Wednesday, April 17, 2013

On the trail of the amphibian chytrid fungus in the Atlantic Forests of Brazil


by guest blogger, Professor Timothy James
University of Michigan Herbarium

This January to March I traveled to Brazil to work on a few projects and to develop international collaborations.  All of these projects involve aquatic or zoosporic fungi.  One important fungus in particular is the disease agent of amphibian chytridiomycosis (Batrachochytrium dendrobatidis). Try to say that fast four times.  One major goal of the trip was to develop an international collaboration with Brazilian scientists.  The funds for the trip came from a joint program funded by the National Science Foundation and the Fundação de Amparo à Pesquisa do Estado de São Paulo (Foundation for Research Support of the State of São Paulo, or FAPESP).  Our primary collaborators for the project are L. Felipe Toledo and Domingos Leite at the Universidade de Campinas (UNICAMP). Besides having a meeting with folks from southern Brazil interested in amphibian disease, we (myself and two graduate students from U. Michigan, Clarisse Betancourt and Thomas Jenkinson) spent a lot of time hunting frogs and trying to isolate the chytrid fungus. We visited localities in these four states: São Paulo, Paraná, Rio de Janeiro, and Santa Catarina. We found chytrid infected tadpoles at each of the localities. The rate of chytrid infection was really high, roughly the 50% previously reported for Brazilian Atlantic Forest tadpoles (Toledo et al. 2006, South American Journal of Herpetology 1:185). This blew me away as we find almost zero percent tadpoles with dekeratinized mouthparts back in Michigan.

Picture of a Phyllomedusa being swabbed.  Swabs are tested in the lab using DNA methods to determine if the fungus pathogen is present.



After leaving Campinas, I moved to São Paulo to visit the lab of Carmen Pires-Zottarelli at the Instituto de Bôtanica.  The place is a holy land of botanical research in the best way.  It’s situated in green oasis right in the middle of the city and has the city’s public garden attached.  There’s at least six faculty doing mycological research there, including lichenologists and agaricologists, and my host lab which studies aquatic fungi.  We were working on molecular phylogenetics of chytrids and oomycetes.  One project involves documenting zoosporic fungi from Ilha do Cardoso, the most pristine habitat I saw while in Brazil.  

Ilha do Cardoso has forest that is dense with bromeliads, which makes great habitat for amphibians as well.  I don’t think any chytridiomycosis surveys have been done here.
Combining toadstools and toads was never something I’d imagined doing when I entered into the world of mycology.  But, since 1998 we’ve been experiencing a global pandemic of this fungus disease.  More research is needed to understand the disease’s origins and to help with amphibian conservation.  There’s no better place to do that than the Atlantic Forest of Brazil, which has over 500 endemic species of amphibians.


Hygrocybe c.f. conica mushrooms and the pumpkin toadlet Brachycephalus ephippium.

Sunday, September 9, 2012

Cowboys, Waterfalls, and Snails: A tale of true grit in the Oregon wild

The purpose of my research was to use molecular and morphological analyses to help establish the species status of a freshwater physid snail in the Owyhee river of southeastern Oregon. On paper, this task did not appear to involve any sweat-inducing, heart-palpitating-causing, shortness-of-breath-producing activities. In reality, however, where most of the things I do take place, it most certainly did. But from the beginning, who would've thought? Here's what I mean...

My summer research began in a lab. Work station, latex gloves, pipettes, centrifuge tubes, tiny dead snail DNA, and a handful of chemicals. I was living the simple life. I would go to work every odd day, perform extractions, PCRs, sequence DNA and make trees. From this life of simplicity, I produced a poster to present at the ESA Conference.


I enjoyed this work. Not only because I knew what I was doing, but also because everyday I was learning something new and interesting. Even so, I was looking forward to the field work. Lab work can only be so satisfying. What I needed were more specimens for morphological analyses and to characterize the species habitat. Thus, after ESA, I prepared to make my way from Ann Arbor to the Owyhee River in Oregon. From here on, the level of simplicity, comfort and ease with which I worked inverted.

