93
Charlesworth, B., and Charlesworth, D. (1978). A model for the evolution of dioecy and
gynodioecy. Am. Nat. 112, 975–997.
Charlesworth, D., Morgan, M.T., and Charlesworth, B. (1990). Inbreeding depression, genetic load,
and the evolution of outcrossing rates in a multilocus system with no linkage. Evol. Int. J.
Org. Evol. 44, 1469–1489.
Chin, C.-S., Peluso, P., Sedlazeck, F.J., Nattestad, M., Concepcion, G.T., Clum, A., Dunn, C.,
O’Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., et al. (2016). Phased diploid genome
assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054.
Coelho, S.M., Gueno, J., Lipinska, A.P., Cock, J.M., and Umen, J.G. (2018). UV chromosomes
and haploid sexual systems. Trends Plant Sci. 23, 794–807.
Coleman, A.W. (1999). Phylogenetic analysis of “Volvocacae” for comparative genetic studies.
Proc. Natl. Acad. Sci. U. S. A. 96, 13892–13897.
Darriba, D., Posada, D., Kozlov, A.M., Stamatakis, A., Morel, B., and Flouri, T. (2020).
ModelTest-NG: A new and scalable tool for the selection of dna and protein evolutionary
models. Mol. Biol. Evol. 37, 291–294.
Darwin, C., and Burkhardt, F. (1861). The correspondence of Charles Darwin. 9. 1861 (Cambridge
University Press).
Dubini, A., Mus, F., Seibert, M., Grossman, A.R., and Posewitz, M.C. (2009). Flexibility in
anaerobic metabolism as revealed in a mutant of Chlamydomonas reinhardtii lacking
hydrogenase activity. J. Biol. Chem. 284, 7201–7213.
Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high
throughput. Nucleic Acids Res. 32, 1792–1797.
Ferris, P.J., and Goodenough, U.W. (1994). The mating-type locus of Chlamydomonas reinhardtii
contains highly rearranged DNA sequences. Cell 76, 1135–1145.
Ferris, P.J., and Goodenough, U.W. (1997). Mating type in Chlamydomonas is specified by mid,
94
the minus-dominance gene. Genetics 146, 859–869.
Ferris, P., Olson, B.J.S.C., De Hoff, P.L., Douglass, S., Diaz-Cano, D.C., Prochnik, S., Geng, S.,
Rai, R., Grimwood, J., Schmutz, J., et al. (2010). Evolution of an expanded sex determining
locus in Volvox. Science 328, 351–354.
Ferris, P.J., Woessner, J.P., and Goodenough, U.W. (1996). A sex recognition glycoprotein is
encoded by the plus mating-type gene fus1 of Chlamydomonas reinhardtii. Mol. Biol. Cell 7,
1235–1248.
Geng, S., De Hoff, P., and Umen, J.G. (2014). Evolution of sexes from an ancestral mating-type
specification pathway. PLoS Biol. 12, e1001904.
Hamaji, T., Ferris, P.J., Coleman, A.W., Waffenschmidt, S., Takahashi, F., Nishii, I., and Nozaki,
H. (2008). Identification of the minus-dominance gene ortholog in the mating-type locus of
Gonium pectorale. Genetics 178, 283–294.
Hamaji, T., Mogi, Y., Ferris, P.J., Mori, T., Miyagishima, S., Kabeya, Y., Nishimura, Y., Toyoda,
A., Noguchi, H., Fujiyama, A., et al. (2016). Sequence of the Gonium pectorale mating locus
reveals a complex and dynamic history of changes in volvocine algal mating haplotypes. G3
Bethesda Md 6, 1179–1189.
Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda,
A., Fujiyama, A., Miyagishima, S., Umen, J.G., et al. (2018). Anisogamy evolved with a
reduced sex-determining region in volvocine green algae. Commun. Biol. 1, 17.
Hanschen, E.R., Marriage, T.N., Ferris, P.J., Hamaji, T., Toyoda, A., Fujiyama, A., Neme, R.,
Noguchi, H., Minakuchi, Y., Suzuki, M., et al. (2016). The Gonium pectorale genome
demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nat.
Commun. 7, 11370.
Hanschen, E.R., Herron, M.D., Wiens, J.J., Nozaki, H., and Michod, R.E. (2018). Repeated
evolution and reversibility of self-fertilization in the volvocine green algae*. Evolution 72,
95
386–398.
