Planning 2021

One of the great things about a break is the down time to reflect and plan. I really haven't done either. I did one article review and my brain is not engaging fully. Still, I need to plan. 

Teaching

This spring I'll be teaching BIO 347 Biostatistics and Experimental Design and BIO 298 Economics of Conservation with a colleague from the Poli Sci department. As of now we're scheduled to teach in person but COVID rates are higher than they were in spring. Although vaccines have been approved I don't see widespread vaccine availability until mid-Spring. Just a guess though. One student in Biostats has requested remote teaching so I'll be recording lectures - live or otherwise.  Live recordings ("synchronous") are easy because the camera is just recording me talking and I use my notes that are all ready to go. Asynchronous recordings require much more time - usually about 5 hours of work for 50 minutes of lecture time. 

I'd also like to teach Field Zoology this summer but I'm skeptical it could happen. I haven't thought about it that much. Probably should soon. Also, I'd like to change it to Wildlife Techniques.

The fall semester is still up in the air. I will possibly teach Ecology. If not, I think Archosaurs again.  

Research

This spring I need to focus on DNA barcoding insects. It's gone horribly slow and it just comes down to following directions.  We are also sorting insects from this summer's pollinator pan experiment. 

This summer I need to survey birds in burned and unburned sites on gamelands. If I can have students we'll work at the same sites and catch bugs, birds, and mammals to work out food webs. I'll need to renew a zillion permits. My least favorite thing to work on. 

I'd like to keep with the pollinator study. I started the pollinator project last August and it went exceedingly well. This coming summer I'll add a blue and white plate to the yellow plate I was putting out. Hopefully, by next summer I'll have better wasp ID skills and the barcoding will be down pat. 

Publishing

Clay caterpillar paper is in review. This has four or five students on it (all graduated). This was rejected the first time around and now resubmitted.

I have Ph.D. data I could try to publish on urbanization and birds. I have a ton of post doc data on bluebirds across an urban gradient. Those data are 15 years old. I have the pollinator data we're working on now - that won't be ready for weeks or a few months. There's the prescribed burning data - if anything that needs serious organizing.

Then there's the Wilson Ornithological Society. I'm the chair of the conservation committee and we've been struggling to come up with some initiatives. It looks like most of us want to publish. But what do we publish? Threats to birds? I think I'll put coffee growing forward as a topic and see if this gets some support. 

Reflections on 2020

Academics

Stretching the brain a bit to go back to the spring. Here's what I remember. We took a number of students to Costa Rica in March for a class. Before the trip, I remember getting promed emails about something happening in China and thinking nothing of it. By the end of the trip people were masked at the airport and furiously wiping down their area. I didn't know if they were over-reacting or I was clueless and underreacting - or a bit of both. 

It wasn't long after we decided to close for two weeks, then to the end of the semester, then we closed until we reopened for the beginning of the fall semester. I was also teaching biostatistics and I recorded a few lectures. 

This last semester was BIO 225 Population and Evolutionary Biology - I did a third of the class and the all the labs. We had the fewest students - 29 and only two sections of lab. Normally we have three and we did have four sections one year. Table tops had clear plastic sheets separating students and we all wore masks. One student did not want to come in so I worked her into the labs as much as possible. She was recorder when we were taking measurements. Worked to some extent although I firmly believe that learning to handle equipment (e.g., micropipetter and thermocycler, etc) are all handy skills (plus you come to understand the work that goes into research on a very visceral level). The one student submitted her work through the LIVE system and it was just a matter of logging in and checking the work. 

I also had conservation biology. Although it could have been completely in person I recorded a number of lectures. I want to make this course completely online at some point (and add a lab). Something has to give (and now that I can't stay awake past 10 - more has to give) and I let the homeworks slide. Instead of 12 articles to read and answer questions I think they only had 4. That and 3 exams and journal club. I'd give myself a C+ for the course. 

Research 

This summer was about surveying burned and unburned sites in various state game lands. I covered new ground and hit a few sites I surveyed previously. This gives me more controlled data on how communities change through time (on short time scales). A few sites I wasn't able to get to but I hope to this coming summer. This makes the data messy but so it goes. I didn't employ the Wildlife Acoustics units. That was probably a mistake - they work great (but expensive). I also purchased a bunch of Audiomoth units. Much cheaper than Wildlife Acoustics but so far I'm not impressed. In fact, I have to get something recognizable off the units. I think they're really sensitive to moisture. The standard is to put them in a sandwich baggie and cross your fingers. I kid you not. 

I just ordered an acoustic vent, which is a membrane that transmits sound but not water. I have small tuperware containers that I'll drill a hole in and place the vent over the hole. I'll post a pic when completed. 

