Big Data = No Brain? Pt. 1: Complete plastomes vs 500+ nuclear genes

Having being ignored by phylogeneticists for over a decade, maples [GE:Wikipedia/The Maple Society] – the second-most diverse extratropical angiosperm tree genus of the Northern Hemisphere – have come into focus again. And going Big Data. Time to sum up what we can learn from the new phylogenomic studies and trees. Which is actually a lot, although the interesting bits are to a large degree ignored by those producing the phylogenomic data; despite (or: because) being published in Q1-journals.

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).

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.

Surviving parsimonists: just tree-naive or tree-blindfolded?

A generation ago, an epic battle took place, largely unnoticed outside mathematical and biological sciences: the Phylogenetic Wars. By the mid-1990s, the war was over and probabilistic methods for tree-inference replaced traditional parsimony. But there is a small, quite dusty realm that still pretends nothing happened: palaeontology. A long read about undervalued data and stubborn old white men.

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.

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?

Miraculous reconstruction of palaeoaltitude and -temperature using the "Coexistence Approach"

It may look (to some) like a good idea to take modern-day altitudinal ranges of genera to infer a palaeo-altitude of a fossil plant assemblage using a mutually shared range approach. A fresh example from the purportedly peer-reviewed Elsevier journal Palaeogeography, Palaeoclimatology, Palaeoecology (PPP).

Dispersing the Impermeable Fog: #3 – declining an invitation to review a pseudo-scientific paper

The Coexistence Approach is a pseudo-science. At least, it's fundamentally flawed in theory and practise. But one journal remains the bastion of true faith. But maybe tides are changing?

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.

Business as usual – PPP keeps on publishing Coexistence Approach pseudo-results

In 2016 we published two papers demonstrating that the so-called Coexistence Approach (CA) to reconstruct past climates is fundamentally flawed, theoretically and in practise. As consequence there was a drop-down in CA papers disseminated, exclusively, by members of NECLIME, a Germany-centred scientific consortium promoting this pseudo-statistic (and pseudo-scientific) method. But one journal remains faithful. And has nothing to fear thanks to peer review confidentiality.

How not to make a phylogeographic study

A citation alert pointed me to the paper of Zhang et al. (2017) to be published in Tree Genetics & Genomes, a failed attempt to make a biogeographic study on a small Ulmaceae genus: Zelkova. The severe concerns raised by at least one peer (not me) were largely ignored by the authors and the editor, providing us with a paper that managed to combine the most important pitfalls in (plant) biogeographic studies.