Conservation Genetics of Threatened, High Ploidy <i>Lepidium</i> (Brassicaceae) Species From Vulnerable Inland Habitats, South Island, New Zealand

Genetic variation in three endangered allopolyploid Lepidium species was assayed using amplicon sequencing of 16 nuclear genesand phylogenetic analysis to distinguish ortholog/paralog (homoeolog) relationships. After phylogenetic analysis, the 16 sets of gene sequences were scored as co‐dominant alleles at a total of 55 putative loci in the target species L. kirkii , L. sisymbrioides , and L. solandri . Lepidium kirkii has perfect flowers and has very low heterozygosity consistent with a predominance of self‐fertilization. In contrast, L. sisymbrioides and L. solandri are dioecious and have high levels of heterozygosity consistent with an obligately outcrossing breeding system. High contemporary heterozygosity in L. sisymbrioides and L. solandri are consistent with the rapid and recent decline in their numbers and suggest that management of the remaining genetic diversity of these species may be required for their survival. Clustering of samples based on allele‐sharing suggests that the distinction between the sympatric species L. sisymbrioides and L. solandri may not reflect kinship relationships well, with three regional groups being recovered instead of groups corresponding with the currently accepted classification. An appreciable fraction (25%) of the gene sequences recovered appear to be pseudogenes.