Evolutionary patterns of the Tamus clade of Dioscorea in
the Mediterranean
Overall evolutionary patterns of Dioscorea lineages have been
thoroughly studied using plastid markers (e.g., Wilkin et al.,2005; Hsu et al., 2013; Maurin et al., 2016; Viruelet al., 2016) and low copy nuclear genes (e.g. Viruel et
al., 2018, Soto Gomez et al., 2019). Previous studies determined
that yams diverged and expanded since the Late Cretaceous, probably from
Laurasia, and that a split of the African-Mediterranean lineage, which
includes the Tamus clade, likely occurred in the Oligocene, following a
westward migration ca. 33 MY (Viruel et al ., 2016). Fossil
records indicate that Dioscorea ancestors persisted in Europe
during the Oligocene (Andreànzky, 1959). Based on data from four plastid
markers, the split between the two Mediterranean clades, Borderea and
Tamus, was estimated to have occurred during the late Oligocene (ca.
25.7 MY) (Viruel et al ., 2016), a similar divergence time to the
one we obtained with our analyses based on 260 nuclear genes, which
indicate that this divergence took place in the early Oligocene
(28.2–28.4 MY); Supplementary Data Figure S4). Two narrowly endemic
species of the Borderea clade survived in refugia in the Pyrenean
mountains, D. chouardii , a critically endangered species with
only one known locality (Martínez & Otano, 2011), and D.
pyrenaica , with a slightly wider distribution in the central Pyrenees
and Pre-Pyrenees (Segarra & Catalán, 2005; Catalan et al ., 2006;
Segarra-Moragues & Catalan, 2008; García et al., 2012). A
previous study (Viruel et al., 2016) estimated a split between
these two species during the early Pliocene (ca. 4.3 MY), whereas our
results indicated that this divergence likely occurred during the late
Miocene (8.1–10.6 MY).
The differences observed in divergence times for the Tamus clade in
comparison with previous studies are a consequence of the newly
recognized species (D. cretica ). In Viruel et al . (2016),
the crown node of the Tamus clade was estimated to be 15.3 MY (D.
edulis (D. communis , D. orientalis )), and the subsequent
split between D. orientalis and D. communis at 10.4 MY.
However, the samples of D. orientalis included in Viruel et
al . (2016) have now been reidentified as D. cretica , and thus
the older age estimates herein for the crown node of the Tamus clade
(20.6–18.2 MY) demonstrate an early split of D. orientalis in
the eastern Mediterranean, followed by a split of D. edulis ca.
16.0-13.5 MY, and the divergence of D. communis s.s. andD. cretica ca. 6.6–5.6 MY. Given the findings presented here,
with a sampling representative of the whole distribution range of the
Tamus clade across the circum-Mediterranean region, we conclude that the
divergence times estimated here are more robust and taxonomically more
representative, which allowed us to reassess the species delimitation in
this group.
The Mediterranean region is considered one of the major biodiversity
hotspots of the world (Médail and Quézel, 1997). Fossil records and
evolutionary studies have confirmed that the ancestors of several plant
lineages were part of a tropical flora that occupied the Mediterranean
region during the Miocene and early Pliocene (Suc et al., 2018).
The drastic subsequent climatic changes that came during the Pliocene
(3.5–2.4 MY), with a significant drop in temperature and a marked
seasonality in thermal and rainfall regimes, impacted the
diversification patterns of plant lineages and resulted in narrow
endemics in the margins of the distribution range of their sister
species (e.g., Ceratonia oreothauma Hillc., G.P.Lewis & Verdc.;
Viruel et al., 2020). The diversification of species in the Tamus
clade likely occurred during the Miocene when subtropical climatic
conditions were present across the Mediterranean (Suc et al .,
2018). The most recent common ancestor of all Tamus clade taxa likely
diversified during the early Miocene (20.6–18.2 MY), when the lineages
that gave rise to the current D. orientalis and the clade
comprising the three lineages of D. communis s.l. likely split.
