Tuesday, December 29, 2015

Aubert's analysis of phylogenetic terminology, part 2: definitions

Continuing the discussion of this paper from here. Originally I had the idea of going through the pages in sequence, but it may be more productive to tackle one by one what appear to be the main claims of the paper as I see them:
  • The various definitions provided in the paper are in some way better than the ones that are currently accepted.
  • There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)
  • A strictly phylogenetic classification is formally impossible.
  • Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".
  • Cladism is built on biologically unrealistic assumptions that have been empirically falsified.
  • There exists an objective approach to delimiting paraphyletic groups.
  • It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.
So this might turn into seven separate posts, although the last few will perhaps be short. This is the first one, dealing with the definitions, and it got rather long.

Monday, December 21, 2015

Aubert's analysis of phylogenetic terminology, part 1: abstract

As always the following is my personal opinion and does not necessarily represent the opinion of any of my friends and relations, of my employer or colleagues, or of anybody whosoever except me.

I have recently set an alert with the key word evolutionary systematics (or similar), and today it delivered the first noteworthy catch: Damien Aubert, A formal analysis of phylogenetic terminology: Towards a reconsideration of the current paradigm in systematics. Published in Phytoneuron, an online journal that has peer review "if deemed appropriate or necessary by the editor, or if requested by the author", this piece of criticism of phylogenetic systematics runs over an astonishing 54 pages. It will certainly have to be tackled in homoeopathic doses.

So for the moment, let's just have a look at the abstract and table of contents.

Thursday, December 17, 2015

Fun with trendline charts

Via Pharyngula I was recently lead to an American blog that had produced the following chart of average annual global temperatures, apparently in an attempt to demonstrate that we need not worry about the greenhouse effect:

This is just so totally awesome, I thought I would do a few myself. First, did you know we don't need to worry about overpopulation either?

Indeed there is absolutely no population growth at all! Next, watch my daughter grow up:

Finally, I tried my hand on one of those Kurzweilian charts of exponential technological progress:

Seems like we won't see a technological singularity any time soon. Checkmate, futurists!

Sunday, December 13, 2015

Wildflowers of Mount Majura Nature Reserve

Living directly next to Mount Majura, we have over time built up quite a list of photos of the plants in the reserve. Perhaps this will be useful to other wildflower enthusiasts. It is obviously far from complete and heavily biased towards the groups we personally find attractive, like daisies and legumes. I may update the list in due course.

Asterisks indicate introduced species. Last updated 23 October 2016.


Ophioglossum lusitanicum
Widely distributed across the globe and apparently not even rare in Australia, but easily overlooked because it is tiny and green. We had been visiting Mt Majura reserve for six years before we saw it the first time.

Cheilanthes sieberi
These ferns are unusually drought-resistant, rolling up their leaves to conserve water as they dry out. There is at least one other very similar species in the genus.

Thursday, December 3, 2015

Australasian Systematic Botany Conference 2015, third day

On the third day I unfortunately had to miss several talks. The main topic of the day was Integrated Floras, Electronic Floras, and Online Keys.

In the morning session chaired by Zoe Knapp, Ilse Breitwieser's keynote lecture gave an overview over the various types of floras or flora-like publications, starting with her first use of the Schmeil-Fitschen field flora of Germany as a student. She explored the definition of a flora, of an integrated flora, and of an electronic flora - not just a digitised book but a flora curated and updated in an electronic data management system. She then covered a variety of 'learnings' from the eFlora of New Zealand including the problem of managing authorship rights and copyrights in an increasingly collaborative, dynamic and openly accessible workspace.

Wednesday, December 2, 2015

Australasian Systematic Botany Society Conference 2015, second day

Writing about the second day of the ASBS Conference 2015 I should first mention that I should now really be considered biased because I chaired the morning session and gave my own talk in the afternoon.

The day started with the session on Genomic Data in Plant Systematics. In his keynote Craig Moritz, the director of the ANU/CSIRO Centre for Biodiversity Analysis, set the scene by providing an overview of next generation molecular and analytic methodologies and their use cases. He also discussed the new possibilities arising in what he called a post-phylogenetic world - not in the sense of 'evolutionary' systematists of course, but in the sense of having achieved more or less complete taxonomic description and the availability of decent backbone phylogenies for at least some taxonomic groups. In particular, he mentioned the integration of population genetics and phylogenetics, the study of speciation mechanisms, and cryptic diversity.

Next, Todd McLay presented results form his research on species delimitation and phylogenetics of the grass tree genus Xanthorrhoea. I was particularly intrigued by a new PCR based reduced representation library preparation method that he developed, because it seemed to be comparatively simple and thus perhaps feasible even in shorter student projects. Benjamin Anderson then gave a very concise talk on this work in the arid zone grass Triodia.

Tuesday, December 1, 2015

Australasian Systematic Botany Society Conference 2015, day one

This week our herbarium is hosting the annual Australasian Systematic Botany Society Conference. For me this is the first time to be involved in conference organisation, specifically the scientific program (deciding on conference theme and major sessions, inviting keynote speakers, organising workshops, deciding on abstract acceptance, grouping talks into sessions, etc.).

Yesterday started with a long session on collections science chaired by Sarah Mathews. Keynote speaker Vicki Funk of the Smithsonian stressed the importance of natural history collections in the genomic age and identified three game changers for the near future of collections science: open access to data and images, improved sequencing of degraded DNA from old specimens, and linking collection specimens with phylogenies and climate data. I was also amused by an anecdote she told of discussing phylogenetic systematics with an older, very influential traditional taxonomist who argued that not being allowed to recognise taxa based on plesiomorphies amounted to "throwing half my data away". Vicki then tried to explain that the data are used, only deeper in the tree, where those character states were apomorphies themselves. The amusing aspect is of course that 'evolutionary' taxonomists still haven't grasped that a generation later.

The collection science session continued with a talk by Jill Brown on crowd sourcing of data entry at the herbarium of the University of Melbourne. They are involving volunteers through the ALA DigiVol portal, and the project appears to be quite successful. Liqin Wu then presented an analysis of environmental lead accumulation in historical lichen specimens, an interesting use case of collections. She also identified possible lead sources (soil/rock, leaded petrol, coal burning) based on isotope ratios.