Augustus (Gus) Pendleton

tmap vs. ggplot2 for mapping – Geospatial Stuff For me at least the choice between ggplot2 and tmap is an ongoing question. Here are my latest thoughts on the subject (with code).

tmap or ggplot2 for maps? 🗺️

David O’Sullivan breaks down the trade-offs in a blog post.

URL: dosull.github.io/posts/2024-1...

#RStats #RSpatial #Maps #tmap #ggplot2

This paper combines so many things I love! Community assembly, an appreciation for absolute abundance, and carefully selected (and interpreted!) alpha and beta diversity. Fun to see generalized concepts we're measuring in freshwater systems also get their due in host-associated microbiomes.

Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.

Pitchfork is down...quick everyone just enjoy the music you like without feeling judged

Prospective PhD students - here is a brilliant opportunity to explore how bacteria and viruses evolve in liquid environments like the ocean 🌊

The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇

Too cool!!

Dream job alert 🚨🚨

Thanks!

Thank you!

Why Is This Lake ‘Burping’?

Anyone have access to this article and would like to share it as a gift link? It's a topic near-and-dear to my heart 😅
www.nytimes.com/2025/10/08/n...

Environmental factors affecting the formation of methylmercury in low pH lakes Abstract. Recent studies have demonstrated elevated levels of mercury in fish from remote, low alkalinity and low pH lakes. The mechanisms of this enhanced

Anyone have access to this and might be willing to send me a pdf?
academic.oup.com/etc/article-...

A pontoon boat loaded with two canoes cruises across a calm Lake Poygon.

Two hands in pink gloves mix a large pile of mayom/manoomin/Zizania/wild rice seed.

Yesterday I headed over to Fremont, WI on the Wolf River to help prep for wild rice seeding that the Brothertown Indian Nation is doing. We collected some sediment at two sites, mixed up seeds for several sources, and made mud balls for seeding. They are seeding today and tomorrow! #restoration

3 year Postdoctoral Research Fellow position in Landscape Multifunctionality here in beautiful Bergen jobbnorge.no/en/available... please repost

Abstract: Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media. For these collective blunders, we now regret our involvement or apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not considered a valid position to reject AI technologies in our teaching and research. This is why in June 2025, we co-authored an Open Letter calling on our employers to reverse and rethink their stance on uncritically adopting AI technologies. In this position piece, we expound on why universities must take their role seriously toa) counter the technology industry’s marketing, hype, and harm; and to b) safeguard higher education, critical thinking, expertise, academic freedom, and scientific integrity. We include pointers to relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI (black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf. Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al. 2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n

Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.

Learn more abt projects: cxli233.github.io/cxLi_lab/res...

Mapping quantitative data to color - Nature Methods Data structure informs choice of color maps.

www.nature.com/articles/nme...

It is a beautiful figure!

New open access paper out! We evaluated the population structure and conservation needs for 3 crested penguin species in NZ. Read it here: journals.plos.org/plosone/arti...

Leaving Academia: Insights from Evolutionary Biologists on Their Career Transitions and Job Satisfaction https://www.biorxiv.org/content/10.1101/2025.08.19.671061v1

This is what's held me back - amazing to see!

Looking for potential fellowship opportunities for final-year writing funding (I understand this might be a moonshot at the moment). Just stipend (no research costs). I'm in the environmental/life sciences, and grateful if there are any directions people could point me towards!

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

A new version of gcplyr (1.12.0) has just been released and is available now from CRAN and github. This update fixes a handful of bugs along with some improvements to the documentation

mikeblazanin.github.io/gcplyr/

This is across ~1000 different species (randomly sampled from NCBI, unique genera representing >10 Phyla with high-quality closed genomes).

This reminds me when I was just messing around with codon usage in Julia and I found this out on my own - look at those AT-rich codons!!

gus-pendleton.github.io/CUBScout_Rel...

This paper is a short, good read, even for those using relative or compositional approaches, who want a clear demonstration of how different distance metrics can be interpreted and how they discern differences between communities. Please reach out to us if you have comments! (4/4)

In fact, most tools to calculate Weighted Unifrac will convert your counts to relative abundance under the hood! (3/4)

Choosing metrics for beta-diversity is important, and interpreting them is non-trivial! But we haven’t seen anyone discussing how phylogenetic similarity, composition, and absolute abundance intersect when calculating Weighted Unifrac. (2/4)

Interpreting UniFrac with Absolute Abundance: A Conceptual and Practical Guide Microbial ecologists routinely use β-diversity metrics to compare communities, yet these metrics vary in the ecological dimensions they capture. Popular for incorporating phylogenetic relationships, U...

Microbial ecologists! Do you use Unifrac distances? Are you curious about absolute abundances? Then I’ve got a paper for you!
www.biorxiv.org/content/10.1... (1/4)

Amazing opportunity! 👇