Towards the end of the summer I realized that I could easily study pollinators with pan traps. These are amazing. Simple, cheap, easy to deploy. A dream, yes?  The problem is the wealth of data you get. 

The picture above was typical of a pan after 24 hours.  That's right - 24 hours. I'll predict we get some 250 species of bee/fly/wasp.  We're also DNA barcoding the insects to see who they are. So far that's been going meh. 

Looks like the standard pan trap deployment is a combination of white, blue, yellow. I definitely want to do this next year so I need to up my pollinator ID skills. We're photographing everything as well but the iNaturalist crew has been slow to ID.  

I did submit a paper with five students as co-authors on Wednesday. Feels good. Years in the making and I had to figure out how to do raster extract in R. Which I did. Need to work on the next thing. 

The next thing... 

Field Season 2020 Week V

6/22/2020 Monday - SGL38
Finding my way around SGL38 and Bethlehem Water Authority I noticed non-burned areas that there cut so I decided to throw these in. I may not be able to find enough to say anything but they are a forest management strategy. A shelterwood cut is a clear cut with a few scattered trees left. At this site in Long Pond, they left oaks and pitch pine. These sites are great for Field Sparrow and Eastern Bluebird. The trees still had Black-and-White Warbler and Red-eyed Vireos. As this site becomes for shrubby, it might host Golden-winged Warblers, Blue Grosbeaks, and Yellow-breasted Chats. What I have noticed about PA's management strategy on game lands is that the scales are very large - hundreds of acres get the same treatment. But many birds will use various habitat types within their territory. Wood Thrush, for example, nest in small patches of an old opening that is filled with dense vegetation and they'll forage in areas with a closed canopy and open understory.  

6/23/2020 Tuesday - Cameras on Jacob's Property/Audiomoth

Finally figured out why I wasn't getting any sound on my Audiomoth - I needed to update by firmware. Ugh.  These units are getting a lot of buzz but I haven't been able to find any publications on their use with birds. They're a fraction of the cost of other ARUs. 

6/24 - 6/28  Rain or meetings 
Some data entry. Had a "low level" manuscript rejected (as expected actually). 

Field Season 2020 Week IV

Monday 6/15/2020

SGL 57. Interesting site with points that were unburned (full of Veery, Black-throated Blue Warbler), very recently burned (with Veery!), and cut and burned (with American Robin - yes, they can live without yards). The bird highlight was two points with Cerulean Warbler in the burned sections. Mammal highlight was a porcupine. 

Tuesday 6/16/2020 - off 

Wednesday 6/17/2020 and Thursday 6/18/2020 - SGL 38 
SGL38 is located in the Poconos and, apparently has many rattlesnakes. In fact, if you go back in this blog you'll find pictures of one I came across. Also the site that had a bear I estimate was over 600 pounds. The two days I was out had no bears and no rattlesnakes. Sites were burned in 2012 - 2014 but I suspect that this placed burned many times before that. It was covered in bear oak and pitch pine with all the hallmarks of having been burned (e.g., epicormic needs coming directly out of the bark). The density of towhees, Prairie Warblers, and Chestnut-sided Warblers is through the roof. No Golden-winged Warblers. 

One dimension I need to add to the research picture is the effect of cutting on bird communities. Thinning as a large effect on understory plant density and cut + burn makes for some interesting habitat. If they were to repeatedly burn, I think some grasses would move in and then they'd get Golden-winged. Just a guess. I remember my one and only GWWA on a territory and it was on a powerline in NJ (seen during my one and only World Series of Birding in 1990). Powerlines in the NE US have scattered shrubs, grasses and forest edges. 

Allegheny Mound Ant mount and ant (below)

Epicormic needles in pitch pine

Friday - Sunday - off 

Field Season 2020 Week III

Monday 6/8/2020 SGL 110

This State Game Land straddles the Appalachian Trail just north of Reading, PA. It's a bit of a drive (1.5 hours) but it has plots that were burned in 2016, 2017, and a plot that will be burned in 2020. So I can get lots on information on birds and burning from one site. The other downer is the distance between sites. I walked almost 20,000 steps. Bird-wise wasn't very exciting but the burn sites were a joy to walk through since the fire took out the very dense mountain laurel. Was able to get 7 points in. Not great. Next time I should bring a mountain bike to take on the game road from plot to plot. 

Met with two colleagues about fancy ways to measure vegetation structure with LIDAR and drones. Still need to start getting measurements with some new (not newest) tools. 

Tuesday - Sunday off

Feeling lazy. Took a fall on Monday that left me a bit sore. Tripped on dewberry and I thought I would turn it into a roll - I just flopped on my side.  

