Wildlife ecology and conservation, metabarcoding, eDNA, disease ecology, mathematical modeling. Prof of Fisheries, Wildlife, and Conservation at Oregon State U
Antibody tests are coming online. Never before have humans needed to understand Bayes rule more. Let's talk about why it's critical NOT to assume you are immune to covid-19 when you have a positive antibody test. Seriously, people need to understand this to prevent many deaths.
Science communication...did you know that there is a population of aquatic jaguars in the Brazilian Pantanal living at extraordinarily high density, eating almost entirely fish and caiman, and cooperatively fishing? I'll post some videos of them every week or so.
These western Oregon wolverine detections are getting more insane by the day. Now running around Eugene! Maybe the same one from Portland and the coast?
Some context. This is not a local animal coming out of the mountains. This is an EPIC journey. When Aubry's wolverine distribution paper came out in 2007, the last record of the animal in the whole state was is 1992! More recent records from NW corner of state near Idaho /1
These western Oregon wolverine detections are getting more insane by the day. Now running around Eugene! Maybe the same one from Portland and the coast?
Sometimes you get lucky. A jaguar decided to sit in front of our camera and relax. Did you know that jaguars are the third largest cat species but still much smaller than lions and tigers? They are largest in Americas after others went extinct ~10k years ago. Know which ones?
We've been working on this paper out today (and open access) for over 7 years, so bear with me while I tell you the story of how we discovered that wolves kill and eat sea otters (Panels A-D) and what this means for wolves, otters, and deer. /1
I failed to regularly post videos because a coauthor smartly suggested we wait until the paper is out. I can't wait to flood Twitter with aquatic jaguar videos. The time has *almost* come.
Science communication...did you know that there is a population of aquatic jaguars in the Brazilian Pantanal living at extraordinarily high density, eating almost entirely fish and caiman, and cooperatively fishing? I'll post some videos of them every week or so.
It's hard to talk to people with strong feelings about Israel, because invariably they know so little about the most complex geopolitical conflict on earth but are sure of their position. A personal story and attempt to explain history. My g-g-grandpa came from Yemen in 1882/1
I've been trying to start a DNA service lab. My department had an abandoned building at forest edge. We got water and heat and then lab members moved out junk and cleaned decades of gunk and mouse poop over 2 days. Welcome to the future OSU Center for Environmental Genetics /1
Dear wildlife biologists, please stop comparing a gazillion models with AIC when you really have some specific research questions you want to make inference about. It's really ok to think first about your question and fit one model to make inference from effect sizes and CIs
If you get a positive antibody test result and think you're immune and quit socially distancing, you are far more likely than not to make a big mistake. When millions of people make the same mistake rather that appreciate conditional probability and Bayes rule, many people die.
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Several companies have tests of varying quality, but Cellex makes a FDA-approved antibody test. The goal is to test for immunity due to prior exposure rather than an active infection. Cellex's test has a "sensitivity" of 93.8% and a "specificity" of 95.6%. Lets interpret this
Aquatic jaguar paper led by
@ceeriksson7
now posted. This started 7 years ago when I asked
@CarlosPeres_
about possible felid projects and he described a place rumored to have extremely high jaguar densities. Ronaldo Morato had just placed GPS collars
If we plug in sensitivity, Pr(test+|are+), the probability a random person is positive, and the probability a random person tests positive, then a randomly tested person who TESTS positive, only has a 17.7% chance of actually BEING positive. More that 82% of people will be wrong!
6. I lied, one more thing. This is not some great insight that I had or a fancy model. This is one of the first things you learn in Bayesian statistics. Every statistician knows this, but many MDs do not (at least that's what statisticians say). I just took the time to tweet it.
The take home is that a high sensitivity, Pr(test+|are+)=0.938, does NOT mean that Pr(are+|test+) is high. 82 of 100 people who get a positive test will still be susceptible to the virus. Once 10% of population has been infected, this drops to 30%, but that is a LOT of people!
I foresee that someone will say that more than 1% of people have now been infected. At a prevalence of 5%, 47 of 100 people who test positive will still be wrong. I found an online tool that lets you explore this for various quantities.
Recently graduated students:
Jobs all want me to know R. Why didn't anyone teach R?
Instructor:
Whew, it was a lot of work but I've added many R labs and training modules to my course!
Undergraduates:
Ugh, R is so hard, why are we learning R? Unfair! What about my grade!
How do bears, bobcats, and coyotes interact with cougars and their kills?
Really excited for new paper from Joel Ruprecht. 51 GPS collared animals from 4 species, 972 DNA metabarcoded scats, 128 cougar kill investigations, and videos from carcasses
Cougar chasing coyote at kill
And this visual summary is great. I like getting into the details since typically there are lots of examples without the math worked out, but somehow I've seen nothing about this false positive problem.
