Introduction
The yam genus, Dioscorea L. (Dioscoreaceae) is a diverse group
currently containing 631 accepted species (POWO, 2022) possessing
underground storage organs and, in most, a climbing habit. Species with
starchy tubers constitute a food staple for millions of people,
resulting in seven to ten species being cultivated on a large scale
(Asiedu and Sartie, 2010), including two (D. alata L. andD. cayenensis Lam.) which together are the most widely cultivated
crops (Price et al ., 2016). More than 40 wild species are
harvested as food sources (Martin and Degras, 1978). In addition, some
yams have been used in traditional medicine and as a source of steroidal
precursors (De Luca et al., 2012; Hua et al., 2017; Priceet al ., 2016). While most wild yam species are found in tropical
regions (Caddick et al., 2002), a few species are distributed in
temperate regions and exhibit unique morphological traits (Viruelet al., 2010). For
example, only six species occur in the Mediterranean-Macaronesian
region: two species of the Stenophora clade (D. balcanica Košanin
native to Montenegro and Albania, and D. caucasica Lipsky, found
in Georgia and Caucasian Russia), the Borderea clade, which contains two
well-defined and narrow endemic species from the Pyrenean mountains
(D. chouardii Gaussen and D. pyrenaica Bubani & Bordère
ex Gren.), and the Tamus clade, which is defined by having berries
rather than winged capsules and is more widely distributed across the
Mediterranean Basin, Macaronesia and Atlantic Europe (Viruel et
al., 2016).
The Tamus clade currently comprises two species (Wilkin et al.,2005): D. communis (L.) Caddick & Wilkin, distributed throughout
the Mediterranean Basin and the Macaronesian Islands (Canary Islands and
Madeira), and with infraspecific variation in ploidy (Viruel et
al., 2019); and D. orientalis (J. Thiébaut) Caddick & Wilkin,
restricted to Lebanon and Israel. However, like in many Dioscoreaclades (Viruel et al., 2010), the Tamus clade has had multiple
previous taxonomic circumscriptions. The Tamus clade was considered as a
separate genus, Tamus L., distinct from Dioscorea , until
2002 (Caddick et al ., 2002). Linnaeus (1753) recognized two
species: T. communis L. with cordate leaves and a Mediterranean
distribution, and T. cretica L, with trilobed leaves and
typified with material from the Greek island of Crete. In the
19th and early 20th centuries, four
Macaronesian endemic species were described (T. edulisLowe, T. parviflora Kunth, T. norsa Lowe and T.
canariensis Willd. ex Kunth), while T. cirrhosa Hausskn. ex
Bornm., T. cordifolia Stokes and T. racemosa Gouan were
treated as distinct Mediterranean species. In the late
20th Century, T. cretica was placed as a
subspecies in T. communis (T. communis subsp.cretica (L.) Nyman), and T. communis f. subtriloba(Guss.) O. Bolòs & Vigo was described as a variety with trilobed leaves
found in the Balearic Islands and northeastern Spain (Catalonia). All
these names were subsequently united under the currently acceptedD. communis (Caddick et al., 2002). The second species
currently recognized in the Tamus clade, D. orientalis , was
originally described as T. orientalis J.Thièbaut named after its
eastern Mediterranean distribution.
From the above, it is clear that species concepts have undergone many
changes since Linnaeus described two Tamus species using
morphology, especially reproductive traits (De Queiroz, 2007). As for
many other species in other plant genera and families, integrative
taxonomic and systematic approaches combining genetic data,
morphometrics and climatic envelope data have successfully helped to
delimit species in challenging groups of plants (e.g., Frajman et
al., 2019). The emergence of high-throughput sequencing (HTS)
techniques and the production of thousands of molecular markers have
massively increased our ability to resolve relationships between and
within species, and subsequently redefine species boundaries (e.g., Fayet al., 2019; Escudero et al., 2020). Among these HTS
methods, Hyb-Seq has become widely adopted across plant phylogenomic
studies due to its ability to generate data from degraded herbarium
materials (e.g., Brewer et al., 2019; Viruel et al., 2019)
and to resolve relationships at different taxonomic scales (e.g.,
Villaverde et al., 2018). Hyb-Seq techniques rely on genome skim
data and target capture probes either designed specifically for some
genera or families (e.g., Soto Gomez et al., 2019) or more widely
across larger groups, including all angiosperms (e.g., Johnson et
al., 2019). In this study, we use a multidisciplinary approach
combining genomic, morphometrics, and environmental niche modelling data
generated from herbarium specimens to identify taxon boundaries in the
challenging Tamus clade of Dioscorea , and to explore their
phylogeographic patterns across the Mediterranean.