Just a single, easily overlooked tip

One thing about phylogenomic studies in the Era of Big Data is that we easily tend to overlook what is new and interesting. Why it may be worth to give each subtree in a phylogenomic tree a closer look

Artkonzepte, in Bildern

Biodiversität, die Artenvielfalt, ist in aller Munde. Grundlage zum Messen der Biodiversität, ist fast immer (noch) die Anzahl der in einem Gebiet gefundenen Arten. Aber was ist eine Art? Ein paar Bildchen. Und Beispiele.

Scientia-ex-machina: explicit biogeographic inferences and the phylogenomic age

The nice thing about huge datasets is that they can give quick results, often trivial to interpret. In phylogenomics: a fully resolved, unambigously supported phylogenetic tree. The not-so-nice thing is that downstream analyses using these fully resolved trees, such as ancestral area analyses, may be utter nonsense because the experimental set-up was fundamentally flawed to start with. A post-review of Areces-Berazain et al. (2021), including the results from Li et al. (2019) and Yu et al. (2022).

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.

Oaks systematics and complete plastome trees

We are living in the era of Big Data. You just need the money and/or workforce, and you drown in data. As consequence an increasing amount of researchers study complete plastomes of organisms, they have little idea about. The oaks (Quercus; beech family: Fagaceae) are becoming a prominent example.

Monophyletic species

Probably the most common line one can read in phylogenetic papers scratching at the surface of evolution is "species xxx is not monophyletic" or "supports species yyy as monophyletic". While appearing to be trivial, clade = monophylum, such statements are often naive, too often incomprehensive or, occasionally, just wrong. A clarification.

A fully resolved, and perfectly misleading, species tree

The ultimate promise of phylogenomics is to get a fully resolved species tree: a tree, where the individuals finely sort per species, and where all branches, especially the deepest ones, have high or, better, unambiguous support. A look behind such a tree, Jiang et al.'s (2021) Tree of Beeches.

Die Wahl der Qual

In meinem Heimatland steht mal wieder das 4-jährliche Abnicken der Legislative an: die Bundestagswahl 2021. Wieder mal Zeit, den Wahl-O-Mat der bpb zu visualisieren, und in allgemeineren Kontext zu stellen.

Wahl der (H)Ampelmännchen

Diesen Sonntag wird in meinen beiden Heimatländern gewählt: Rheinland-Pfalz (meinem Geburtsland) und Baden-Württemberg (meinem Zweitland, bevor die DFG mich ins schwedische Exil schickte). Zeit die Wahl-O-Maten der Bundeszentrale für politische Bildung zu vernetzen.

Where have all the Mondays gone

Who likes Mondays? Probably no-one, really. Thus, inspired by a tweet of a fellow Monday-victim and two great classics, a songtext.

Caesar's EU, Hitler's EU, EU, future Xi's EU – all the same?

I got a comment to my Fare well Brittania! post drawing that line, which got me thinking. A reflection and response.

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.

Palynology from A to Z: People

Five of my palynology advertising tweets (have/will) introduce(d) researchers pushing forward the importance of palynology in contemporary organismal science. With four, I worked, and we published a good deal of papers including some pretty unique ones, which hopefully will provide templates for future cross-disciplinary research.

Palynology from A to Z: A as in Aponogeton

One thing, full-blood scientists usually forget, is to advertise their work. Usually because they lack the time. I have plenty and started a series of daily threads on Twitter advertising palynological research. But my reach there is miniscule and the half-life of tweets is extremely short. Hence, this post series.

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.

Inferring a ML tree with 12000 (or more) virus genomes

Somebody on the RAxML group posted this as a bold question, asking for tips how to speed up the analysis. Since I recently looked at virus genomes (infamous SARS group) myself, I have some ideas for this.

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.