2. Prevalence varies locally, so testing random New Yorkers for antibodies will produce fewer errors than random Oregonians.
3. Point of this tweet was to teach some math and an important qualitative message about being careful with a single + test.
But it gets worse. If you never had symptoms but test positive and conclude you're one of the lucky people who had an asymptomatic infection, you're even more likely to make a big mistake. Of course, as a higher proportion of population becomes infected, this mistake diminishes.
The conditionality is reversed. Probability you are + given that you test positive can be written as Pr(are+|test+). Let's just derive Bayes theorem real quick in this context so you don't have to just trust me. Pr(are+|test+) equals the sensitivity Pr(test+|are+) multiplied by..
The Cellex test appears to have higher rates than others. Sensitivity: Probability person tests positive if they are infected. Specificity: Probability person tests negative given that they are negative. 93.8% and 95.6% sound good, they mean that only 6.2% of + people test -, and
My bad, it's 4.4% of negatives. So 4.4%* (1,000,000-10,000)=43560. 43560/(43560+9380)= 0.82. So still 82% but the math was off slightly. This is how you get in trouble with quick tweets while morning coffee hasn't sunk in!
I've been losing a lot of followers lately by supporting Black people and Black Lives Matter. People, how can't you see that the US has never dealt with the legacy of slavery and segregation and that we still have a major problem with racism? For the rest of you - enjoy jaguars
Since this tweet is being spread around, some addendums and an attempt at communicating with a general audience. 1. Context is testing of random population. If you had severe symptoms in the past, the probability of false positive is lower because Pr(are+) is higher.
only 4.4% of - people test +. But what does it mean when you test positive? Since the sensitivity is high, you'd assume that you're positive and immune to covid-19. But sensitivity measures prob testing + given that you are +. We want prob of BEING + GIVEN that you TEST +
But that is 4.4%*1,000,000=44,000 false positives. 44,000/(44,000 + 9380) = 0.82. So in this example, 82% of the people with positive tests were never infected and are still at risk. There it is w/out math lesson. If you didn't have severe symptoms, a second + test really helps.
@rabiasquared
@taaltree
Say a test has a 95% specificity rate. 95% of people who are neg test neg. 5% test positive. For a rare condition, occurring say in 1 out of 100, you test everybody. 1 true positive tests positive. ~5 in 99 true neg also test positive. Ergo. Only 1/6 positive tests are a true pos
I don't think people are marveling enough that we're about to introduce mRNA into billions of people so that their own cells can translate that mRNA into a SARS-CoV-2 protein, which then triggers an immune response that can recognize the real SARS-CoV-2 virus. How cool is that!
4. Now an attempt at explaining this idea for general audience. Say you test 1,000,000 random people and prevalence is low so only ~10,000 had been infected. Those 10,000 will be picked up with sensitivity 93.8%, so 9380 will get positive test. Only 4.4% of negative people test +
The most disconcerting trend in conservation science is the growing antipathy toward protected areas. Here is another jaguar video to remind you that earth needs many more protected areas because nature has intrinsic value.
This is a site where a powerful cattle rancher illegally deforested a large swath of land. The land was forcefully reclaimed and is now managed by a community group harvesting non-timber forest products. Great wildlife recovery. It's a rare win-win-win.
I'm excited to share some incredible news from the recuperation area of La Colorada in the Maya Biosphere Reserve, Guatemala. It is the first time that we are able to sight tapir with offspring in our camera traps monitoring there.
There has been so much discussion on Twitter about who is an "expert". There are people with domain knowledge, and then there are people who are leaders in their field, and then there are good science communicators.
@trvrb
is all of these and his content has been wonderful.
Given my statement that the US has 300k - 600k new infections per day, I've had a bunch of responses telling me that
#TestTraceIsolate
is futile and we should give up on it. This thread demonstrates the benefits of reducing transmission even if suppression is not attainable. 1/9
the probability you are+ irrespective of how you test, which is the same as the proportion of positives in the population. Let's assume that in the USA this is ~1% or ~3.3 million people are really infected. The final term in the denominator is the probability you test positive.
