayes: Not so stupid after all?International Statistical Review / Revue Internationale de
Statistique, 69 (3), 385–398. doi: 10.2307/1403452.
Hughes, A. R., Inouye, B. D., Johnson, M. T. J., Underwood, N., &
Vellend, M. (2008). Ecological consequences of genetic diversity.Ecology Letters, 11 (6), 609–623. doi:
10.1111/j.1461-0248.2008.01179.x.
Hughes, A. R., & Stachowicz, J. J. (2004). Genetic diversity enhances
the resistance of a seagrass ecosystem to disturbance. Proceedings
of the National Academy of Sciences of the United States of America,
101 (24), 8998–9002. doi: 10.1073/pnas.0402642101.
Kendrick, G. A., Orth, R. J., Statton, J., Hovey, R., Montoya, L. R.,
Lowe, R. J., . . . Sinclair, E. A. (2017). Demographic and genetic
connectivity: The role and consequences of reproduction, dispersal and
recruitment in seagrasses. Biological Reviews, 92 (2), 921–938.
doi: 10.1111/brv.12261.
Kendrick, G. A., Waycott, M., Carruthers, T. J. B., Cambridge, M. L.,
Hovey, R., Krauss, S. L., . . . Verduin, J. J. (2012). The central role
of dispersal in the maintenance and persistence of seagrass populations.BioScience, 62 (1), 56–65. doi: 10.1525/bio.2012.62.1.10.
Lewis, W. M. (1987). The cost of sex. In S. C. Stearns (Ed.), The
evolution of sex and its consequences (pp. 33–57). Basel, Switzerland:
Birkhäuser Basel.
Liddell, H. G., Scott, R., Jones, H. S., & McKenzie, R. (1940). A
Greek-english lexicon . Oxford, UK: Clarendon Press.
Loxdale, H. D., Schöfl, G., Wiesner, K. R., Nyabuga, F. N., Heckel, D.
G., & Weisser, W. W. (2011). Stay at home aphids: Comparative spatial
and seasonal metapopulation structure and dynamics of two specialist
tansy aphid species studied using microsatellite markers.Biological Journal of the Linnean Society, 104 (4), 838–865. doi:
10.1111/j.1095-8312.2011.01761.x.
Marbà, N., & Duarte, C. M. (1998). Rhizome elongation and seagrass
clonal growth. Marine Ecology Progress Series, 174 , 269–280.
doi: 10.3354/meps174269.
Marshall, D. R., & Weir, B. S. (1979). Maintenance of genetic variation
in apomictic plant populations. Heredity, 42 (2), 159–172. doi:
10.1038/hdy.1979.20.
Massa, S. I., Paulino, C. M., Serrão, E. A., Duarte, C. M., &
Arnaud-Haond, S. (2013). Entangled effects of allelic and clonal
(genotypic) richness in the resistance and resilience of experimental
populations of the seagrass Zostera noltii to diatom invasion.BMC Ecology, 13 (1), 39. doi: 10.1186/1472-6785-13-39.
McCulloch, S., Kunkel, T. (2008). The fidelity of DNA synthesis by
eukaryotic replicative and translesion synthesis polymerases. Cell
Research , 18 , 148–161. Doi:10.1038/cr.2008.4
McMahon, K. M., Evans, R. D., van Dijk, K.-J., Hernawan, U., Kendrick,
G. A., Lavery, P. S., Waycott, M. (2017). Disturbance is an important
driver of clonal richness in tropical seagrasses. Frontiers in
Plant Science, 8, 2026. doi: 10.3389/fpls.2017.02026.
Navascués, M., Stoeckel, S., & Mariette, S. (2010). Genetic diversity
and fitness in small populations of partially asexual, self-incompatible
plants. Heredity, 104 (5), 482–492. doi: 10.1038/hdy.2009.159.
Nougué, O., Rode, N. O., Jabbour-Zahab, R., Ségard, A., Chevin, L. M.,
Haag, C. R., & Lenormand, T. (2015). Automixis in artemia: Solving a
century-old controversy. Journal of Evolutionary Biology, 28 (12),
2337–2348. doi: 10.1111/jeb.12757.
Orantes, L. C., Zhang, W., Mian, M. A. R., & Michel, A. P. (2012).
Maintaining genetic diversity and population panmixia through dispersal
and not gene flow in a holocyclic heteroecious aphid species.Heredity, 109 (2), 127–134. doi: 10.1038/hdy.2012.21.
Payseur, B. A., & Cutter, A. D. (2006). Integrating patterns of
polymorphism at SNPs and STRs. Trends in Genetics, 22 ,
424-429. doi: 10.1016/j.tig.2006.06.009
Piñeiro, G., Perelman, S., Guerschman, J. P., & Paruelo, J. M. (2008).
How to evaluate models: Observed vs. predicted or predicted vs.
observed? Ecological Modelling, 216 (3-4), 316–322. doi:
10.1016/j.ecolmodel.2008.05.006.
Putman, A. I., & Carbone, I. (2014). Challenges in analysis and
interpretation of microsatellite data for population genetic studies.Ecology and Evolution, 4 (22), 4399–4428. doi: 10.1002/ece3.1305.
Reichel, K., Masson, J.-P., Malrieu, F., Arnaud-Haond, S., & Stoeckel,
S. (2016). Rare sex or out of reach equilibrium? The dynamics of F IS in
partially clonal organisms. BMC Genetics, 17 (1), 76. doi:
10.1186/s12863-016-0388-z.
