Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

© 2020 International Phycological Society. Ancient lakes are centres of adaptive radiation and speciation. The Cladophoraceae endemic to ancient Lake Baikal is a morphologically diverse group nested within Rhizoclonium that may represent a case of sympatric speciation. Recent research using ribosomal DNA markers indicates that these taxa form a monophyletic group but was not able to resolve boundaries between all of the investigated morphospecies due to very low genetic diversity. For this reason, a population genetics approach using more variable markers was investigated. In this study, we developed a set of microsatellites (SSRs) using high-throughput sequencing (HTS) data obtained from three morphospecies of Cladophoraceae from Lake Baikal. To increase amplification rate of the microsatellites across taxa, we performed an in silico cross-validation step comparing the microsatellites retrieved from three HTS datasets and tested the most promising loci on 14 of the mostly endemic morphospecies. We obtained 11 SSRs that cross-amplified among morphospecies, eight SSRs in 12 taxa and three in only four taxa. Our results showed that most loci had more than two alleles, but also displayed variation between and within morphospecies. These results indicate that this group may have gone through polyploidisation. Polyploid systems require a different approach from standard population genetic analyses. We produced ‘allelic phenotypes’ (presence/absence matrices) to analyse genetic diversity. We showed that similarity indices mostly grouped morphospecies, suggesting that this scoring method will be useful in species delimitation, but further work is needed to elucidate the speciation process in this algal species flock in Lake Baikal.