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Phylogenetic Tree for the Gomphales

Submitted by cooperj on Mon, 03/07/2023 - 11:07am
The order Gomphales contains the colourful coral fungi in the genus Ramaria, as well as some of our unusual and uncommon species like the toothed Beenakia dacostae and the 'gomphoid' species of Gloeocantharellus. The coral fungi were last revised in New Zealand by Ron Petersen in 1988 (The clavarioid fungi of New Zealand. DSIR Science Information Publishing). That was pre-molecular era work and species concepts have changed over time. Species with a broad distribution are now usually found to represent multiple phylogenetic species with narrower distributions, and sometimes crptic morphological differenecs. That is true for the clavarioid fungi, where northern hemisphere names have been incorrectly applied in New Zealand, and where we have many undescribed species. The phylogenetic tree linked here was produced primarily with mult-gene data already available in GenBank. There are existing published trees in various papers on various groups in the order, but none of them seem to stitch together all the available data. The resulting super-matrix used for this tree is sometimes sparse, but it does suggest some interesting relationships, and does support at least some recently recognised genera. However, the tree also contains many poorly supported branches and there is no doubt that more extensive sampling is needed to adequately resolve the genera in the family, and to sort out potential generic synonyms and older names that might be resurrected. The tree has been supplemented with data from sequences New Zealand species, highlighted in red. Further information on these species and collections may be found on the NZ Biota website (

Update July 2023. I added some recently published sequences for a couple of new genera and more muti-gene sequences that separate Turbinellus from Gomphus. I was also more thorough in removing poorly aligned regions. ITS, whilst useful for separating species, is saturated when the alignment includes representatives across the order. Removal of poorly aligned regions essentially reduces ITS to the 5.8 region and few small islands of stability. Consequently, Phylogenies using just ITS+LSU will be relatively poor, especially without alignment pruning (using an objective tool such as CIAlign, and not biased pruning by eye). Ditto ATP6+mtSSU should not deliver anything significantly different for the deeper structure because they are tightly coupled mitochondrial genes. The inclusion of Tef and RPB2 is critical, but the number of available sequences remains relatively low. The updated phylogeny is the file 202JulMulti2.pdf


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