DOI: 10.5061/dryad.f7m0cfxrq
title: Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian‐ eastern North American Nyssa (Nyssaceae)

description: Nyssa (Nyssaceae, Cornales) represents a classical example of the
 well‐known eastern Asian‐eastern North American floristic disjunction. The
 genus consists of three species in eastern Asia, four species in eastern
 North America, and one species in Central America. Species of the genus
 are ecologically important trees in eastern North American and eastern
 Asian forests. The distribution of living species and a rich fossil record
 of the genus make it an excellent model for understanding the origin and
 evolution of the eastern Asian‐eastern North American floristic
 disjunction. However, despite the small number of species, relationships
 within the genus have remained unclear and have not been elucidated using
 a molecular approach. Here we integrate data from 48 nuclear genes,
 fossils, morphology, and ecological niche to resolve species
 relationships, elucidate its biogeographic history, and investigate the
 evolution of morphology and ecological niches, with the goal toward a
 better understanding of the well‐known EA‐ENA floristic disjunction.
 Results showed the Central American (CAM) N.
 talamancana was sister to the remaining species, which were
 divided among three, rapidly diversified subclades. Estimated divergence
 times and biogeographic history suggested Nyssa had an
 ancestral range in Eurasia and western North America in the late
 Paleocene. The rapid diversification occurred in the early Eocene,
 followed by multiple dispersals between and within the Erasian and North
 American continents. The genus experienced two major episodes of
 extinction in the early Oligocene and end of Neogene, respectively. The
 Central American N. talamancana represents a relic
 lineage of the boreotropical flora in the Paleocene/Eocene boundary that
 once diversified in western North America. The results supported the
 importance of both the North Atlantic land bridge and the Bering land
 bridge (BLB) for the Paleogene dispersals of Nyssa and
 the BLB for the Neogene dispersals and the role of Central America as
 refugia of the Paleogene flora. The total‐evidence based dated phylogeny
 suggested that the pattern of macroevolution
 of Nyssa coincided with paleoclimatic changes. We found
 a number of evolutionary changes in morphology (including wood anatomy and
 leaf traits) and ecological niches (precipitation and temperature) between
 the EA‐ENA disjunct, supporting ecological selection driving trait
 evolutions following geographic isolation. We also demonstrated challenges
 in phylogenomic studies of lineages with rapid diversification histories.
 The concatenation of gene data can lead to inference of strongly supported
 relationships incongruent with the species tree. However, conflicts in
 gene genealogies did not seem to impose a strong effect on divergence time
 dating in our case. Furthermore, we demonstrated that rapid
 diversification events may not be recovered in divergence time dating
 analysis using BEAST if critical fossil constraints of the relevant nodes
 are not available. Our study provides an example of complex bi‐directional
 exchanges of plants between Eurasia and North America in the Paleogene but
 “out of Asia” migrations in the Neogene to explain the present disjunct
 distribution of Nyssa in EA and ENA.