Emerging pathogens have been increasing exponentially over the last
century. The knowledge on whether these organisms are native to
ecosystems or have been recently introduced is often of great
importance. Understanding the ecological and evolutionary processes
promoting emergence can help to control their spread and forecast
epidemics. 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 west to east: from Malaysia to 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 it
was recently introduced in multiple areas. Our results suggest that
recent emergence of P. noxius in east Asia, Australia, and the
Pacific Islands is likely driven by anthropogenic and natural
disturbances, including deforestation, land-use change, severe weather
events, and introduction of exotic plants. This study provides a novel
example of utilization of genome wide allele frequency data to unravel
dynamics of pathogen emergence under conditions of changing ecosystems.
INVESTIGATING THE EVOLUTIONARY HISTORY OF THE PACIFIC NORTHWEST MESIC FOREST ECOSYSTEM: HYPOTHESIS TESTING WITHIN A COMPARATIVE PHYLOGEOGRAPHIC FRAMEWORK
