weecology

Portal Regime Shift Update: How bad can it get? Well, 2025 was a wild ride. The lack of updates on the potential regime shift at Portal isn’t because it fizzled, but because [wave hands at the world]. And Portal was not immune to [waves hands at…

New update on the regime shift at our long-term study site from
@skmorgane.bsky.social

"...our kangaroo rats losing their battle with the forces of dryness, but if you squint real hard you might be able to see them pushing themselves back up. Maybe."

doi.org/10.59350/4y0...

Workforce development has long been a key component of NSF's mission. An educated workforce, trained for the jobs of tomorrow, is regularly considered a public good.

Forgot:

University of Florida
Probably a few others

Not to mention folks that work at these places that benefited from interactions with NSF funded folks/projects:

Amazon Web Services
Chicago Trading Company
Chewy
Goldman Sachs
Deutsche Bank
Bloomberg
MathWorks
and a bunch of others.

#WithoutNSF

Why is the U.S. National Science Foundation important?

Please share your stories!

Use the hashtags #WithoutNSF or #WithoutScience

...
Rush University Medical Center
Terra Global Captial
University of Arizona
University of Pennsylvania
USGS

This is just the folks funded directly through NSF. #WithoutNSF we won't have the people with the skills to solve the problems, and fill the jobs, of tomorrow

#WithoutNSF we wouldn't have been able to train folks in the skills they need for their jobs at:

College of Charleston
Denison University
Instacart
Institute for Ecosystems Studies
National Ecological Observatory Network
Netflix
NIH
Oregon Department of Human Services
...

Regime Shift: A Winter of Grim Every episode in a tv series starts with a recap. So… Previously, on Portal: the Regime Shift — In fall of 2023, one of the ruling families of Portal — the Desert Pocket Mouse (Ch…

New update on the regime shift at our long-term study site. With a little levity thanks to @skmorgane.bsky.social.

"No species was safe, and populations began to drop like characters in a George R.R. Martin book. Only kangaroo rats... were making a valiant stand against the forces of dryness"

🌎 🧪

One of my favourite papers I've been involved in was just published in @peerj.bsky.social. Working with a wonderful team of ecologists at @weecology.bsky.social, we used multivariate ecological forecasts to understand the population dynamics of desert rodents peerj.com/articles/189... 🌎 #rstats

VectorByte (VecTraits and VecDyn databases) The VectorByte initiative is establishing a global open access data platform to study disease vectors. This project will not only serve as a hub for biological trait and abundance data for human and n...

Excited to see @vectorbyte.bsky.social joining Bluesky www.vectorbyte.org

We’re hiring a computer vision developer! Interested in using computer vision to help understand, manage, and conserve nature? We hiring for a new position to join our team working on models, software, and community outreach in our existing projects using airborne imagery to monitor and understand natural systems at large scales.

Interested in using computer vision to help understand, manage, and conserve nature? We looking for someone to join our team to work on models, software, and community outreach in projects using airborne imagery to monitor and understand nature at scale.

Near-term ecological forecasting for climate change action - Nature Climate Change In this Perspective, the authors discuss the current status of ecological forecasting research, its role in helping to address the climate and biodiversity crises facing society and potential future d...

New paper on "Near-term ecological forecasting for climate change action" by a group of folks from the Ecological Forecasting Initiative led by Mike Dietze w/me @skmorgane.bsky.social @cboettig.bsky.social @careylab.bsky.social @waterpotential.bsky.social and lots of other (non-Bluesky) folks 🌎🧪

I tried to build a starter pack for researchers in ecology sensu lato. Who am I missing? go.bsky.app/2MdGeqi I can add more people and spread it around.

Really pleased to share the preprint of Ms Simrik Bhandari's primary thesis paper examining spatial patterns in Nepal's record outbreaks of dengue in 2022 and 2023. (1/n)

If I had known a career in “weecology” was an option, I might have made some very different decisions.

There are still 5 days left to apply to join me teaching interdisciplinary data analytics at Denison University!

It's an exciting place w/ great resources. PhD in any field + ability to teach using R and/or Python; @ Assistant or Associate Professor rank, apply by Oct 7 apply.interfolio.com/151230

PhD Student Opening: Small Mammal Community Dynamics Interested in understanding how ecological systems change through time? Morgan Ernest’s Lab at the University of Florida has an opening for a PhD student to start Fall 2025. The new student will wo…

We're looking for a PhD student to join us starting Fall 2025 to work on our long-term study (almost 50 years!) of small mammals and plants to understand and predict changes in species abundances and biodiversity in response to changing climate and biotic conditions. 🧪🌎

PhD Student Position In Ecological Forecasting Of Everglades Wading Birds Ethan White’s lab at the University of Florida has an opening for a PhD student starting in Fall 2025 to study ecological forecasting of wading birds in the Everglades.

I'm looking for a PhD student to join @weecology.bsky.social to study ecological forecasting using wading birds in the Everglades. The position will be focused on data science, time-series modeling, and forecasting. There will also be opportunities for field, drone, and computer vision work. 🌎

PhD Student Position In Ecological Forecasting Of Everglades Wading Birds Ethan White’s lab at the University of Florida has an opening for a PhD student starting in Fall 2025 to study ecological forecasting of wading birds in the Everglades.

We're looking for a new #PhD student to join weecology! Come learn and work with us studying ecological forecasting and dynamics with wading birds in the Everglades.

