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michael catchen

michael catchen

@mdcatchen.bsky.social

3.9K followers 450 following 65 posts

postdoc in the Poisot Computational Ecology Research Group at Université de Montréal

species distribution models, optimal biodiversity monitoring, and network science using machine learning and hierarchical bayes

he/him

gottacatchenall.github.io .. more

Environmental science 57%

Agriculture 17%

more

Posts Replies Media Videos

michael catchen @mdcatchen.bsky.social · 11d

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

A protocol for biodiversity-informed wildlife disease surveillance

michael catchen @mdcatchen.bsky.social · 11d

🚨🐭🦠 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.

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

Reposted by Michael Catchen

Timothée Poisot @ctrlalttim.com · 11d

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...

Reposted by Michael Catchen

ÉPICBiodiversity @epic-biodiversity.org · 11d

🧪 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.

Effective sampling of wildlife disease from biodiversity data | ÉPICBiodiversity

epic-biodiversity.org

Reposted by Michael Catchen

Jelena Pantel @jhpantel.bsky.social · 13d

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)

Reposted by Michael Catchen

ÉPICBiodiversity @epic-biodiversity.org · 15d

We have added support for ESRI administrative areas to our species distribution #JuliaLang package — a lot more stable than GADM (although limited to level 1 divisions).

📗 Read more: poisotlab.github.io/SpeciesDistr...

GBIF occurrences of Mastomys natalensis in Tanzania

using SpeciesDistributionToolkit
const SDT = SpeciesDistributionToolkit
using CairoMakie

# Get the data
const DATA_DOI = "10.15468/dl.7ddsb7"
presences = GBIF.download(DATA_DOI)

# Get the country-level data
borders = getpolygon(PolygonData(ESRI, Places))["Country" => "Tanzania"]

# Make a plot
poly(borders, color=:grey95)
lines!(borders, color=:grey40, linewidth=0.5)
scatter!(presences, color=:white, strokecolor=:forestgreen, strokewidth=1)
current_figure()

Reposted by Michael Catchen

Nicholas Landry @nwlandry.bsky.social · Nov 25

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...

How to Apply to the Graduate Program

bio.as.virginia.edu

michael catchen @mdcatchen.bsky.social · Nov 24

sometimes you write interesting sentences in ecology

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

Reposted by Michael Catchen

Patrick Cosmos @veryimportant.lawyer · Nov 9

i do not care about "the future of the democratic party" as discussed by professional-class bozos who cannot see beyond their next client. i care about not living under a military occupation that is disappearing my neighbors

michael catchen @mdcatchen.bsky.social · Nov 7

just gonna leave @ecoevorxiv.bsky.social here

Carl T. Bergstrom @carlbergstrom.com · Nov 7

A week after the arXiv was forced to tighten down on submissions because of overwhelming volumes of AI slop, bioRxiv is throwing the doors wide open.

samuel mehr @mehr.nz · Nov 7

disappointed that @biorxivpreprint.bsky.social is implicitly endorsing the use of LLMs to replace scientific thought

@richardsever.bsky.social this is a short-sighted move and a net negative for science

Reposted by Margot C. Finn, Michael Catchen

Carl T. Bergstrom @carlbergstrom.com · Nov 7

A week after the arXiv was forced to tighten down on submissions because of overwhelming volumes of AI slop, bioRxiv is throwing the doors wide open.

samuel mehr @mehr.nz · Nov 7

disappointed that @biorxivpreprint.bsky.social is implicitly endorsing the use of LLMs to replace scientific thought

@richardsever.bsky.social this is a short-sighted move and a net negative for science

Oded Rechavi @odedrechavi.bsky.social · Nov 6

IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇

Reposted by Michael Catchen

David Berman Bot @davidbermanbot.bsky.social · Nov 6

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

Reposted by Michael Catchen, Benjamin Wildermuth

Vadim Karatayev @lifenonlinear.bsky.social · Oct 30

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/

resiliencelab.github.io

Reposted by Michael Catchen

David Berman Bot @davidbermanbot.bsky.social · Oct 25

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

michael catchen @mdcatchen.bsky.social · Sep 18

Thanks Austin!

Reposted by Richard McElreath, Michael Catchen

Timothée Poisot @ctrlalttim.com · Sep 18

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

A Julia toolkit for species distribution data

peercommunityjournal.org

Reposted by Michael Catchen

David Berman Bot @davidbermanbot.bsky.social · Sep 12

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

Reposted by Michael Catchen

David Berman Bot @davidbermanbot.bsky.social · Sep 7

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.

Reposted by Michael Catchen

Johan Ugander @jugander.bsky.social · Aug 24

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

Adventures in State Space

YouTube video by 2swap

www.youtube.com

Reposted by Alex Long, Michael Catchen

stuart @stuartp.bsky.social · Jul 1

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

Reposted by Garry Peterson, Jesse M. Shapiro, Michael Catchen

Timothée Poisot @ctrlalttim.com · Jun 30

🦠🌿🐦🧪 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...

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

academic.oup.com

Reposted by Michael Catchen

David Berman Bot @davidbermanbot.bsky.social · Jun 25

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

Reposted by Michael Catchen

Verena @viralemergence.org · Jun 2

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

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. 🦟 🦇 🦠

michael catchen @mdcatchen.bsky.social · May 31

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

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.

web.archive.org

michael catchen @mdcatchen.bsky.social · May 31

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?

Reposted by Laura J. Pollock, Michael Catchen

Katherine Hébert @katherinehebert.bsky.social · May 26

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

Blitz the Gap 2025

www.blitzthegap.org

Reposted by Michael Catchen

David Berman Bot @davidbermanbot.bsky.social · May 14

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

Reposted by Michael Catchen

CSEE SCEE Meetings @csee-sceemtgs.bsky.social · May 9

🐾 #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...