Reusch, T. B., & Lampert, W. (2004). Role and maintenance of
genetic diversity in natural populations . Kiel, Germany:
Christian-Albrechts-Universität Kiel.
Riginos, C. (2015). Clones in space—how sampling can bias genetic
diversity estimates in corals: Editorial comment on the feature article
by Gorospe et al. Marine Biology, 162 (5), 913–915. doi:
10.1007/s00227-015-2638-4.
Rouger, R., Reichel, K., Malrieu, F., Masson, J. P., & Stoeckel, S.
(2016). Effects of complex life cycles on genetic diversity: Cyclical
parthenogenesis. Heredity, 117 (5), 336–347. doi:
10.1038/hdy.2016.52.
Schön, I., Van Dijk, P., & Martens, K. (2009). Lost sex: The
evolutionary biology of parthenogenesis . Dordrecht, Netherlands:
Springer.
Sinclair, E. A., Krauss, S. L., Anthony, J., Hovey, R., & Kendrick, G.
A. (2014). The interaction of environment and genetic diversity within
meadows of the seagrass Posidonia australis (Posidoniaceae).Marine Ecology Progress Series, 506 , 87–98. doi:
10.3354/meps10812.
Stoeckel, S., Grange, J., Fernández‐Manjarres, J. F., Bilger, I.,
Frascaria‐Lacoste, N., & Mariette, S. (2006). Heterozygote excess in a
self‐incompatible and partially clonal forest tree species —Prunus avium L . Molecular Ecology, 15 (8), 2109–2118. doi:
10.1111/j.1365-294x.2006.02926.x.
Stoeckel, S., & Masson, J.-P. (2014). The exact distributions of FIS
under partial asexuality in small finite populations with mutation.PLoS One, 9 (1), e85228. doi: 10.1371/journal.pone.0085228.
Tibayrenc, M., Avise, J. C., & Ayala, F. J. (2015). In the light of
evolution IX: Clonal reproduction: Alternatives to sex.Proceedings of the National Academy of Sciences of the United
States of America, 112 (29), 8824–8826. doi: 10.1073/pnas.1508087112.
Tibayrenc, M., & Ayala, F. J. (2012). Reproductive clonality of
pathogens: A perspective on pathogenic viruses, bacteria, fungi, and
parasitic protozoa. Proceedings of the National Academy of
Sciences of the United States of America, 109 (48), E3305–E3313. doi:
10.1073/pnas.1212452109.
Tibayrenc, M., Kjellberg, F., Arnaud, J., Oury, B., Breniere, S. F.,
Darde, M. L., & Ayala, F. J. (1991). Are eukaryotic microorganisms
clonal or sexual? A population genetics vantage. Proceedings of
the National Academy of Sciences of the United States of America,
88 (12), 5129–5133. doi: 10.1073/pnas.88.12.5129.
Tibayrenc, M., Kjellberg, F., & Ayala, F. J. (1990). A clonal theory of
parasitic protozoa: The population structures of Entamoeba ,Giardia , Leishmania , Naegleria , Plasmodium ,Trichomonas , and Trypanosoma and their medical and
taxonomical consequences. Proceedings of the National Academy of
Sciences of the United States of America, 87 (7), 2414–2418. doi:
10.1073/pnas.87.7.2414.
Van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M., & Shipley, P.
(2004). micro-checker: Software for identifying and correcting
genotyping errors in microsatellite data. Molecular Ecology Notes,
4 (3), 535–538. doi: 10.1111/j.1471-8286.2004.00684.x.
Villate, L., Esmenjaud, D., Van Helden, M., Stoeckel, S., & Plantard,
O. (2010). Genetic signature of amphimixis allows for the detection and
fine scale localization of sexual reproduction events in a mainly
parthenogenetic nematode. Molecular Ecology, 19 (5), 856–873.
doi: 10.1111/j.1365-294x.2009.04511.x.
Webb, G. I., Boughton, J. R., & Wang, Z. (2005). Not so naive bayes:
Aggregating one-dependence estimators. Machine Learning, 58 (1),
5–24. doi: 10.1007/s10994-005-4258-6.
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the
analysis of population structure. Evolution, 38 (6), 1358–1370.
doi: 10.2307/2408641.
Wright, S. (1921). Systems of mating. II. the effects of inbreeding on
the genetic composition of a population. Genetics, 6 (2),
124–143.
Wright, S. (1931). Evolution in mendelian populations. Genetics,
16 (2), 97–159.
Wright, S. (1969). Evolution and the genetics of populations,
volume 2: Theory of gene frequencies . Chicago, IL: University of
Chicago Press.
Yonezawa, K., Ishii, T., & Nagamine, T. (2004). The effective size of
mixed sexually and asexually reproducing populations. Genetics,
166 (3), 1529–1539. doi: 10.1534/genetics.166.3.1529.
Yu, F.-H., Roiloa, S. R., & Alpert, P. (2016). Editorial: Global
change, clonal growth, and biological invasions by plants.Frontiers in Plant Science, 7 , 1467. doi:
10.3389/fpls.2016.01467.
Zhang, H. (2004). The optimality of naive bayes . Menlo Park, CA:
American Association for Artificial Intelligence.