3.4.1 Genetic diversity and clonal diversity
Parthenogenetic populations often showed lower gene diversity (He ; Table 1); gene diversity was around 0.10 in most sexual populations, while that of parthenogenetic populations was often below 0.05. The high gene diversity of parthenogenetic populations p24 and p27 is probably because individuals in these populations have two distinct genomes.
Genetic distances between individuals showed that parthenogenetic populations included more genetically identical/nearly identical individuals than sexual populations (Figure 4). Histograms of the genetic distances based on haploid and diploid datasets were similar in shape, except for that the genetic distances based on the diploid dataset (Figure S2) doubled those of the haploid dataset (Figure 4). Histograms based on haploid dataset showed that pairs of individuals having genetic distance of less than 11 were rare in sexual populations (i.e., seven pairs), but abundant in parthenogenetic populations (i.e., 221 pairs; Figure 4). A previous study showed that parthenogenesis rarely occurred in a sexual population of Scytosiphon shibazakiorum (as Scytosiphon species IIa; Hoshino & Kogame, 2019), a close relative of S. lomentaria . Therefore, we considered that the genetic distances observed in sexual populations (larger than 11) are the genetic distances mostly between sexually produced individuals (i.e., gametophytes generated through meiosis in sexually produced sporophytes), and the genetic distances between individuals belonging to the same clonal lineage are smaller than those. Thus, a threshold distance distinguishing whether pairs of individuals belonging to the same clonal lineage was set to 10 (shown in Figure 4 as broken lines). For the diploid dataset, a threshold distance was set to 20. In the haploid dataset, 27 clones were assumed from 93 parthenogenetic population individuals, 114 clones were assumed from 119 sexual population individuals, and 138 clones were assumed in total (three clonal lineages c5, c28, and c53 were shared by both parthenogenetic and sexual populations; Table 1). In the diploid dataset, 33 clones were assumed from 118 parthenogenetic population individuals, 115 clones were assumed from 119 sexual population individuals, and 145 clones were assumed in total (three clonal lineages were shared by both parthenogenetic and sexual populations).
Most sexual populations had genetic diversity (Div ) and clonal diversity index (R ) of nearly 1.0, while those of parthenogenetic populations were usually below 0.5 (Table 1). Each parthenogenetic population usually had unique clonal lineages, but several clonal lineages were shared by multiple populations. For example, lineage c5 was found in three parthenogenetic populations (p28, p29, and p32) and also in a sexual population p6, and lineage c28 was found in a sexual population p25 and also in a parthenogenetic population p26 (Table 1). Argentinean populations had clonal lineages (c44 and c98) which were found from Japanese parthenogenetic populations p2 and p29.