This study uses phylogenetic relationships of the species-rich section
Astragalus (Incani), to follow up on recent evidence pointing to rapid and
recent plant diversification patterns in the west of Iran. Section Incani is
introduced for its taxonomic complication resulting from overlapping
morphological characters, but few studies have been done on this section;
hence, we also lack a robust time-calibrated chronogram to address
hypotheses (e.g., biogeography and diversification rates) that have implicit
time assumptions. Two loci (rpl32-trnL(UAG) and nrDNA ITS) were amplified
and sequenced for 87 taxa across Incani for phylogenetic reconstruction and
a chronogram in BEAST. Incani is identified as the sister clade to all
remaining sections with high support, and within the clade Incani, two
strongly supported groups are seen: (1) Clade I includes nine species
restricted to eastern Iran and Central Asia, and (2) clade II includes a
bulk of the species from west and northwestern Iran, Turkey and southern
Europe. Divergence time estimates suggest Incani diverged from remaining
sections 3 Mya during the late Pliocene. The crown date for Incani is
estimated at 1.5 Mya (Pleistocene). Biogeography showed significant
improvement in the likelihood score when the ??jump dispersal? parameter was
added. An eastern origin (Central Asia) is implicated as important ancestral
area in all deeper nodes. BAMM analyses indicate that the best configuration
included one significant shift in diversification rates within Incani: near
the crown of Incani (1.5-2 Mya) including clade II. Issues with conducting
diversification analyses more generally are examined in the context of
scale, taxon sampling, and larger sets of phylogenetic trees.