The easiest part of my field work was arriving at the Boise, Idaho airport. There, I met Dave Hopper of the US Fish and Wildlife Service, who was the driving force behind this research project. During my first night in his neck of the woods, he and his wife showed me the sights of Boise: a local co-op grocery store, a family-owned Mexican restaurant (including an adorable Mexican man singing karaoke), and the state capitol. It was calm, quaint and, in retrospect, the perfect juxtaposition with the next two days.

The plan was to leave by 7am. We hit the road, bags packed, sleeping bags secured, and canoe laced tightly to the top of the Jeep. The highway was beautiful. We took it for 2 hours before turning off onto a rarely-traveled but moderately well-maintained dirt road.



Then the simple life I had learned to both love and expect evaporated and in it's stead was a stampede of cows and cowboys, which apparently are still real. 

 



We waited on the side of the road for 20 minutes as cow after cow, urinating, drooling, and doing a lot of staring into my soul with their dark and lucid eyes, walked up to and around our car. Moos came from every direction with cowboys on horses and 4-wheelers herding to their heart's content.

Once the procession passed, we traveled the remainder of our 3.5 hour journey to our destination. Between our camp site and the gate entrance was a drive down the mountain side, spiraling, precarious, and rock-slide susceptible. Pictures of this portion of the drive don't exist because terror prevented me from taking them. Several minutes, two sweaty palms, one dry throat, and an unhealthy new-found fear of dirt roads later, we arrived.


After setting up camp, we canoed a mile up river to the study site where the snails are found. Two of Dave's friends had joined us, along with their dog (who the owner originally thought was a female and named Cindy, only to "discover" it is actually a male and began to call him Sydney) and they partook in some fly-fishing in their inflatable.

Once we reached the study site, the following happened:
 
 
  
 
 
We located hot water streams that fed into the main river, GPS'd and surveyed them for snail presence/absence, I took pictures, we climbed a waterfall, Dave told me to be very careful of the wet rocks, then I slipped on some wet rocks, caught myself, paused to decide between fight or flight, then both strategically and with some well-placed prayer made my way up the rest of the way. All of which made me realize that I'm literally nothing like Bear Grylls or Les Stroud.
 
At the top of the waterfall sat an artificially constructed hot spring occupied by four overly-friendly half-naked middle-aged men, who suggested that I join them but I politely declined. Beyond this semi-nude congregation, a hot-water stream flowed down from the mountain and into the hot spring. The water flow was strong enough to cause a constant sense of uneasiness; wet-rocks abound and surety of balance a thing of the past, we traversed the landscape. For the next several hours, Dave and I hobbled and tight-roped our way up-stream, occasionally visited by the bounding and roaming Cindy/Sydney, and measured physid population densities, stream depth, temperature, pH, dissolved solids, and conductivity. 
 
Once finished, we tip-toed our way back down the waterfall, canoed downstream and settled back in at our campsite. So close to the finish line, I relaxed most of the evening away in a folding chair with a book in one hand and what we will call water in the other. But relaxation was short-lived as there was one more test to pass: the Oregon wild at night. Coyotes. Rattlesnakes. Mountain lions.

For emphasis: MOUNTAIN LIONS.

Dave had mentioned casually that they were in the area, though rarely sited, and this remained in the back of my mind since the morning when I walked the 100 yards, alone, to the only port-a-john around for miles and saw not only hooves, but very large, very un-dog like prints in the sand. Needless to say, I did not sleep well. Rustling leaves, footsteps around my tent, the dog occasionally growling. At who? Dave walking to the bathroom? A mountain trying to sneak in and kill me? Unsolved mysteries.

However, in the end, I didn't die. I held my breath the night away and the next morning, we took the liberty to do some quick canyoning and explore the area before vacating. As clouds rolled in, it was important to leave ahead of the weather to avoid being stranded in the canyon for days (with mountain lions prowling, which is what they do I bet). As we drove back up the narrow, gut-wrenching mountain-side road, I took the opportunity to remember every sight I saw, every fear I felt, and every smile I shared because through all the nit and the grit, I wouldn't have altered my experience. The fear and uncertainty were a part of the learning and if they weren't, this wouldn't be my story. 
 
