Background and Aims Hybridization is known to drive plant speciation through the establishment of homoploid or allopolyploid hybrid species. Here we investigate the origin of Pulmonaria helvetica, a narrow endemic species described across a restricted area of Switzerland that was entirely covered by ice during the last glacial maximum. This species presents an original number of chromosomes (2n = 24) and morphological traits suggestive of a hybrid origin. Methods We sequenced a plastid locus and 1077 double-digest restriction site associated DNA (ddRAD) loci in 67 individuals from across the distribution range of P. helvetica and candidate progenitor species growing in the same area. Assignment of genotypes to main genetic clusters within and among taxa using STRUCTURE tested whether P. helvetica represents a genetically differentiated lineage and addressed the hypothesis of its hybrid origin. Comparative ecological modelling further addressed possible niche differentiation among taxa. Key Results P. helvetica was highlighted as a genetically homogeneous species distinct from co-occurring taxa. Consistent with a scenario of hybrid speciation, it presented clear evidence of balanced admixture between P. officinalis (2n = 16) and P. mollis s.l. (2n = 18, 22) that was also highlighted as maternal progenitor based on plastid sequences. Limited genetic structure within the maternal progenitor is consistent with an origin of P. helvetica through either homoploid hybridization with considerable karyotype changes or via complex scenarios of allopolyploidy involving a dysploid taxon of P. mollis s.l. Comparative niche modelling indicated non-significant ecological differences between P. helvetica and its progenitors, supporting intrinsic factors resulting from hybridization as main drivers of speciation. Conclusions Hybridization appears as a major process having promoted the postglacial origin of the narrow endemic P. helvetica, suggesting hybrid speciation as an effective process that rapidly produces new species under climate changes.

Climatic oscillations of the Quaternary rapidly compelled plant species to shift their geographical range. How alpine plant species responded to climate change, however, remains elusive and remnants of the cold-adapted flora that currently strive in restricted ranges as small, isolated populations have been particularly overlooked. To address the evolutionary history of such a ‘glacial relict’, we here sampled and genotyped all known native populations of a narrow endemic species from the northwestern Alps, Papaver occidentale, as well as closely related taxa with double digest restriction-site Associated DNA (ddRAD) sequencing. Spatial patterns of genetic variation across populations coupled with insights from climatic niche modelling through time address underpinings of the long-term persistence of the species in face of climate changes. Evidence from population genetics and ecological modelling indicates that P. occidentale likely persisted through the last glacial maximum outside of the Western Prealps and that a major lineage recolonized the area from lower elevation, external regions. Differentiated lineages at the Northern margins of the species distribution range highlight highly divergent and geographically restricted populations that include considerable share of private markers and may indicate local glacial survival in isolated conditions. Our data thus imply that processes having shaped intraspecific spatial genetic structure within the Alps can be complex and lead to mosaic of populations with a mixed-history of local survival and immigration. A better understanding of spatio-temporal aspects of range contraction–expansion is crucial to shed light on processes underlying the evolution of remnant populations of such endemic species and set conservation priorities considering current climate changes.

Although there exist over 7000 crop species, only a few are commercially valuable and grown on a large scale in monocultures worldwide. However, underutilised crops (also called orphan crops) have significant potential for food security and Telfairia occidentalis Hook. F. (Cucurbitaceae) is one such orphan crop grown in West Africa for its nutritious leaves, oil and protein-rich seeds. In this dioecious crop, farmers like to eliminate male plants and keep mostly females to increase their yield. However, they face the challenge of determining sex due to limited morphological differences between females and males before flowering. This study used double digested restriction site-associated DNA sequencing data (ddRADseq) to examine the genetic diversity within and among landraces of T. occidentalis, identify common sex-determining loci, and establish reliable assays to characterize the sex of immature plants in the vegetative state. To differentiate males from females of T. occidentalis, two molecular assays were thereupon developed based on polymerase chain reaction (PCR) to genotype sex-specific sequence variation either through restriction by Mfe1 or the direct use of sex-specific primers. Both assays require standard laboratory conditions to reach a certainty of 94.3% for females and 95.7% for males from the studied samples. With the inclusion of additional landraces, medium to largescale farms growing T. occidentalis as a crop can readily benefit from an early determination of the sex of plants.

Although there exist over 7’000 crop species, only a few are commercially valuable and grown on a large scale in monocultures worldwide. However, underutilised crops (also called orphan crops) have great potential for food security and Telfairia occidentalis (Cucurbitaceae) is one such orphan crop grown in West Africa for its nutritious leaves and oil and protein-rich seeds. In this dioecious crop, farmers like to eliminate male plants and mostly keep females to increase their yield but face the challenge of determining sex with limited morphological differences between females and males before flowering. This study used double digested restriction site-associated DNA sequencing data (ddRADseq) to examine the genetic diversity within and among landraces of T. occidentalis, identify common sex-determining loci, and establish reliable assays to characterize the sex of immature plants in the vegetative state. Two molecular assays for distinguishing males from females of T. occidentalis were thereupon developed based on polymerase chain reaction (PCR) to genotype sex-specific sequence variation either through restriction by Mfe1 or the direct use of sex-specific primers. Both assays require standard laboratory conditions to reach a certainty of 94.3% for females and 95.7% for males from studied samples. With the inclusion of additional landraces, medium to large scale farms growing T. occidentalis as a crop can readily benefit from an early determination of the sex of plants.