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.

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.

European Not-Really-A-Union #3 – the Happiness Divide

The European Union is drifting farther and farther from being a union. The reasons for the drift are as manifold as they are obscure, so let's focus on what makes us different. For example, how happy we are.

Hessenwahl 2018 – wie nah sind sich die Parteien?

Auch zur Hessenwahl versorgt uns das bpb mit einem Wahl-O-Mat mit 38 Thesen. Hier die Distanznetze dazu. Und natürlich der Plot der Thesen, die hinter den politischen Splits stehen. Für jeden, der die Wahl-O-Mat %-Balken nicht sonderlich hilfreich findet.

Bayernwahl 2018 – wie nah sind sich die Parteien?

Eine deutsche Tradition für Wahlen sind die Wahl-O-Mat Angebote der Bundeszentrale für politische Bildung (bpb). Der für die Bayernwahl 2013 war (ist) noch online und auch für die Bayernwahl 2018 gibt es natürlich eine Neuauflage des Bayernwahl Wahl-O-Mats.  Eine gute Gelegenheit zu sehen (und zu zeigen) wie nah oder fern sich zukünfte Koalitionäre stehen.

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).

Digging deeper: Population dynamics and individual-based fossil phylogenies

In one of my last posts, I argued for looking out for ancestor-descendant relationships when putting up an evolutionary hypothesis based on fossil data. In this post, I will explore a bit the background of individual-based phylogenies and why we should keep in mind population processes, when analysing such data sets.

The challenging and puzzling ordinary beech – a (hi)story

While working on another post, I noticed I could need an example for a pretty well-understood evolution of a plant genus through space and time. But to keep the other post a short-as-possible, the example merits its own. So here's the history of the beeches, which is a nice story to tell, also regarding how it developed scientifically.

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.

Age of angiosperms, may palaeobotany rest in peace (and pieces)

How old are the angiosperms? Very trivial to answer, more or less as old as all the other main lineages of living seed plants. Unless you define them in a particular way. And because you are who you are, no-one dares to criticise it. But thanks to predatory publishers, someone did. A tale about ivory towers, opinions presented as facts, the Impermeable Fog shrouding the Forest of Reviews, and the creeping death of palaeobotany. Although it could been the spark to ignite something beautiful.

What I was not allowed to show #2: Networks explaining molecular evolution in wax plants

Thanks to the confidentiality of the review system, experimental research that goes beyond the standard applications may be lost to the Impermeable Fog. In this post, I'll will show several reconstructions I made for a paper of a colleague on Hoya (Asclepioideae), the wax plants.

What I was not allowed to show #1: A neighbour-net of seed plants

Even as a professional scientist, I always put a lot of effort in enhancing the graphics of our papers. In some cases, the mighty Wizards of the Forest of Review appreciated the effort, but most didn’t bother. In some cases, the circumstances forced me to dump some pretty nice graphs. In this series of posts, I’ll show what has been lost because of the Impermeable Fog, or because my co-authors were vary it might wake dogs and more evil things lurking in the Forest of Review.

Changing sides – voter migration mapped in 2- and 3-dimensional space

Migration of voters in elections is usually figured as a 1-dimensional graph, showing on one side what voters voted in the last election, and on the other, their new party. But this hardly show how far (some of them) migrated.

Two papers you may want to read before inferring trees from morphological (or other) data

In this post, I'll advertise two probably undercited papers published in 2004 by Richard H. Zander regarding “Minimal values of reliability of Bootstrap and Jackknife proportions, Decay index, and Bayesian posterior probability”, and Matthew Spencer and co-workers on the “Phylogenetics of artificial manuscripts”. Two papers that should have been read by anyone trying to infer trees from morphological data including fossil taxa, or non-trivial data in general.

Wahl-O-Mat 2017 – wie nah sind sich eigentlich die Parteien?

Als in Frankreich (EU-Land) lebender Deutscher (anderes EU-Land), habe ich leider keinen Einfluß auf die Zusammensetzung des Parlaments und der Regierung, deren Politik mein tägliches Leben bestimmt. Aber – zumindestens theoretisch – könnte ich an der Bundestagwahl teilnehmen.