Fig. 1. Strict consensus of 12 trees from the phylogenetic analysis of species in sections Exsertaria (SE), Latoangulatae (SL), and Maidenaria (SM) using the CCR gene fragment. Phylogenetic trees were constructed using the branch and bound algorithm in PAUP. Numbers above branches represent bootstrap percentages after 10,000 bootstrap replicates.

Fig. 2. Representation of the recombination event in CCR depicting E. botryoides 1 (Latoangulatae, SL) as the recombinant progeny of the parental sequences E. nudicaulis (Exsertaria, SE) and E. scias ssp. apoda (SL). Only the variable sites between the three sequences are shown for the recombinant region of the CCR gene fragment. Numbers above the nucleotide alignments refer to base pair positions (read vertically). The recombinant E. botryoides 1 is very similar to E. scias ssp. apoda from nucleotide positions 1–968 and 1212–1418. However, it is more similar to E. nudicaulis at positions 969–1211. Sequences closely related to E. botryoides 1 (E. grandis 1, E. grandis 2, E. saligna 1, and E. saligna 2) were also identified as recombinants.

Fig. 3. Representation of the recombination event in CCR where E. globulus 1 (Maidenaria, SM) was identified as the recombinant progeny of parental sequences similar to E. grandis 1 (Latoangulatae, SL) and an unknown parent (outside the dataset) that was most similar to E. scias ssp. apoda (SL). Only the variable sites between the three sequences are shown for the region of CCR at which recombination is thought to have occurred. Numbers above the nucleotides refer to base pair positions (read vertically). The sequence of E. globulus 1 is most like E. grandis 1 in the recombinant region between positions 774–1211, however, in the rest of the sequence (1–773 and 1212–1418) it is more similar to E. scias ssp. apoda.

Fig. 4. Phylogenetic evidence for a potential recombination event in CCR of Eucalyptus species from sections Maidenaria (SM), Latoangulatae (SL), and Exsertaria (SE). Neighbour joining trees were constructed using phylip with Kimura-2 parameter distances and 1000 bootstrap replicates. The tree on the left used nucleotide sequences depicted in white in the schematic representation of the alignment above the trees (positions 1–968 concatenated with positions 1212–1418). The tree on the right used nucleotide sequences depicted in black in the schematic representation of the alignment (positions 969–1211). Numbers above the branches represent bootstrap percentages. The common ancestor of Group 1 (SL E. botryoides 1, SL E. grandis 1, SL E. grandis 2, SL E. saligna 1, and SL E. saligna 2) was a recombinant sequence, and sequences related to the parental sequences involved in the recombination event are indicated by Group 2 (SE E. nudicaulis) and Group 3 (SL E. scias ssp. apoda). A second recombination event occurred where SM E. globulus 1 was identified as a recombinant sequence, for which the most likely parents were SL E. grandis 1 (Group 1) and a sequence similar to that of SL E. scias ssp. apoda (Group 3). This caused the placement of E. globulus 1 in Group 1 in the tree on the right.

Fig. 5. Potential recombination hotspots within the alignment of 26 CCR gene fragments for species from sections Maidenaria, Latoangulatae, and Exsertaria of Eucalyptus. Detectable breakpoint positions (indicated by small vertical lines at the top of the graph) suggest the location of two potential recombination hotspots (indicated by horizontal lines above the graph). The bar at the top of the graph represents the CCR fragment: black represents exon regions and white depicts the intron. A 200 nucleotide window was moved along the alignment one nucleotide at a time and the number of breakpoints detected within the window region were counted and plotted. The upper and lower broken lines represent confidence levels; anything above those lines represents significant clustering based on a permutation test.

Specimen details for the Eucalyptus samples from sections Latoangulatae, Exsertaria, and Maidenaria used in the phylogenetic and recombination analyses of the CCR gene

Samples with two GenBank numbers have separate 5′ and 3′ sequence fragments, due to the presence of a long microsatellite in the middle of those two regions, which was difficult to sequence. CCA refers to the Currency Creek Arboretum, South Australia.

Insertions/deletions (indels) found in intron 4 of the CCR gene fragment from 29 Eucalyptus samples of sections Latoangulatae, Exsertaria, and Maidenaria

Deletion of sequence in each position was coded as zero; each insertion was coded as shown.

Sequence polymorphisms (including substitutions and one base pair insertion/deletions) found in the CCR gene fragment for 29 Eucalyptus samples from sections Latoangulatae, Exsertaria, and Maidenaria

The size of a region was calculated from the aligned sequences and excluded the insertion/deletion sequences described in Table 2.