Near real-time monitoring of long legged wading birds using uncrewed aircraft systems and computer vision bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

New preprint on our work monitoring Everglades wading birds in near real-time using drones, computer vision models, & automated workflows. 🧪🌎

Preprint: doi.org/10.1101/2024...
#rstats data viz website: everwatch.weecology.org
Open data: zenodo.org/doi/10.5281/...
Code: github.com/weecology/ev...

Screenshot of https://everwatch.weecology.org. Map showing the general location of the colony, CypressCity. Time-series showing the total counts of all birds in that colony weekly during the February-April for 2000-2023. A zoomed in image showing individual bird detections on top of the imagery.

One-to-one plot showing counts of birds from the bird detector on the x axis, human counts on the y axis, and a tight clustering of points along the one-to-one line.

Diagram of workflow showing: 1) imagery moving from drone to laptop and then syncing to a workstation; 2) ground control point alignment; 3) combine individual drone images into a single orthomosaic; 4) syncing the orthomosaic to the HPC; 5) cropping the ortho into pieces for the model; 6) DeepForest model prediction; 7) output the predictions; archive the predictions and transfer them to a web server for visualization. It also shows: 1) orthomosaic converted to mbtiles and geospatial raster data; 2) syncing this data to a tiling service in the cloud; 3) that data being pull to the data visualization platform.

We (@weecology.bsky.social) monitor Everglades wading birds using drones & turn this imagery into data in near real-time using computer vision models to detect birds & automated workflows to immediately process new imagery. 🧪🌎

Preprint: doi.org/10.1101/2024...
Blog post doi.org/10.59350/b5b...

New NSF Postdoc Fellowship track.

“…will support Fellows that leverage large data, such as those from the National Ecological Observation Network (NEON), and innovative approaches, including Artificial Intelligence (AI), Machine Learning (ML), and modeling…”

www.nsf.gov/pubs/2024/ns...

🧪 Very cool results on food webs by lab members:

[1] Banville et al.: what does it mean to use probabilities to represent interactions?

[2] @gabdans.bsky.social et al.: local reconstruction of regional food webs

[1] ecoevorxiv.org/repository/v...
[2] royalsocietypublishing.org/doi/10.1098/...

Chasing Ghosts: Race, Racism, and the Future of Microbiome Research | mSystems In this article, we argue that a careful examination of human microbiome science’s relationship with race and racism is necessary to foster equitable social and ecological relations in the field. We p...

#BeneficialMicrobes day 3 starts with Elizabeth Mallott discussing human gut microbiome. Mallot has a background in sociology and looks outside of race/ethnicity for variables that alter the gut microbiome. Love this shift in microbiome research. Cites this paper:

journals.asm.org/doi/full/10....

New dataset on 100 million canopy trees across the National Ecological Observatory Network New dataset of canopy tree maps for 100 million trees in the National Ecological Observatory Network with information on location, species identify, and size. Paper: Interactive web visualization: …

We published a dataset of canopy tree maps for 100 million trees in the National Ecological Observatory Network with info on location, species identify, & size 🧪🌍

Paper: doi.org/10.1371/jour...
Interactive DataVis: visualize.idtrees.org
Data: doi.org/10.5281/zeno...
Blog: doi.org/10.59350/zb2...

Individual canopy tree species maps for the National Ecological Observatory Network Detailed maps of tree species can be used for forest analysis, biogeographic research and ecosystem monitoring. This study provides individual tree species maps for 24 sites in the United States Natio...

We made maps of 100 million trees in the National Ecological Observatory Network with info on location, species identify, and size 🧪🌎

Paper: doi.org/10.1371/jour...
Interactive #DataViz: visualize.idtrees.org
#OpenData on Zenodo: doi.org/10.5281/zeno...
Blog Post: doi.org/10.59350/zb2...

Regime shift cometh? Saga Continues Welcome back to our next installment of: what the heck is happening with the Portal rodents? For those just tuning in, I might recommend reading our first two installments: Regime Shift Cometh? and…

Our @skmorgane.bsky.social has been chronically a potentially rapid shift in species composition happening at one of our long-term study sites. Check out her most recent update 🌎🧪

Regime shift cometh? Saga Continues Welcome back to our next installment of: what the heck is happening with the Portal rodents? For those just tuning in, I might recommend reading our first two installments: Regime Shift Cometh? and…

Latest update on the rodent community dynamics at Portal - is a regime shift still in the cards? Read and find out! jabberwocky.weecology.org/2024/07/08/r...

Developing a modern data workflow for regularly updated data This Community Page article describes a data management workflow that can be readily implemented by small research teams and which solves the core challenges of managing regularly updating data. It in...

Our near real-time data processing including QA/QC and integration of data from both local and remote sensors (we also post everything as #OpenData and archiving for long-term preservation; doi.org/c82f) and software for quickly extracting key data from the project (doi.org/mv34).

Regime shift still cometh? Back when I had optimistic views of my time, I vowed to do more blogging this year. Sadly, life had other plans. But I return with an update to an earlier post on the Portal rodent community. To re…

We've been monitoring what appears to be the start of an active regime shift at one of our long-term study sites. The ecosystem is likely rapidly transitioning from a decade long stable state to a new state & we can watch the transition happen. We can do this thanks to... 🌎🧪

Has anyone we know gone through the NSF LTREB renewal process (the renewal proposal for the 2nd 5 years of funding)? We're starting work on the renewal for the Portal Project (portal.weecology.org) and are hoping to see an example of what this looks like since it's our first time doing one. 🌍