A recent paper and website promote the need for "inclusive" language in EEB and maintain a list of words to avoid. I'm going to try to have a nuanced discussion on Twitter about why I think this is a very bad idea. No hate to the authors, which include friends and colleagues./1
Out now in
@Trends_Ecol_Evo
, we discuss the power of terminology and outline a path forward for identifying and revising harmful terms in ecology and evolutionary biology (EEB) to foster inclusion in the field. (1/5)
A thread on why ecologists interested in animals should consider applying to wildlife graduate programs. I wasn't exposed to wildlife programs until being a prof in one and there are lots of benefits I didn't know
1. A peer community interested in organismal and applied research
The probability you test positive must be decomposed into the people who test positive and are positive plus the people who test positive and aren't. We have all the necessary numbers for this probability expression and get a denominator of 0.053. Plugging it all in to Bayes rule
Coming soon funded PhD position Fall 2022 on landscape scale biodiversity and its response to sudden oak death in SW Oregon marten/fisher range. Lots of flexibility in research questions. Planning cameras, bioacoustics, Malaise and pitfall traps, tick drags, genetics/genomics
5. Finally (maybe), RT-PCR, which is used to test for current infections is much less susceptible to this issue because false positives are much more rare. Someone "PCR-splained" me about this (Our genetics lab does many thousands of PCRs every year and designs assays)
Important context that people seem to forget. The world was already hostile for North African and Middle Eastern Jews, but after the UN partition plan in 1947 it became unbearable with massacres and mass expulsion. This is why Israel is now primarily not European. In Yemen/1
What do wolves eat in the SE Alaska island Archipelago? Lots of cool stuff and spatial variation revealed by DNA metabarcoding of scats collected across a geographic gradient spanning deer, moose, mountain goat systems. Marine mammals dominant food in one year. Guess which? /1
If you ever wonder if you *really* need separate lab spaces for pre-PCR and post-PCR work, try swabbing your post-PCR lab and metabarcoding to see what you get. We just found...wolverine, bobcat, puma, moose, deer, bear, and fox. Don't even sort samples in post-PCR spaces!
So seeing a wolverine in Western Oregon is extremely unusual. But, wolverines are legendary movers. They have huge ranges. This is almost certainly a male on walk about. Hopefully he finds his way. /5
Fall is coming. Some advice for prospective graduate students in ecology and wildlife science in particular. Feel free to contribute.
1. Hear from multiple people and triangulate advice. People give advice that works for them, but we're all different with distinct goals
Mule deer are in long term decline and we don't know why. Joel Ruprecht mined the literature to find 722 estimates across 8 vital rates. Using these vital rates and their correlation structure, he ran a life stage simulation analysis to see which most explain population growth /1
My 7 year old looking doing a straight up artist pose with her recent carnivore paintings. They're definitely not things I hang up just because by kid made them.
By 2020, wolverines recolonized Mount Rainier in Washington, back for the first time in a century. They successfully denned. We started sequencing their scats collected at the den. If I had to guess, this is a male disperser from that new population /2
Our department
@OregonState
is hiring an Assistant Professor in Wildlife Ecology with a future research program tha includes small mammals in agricultural ecosystems. Please share widely. Full consideration by March 3rd. Happy to answer questions
Finishing a MS or PHD in Molecular Ecology? Or are you a postbac with lab skills? Want a job with full benefits (including a pension) in Corvallis, OR? Get in touch! We'll be hiring for multiple positions doing fecal DNA metabarcoding and genotyping across multiple study areas
So, I would propose that we actually try to make the world a more inclusive and better place with actions rather than a snobby and humorless one in which we try to sanitize language under the assumption that we're all so brittle as to be unable to hear ordinary language/7
After years of development, we just got a complete eDNA autosampler prototype for field testing. So excited about the possible applications. It can filter 24 samples on a schedule and preserve them. Fits in a "bear-proof" cooler.
So you're stuck at home with the kids. Why don't you and/or your kids learn some math with this *long* thread on exponential growth? I'll try to make it accessible given twitter limitations, but feel free to ask questions! Exponential growth today and epidemic models tomorrow.
7. This is an educational thread. I'm in no way stating that effective serology to test for prior exposure can't be done. For instance, people testing positive for HIV with an ELISA would then follow up with a Western Blot. I have seen no such proposal. Point is...think carefully
Our Ecology, Evolution, and Conservation Biology Seminar is free and open to the public. We'll start with
@ChrisDarimont
next Wednesday 4pm PST. Chris will present "Bears, salmon, and people: Applied conservation science in the Great Bear Rainforest"
Zoom:
Kid back in school so I thought, let me dust off this unfinished manuscript with all this newfound glorious time. Checked the date....2015. I've let this thing sit unfinished for 6 years. Hopefully this helps someone not feel bad about their languishing project.
Recovering America's Wildlife Act was reintroduced in the senate where it has bipartisan support. Its passage will produce many wildlife jobs nationwide and a significant portion of the money will end up in university wildlife departments.
