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 ghost population to Malaysia and the
Pacific Islands, with subsequent spread to Taiwan and Australia.
Furthermore, ABC analyses indicate that 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. noxius in 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 Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history