michael catchen

Read it here: ecoevorxiv.org/repository/v...

A conceptual figure outlining a protocol for using species distribution models to prioritize sampling for pathogens in wildlife

A scientific figure showing a case study of the protocol applied to Arenaviridae in rodents in India

🚨🐭🦠 New preprint!

Monitoring wildlife disease is expensive, so we need to be smart about where we sample to get as much useful info as possible.

We show how SDMs can guide adaptive sampling for zoonotic disease surveillance, using case studies in rodents.

This is, not a joke, one of my favourite papers in a long time. Absolutely stellar co-authors, but also a straight line from "nitpicky little nerds obsessing over sampling" to "translational research with clear implications for management". Go read all about it here: ecoevorxiv.org/repository/v...

🧪 New @mdcatchen.bsky.social preprint!

Here's how we can decide where to look for wildlife disease, based on combinations of biodiversity, uncertainty, and prevalence data. This is a really cool paper, that is pushing the boundaries of what we can do with sampling and monitoring techniques.

I'm just worried. Even pre-AI, it was really pulling teeth to get some (not all) PhD students to take the time to look up the formula the R package used, make sure its what they actually want to calculate, and validate what R spits out (note: I don't take students like this anymore)

Noteworthy because it was my first time adding a polygon provider using the interface @mdcatchen.bsky.social built for one of our component packages 🎉

One week left to apply to the UVA Biology PhD program! If you or someone you know are interested in contagion from a complex systems perspective, please reach out! I'm looking for a grad student! bio.as.virginia.edu/how-apply-gr...

the phrase "but we see a large increase in absolute loser bees" in an excerpt from a draft scientific manuscript

sometimes you write interesting sentences in ecology

just gonna leave @ecoevorxiv.bsky.social here

And like a brown bird nesting in a Texaco sign
I got a point of view

Hi all! I am seeking an ecology or applied math PhD student interested in quantitative ecology, specifically ecological theory, food web modeling, or population dynamics. If you are interested, have a look at our lab website below and reach out to me.
resiliencelab.github.io/join/

My friends, don’t you know
that I never want this minute to end?
And then it ends.

Thanks Austin!

Our software paper on SpeciesDistributionToolkit.jl is now published in @peercomjournal.bsky.social - peercommunityjournal.org/articles/10....

What kind of animal
Needs to smoke a cigarette?
Grass in the pasture
Is sharper than a bayonette

Sometimes a pony
Sometimes a pony
Sometimes a pony gets depressed

When I go downtown, I always wear a corduroy suit,
’cause it’s made of a hundred gutters,
that the rain can run right through.

YouTube video by 2swap Adventures in State Space

A beautiful visualization of the state space of puzzles, 11 min of joy, h/t @danlarremore.bsky.social

you have been visited by "Le Boulanger Quebecois"
repost to receive his blessing

Biodiversity science and biosurveillance are fellow travelers The failure to meet the Aichi targets to alleviate global biodiversity decline (Nature 2020) was a wake-up call to the biodiversity monitoring community (T

🦠🌿🐦🧪 How can biodiversity monitoring help global efforts in disease surveillance?

With ✨ fantastic ✨ colleagues from @viralemergence.org and the @geobon.org working group on One Health, we try to identify three key lessons for the future.

🧵 A short thread!

academic.oup.com/bioscience/a...

Poor as a mouse every morning
Rich as a cat every night

Some difficult news from the team: In NSF's FY25-26 Budget Request to Congress, we learned that our program will take a whopping 50% cut - meaning that in September, we'll be $1.25m short of an operating budget that currently supports a cohort of seven PhD students, four postdocs, and three full-time staff. Verena is one of the largest and last pandemic prevention-focused programs in the United States: since 2020, we've supported the training of over 60 postdocs, graduate students, and undergraduates. Our researchers have established unique laboratory resources for studying animal immune systems, and discovered new antiviral immune adaptations in bats; developed risk assessment algorithms for wildlife and livestock viruses, and diagnostic algorithms for viruses like dengue, Ebola, and Zika; and quantified the effects of climate change, deforestation, and factory farming on spillover risk. Everything we develop is 100% open source, and our data has supported the research of nearly 150 external researchers in 21 countries to date. We have three months to make up our budget shortfall. Every dollar spent on Verena supports not just our team, but the community of researchers who use our data, code, and resources. You can help us by sharing this post, and reaching out if you're able to support a unique and vulnerable program. Or just head over to viralemergence.org, and take a look at what we do. 🦟 🦇 🦠

An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠

2022 Release - North American Breeding Bird Survey Dataset (1966-2021) The 1966-2021 North American Breeding Bird Survey (BBS) dataset contains avian point count data for more than 700 North American bird taxa (species, races, and unidentified species groupings). These data are collected annually during the breeding season, primarily in June, along thousands of randomly established roadside survey routes in the United States and Canada. Routes are roughly 24.5 miles (39.2 km) long with counting locations placed at approximately half-mile (800-m) intervals, for a total of 50 stops. At each stop, a citizen scientist highly skilled in avian identification conducts a 3-minute point count, recording all birds seen within a quarter-mile (400-m) radius and all birds heard. Surveys begin 30 minutes before local sunrise and take approximately 5 hours to complete. Routes are sampled once per year, with the total number of routes sampled per year growing over time; just over 500 routes were sampled in 1966, while in recent decades approximately 3000 routes have been sampled annually. No data are provided for 2020. BBS field activities were cancelled in 2020 because of the coronavirus disease (COVID-19) global pandemic and observers were directed to not sample routes. In addition to avian count data, this dataset also contains survey date, survey start and end times, start and end weather conditions, a unique observer identification number, route identification information, and route location information including country, state, and BCR, as well as geographic coordinates of route start point, and an indicator of run data quality.

The 2022 release is here, in case others need it web.archive.org/web/20220705...

It looks like Breeding Bird Survey data has disappeared from ScienceBase. I've found a copy of the 2022 version on the Internet Archive, but I'm curious if anyone downloaded the most up to date data before the administration change?

Blitz the Gap 2025

One week until Blitz the Gap (www.blitzthegap.org) starts - a Canada-wide event to fill biodiversity data gaps with iNaturalist! @laura-pollock.bsky.social

There were no new ways to understand the world, only new days to set our understanding against.

🐾 #CSEE2025 Workshop Highlight 🐾

"Interpretable machine learning for species distribution modelling"

💻 Discover how to use reproducible ML tools to tackle diverse ecological questions!

🔗 Register here: event.fourwaves.com/scee2025/reg...

What kind of animal
Needs to smoke a cigarette?
Grass in the pasture
Is sharper than a bayonette

Sometimes a pony
Sometimes a pony
Sometimes a pony gets depressed

Boy wants a car from his dad
Dad says, "First, you got to cut that hair"
Boy says, "Hey, Dad, Jesus had long hair"
And Dad says, "That's right, son, Jesus walked everywhere"

only if the title is: okay, this is epic

People gotta synchronize to animal time