Data from: Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living
member of the sister group to all other extant Angiosperms, is endemic to
New Caledonia. We addressed the intraspecific phylogeography of Amborella
by investigating whether its present population genetic structure could be
related to its current and past habitats. We found moderate range-wide
genetic diversity based on nuclear microsatellite data, and detected four
well-differentiated, geographically distinct genetic groups using Bayesian
clustering analyses. We modeled the ecological niche of Amborella based on
current climatic and environmental conditions. The predictive ability of
the model was very good throughout the Central East mainland zone, but
Amborella was predicted in the northern part of the island where this
plant has not been reported. Furthermore, no significant barrier was
detected based on habitat suitability that could explain the genetic
differentiation across the area. Conversely, we found that the main
genetic clusters could be related to the distribution of suitable habitat
at the last glacial maximum (LGM, ca. 21 000 years BP), when Amborella
experienced a dramatic 96.5% reduction in suitable area. At least two
lineages survived in distinct putative refugia located in the Massif des
Lèvres and in the vicinity of Mount Aoupinié. Our findings finally
confirmed the importance of LGM rainforest refugia in shaping the current
intra- and inter-specific diversity in New Caledonian plants, and revealed
the possibility of an as-yet unreported refugium. The combination of niche
modelling and population genetics thereby offered novel insight into the
biogeographic history of an emblematic taxon.