Subspecies variation of Daucus carota coastal ("gummifer") morphotypes (Apiaceae) using genotyping-by-sequencing

The genus Daucus is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. The D. carota complex presents the greatest taxonomic problems in the genus. We focus on a distinctive phenotypic group of coastal morphotypes of D. carota, strictly confined to the margins to within about 0.5 km of the Mediterranean Sea and the Atlantic Ocean, which we here refer to as coastal morphotypes or D. carota subsp. "gummifer" complex, the earliest name for taxa in this group. They are loosely morphologically coherent, sharing a relatively short stature, thick, broad, sometimes highly glossy leaf segments, and usually flat or convex fruiting umbels. We analyzed 288 accessions obtained from genebanks in England, France, and the USA, and an expedition to Spain in 2016, covering the Mediterranean and Atlantic coasts and Balearic Islands, where much of the gummifer complex variation occurs. Our study includes 112 accessions not examined before in this context. Genotyping-by-sequencing identified 29,041 filtered SNPs. Based on high bootstrap support from Maximum likelihood and Structure analysis we highlight three main clades. The gummifer morphotypes are intercalated with members of Daucus carota subspecies carota and subspecies maximus in two of these main clades, including a clade containing accessions from Tunisia (also including D. carota subsp. capillifolius) and a clade containing accessions from western Europe (including the British Isles), southern Europe (including the Balearic Islands and the Iberian Peninsula) and Morocco. These results support five independent selections of the gummifer morphotypes in these narrowly restricted maritime environments in the Mediterranean Region and nearby Atlantic coasts. Daucus annuus (=Tornabenea annua) and Daucus tenuissimus (=Tornabenea tenuissima; Cape Verde) also fall firmly within Daucus carota, supporting their classification as morphologically well-defined subspecies of D. carota, which are accepted here with new combinations. Types are indicated for most of treated names, including designation of four new lectotypes and two new epitypes, which contribute to fixation of further use of these names.Figure 1. Maximum likelihood reconstruction and structure of the genetic diversity of 288 accessions of the Daucus carota complex and outgroup, using 29,041 SNPs obtained by genotyping-by-sequencing. Each accession is represented by a horizontal bar, and each color corresponds to a theoretical population (nine in total). Numbers above the branches represent bootstrap values. Daucus syrticus is the outgroup. Accessions previously studied in Arbizu et al. (2016) and Mezghani et al. (2018) are marked in green. Supplemental Table 1. The 288 accessions of Daucus included in this study: accession number, clade, corresponding number on Fig. 3 map, new identification, and locality information. Maximum likelihood file and VCF file that was produced before the Maximum likelihood file