SNP sets of Bolivian Parajubaea species

Conservation and sustainable management of lineages providing non-timber
forest products are imperative under the current global biodiversity loss.
Most non-timber forest species, however, lack genomic studies that
characterize their intraspecific variation and evolutionary history, which
inform species’ conservation practices. Contrary to many lineages in the
Andean biodiversity hotspot that exhibit high diversification, the genus
Parajubaea (Arecaceae) has only three species despite the genus’ origin 22
million years ago. Two of the three palm species, P. torallyi and P.
sunkha, are non-timber forest species endemic to the Andes of Bolivia, and
are listed as IUCN endangered. The third species, P. cocoides, is a
vulnerable species with unknown wild populations. We investigated the
evolutionary relationships of Parajubaea species, and the genetic
diversity and structure of wild Bolivian populations. Sequencing of five
low-copy nuclear genes (3,753 bp) challenged the hypothesis that P.
cocoides is a cultigen that originated from the wild Bolivian species. We
further obtained up to 15,134 de novo single-nucleotide polymorphism
markers by genotyping-by-sequencing of 194 wild Parajubaea individuals.
Our total DNA sequencing effort rejected the taxonomic separation of the
two Bolivian species. As expected for narrow endemic species, we observed
low genetic diversity, but no inbreeding signal. We found three genetic
clusters shaped by geographic distance, which we use to propose three
management units. Different percentages of missing genotypic data did not
impact the genetic structure of populations. We use the management units
to recommend in-situ conservation by creating new protected areas, and
ex-situ conservation through seed collection.