Field Season 2020 Week II

Monday (6/1/2020)

• Bird surveys on SGL091. This section was cut and burned. Tons of birds and all the usual suspects for early successional forests, including Chestnut-sided Warbler, Common Yellowthroat, Field Sparrow. The last being one of the first birds to leave an area that converts to a forest. 

Tuesday (6/2/2020)

• Went to survey SGL 326 which has three burning years  (https://paprescribedfire.org/map)  so an ideal site if you want to know how bird communities change after a burn. The gate to the "road" was closed and I don't have permission to drive on the site so it was a bit of a bust. The nearest site was just over a mile walk and I don't just don't have it in me. 
• Met up with an ornithologist from the Schuylkill area and gave me back a camera I had left behind last year. Set on video and put onto a Wood Thrush nest. Lasted about three days and then stopped recording for whatever reason. Unfortunately, the angle was too high so we could only see the adults. Problem with nature - doesn't always give you the perfect opportunities
• Went to the Jacob's property to check out the game cameras. Captured chipmunk, squirrel, raccoon and deer. Still hoping to get video of bear, beaver, etc. 

Wednesday 

• Field day off. Three meetings. 
• Read a paper "The worldwide impact of urbanisation on avian functional diversity" in Ecology Letters. Great paper. Stats will take some time to figure out but interesting paper. 

Thursday 

• Surveyed a few points on SGL91- same state game land as Monday but very different section near Pittston. Burned sites were logged then burned. The regrowth was shoulder height and just above. Soaked to the point of saturation - everywhere. I have data (I should) from when I surveyed in 2017. Last time I was here the trees were chest high and exceedingly thick - mostly oak saplings. Now the oaks are just over the my head slightly less dense as they start to self thin. The ground cover was slight (if one defines ground cover as <1 m from the ground). I think there fewer birds. We'll see. 

Friday 

• Took a field day off. Entered a bunch of data. Called the vet. Laundry. Bottle of wine.

Saturday 

• Survey at SGL55. Some of it was cut over and burned (a mess) and some was just burned (glorious). Lot's of Hooded Warblers. Lot's of rocks flipped over by bears. Lot's of American Chestnut sprouts 

Sunday 

• Day off for chores 

Field Season 2020 Week I

Kicked off the field season with bird surveys 

Tuesday (5/26/2020)

• SGL40 - site near Francis Walter Dam, Turned 51
• Burn sites and reference sites
• Least flycatchers were back - must have social breeding. Breeding site in the burned area - I suspect they don't care as long as the mid-story and canopy are intact. Lots of Veery in the unburned site. 

Wednesday (5/27/2020) 

• SGL292 - site near Laurel Run, PA
• found sites that were burned last year I didn't get to. Lots of hiking. There is a creek on a north facing slope that has huge hemlocks and very awe inspiring. 

Thursday (5/28/2020)

• Took the day off for personal reasons 

Friday (5/29/2020)

• SGL207 part 1 - site near Mountain Top, PA
• I assumed this site was smaller but after looking at maps this site is huge but today I just surveyed sites I did last year including sites that were burned in 2018 and reference sites. Heard one wood thrush pair although there were at least 5 pairs last year 

Saturday (5/30/2020)

• SGL207 -  surveyed six points - 3 points that were burned 
• Walking to new sites heard a few Wood Thrush I didn't hear the day before. 
• Probably the second hardest day in the field in three years. The new sites were at least a km from the car and then several hundred meters apart. The slopes were steep and undulating. I wonder if there was copper mining at this in the past (at least 100 years ago). Huge granite boulders and slabs created lots of smaller cliff faces and caves. Shocked I didn't see bears or a rattlesnake. Did find a small patch of pink lady's slipper. The big problem of the day were the gnats. 

Sunday (5/31/2020) 

• SGL13 - surveys 4 points that will be burned this year (at least scheduled to). Super dense blueberry bushes and swamp. Also, a branch swung up my nose and I gushed blood for a few minutes. Did see a huge (maybe 400 pounds) bear cross the road and head to where I surveying. Awesome. 

When I wake up Tuesday

We're getting close to the safe dates for surveying birds. A safe date in this context implies that a bird you detect (hear/see) is a resident. This morning I will see hearing Scarlet Tanagers and Tennessee Warblers in my suburban neighborhood so these species are not within safe dates. I'm going to assume that nearly all species will be "safe" to survey by May 26. I have a bunch of project I can work on this summer that do not require students. All have advantages and disadvantages. I guess the larger goal is to do science that gets published. 