Heesch, S., Serrano-Serrano, M., Luthringer, R., Peters, A.F., Destombe, C., Cock, J.M., Valero,
M., Roze, D., Salamin, N., and Coelho, S. (2019). Evolution of life cycles and reproductive
traits: insights from the brown algae. BioRxiv 530477.
Herron, M.D., Hackett, J.D., Aylward, F.O., and Michod, R.E. (2009). Triassic origin and early
radiation of multicellular volvocine algae. Proc. Natl. Acad. Sci. 106, 3254–3258.
Hiraide, R., Kawai-Toyooka, H., Hamaji, T., Matsuzaki, R., Kawafune, K., Abe, J., Sekimoto, H.,
Umen, J., and Nozaki, H. (2013). The evolution of male-female sexual dimorphism predates
the gender-based divergence of the mating locus gene MAT3/RB. Mol. Biol. Evol. 30, 1038–
1040.
Isaka, N., Kawai-Toyooka, H., Matsuzaki, R., Nakada, T., and Nozaki, H. (2012). Description of
two new monoecious species of Volvox sect. Volvox (Volvocaceae, Chlorophyceae), based on
comparative morphology and molecular phylogeny of cultured material. J. Phycol. 48, 759–
767.
Jarne, P., and Auld, J.R. (2006). Animals Mix It up Too: The Distribution of self-Fertilization
among hermaphroditic animals. Evolution 60, 1816–1824.
Jones, D.T., Taylor, W.R., and Thornton, J.M. (1992). The rapid generation of mutation data
matrices from protein sequences. Bioinformatics 8, 275–282.
Kalanon, M., and McFadden, G.I. (2008). The chloroplast protein translocation complexes of
Chlamydomonas reinhardtii: a bioinformatic comparison of Toc and Tic components in plants,
green algae and red algae. Genetics 179, 95–112.
Kasai, F., Kawachi, M., Erata, M., Mori, F., Yumoto, K., Sato, M., and Ishimoto, M. (2009). NIESCollection, List of strains, 8th edition. Jpn J Phycol 57, Supplement: 1–350, plates 1–7.
KATO, S. (1982). Laboratory culture and morphology of Colacium vesiculosum Ehrb.
(Euglenophyceae). Jpn J Phycol 30, 63–67.
96
Kianianmomeni, A., Ong, C.S., Rätsch, G., and Hallmann, A. (2014). Genome-wide analysis of
alternative splicing in Volvox carteri. BMC Genomics 15, 1117.
Kirk, D.L. (2005). A twelve-step program for evolving multicellularity and a division of labor.
BioEssays News Rev. Mol. Cell. Dev. Biol. 27, 299–310.
Kirk, D.L., and Kirk, M.M. (1983). Protein synthetic patterns during the asexual life cycle of
Volvox carteri. Dev. Biol. 96, 493–506.
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. (2018). MEGA X: Molecular
Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 35, 1547–1549.
Le, S.Q., and Gascuel, O. (2008). An improved general amino acid replacement matrix. Mol. Biol.
Evol. 25, 1307–1320.
Liss, M., Kirk, D.L., Beyser, K., and Fabry, S. (1997). Intron sequences provide a tool for highresolution phylogenetic analysis of volvocine algae. Curr. Genet. 31, 214–227.
M. Kawachi et al. (2013). MCC-NIES list of strains, 9th Edition, microbial culture collection at
National Institute for Environmental Studies, Tsukuba, Japan.
McDaniel, S.F., Atwood, J., and Burleigh, J.G. (2013). Recurrent evolution of dioecy in bryophytes.
Evolution 67, 567–572.
Miller, S.M., Schmitt, R., and Kirk, D.L. (1993). Jordan, an active Volvox transposable element
similar to higher plant transposons. Plant Cell 5, 1125–1138.
Nei, M., and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and
nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426.
Nei, M., and Kumar, S. (2000). Molecular Evolution and Phylogenetics.
Noé, L., and Kucherov, G. (2005). YASS: enhancing the sensitivity of DNA similarity search.
Nucleic Acids Res. 33, W540-543.
Nozaki, H. (1983). Sexual reproduction in Eudorina elegans (chlorophyta, volvocales). Bot. Mag.
Shokubutsu-Gaku-Zasshi 96, 103–110.
97
Nozaki, H., Mori, T., Misumi, O., Matsunaga, S., and Kuroiwa, T. (2006). Males evolved from the
dominant isogametic mating type. Curr. Biol. CB 16, R1018-1020.
