Is evolution of apomicts driven by the phylogeography of the sexual ancestor? Insights from European and Caucasian brambles (Rubus, Rosaceae)

Abstract

Aim Apomixis, i.e. asexual reproduction via seeds, occurs in many plant taxa of diverse phylogenetic origins and has resulted in a high abundance and wide distribution of some groups. When and where apomicts arose and how their evolution is linked to their sexual ancestors is poorly understood. We aimed at detecting phylogeographical patterns in Rubus ulmifolius–R. sanctus agg., a diploid sexual species aggregate from Rubus series Discolores (Rosaceae), and asked where and when its polyploid apomictic descendants originated. Location Europe and adjacent regions (Caucasus, Macaronesia, Morocco). Methods Next‐generation sequencing of 10 nuclear microsatellite loci, Sanger sequencing of two plastid loci and ecological niche modelling. Results The data reveal strong, continental‐scale genetic structuring within Rubus ulmifolius–R. sanctus agg. Geographical patterns of genetic diversity and ecological niche models indicate its survival mainly on the Iberian Peninsula and in Morocco during the Last Glacial Maximum, as well as population bottlenecks in the eastern Mediterranean and the Caucasus, whereas low allelic diversity in north‐western Europe stems from post‐glacial re‐colonization from southern refugia. The distribution of alleles among diploids and polyploids indicates that the first allopolyploidization events occurred prior to the last glaciation, but also reflects post‐glacial gene flow from diploids to polyploids. Main conclusions Polyploid apomicts both preserve ancestral alleles lost in their diploid ancestors because of ice‐age bottlenecks and harbour also derived, i.e. younger, alleles obtained from diploid taxa via recent gene flow. Diversification of apomicts as a result of the diploid's genetic deterioration is hypothesized. Then, geographical parthenogenesis in Rubus could also be explained by genetic diversity patterns in the diploid, sexual ancestor.

SSR‐seq: Genotyping of microsatellites using next‐generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring

“…The presented method allows using longer fragments (mean locus length was 329 bp over all loci and species with a maximum length of 418 bp), as compared to the traditional way of SSR scoring, increasing the likelihood that the FR contain genetic variation. This, in fact, does not prevent short fragments of already available primers and SSR loci to be successfully genotyped applying our method (Sochor, Šarhanová, Pfanzelt, & Trávníček, ). Nevertheless, the degree of size homoplasy did not correlate with mean fragment length, number of variable sites or number of SNPs or SSR units.…”

“…The presented method allows using longer fragments (mean locus length was 329 bp over all loci and species with a maximum length of 418 bp), as compared to the traditional way of SSR scoring, increasing the likelihood that the FR contain genetic variation. This, in fact, does not prevent short fragments of already available primers and SSR loci to be successfully genotyped applying our method (Sochor, Šarhanová, Pfanzelt, & Trávníček, 2017 (Table 3). In the case of eventual correlations of size homoplasy and the number of variable sites, it should be considered that the way of calculating size homoplasy in the present study does not take into account how many alleles of the same fragment size class (differing in sequence, but not in length) are present.…”

Geographical Parthenogenesis in Alpine and Arctic Plants

“…Due to the bypass of meiosis, apomicts avoid loss of heterozygosity and inbreeding depression in the offspring, which otherwise reduces the fitness of selfing diploid populations. Inbreeding in small, diploid self-incompatible populations results in lower fitness and is disadvantageous to diploid sexual progenitors [ 76 , 103 , 104 , 105 ]. Third, polyploids, specifically allopolyploids, have higher levels of heterozygosity, both on the population level [ 106 ], but also as intragenomic heterozygosity ([ 65 ]).…”

Sperm-dependent asexual species matter in ecology and evolution

“…The examples are hybridogenetic frogs P. esculentus which serve as a "vector" transmitting clonal genomes of a parental species, P. ridibundus, to western Europe, far beyond its original range (Arano et al 1994;Pagano et al 2001), gynogenetic Cobitis hybrids that transmit genes of its Danubian parent, C. elongatoides, hundreds of kilometers outside its range to the Rhine River region and to the southern Ukraine (Choleva et al 2008), or Corbicula clams, whose asexual hermaphroditic reproduction increases invasive success (Pigneur et al 2011(Pigneur et al , 2012. Similarly in plants, such as in the genus Rubus, polyploid apomicts may preserve ancestral alleles lost in their sexual ancestors during Pleistocene ice-age bottlenecks and spread younger alleles obtained from diploids via recent gene flow (Sochor et al 2017).…”