Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Abstract

Abstract. Eucalyptus is a genus that occurs in a range of habitats in Australia, Papua New Guinea, Timor, Sulawesi and the Philippines, with several species being used as sources of timber and fibre. However, despite its ecological and commercial significance, understanding its evolutionary history remains a challenge. The focus of the present study is the green ashes (subgenus Eucalyptus section Eucalyptus). Although previous studies, based primarily on morphology, suggest that the green ashes form a monophyletic group, there has been disagreement concerning the divergence of taxa. The present study aims to estimate the phylogeny of the green ashes and closely related eucalypts (37 taxa from over 50 locations in south-eastern Australia), using genome-wide analyses based on Diversity Arrays Technology (DArT). Results of analyses were similar in topology and consistent with previous phylogenies based on sequence data. Many of the relationships supported those proposed by earlier workers. However, other relationships, particularly of taxa within the Sydney region and Blue Mountains, were not consistent with previous classifications. These findings raise important questions concerning how we define species and discern relationships in Eucalyptus and may have implications for other plant species, particularly those with a complex evolutionary history where hybridisation and recombination have occurred.

Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

“…The phylogeny of the green ashes was previously estimated using the DArT microarray method (Rutherford et al 2016). It was found that while some of the lineage relationships were consistent with previous taxonomic classifications primarily based on morphology, other relationships were not.…”

“…The advent of next-generation sequencing (NGS) and associated technologies has enabled a much higher genomic resolution for the study of speciation mechanisms compared with traditional molecular methods (Keller et al 2013). One technique that is increasingly being used in Eucalyptus is Diversity Arrays Technology sequencing (DArT, e.g., Steane et al 2011;Rutherford et al 2016). DArT is based on genome complexity reduction using restriction enzymes, followed by hybridisation to microarrays to simultaneously assay thousands of markers across the genome (Jaccoud et al 2001).…”

A dated molecular perspective of eucalypt taxonomy, evolution and diversification

“…Much more data than the four loci used here will be necessary to achieve higher resolution of the eucalypt relationships. Previous eucalypt studies using a greater proportion of the 55 nuclear or plastid genome than in the present study have still led to non-monophyly of lower-level groups (Nevill et al 2014;Rutherford et al 2015;Jones et al 2016). It may be possible to resolve relationships in cases of incomplete lineage sorting using a coalescent approach, which is being improved in programs such as STAR BEAST (ver.…”

“…Further, the hybridising ability of what are considered to be more distantly related groups, as also illustrated by Schuster et al (2018), means that a resolved bifurcated tree might not be appropriate, and that nodes closer to the tips of the phylogeny might be better represented as evolutionary networks (e.g. appendix 4 of Rutherford et al 2015).…”

Phylogenetic studies of eucalypts: fossils, morphology and genomes

“…et al 2006Parra-O. et al , 2009, microsatellites Ochieng et al 2007b), AFLPs (McKinnon et al 2008), and Diversity Array Technology (DArT) markers Woodhams et al 2013;Hudson et al 2015;Rutherford et al 2015).…”