Nozaki, H., Matsuzaki, R., Yamamoto, K., Kawachi, M., and Takahashi, F. (2015). Delineating a
new heterothallic species of volvox (volvocaceae, chlorophyceae) using new strains of
“Volvox africanus.” PLOS ONE 10, e0142632.
Nozaki, H., Takusagawa, M., Matsuzaki, R., Misumi, O., Mahakham, W., and Kawachi, M. (2019).
Morphology, reproduction and taxonomy of Volvox dissipatrix (Chlorophyceae) from
Thailand, with a description of Volvox zeikusii sp. nov . Phycologia 58, 1–8.
Ohtsubo, Y., Ikeda-Ohtsubo, W., Nagata, Y., and Tsuda, M. (2008). GenomeMatcher: a graphical
user interface for DNA sequence comparison. BMC Bioinformatics 9, 376.
Pannell, J.R. (2002). The Evolution and maintenance of androdioecy. Annu. Rev. Ecol. Syst. 33,
397–425.
Piel, W. H., Chan, L., Dominus, V. Tannen, M. J., Ruan, J, and ., Vos, R. A., (2009). TreeBASE v.
2: A Database of Phylogenetic Knowledge. E-BioSphere.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu,
L., Suchard, M.A., and Huelsenbeck, J.P. (2012). MrBayes 3.2: efficient Bayesian
phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542.
Russell, J.R.W., and Pannell, J.R. (2015). Sex determination in dioecious Mercurialis annua and
its close diploid and polyploid relatives. Heredity 114, 262–271.
Smith, G.M. (1944). A Comparative study of the species of Volvox. Trans. Am. Microsc. Soc. 63,
265–310.
Starr, R.C. (1969). Structure, reproduction and differentiation in Volvox carteri f. nagariensis
Iyengar, strains HK9 & 10. Arch Protistenkd. 111, 204–222.
Starr RC (1971). Sexual reproduction in Volvox africanus. In Contribution in Phycology, (Allen
Press), pp. 59–66.
98
Tamura, K., Battistuzzi, F.U., Billing-Ross, P., Murillo, O., Filipski, A., and Kumar, S. (2012).
Estimating divergence times in large molecular phylogenies. Proc. Natl. Acad. Sci. 109,
19333–19338.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: Molecular
evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729.
Tamura, K., Tao, Q., and Kumar, S. (2018). Theoretical foundation of the reltime method for
estimating divergence times from variable evolutionary rates. Mol. Biol. Evol. 35, 1770–1782.
Tao, Q., Tamura, K., Mello, B., and Kumar, S. (2020). Reliable confidence intervals for reltime
estimates of evolutionary divergence times. Mol. Biol. Evol. 37, 280–290.
Umen, J., and Coelho, S. (2019). Algal sex determination and the evolution of anisogamy. Annu.
Rev. Microbiol. 73, 267–291.
Vos, R., Balhoff, J., Caravas, J., Holder, M., Lapp, H., Maddison, W., Midford, P., Priyam, A.,
Sukumaran, J., Xia, X., et al. (2012). NeXML: rich, extensible, and verifiable representation
of comparative data and metadata. Syst. Biol. 61, 675–689.
Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng,
Q., Wortman, J., Young, S.K., et al. (2014). Pilon: an integrated tool for comprehensive
microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963.
Wong, J.L., and Wolfner, M.F. (2017). Is gender just a category? The two-plus sex advantage. Mol.
Reprod. Dev. 84, 89–90.
Yamamoto, K., Oda, Y., Haseda, A., Fujito, S., Mikami, T., and Onodera, Y. (2014). Molecular
evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at
different loci in a chromosomal region. Heredity 112, 317–324.
Yampolsky, C., and Yampolsky, H. (1922). Distribution of sex forms in phaerogamic flora (Biblio.
Genet.).
Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24,
99
1586–1591.
Yang, Z., and Nielsen, R. (2000). Estimating synonymous and nonsynonymous substitution rates
under realistic evolutionary models. Mol. Biol. Evol. 17, 32–43.
Zhu, B., Zhu, X., Wang, L., Liang, Y., Feng, Q., and Pan, J. (2017). Functional exploration of the
IFT-A complex in intraflagellar transport and ciliogenesis. PLOS Genet. 13, e1006627.
100
...