Here are the possibilities I'm considering:

Project	Advantages	Disadvantages
Wood Thrush nest success	Interesting, can add data to sparse data set. Can be done any time	Finding nests is super time consuming. Lots of squeeze for so little juice. Unlikely publishable
Urban bird diversity	Easy, interesting, possibly publishable. Done by 11 AM	Need lots of data and an interesting spin to make it publishable.  Up early.
Fire and bird diversity	Potentially publishable. Interesting. Done by 11 AM. Data used for other projects	Need to get permits, sites may or may not be burned (no experiment), up really early. Need to figure out how to assess vegetation structure quickly.
Nothing	I can write, get papers out, work on lectures	Boring

For my mental state, I finished the semester much better year than I have the past two years. This is good. Still, a rapid transition from classroom (recently my sofa) to the field leaves no room for downtime. However, things have to happen. 

I'm leaning towards Fire and Bird Diversity. I have a state grant to study birds and prescribed burning but that research is put off a year due to COVID. Having the diversity part settled will allow me to focus on food webs next year when I can have students in the field with me. The big downer of this research is that State Game Lands are not in my backyard and I need to get at some sites at sunrise that are over and hour away. Oh well, there's always coffee. On the upside, I'm done by 11 (that's the protocol) so I can still work on papers (although when you're in bed by 7 I'm not super productive). I can also listen for Wood Thrush and look for their nests when wrapped up. 

The more I think about it. The more I should the fire project. So be it. 

Tropical Ecology Course Online

Course Description: This course explores ecology and conservation with a focus on tropical forests. 

The textbook: John Kricher's Tropical Ecology

This page: Going to paste links to my lectures, a reading list, and random stuff. Assignments and readings will be through the portal. I'm making this public so anyone can see what is taught in the course. 

Topics 

• The stage
• Biomes of the world and their drivers
• Major habitats within the tropics 
• Global diversity and history of tropical forests 
• The players: Tour of tropical diversity 
• Plants and Forests 
• Fungi 
• Invertebrates 
• Vertebrates 
• Fish 
• Amphibians and Reptiles 
• Mammals 
• Archosaurs
• The ecological play 
• Ecosystem services
• Nutrient cycling 
• Disturbances 
• Predation and coevolution in the tropics
• Threats to tropical forests 
• Conservation in the tropics 
• 
  

Reading list for the tropical ecologist (or enthusiast)

• Charles Darwin's Voyage of the Beagle - Could be called "Tales of a twenty-year old naturalist" 
• The Shaman's Apprentice - if you dig ethnobotany, this is a must
• 
  

Coffee Course 2020 - Trip to Costa Rica: Foods

I have started co-teaching a course on coffee. This is an interdisciplinary course and the other professor teaches some history of Costa Rica and Latin America as well as the economics of coffee. I teach the biology of coffee but narrowly (e.g., the parts of the coffee cherry = bean + surrounding fruit) and broadly (e.g., tropical climates, soil, photosynthesis). As part of the course, we go to the Tarrazu region of Costa Rica, which is southwest of San Jose. I wanted to make a post about the foods there - all of which were fresh from markets (at least the food we ate). We stopped at a market in Cartago and it was glorious! 

You like beans? We got beans. All kinds! Sold by the kilo. 

Edge of the Cartago market. Every inch of these markets are used. 

             

Chayote root. Apparently delicious and expensive. This was at a roadside vendor near a chayore farm. I assume chayote is perennial so the vine (not shown) would regrow from the root. Given the fruit (below) are valuable the roots must be even more valuable. So I wonder if the plants has lower production after a number of years and that's when the root can be sacrificed. Question for the next trip. 

Cayote fruits. We ate them in a salad (not shown) but apparently they're very flexible and can be eaten like tomatoes (raw, steamed, fried, pickled, etc) 

   

An edible palm fruit, the pejibaye. This we had buttered and steamed and I loved it. Starchy like yucca. 

Lots of chayote to be found

Fish, chayote, salad, rice, and black beans - standard fare of Costa Rica. No hot sauce is typically used.

I can't remember the name but I think this was in the genus Inga. I believe this to be a large bean pod of a plant in the Fabaceae (bean family). The white part is the edible part and is very sweet. 

This looks like passionfruit but I believe it's just related to it. Grows on a vine (below) and it eaten green (unlike passionfuit, which is yellow) 

Sausage, chicken, nachos = goodness

Cas, very popular in juices. Very tart. 

This and below. No idea. Sweet and delicious. 

Gallos en hoja de platano. This was made special for us by our caterer but this is considered field food. It is a meal by itself: potatoes, beans, sausage, and two corn tortillas that are fitted like a pita. 

Boiled down sugar cane juice and poured them into molds to make a candy. This guy had several acres of coffee and sugar cane that he purchased after working at a diner in New Jersey for four years. I kid you not.

Cashew. Yep. That curly thing at the bottom contains the nut.