10.5061/DRYAD.C866T1G89
Kozhar, Olga
0000-0002-0976-7334
Colorado State University
Kim, Mee-Sook
Pacific Northwest Research Station
Ibarra Caballero, Jorge
Colorado State University
Klopfenstein, Ned B.
Rocky Mountain Research Station
Cannon, Phil
US Forest Service
Stewart, Jane
Colorado State University
Long evolutionary history of an emerging fungal pathogen of diverse tree
species in eastern Asia, Australia, and the Pacific Islands
Dryad
dataset
2022
FOS: Agriculture, forestry, and fisheries
2022-03-03T00:00:00Z
2022-03-03T00:00:00Z
en
https://doi.org/10.5281/zenodo.5940863
51718293 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Emerging plant pathogens have been increasing exponentially over the last
century. To address this issue, it is critical to determine whether these
pathogens are native to ecosystems or have been recently introduced.
Understanding the ecological and evolutionary processes fostering
emergence can help to manage their spread and predict
epidemics/epiphytotics. Using restriction site-associated DNA sequencing
data, we studied genetic relationships, pathways of spread, and
evolutionary history of Phellinus noxius, an emerging root-rotting fungus
of unknown origin, in eastern Asia, Australia, and the Pacific Islands. We
analyzed patterns of genetic variation using Bayesian inference, maximum
likelihood phylogeny, populations splits and mixtures measuring
correlations in allele frequencies and genetic drift, and finally applied
coalescent based theory using Approximate Bayesian computation (ABC) with
supervised machine learning. Population structure analyses revealed five
genetic groups with signatures of complex recent and ancient migration
histories. The most probable scenario of ancient pathogen spread is
movement from an unsampled population to Malaysia and the Pacific Islands,
with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses
indicate P. noxius spread occurred thousands of generations ago,
contradicting previous assumptions that this pathogen was recently
introduced to multiple geographic regions. Our results suggest that recent
emergence of P. noxiusin eastern Asia, Australia, and the Pacific Islands
is likely driven by anthropogenic and natural disturbances, such as
deforestation, land-use change, severe weather events, and/or introduction
of exotic plants. This study provides a novel example of applying
genome-wide allele frequency data to unravel dynamics of pathogen
emergence under changing ecosystem conditions.
The dataset contains three input files obtained from raw RADseq reads with
Stacks v.2 to generate results in our paper. It also contains
configuration files of five DIYABC analyses performed with DIYABC Random
Forest v.1.
Users will need sequence data () and some knowledge of linux.