So
@ellendymit
had this idea of setting cameras vertically from high lateral branches to avoid theft and identify individual jaguars by the same spot patterns on the top of their back rather than only seeing 1 flank per detection. Pretty cool vantage point actually!
thrilled to report that our โbirdโs eyeโ camera setups worked very well! we were able to detect even small animals, like this super cool Tamandua mexicana ๐
Let me tell you a story about 3 black bears and 2 cougars in a new natural history paper by MS student and amazing naturalist Marcus Bianco. Cougar C256 gave brith on June 14 at a nursery site. She killed an elk on June 29. A 129 kg male bear U2 arrives/1
Was just working up budgets. With new tuition and overhead increases at OSU, it now costs $70k per year to support a PhD student on an NSF grant! Why do graduate students taking no courses pay $20k in tuition? That is a very good question indeed.
Hey wildlife folks. I think this is an important paper. Marked GPS collars on cougars, bears, bobcats, and coyotes+Scat-detection dogs and genotypes+camera traps. We compared models with no to full individual identifiability and develop integrated model.
The journey from Rainier to Eugene would be formidable, crossing the mighty Columbia River, Portland (where one was seen). Assuming it's one animal, it then went to Newport, Florence, and now Eugene. In 2011, wolverines were detected around Eagle Cap Wilderness, another option/3
"Inclusive" is good branding because who doesn't want to be inclusive? But this practice is *exclusive*. It creates in-group language generated in elite academic spaces and imposes it on others often contrary to group wishes. E.g researcher referred to "proper terminology" page/2
Today I learned that Frank Herbert's "Dune" was motivated by the Oregon dunes that, now stabilized by invasive beachgrass planted by USFS, retain the last remaining population of coastal martens in Central Oregon. Here's a compilation monitoring berry consumption on the dunes.
Interesting mountain goat behavior observed by colleague Kevin White near Haines, AK. They've dug some nice beds in deep snow presumably to provide protection from strong winds during a recent big winter storm. A collared male and nanny/kid pair
Dear person who graciously gave an unsolicited donation to Oregon State University Foundation for our lab. You're the only person ever to do this, and we're so appreciative. If you're out there, please contact us.
We'd like to send you a thank you card and tell you about our work
Here is some footage of the first camera trapping evidence of wolverines in the Wallowas (NE Oregon). As far as I know, only this male, named "Stormy", has been detected repeatedly. USFWS thinks there are only about 300 wolverines in the contiguous US /4
Dear ecologists. Awesome job coming. The USGS Coop unit at OSU Fisheries and Wildlife will soon post a landscape ecologist position on USAjobs. Be on the lookout. I understand they'll be looking for someone who can work on multiple taxa with quantitative and spatial methods.
in the West Bank, controls their borders, retaliates violently, razes homes. Gaza has very high population density and is by all accounts a terrible place to live. The Palestinian people deserve full self governance, but how to achieve this has failed for many decades. /23
I keep reading papers that misuse model selection by AIC. If you add a parameter to a linear model and the fit doesn't improve at all, the more complex model will be 2 AIC units higher - ergo being within 2 AIC of a simpler model is evidence of nothing. In the reverse case, /1
OK, I'll oblige. Twitter will give you the false impression that there is some consensus of hate for academia. Many of us really love this job and feel grateful for it. There are many legitimate complaints, and it can be hard to make it, but it can also be pretty wonderful...
Give Charlotte Eriksson
@ceeriksson7
a follow for some jaguar content. She just submitted a paper from her dissertation about the diet, density, social interactions, and space use of this aquatic jaguar population.
Life mimics art. This reminds me of the scene from The Office where Michael asks Oscar to use something less offensive than "Mexican". Almost this exact scenario happened to me in our department's microaggression training. Well-meaning trainer assured me that Jew was offensive /3
I gained followers tweeting about covid. Although we research disease ecology (landscape epidemiology of Leishmaniasis led by
@masseyaimee1
and white-nose syndrome led by
@jnyurbina
), expect wildlife tweets. Especially carnivores like this giant aquatic jaguar. Enjoy the big boy
Watching the Warriors game and they just said that Steph Curry started buying food for Oakland families when the pandemic began. Get this. The Curry family has apparently supplied **15 MILLION** meals for Oakland residents over the past year.
These lists wish to change common language to *make* people take offense not remind people to be kind and welcoming. This undermines the credibility of universities and scientists, making us look like oversensitive and out of touch whiners to the broader community that we serve/5
I'm optimistic that integrating ChatGPT into R like this will be an equalizing force in ecology so that people with field and natural history expertise can more easily produce complex analyses. On the other hand, analytical skills alone will be of less value.
Fulbright scholars only get a portion of their salary funded, which can make it hard to bring them on for a PhD. My department head just pledged to cover the remaining costs to a full
@OregonState
grad salary. This will make it much easier to accept int'l students in wildlife!