This was followed by a subsequent split of the Macaronesian D.
edulis that would have taken place in the mid-Miocene (16.0–13.5 MY),
after the formation of some of the Canary Islands, which has been
estimated to start around 23 MY (Sanmartín et al., 2008;
Florencio et al ., 2021). The most recent split between D.
communis s.s. and D. cretica is estimated to have
occurred during the Messinian (Miocene, 6.6–5.6 MY). During this
period, the significant and rapid lowering of the sea level of the
Mediterranean also resulted in new terrestrial biogeographical
connections allowed by the formation of land-bridges.
Several phylogeographic studies have attempted to explain the
biodiversity patterns and processes that shaped the Mediterranean region
and its development into one of the world’s biodiversity hotspot (e.g.,
Nieto Feliner, 2014; Thompson, 2021). Two main areas of high plant
endemism were identified in the western (Iberian Peninsula and Morocco)
and eastern Mediterranean (including Turkey and Greece) (Médail and
Quézel, 1997). In both these areas, Quaternary glaciations likely played
a major role shaping the distribution of species and left a footprint in
the genetic structure of many Mediterranean species, particularly in
refugia (Médail and Diadema, 2009). Western and eastern genetic groups
have been identified in phylogeographic patterns of several
Mediterranean plants, leading to disjunct distributions in some cases,
such as in Microcnemum Ung.-Sternb (Amaranthaceae) andMandragora L. (Solanaceae) (Kadereit and Yaprak, 2008; Voliset al., 2018), or by differentiating morphotypes that later
hybridized in intermediate zones (e.g., Quercus ilex L., Lumaretet al., 2002). The strong geographic influence in the genetic
structuring of D. communis across the Mediterranean may have also
been slightly influenced by bird dispersal. Bird dispersals have
contributed to shaping the postglacial recolonization of the
Mediterranean, such as seen in Frangula alnus Mill. (Hampeet al ., 2003). The birds that consume berries produced by species
of the Tamus clade, mainly blackbirds (Turdus merula L.), robins
(Erithacus rubecula L.) and blackcaps (Sylvia communisLatham) (Chiscano, 1983; Herrera, 1984), are predominantly sedentary
birds or have modern migratory routes that do not strictly coincide with
the past and current distribution patterns estimated in this study
(Adriaensen, 1988; Burfield and Van Bommel, 2004). It would thus be
useful to analyse the patterns of genetic structure at the population
level of D. communis s.s. in more detail and in connection with
the possible magnitude of ornithochory, which has never been studied in
detail to our knowledge.
Changes in ploidy, morphological differences and introgression between
the central Mediterranean and western European populations have been
shown to have occurred between the D. communis s.s. and D.
cretica lineages (Figures 2, 5). The central-eastern Mediterranean area
constitutes the contact region between these two species and is
congruent with the introgression patterns found in our study (Figure 2).
Five out of 16 samples studied of D. cretica exhibited
<20% of admixture index with D. communis s.s. , and all
individuals of D. communis belonging to the eastern clade ofD. communis s.s. showed <20% of admixture index withD. cretica (Figure 2). However, only four individuals from the
central Mediterranean and western European subclades of D.
communis were detected as introgressing with a sister species, and one
sample of D. cretica was placed in a clade of D. communis
s.s. in the phylogenetic tree based on plastid data (R32, Figure 1).
These results are congruent with their potential distribution in
disjunct refugia followed by secondary contact through recolonization,
and by maintaining some capacity of interspecific gene flow between
closely related species (see Viruel et al., 2021). The
topological incongruencies found between the nuclear and plastid
phylogenetic trees, indicative of plastid capture events (Figure 1), are
congruent with these hypothesized introgression patterns: plastid clades
I and II are found in the central and eastern Mediterranean lineages
without a clear geographic separation (Figure 6), whereas clade III is
uniquely found in the western part of the Mediterranean where lower
introgression events have been inferred.