Multiple independent origins of asexuality and polyploidy among cryptic species of the brown alga <i>Scytosiphon promiscuus</i> (Scytosiphonaceae, Ectocarpales)

SUMMARY Although asexual populations and species have been frequently reported in seaweeds, their nature (e.g. origins and distribution patterns relative to closely related sexual counterparts) remains largely unknown. This is likely because determining the species identity, sex, and phase of individual organisms is often troublesome, making it difficult to comprehensively survey reproductive modes across many populations within a single species. In this study, we demonstrated that reduced‐representation sequencing (RRS), a method of sequencing a fraction of the genome using high‐throughput DNA sequencing platforms, is a simple and effective tool to investigate the reproductive modes of populations. To uncover the evolutionary trajectory of asexuals in S. promiscuus , which is known to include both sexual and asexual populations, we performed an RRS approach, MIG‐seq. By applying MIG‐seq to 122 individuals from 20 localities, mainly across Japan, we were able to: (i) estimate genetic diversity and phylogenetic relationships of populations; (ii) detect possible cryptic species ( spro1 and spro2 ); (iii) develop a pair of polymerase chain reaction‐based sex markers to identify the sex and ploidy of individuals; and (iv) discover polyploid populations in spro1 and female‐dominant populations in spro2 , both of which appear to be maintained asexually. By subsequently conducting crossing experiments and phylogenetic analysis using the mitochondrial gene cox1 and nuclear gene cetn‐int2 , we confirmed that spro1 and spro2 are reproductively isolated. We also uncovered that polyploid populations have emerged multiple times in spro1 , and one of these populations originated from hybridization between S. promiscuus and S. shibazakiorum , while the other populations originated from intraspecies crossing within S. promiscuus . It is surprising that multiple pathways to asexuality were found within such a narrow phylogenetic scope.