Searching for a research object? Why not maples!

In course of my career as a professional scientist, I had to leave a lot of threads open. Mainly, because I need to make sure to fund my own position, which consumed 80–90% of the money the mighty research councils granted me. One easy pick for those that have money to do molecular research are the western Eurasian super-species of Acer sect. Acer.

How to pimp up a palaeobotanical monograph

I got a request via ResearchGate to give feedback to a recently published palaeobotanical monograph. I'd love to, but I can't, really; I'm simply not qualified. But I can give some tips how to enrich a description of a palaeoflora to put palaeobotany in a better light.

Are complete plastome trees always better? Maples, for instance.

With the advances in sequencing, it has become easy to compile complete chloroplast genomes (plastomes) for plants. Given you have the money and workforce. The People's Republic of China is rich in both; hence, gene banks fill up with complete plastomes of tree genera, otherwise ignored by the scientific world. Such as maples (Acer). Beware the fully resolved trees.

The stag cracked the 30

One of my favourite hobbies as a tax-paid scientist was to check and groom, once in a while, my "impact". I still check, out of curiosity and vanity, and just noticed that my stag cracked the thirty. A little reflection of self-inflating impact with some tips for the game.

Now that RAxML includes all models – a practical tip

The new, faster and (meanwhile) very option-rich version of RAxML, RAxML-NG provides the full plethora of nucleotide substitution models, which can be confusing to the normal user. Hence, a practical tip based on my experiences with very different sets of nucleotide data (and from very different organisms).

Why I never published a "total evidence" tree

Triggered by a support question on the RAxML google group, I pondered the question whether it makes sense (anymore) to use the total evidence approach to place fossils.

The Easter Egg featuring Earth, live

For this Eastern, I'll advertise something colourful to turn our eyes back from ourselves to the planet we inhabit: a live simulation/representation of Earth's dynamic surface and atmosphere.

A Wikipedia list everyone should know

Wikipedia has changed the world how we access knowledge. And despite recent (and fair) criticism, it's still an invaluable social project because it provides easy entry portals and an enormous wealth of quick-to-access data. Approaching Christmas, the Feast of Love and Peace, I'd like to point towards a Wikipedia page dealing with something, we tend to quickly forget about: Wikipedia's List of ongoing armed conflicts.

When dating is futile – plastome-based chronograms for oaks

With most-versatile programmes like BEAST at hand, everyone can do a molecular dating. Which makes it even more important that editors and peers check the priors and reasoning behind it. And always should make sure a palaeobotanist (or at least, a palaeogeographer) is one of the peers.

The Easter Egg – everyone can (visually) dive into Earth's past

As my first Easter Egg post, I advertised the most important French hebdomaire, weekly newspaper, Le Canard enchainé (lit. the Chained Duck), something you can't find in the virtual world. This year it is something more peculiar, literally a virtual (version of our) world. Well, worlds, the bygone ones.

How to interpret bootstrap values?

A search led me to a question on ResearchGate (RG) issued five years ago: How can I interpret bootstrap values on phylogenetic trees built with maximum likelihood? Quite a bunch people answered it, but, to my mind, only provided easy answers, not the critical ones.

There's no need to do what you can't

Modern science thrives on pretention. We can't just publish something interesting, we always feel compelled arguing why it's important and stress its ground-breaking novelty. On the other hand, everyone can use computers, and those computers can do fancy analyses provided you have some data. And they always get it right, so why should editors and reviewers bother about the results?

European Not-Really-A-Union #2 – A Game of Cards

Although, it would make the world an even less social place, there are a lot of good arguments to get rid of cash. My beloved Sweden has always been on the foremost front of this. However, the technological advances have made this quite impractical, as anyone can find out when living/travelling in more than a single EU country.

Trivial but illogical – reconstructing the biogeographic history of the Loranthaceae (again)

In 2007, a short but nice paper by Vidal-Russell & Nickrent provided a scenario for the unfolding of the Loranthaceae, a plant family of mostly epiphytic tree parasites. Recently, they teamed up with a Chinese group (Liu, Le et al. 2018) to provide a new, and totally unexpected hypothesis.

Elsevier's research data "not available/will be made available on request" – what will be your choice?

What do you do when authors claim something (showing nothing) that you know can't be true (because you showed otherwise)? Just request the data they used and re-analyse it to check. But this is not how it works. An example from Elsevier's Molecular Phylogenetics & Evolution.

What you should show in a palaeophylogenetic study

Far the most palaeophylogenetic studies rely exclusively on tree-inference as methodological framework. Thus, ignoring the fundamental properties over the underlying data: matrices that provide few tree-like signals. A recommendation what to show (and why).

The Easter egg: Le Canard enchaîné – a weekly must read (also for French aliens)

In this Easter post, I'll cherish a light-house of French publications, Le Canard enchaîné.  My occasional French readers will probably know it, but maybe those outside of France have never heard of it. Which would be a pity, as the "palmipède" is a must-read (if you can read French or attempt to).

Wladimir Köppen – a climate-vegetation genius, and what this has to do with wine

The Köppen-Geiger system is the most widely used climate classification. Thanks to a group at the Veternary Medical University in Vienna (Institute for Veterinary Public Health), everyone can check out the beauty of the system. Scientists and non-scientists. E.g. for picking the next holiday or long-burning questions such as: Why can't I find a Brazilian wine?

How did I do it – a short guide to a nice graph

At the end of the 20^th and into the new 21^st century, phylogenies have been largely reduced to stick graphs, often quite unappealing ones. In the papers I co-authored, I always tried to enhance the graphics, and I have not rarely been asked how I do it. So here's my protocol for a little basic tree-and-networks magic.

20/01/2017 – the day we lost a great word: "great"

Things happened one year ago that not a few still can't fathom (personally, I was not overly surprised; but I am a realist). And I'm sure there will be an endless number of articles summarising the year. But for me, the election of a TV clown and orange-billionaire (not to be confused with orange-utans) as 45^th president of the U.S., meant a personal loss. I lost a word, I liked to use: the English word "great".