Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

Abstract

Understanding the evolution of sexual vs asexual reproduction and their consequences in population genetics is a central tenet of evolutionary biology. Nevertheless, until now, it has proved unachievable to assess partially clonal reproduction when the rate of clonality is less than 95%, especially without the use of genome-wide data or temporal samples. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. The results of these investigations have been interpreted by comparison with the sexually reproducing congeneric species Laminaria digitata. Genome-wide variation was assessed by dd-RAD sequencing using 4077 SNPs in L. rodriguezii and 7364 SNPs in L. digitata. As predicted for partially clonal populations, the distribution of FIS within populations of L. rodriguezii was centered in negative values, with heterozygote excess at most loci along the genomes. This finding is the opposite of what we reported within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, two distinct distribution patterns of FIS were reported among populations of L. rodriguezii, consistent with the results predicted by the theoretical model for different levels of clonality. These findings highlight that the investment in clonal growth could differ among populations of L. rodriguezii, confirming that the full distribution of FIS is a promising feature to take into account for the study of asexuality in natural populations. We discuss the implications of these results for the conservation of the rare deep water kelp L. rodriguezii.

Population Genomics and Lagrangian Modeling Shed Light on Dispersal Events in the Mediterranean Endemic Ericaria zosteroides (=Cystoseira zosteroides) (Fucales)

“…Populations of Ericaria zosteroides are genetically differentiated from each other, including at short distances, as reported in the Mediterranean related species Ericaria amentacea and Gongolaria elegans (synonym: Cystoseira elegans) (Susini et al, 2007;Thibaut et al, 2016;Buonomo et al, 2017;Medrano et al, 2020). Such local genetic differentiation has already been observed in other brown algae, such as in the Mediterranean Kelp Laminaria rodriguezii (Reynes et al, 2020), the Atlantic Kelp Laminaria digitata (Billot et al, 2003;Robuchon et al, 2014), Saccharina latissima (Mao et al, 2020), Undaria pinnatifida (Grulois et al, 2011;Guzinski et al, 2018;Salamon et al, 2020), as well as in the Fucoids Hormosira banksii (Coleman et al, 2018), and Fucus ceranoides (Neiva et al, 2012). These studies, from low to high-throughput genotyping approaches, point to the important genetic structuring generally observed in these species.…”

“…Then, SNP discovery was performed using double digest RAD sequencing libraries (dd-RADseq; Peterson et al, 2012). The protocol used to build ddRAD-seq libraries for sequencing is identical to that previously described in Reynes et al (2020). Two hundred and seventy-one individuals of Ericaria zosteroides were randomly distributed across two sequencing libraries, including 10 replicates (one per sampling site), and 100 ng of genomic DNA per individual was double digested using the PstI and HhaI enzymes (NEB).…”

Impact of roadside burning on genetic diversity in a high‐biomass invasive grass

“…In plants, F IS in partially clonal lines has lower mean values, higher standard deviation and negatively skewed distributions compared with sexually reproducing lines (Reynes et al, 2021). Thus, to further investigate variation in clonality among the K genetic clusters identified by fastSTRUCTURE, we visualized the frequency distribution of F IS (from hierfstat) and calculated the mean and interlocus standard deviation of F IS for each cluster separately (Reynes et al, 2021). We did this using the partially filtered data (Filter 1:40,711 SNPs) to include loci with extreme F IS that would be removed with following filters.…”

“…Filter 1 removed SNPs on the same sequence, monomorphic loci and SNPs with a low call rate (<50%). SNPs on the same 69-bp sequence as another were removed to reduce the chance of disequilibrium from physical linkage, keeping the one with the highest call rate (Reynes et al, 2021). Filter 1 was applied before all further processing steps and analyses.…”

Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

“…Microsatellites are commonly employed in tandem with DNA barcoding of organellar markers as a means to fetch genetic information from the nuclear genome (e.g., Neiva et al 2018, Grant andBringloe 2020). Restriction-site-associated DNA sequencing (RADseq) has proven a significant step forward in improving the resolution of genetic datasets (i.e., 1,000s of single-nucleotide polymorphisms, SNPs), particularly in non-model organisms for which reference genomes remain unavailable (e.g., Kobayashi et al 2018, Guzinski et al 2020, Le Cam et al 2020, Mao et al 2020, Reynes et al 2021. Showcasing the power of genome scale genotyping, Flanagan et al (2021) used >62K SNPs to pinpoint the source of global introductions of Agarophyton vermiculophyllum to a ˜50 km section of coastline in Japan.…”