Dean Nicolle

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.

Novel Distances for Dollo Data

We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), that applies to data generated under a Dollo model and show that it has some useful theoretical properties including an intriguing link to the LogDet/paralinear distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, a restriction-site-based distance, and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process; this may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology data sets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyze gene family presence/absence data from bacterial genomes obtained from the COG database and compare the results with previous phylogenies estimated using the conditioned genome reconstruction approach. The results for these case studies are largely congruent with previous studies, in some cases giving more phylogenetic resolution.

Phylogenetic positioning of anomalous eucalypts by using ITS sequence data

We investigated the phylogenetic affinities of the following six taxonomically anomalous species of Eucalyptus: E. cladocalyx, E. cosmophylla, E. gomphocephala, E. longifolia, E. paludicola and E. pumila. ITS sequence data were obtained from these species and combined with an existing large ITS data set for subgenus Symphyomyrtus. Phylogenetic analysis using maximum parsimony and Bayesian approaches showed that E. longifolia belongs in section Maidenaria and E. gomphocephala belongs in section Bisectae I. The phylogenetic affinities of the other four species were not fully resolved by ITS sequence data. E. cladocalyx has affinities with sections Adnataria, Dumaria and Bisectae I; E. cosmophylla and E. paludicola have affinities with sections Exsertaria, Latoangulatae and Maidenaria; and E. pumila appears to be a morphologically divergent member of section Latoangulatae or Exsertae. The implications of the results for conservation of native eucalypt gene pools are discussed.

Variation in the Eucalyptus flocktoniae complex (Myrtaceae) and the description of four new taxa from southern Australia

Eucalyptus flocktoniae is considered to be a complex distinguished within EucalyptusseriesSubulatae by decurrent juvenile leaves and glossyadult leaves. The geographical range of E. flocktoniae(Maiden) Maiden was examined to quantify the patterns of variation in bothadult and seedling morphology. The putatively related speciesE. aspersa Brooker & Hopper,E. cooperiana F.Muell.,E. socialis F.Muell. exMiq.,E. transcontinentalis Maiden sens.lat.and E. yumbarrana Boomsma werealso studied to assess similarity and relationships toE. flocktoniae sens. lat. Phenetic analysis of adult andjuvenile data sets (46 and 21 characters, respectively) indicated that theE. flocktoniae complex consisted of five distinct taxa,distinguishable from one another in habit, branchlet pruinosity, leaf colourand gloss, inflorescence pruinosity, umbellaster orientation, bud size andornamentation, and fruit shape and ornamentation. These taxa areE. flocktoniae subsp. flocktoniae,here redefined, as restricted to between Three Springs and the Oldfield Riverin Western Australia (WA); subsp. hebes Nicolle subsp.nov. from Balladonia to north-east of Ravensthorpe, WA;E. neutra Nicolle sp. nov., from the south-centralwheatbelt of WA; E. peninsularis Nicolle sp. nov. fromlower Eyre Peninsula in SA; and E. urna Nicolle sp.nov., a common and widespread species between Kondinin and Caiguna in WA. Akey and distribution maps are provided for taxa of theE. flocktoniae complex.

High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus

We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies.