Saturday, February 28, 2015

Conservation Biology Hero #4 Eugene Clark

I had not heard of Eugene Clark but this only shows my terrestrial bias in my reading. Unfortunately, she just passed away and I saw a Facebook post by a marine-biologist friend that linked to her obituary. 

There are many biographies about her (here, here) so I'll just give the skinny on why she was chosen to be a conservation biology hero

1. She was a pioneer. She was a Japanese-American female working in field biology in the 1940's. Despite that she excelled as a scientist

2. She created a marine biology lab in Florida. Research labs are incredibly costly so hats off to her for getting it done. 

3. She was an advocate for shark and marine conservation (hear a NPR story here). 

4. She could talk the talk and walk the walk. She was an advocate and a great scientist. I looked her up on Web of Science and found a number of papers - including those in the late 1990's. She also had a Science paper - the top journal in the US. 

Well done Eugene Clark, well done. 

Go to Conservation Biology Hero #3 Jane Lubchenco

Chikungunya in the US: two months into 2015

I predicted that chik would become an issue in the US and be as much as a problem as West Nile virus. The two are related viruses and share the same vectors (common mosquitoes) so you could potentially be coinfected (that would suck). In 2014, there were only a few locally acquired cases in the US. There have been no local cases in 2015 so far - BUT - it's winter. And winter means the vectors are asleep in much of the US and this winter in particular means they are sleeping even farther south than normal. I suspect we'll have a number of local cases this year in the southeast - most likely Florida. 

Two months into 2015 and there has been 43 cases of chik in travelers coming back to the US. These cases have been peppered across the US (see figure) but the majority have been in Florida (n=12) and New York (n=9). I have not seen where these cases were identified to their origin. There has been one local case in the US Virgin Islands so we can assume it is established there. 

Map of the United States showing travel-associated cases reported in Arkansas, Colorado, Florida, Indiana, Kentucky, Maryland, Missouri, New Jersey, New York, Ohio, Pennsylvania, Texas, Washington

Cases, outside the US

Costa Rica: 121 
El Salvador 138,617 
French Guiana 12,308
Puerto Rico 24,281
Antigua + Barbados + Cayman + Jamaica 5000

So here's a prediction: we'll see a spike next month as spring breakers go down to the islands to escape the heat and Florida thaws. 

Fun, fun, fun. 

Wednesday, February 25, 2015

Bugs that cost the US billions

Just completed a lecture on Pennsylvania forests today. I was surprised and I think the students were surprised to hear that PA is gaining forests and the state is now well over 60% forest.

Wilkes property in the Poconos

Yet there are threats to PA forests - not in losing forests per se but our forests are changing - and fast. The forests we had a few decades ago are not the forests we have now or will have a few decades from now.

Some perspective: if we look at Eastern Deciduous Forests on geological time scales, even recently, they have changed dramatically. During the Pleistocene, Pennsylvania would have been covered in boreal forests (spruces, birches, alders) or ice sheets across the northern half. But for the last few thousand years, the forests have been relatively stable (Askins, 2014).  Forest change naturally - even dramatically but recently the change has been rapid. Invasive insects and fungi have altered the composition of PA forests. Examples I gave today were chestnut blight (Cryphonectria parasitica) that obliterated native American chestnut (Castenea dentata) trees across the northeast US and Dutch elm disease, caused by the fungi Ophiostoma ulmi and O. novo-ulmi. More recently the woolly adelgid has been killing hemlocks and the emerald ash borer is picking up steam. There are native pests as well, such as the forest tent caterpillar (Malacosoma disstria), which is more damaging than the invasive gypsy moth (Lymatria dispar). 

Dead barkless American elm tree

I just came across this 2011 PLoS paper by Aukema and colleagues. There are 455 invasive plant-eating insects in the US and they looked at the 62 species that have economic impacts. I dig their quantitative approach using Bayesian analysis but I was floored by this statement "We considered 39 parametric families of curves [19], and reduced these to four non-redundant families with appropriate theoretic properties: the gamma, Weibull, power function and log-normal distributions."  I think I know eight or nine parametric families but there are more than thirty-nine? Jeesh. They also predicted the probability of new expensive pest invaders. Here were the major findings:

  • borers cost the most with $1.7 billion per year in local costs, $92 million in federal costs, $830 million lost in property value, and $760 million in household costs per year... PER YEAR!!
  • lots of sap feeders but they were not as costly ($14 million per yer)
  • foliage eaters cost the most for federal costs at $110 million per year
  • there's a 32% chance a more expensive wood borer than the emerald wood borer will be established in ten years
I added up all the costs (federal, local, household, lost timber, property value loss) and this amounted to just under $5 billion per year. And we will be getting more. 

Good to get a post out. 


Askins, R. A., 2014. Saving the world's deciduous forests: ecological perspectives from East Asia, North America, and Europe. Yale University Press.

Saturday, February 21, 2015

Latest stats on Ebola

I don't have cable so I don't get all the latest news about Ebola - or know if it still makes the news but I'm interested so below is the latest stats from the Wold Health Organization. The good news is that the mortality rates are not like they were historically (> 80%). This is less than 50%. 

All 3 countries
Cumulative cases (deaths):
Total cases 23 371 (9342)


Confirmed cases 2734 (1688)
Probable cases 384 (384)
Suspected 2 (NA)
Total cases 3120 (2072)

Cumulative cases (deaths):
Confirmed cases 3152 (not available)
Probable cases 1882 (not available)
Suspected 4062 (not available)
Total cases 9096 (3947)

Sierra Leone
Cumulative cases (deaths):
Confirmed cases 8223 (3057)
Probable cases 287 (208)
Suspected 2645 (158)
Total cases 11 155 (3423)

My paper: edge effects aren't good for ground-foraging birds

These data are older than my high-school-senior son. I collected these data when there was no gray, no beard, no health issues, and I made $6000/year as a graduate student. Economically, it was the worst of times. Socially and scientifically, living in Louisiana and working in Brazil was amazing and loved so much of it. These were the days before cheap digital cameras so I have no photos (at least that I'm willing to show in public).

Here's the article in a nutshell: the edges of tropical forest fragments are exposed to wind, more sunlight, and lower humidity and the modifies the vegetation in several ways. The canopy becomes more open because more trees blow down and the understory becomes thicker because there is more light. There are more dead leaves on the ground because - well that part I'm less sure about - but there is a dense leaf litter layer. The vegetation is the habitat and the ground-foraging birds I worked on are particularly sensitive to vegetation (why? - that's an interesting question!) so this modified vegetation in fragments may make them unusable to the study birds. To test this hypothesis, I sampled bird habitat (>20 vegetation variables) by looking for foraging birds and I compared these sites to random sites in the interior of fragments - the "best" the fragment has to offer. Ends up that we found differences between bird habitat and fragment habitat and, as expected, the smaller the fragment the larger the differences.

My favorite part of this article is that we didn't use p-values! We took a Bayesian approach and report the probabilities of our predictions being correct. The coding was a bit tedious (because I don't know crap about it) but I love the results.  

We did all of our work at the Biological Dynamics of Forest Fragments Project, just north of Manaus Brazil. I had a ton of support and I have to really thank my advisor, Phil Stouffer, who took a chance on me in 1993. This is our fourth paper together (two in Conservation Biology, one in Biological Conservation and one in J. Field Ornithology). I had a ton of help in the field from Flecha. This was a terribly tedious project - we counted every plant taller than 2 m in a 16 m diameter circle. It became a game to call out the dbh of a tree before we measured it. He also brought me breakfast every day (the trade off was that he didn't have to come out to the field until 930... I was there at 530). 

Edge of a 100-ha forest fragment. 

Friday, February 20, 2015

Torture, abuse, or just bugs

Scattered in a few places around the United States are research stations where bodies are dumped  in the field so that we can do better forensics. In the  latest issue of Journal of Medical Entymology, there is a report from Texas of pillbugs (a.k.a. rolly-pollys) and katydids that fed on human remains.  The sites where they fed produced marks that could be interpreted as "attack, abuse, neglect, or torture." 

Wednesday, February 18, 2015

Amur (Siberian) tigers back in China!

And you probably didn't know there were gone. But they were. Through hunting and habitat loss, the population dwindled to 40. FORTY. Now there are 400 and about 380 of these are in Russia. We tend to think of tigers as living in the jungle - and Bengal tigers do- but this subspecies live in temperate forests. 

I find tigers terrifying. Even more so that they live in temperate forest. If I went to the Arctic, I'd expect polar bears; when I was in Brazil, I expected jaguars (and yes, they followed me a number of times); but it wouldn't occur to me if I was in China  and in habitat like Pennsylvania that I might be killed and consumed by a tiger. 

Of course it's millions of times more likely that me and anyone reading this will be killed by a microbe.

Spring has begun!

Increasing daylength kicks in reproductive behaviors for some resident birds. This morning, despite it being -17 C and snow everywhere, was filled with singing birds.

I heard

Cardinals - two males calling (whip whip whip brrrrrrr)
Song Sparrow
House Finches

There are anatomical and physiological changes occurring that are driving these behaviors - and that is for another post.  

Tuesday, February 17, 2015

This snake loves omlettes... al fresco!

An amazing phenomenon in the bird world is the fact that nearly every species of bird lays two eggs in the tropics. There is a general trend to have larger clutches as one moves towards the poles. This is partially due to different evolutionary lineages replacing each other as one moves away from the tropics but, even in the few species with huge ranges, clutches increase.  

Even with just two eggs/breeding season, most species in the tropics could potentially double their population in a single year should every egg turn into an adult. But tropical species can live for several years so populations could increase several-fold. However, avian population in the tropics are relatively stable. This means that a pair of birds, on average, only replace themselves. So if a bird lays 16-30 eggs in a lifetime, only 2 survive. 

That would be an average per individual in a population. The reality is much more noisy. There are probably birds that are never successful and don't replace themselves and other birds are extremely productive and have enough offspring to offset the losses from other birds. 

But why is failure so common? Could it help explain why birds are lost from forest fragments? 

Ph.D. Candidate Deb Visco and her advisor Dr. Tom Sherry from Tulane University (now deeply immerse in Carnival!) set out to measure nest predation in the Chestnut-backed Antbird in a large forest tract and a forest fragment in Costa Rica. 

Costa Rican understory at La Selva

To get predation rates and identify predators they set up digital video recorders. And record they did - over 22,000 hours of video were taken. What did it reveal? They captured forty-six predation events: one ocelot, one four-eyed possum (no idea what that is), a semiplumbeous hawk, two fire (not army!) ant swarms, and forty-one snake predation events. Amazingly, 80.4% of predation events were by one species of snake, Pseustes poecilonotus (see below). Please follow the link to the article to see pictures of the snake in action. I've seen my Ph.D. advisor give a talk to packed room on nest videography in the tropics and it makes for a great presentation. 

Photo credit Maxime Aliaga see for more photos
Were nest predation rates higher in the fragments? Nope. So why are forest fragments losing species. Nobody knows for sure but I strongly suspect it may have to do with a combination of dispersal abilities (can they get there?) with microclimate/microvegetation preferences (is there the right habitat if they do get there?). 

Hats off to the investigators for one of the most thorough investigations of nest predation in the tropics! Well done guys! 

Monday, February 16, 2015

Two Chinese tigers die from influenza

China is a hotspot for influenza types - many affecting humans. Influenza commonly infects birds and pigs as well and there they mix and emerge as new strains. These are common events and cause pandemics in humans. 

Less frequently we think of influenza affecting other animals but China's Ministry of Agriculture reports of two tigers that recently died of H5N1. Just over 10 year's ago Thailand lost 150 tigers from influenza. 

Get your shot! Not that you'll protect tigers but you may protect the people around you. 

Thursday, February 12, 2015

Darwin Day: hell yea!

Happy Darwin Day! 

As a Darwinphile (Darwinophile?), today is a day to be celebrated. Darwin was born February 12, 1809 and changed the world with his publication The Origin of Species

Last year, I posted a quote a day about Darwin and I hope to get to more as I finish Origin and some other writings (I'm getting a ton of stuff of my plate so hope to get back on the blogging train).

I found two resources tonight that are worth sharing.

1. National Science Foundation's Evolution of Evolution (I couldn't get the audio to work!)

2. English Heritage's Down House Online Exhibit

Plastic oceans

I haven't seen the entire article, but here's a depressing abstract from the latest issue of Science:


Plastic debris in the marine environment is widely documented, but the quantity of plastic entering the ocean from waste generated on land is unknown. By linking worldwide data on solid waste, population density, and economic status, we estimated the mass of land-based plastic waste entering the ocean. We calculate that 275 million metric tons (MT) of plastic waste was generated in 192 coastal countries in 2010, with 4.8 to 12.7 million MT entering the ocean. Population size and the quality of waste management systems largely determine which countries contribute the greatest mass of uncaptured waste available to become plastic marine debris. Without waste management infrastructure improvements, the cumulative quantity of plastic waste available to enter the ocean from land is predicted to increase by an order of magnitude by 2025. 

Tuesday, February 10, 2015

Last thought before bed: ecology videos - soliciting ideas

I like the idea of vodcasting and online courses but me lecturing with powerpoints seems terribly boring. I thinking about producing short (15-20 minute) videos about ecology. Not "here's what I caught and how quickly it can kill you" but something more academic:

  • how organisms survive the winter
  • how do organisms navigate
  • territoriality
  • what are the major habitat types in PA (and NJ!)
  • population regulation and so on
But what to call it?  I was thinking eco... something but every damn time you put "eco" in the front of something these days it means recycling, planting a tree, etc. My god where is the "ology" in ecology??

La Vie En Rose and how you're on this planet

This is turning into a music blog for now. But this is the music I listen to when I work and I'm in a writing grove - which doesn't occur often so I'm going with. 

I finished a section in a paper about threats to tropical birds on climate change and emerging infectious disease - what fun. 

Kind of a downer but this came on and I felt better for a few minutes. Romantic and sweet. Made me think of my grandparents and maybe how my parents were created. Ugh. Better feeling gone.

Monday, February 9, 2015

Astrud Gilberto's Berimbau

When I was a kid and I or one my sisters brought home a new record it always took me a few iterations to see what songs I liked best - something you did while studying the cover and reading the lyrics. One of the downers of the digital age is the ease of getting singles so nobody ever need listen to a song until it grows on you - then you end up loving it. I think all John Prine songs are like this. 

I do appreciate Pandora and other streaming services in that they provide a venue for hearing new songs. Every once a while a song strikes you. I can't even point to why I like this song so much. A great sound of course. But there's something extra. This song pays homage to Capoeira with sounds of traditional instruments. It's all done so well. 

Capoeira is a dance-fighting originally practiced by Brazilian slaves and now practiced by smelly dread-toting Americans from middle-class families who do it terribly. These guys know capoeira:

Saturday, February 7, 2015


1. Working on the introductory paper for the special issue - reviewers have suggested a "total rewrite of some sections"

2. I have to make small edits to my paper in the Special Issue

3. I have six species evaluations to do for the state - past due now. I offered to give population and habitat evaluations for a few grassland species that I've been studying 

4. I'm chair of the Academic Planning Committee that oversees new programs at Wilkes. We have our biggest meeting since I've been a member or chair (6 years worth). We have proposals: a neurotraining facility (if you're feeling overworked and stressed - hmmm), a neuroscience major, two new nursing programs, and a 4 + 1 masters program in bioengineering. Each proposal consists of a narrative and a budget. Yuck. That's Tuesday. 

5. I have to edit a paper that was recently accepted in Restoration Ecology. We use C isotopes to show an entire ecosystem is produced from planting grasses at a once toxic site that was completely unvegetated at one point. This needs to be done by Monday or Tuesday

6. Regular professor stuff: teaching two upper levels to homeworks, quizzes, and lectures to prepare. 

But I did take a mental health break to do some of this:

Enough of that - back to work and jazz

Thursday, February 5, 2015

A coffee & birds study from the home of coffee

There are a number of bird studies looking at the effects of coffee plantations versus forests or shade coffee versus sun coffee. Most of these studies are from Central and South America and very few from Africa. 

Recently accepted in a special issue of Biological Conservation is a study by graduate student Even Buechley and colleages on shade coffee in a region of Ethiopia where coffee is a native species. I love thinking about locals picking coffee beans in the area for hundreds (thousands?) of years. My long lost coffee cousins. Unfortunately, there isn't a link from the journal but the University of Utah published a press release. The link from Biological Conservation should be appearing soon. 

Coffee is a shrub and shade coffee plantations grow under large trees that shade the plants below. Studies from the Americas show, very strongly, that shade coffee is much better for birds than sun coffee. You can now buy coffee from shade coffee plantations if you wish to support birds - I do. In Ethiopia, this study showed that coffee plantations had more species than forest and coffee plantations served as adequate habitat for several forest species as well as migrant birds from Europe (yes, birds migrate there too!). 

Shade coffee plantation with coffee below and canopy above.
Photo Credit: Evan Buechley, University of Utah.

This study is going to get some great press - as it deserves. Large portions of the tropics and near tropics are coffee plantations. How we manage coffee plantations will likely have huge effects on tropical diversity. National Geographic just ran a story here

I need to get to Africa and see some birds and, damn it, I need a cup of coffee. 

Wednesday, February 4, 2015

Death in the hedges

I have a thick hedge in the back yard. Below is a picture from the summer (aaahh, summmer) and now there's about a foot of snow on the ground. We're in a suburb of Wilkes-Barre and I put out bird seed. We don't get Redpolls, Evening Grosbeaks, or crossbills but we do get House Sparrows - hordes of them. Lately, we have about 30-40 at a time. All that chirping might attract some attention. It did. 

Watched a Cooper's Hawk dive in to the hedge and emerge with a sparrow. This hedge is dense enough that it's difficult to put your hand in and pull those stupid nightshade vines out.  

One down, thirty-nine to go. 

Monday, February 2, 2015

Alice the heart-melting puppy

My dog just died a month ago so I'm still a little sensitive and hurting and it may explain why I'm a tearing up mess. But here's a puppy I find so damn cute. 

Meet Alice. 

Today is World Wetlands Day!

I grew up in Karrsville, NJ (not sure that's even on a map). There was a small stream that went by the house, Pohatcong Creek was just down the road, and my neighborhood had five ponds that I fished from (and not always... openly).  I loved these places but after getting into ferns - this is a real thing OK - I got into swamps. So I love wetlands of all flavors. I realize how few pictures I have of wetlands so I better step it up. 

Today we can celebrate wetlands because it is World Wetlands Day!

As cold as it is, and this boggles my mind, Ambystoma salamanders are moving into small fishless ponds and breeding - now - beneath the ice!!! How cool is that?  

Sandpipers at Forsythe National Wildlife Refuge

Stream running through La Selva Biological Station, Costa Rica

Wetlands outside Williamsburg, VA

Wetland (complete with cranberries) on Wilkes property 

Great blue with flounder - Forsythe National Wildlife Refuge