Cowboys, waterfalls, and all of the above, this was a tale of true grit in the Oregon wild.


Thursday, September 6, 2012

Beatriz Otero - Of mice and coffee


 What is the effect of different agricultural practices on the population structure of animals? How does the population structure vary (or not) between different management practices? Which ones serve as better matrices? These are some of the questions I am interested in and to help answer them I spent 9 weeks in a coffee farm in Mexico collecting ear tissue samples from a common mouse species.

This is my attempt of a illustrated chronicle of my field season...



View from Finca Irlanda one of my sampling sites in Chiapas, Mexico. This summer I collected ear tissue samples from Heteromys desmarestianus (Demarest's spiny pocket mouse) in coffee farms and adjacent forested fragments. 
These are some pictures H. desmarestianus. They are one of the most common species rodent species found in moist forest areas from Mexico to Panama.








This genus can be recognized by the pocket it has next to it's mouth. In this picture you can see the full pocket.

After collecting the tissue samples, they were stored in buffer to keep the DNA from deteriorating. I brought my samples back to Michigan and now I am in the process of extracting the DNA.


Wednesday, September 5, 2012

The 2012 Summer Adventures of Marcella Baiz


I went to México this summer to do field work with two closely related howler monkey species (Alouatta palliata and A. pigra) that are hybridizing in the state of Tabasco.

Range of Alouatta palliata and A. pigra in Central America and some of the sampling locations we visited (in red).

During the first part of the trip, I spent time in the states of Veracruz and Tabasco with my advisor, Liliana Cortés Ortiz collecting samples (blood, fecal, hair) from which we will be extracting DNA. I will be using many of these samples for my thesis project, which investigates genetic relatedness among intragroup adult females of both species. 

Collecting samples and taking morphometric data from an adult A. palliata individual

I also assisted in data collection for Lucy Ho’s dissertation project. She is a Ph.D. student in the UM department of PsychologyLucy is interested in female howler monkey social behavior, more specifically, the effect of hybridization on female-female social interactions. So, we spent a lot of time staring up trees recording the monkey’s behaviors and movements.

Lucy trying to locate an A. pigra study group in Macuspana

To end, here are some of my favorite moments in snapshots!





Monday, October 10, 2011

A little adventure in Adamawa, Cameroon--the mosquito sampling trip 1

It has been two days since I came back from the mosquito sampling trip in the Adamawa Province. It is the 2011 president election day today. I am enjoying the tranquility of this special Sunday in Yaoundé, the capital city of Cameroon, while there came the melodious call to the prayers from a mosque nearby, which reminded me of most days in the Adamawa Province, where Muslim culture dominates.

view of Yaoundé; minaret of a mosque at a distance


"Why did you come to Cameroon for research on mosquitoes?" As I was asked this question often enough, I'd say it all started from a paper I discussed with my advisor Prof. Lacey Knowles three years ago. It simulated situations where a chromosomal structural mutation which reverses the gene orders--inversions--in mosquito populations can promote rapid adaptation to different habitats. The alternative inversions copies from parents might leave no direct fitness cost on the hybrids, but indirectly influencing offspring of them by largely suppressing recombinations around the inversion regions. And if luckily, genes that are crucial to the local adaptation reside in the region, the combination of them can be preserved longer without being shuffled with maladapted alleles from different habitats. I got really interested in the biological and modeling aspects of the evolution of inversions in promoting adaptation and found that the malaria vector in sub-Sahara, Anopheles gambiae was an ideal system to answer my questions, which later on became the major focus on my dissertation proposal. With the aid of grants from the Museum of Zoology and The International Institute as well as the support from Center for Tropical Research in UCLA and the vector genetics lab in UCDavis this year, I'm able to come here for the field work I've been dreamed of for two years.

Although my research interest is very much evolution-based, my field trip felt more like a public health study because of the nature of the species. Anopheles gambie females spend a lot of time inside human houses, hiding at dark spots near beds, on walls, roofs, inside bed nets, either waiting for chance to bite or resting to digest a delicious blood meal. We have to catch blood-fed females for chromosomal karyotyping work, which means we need to enter people's houses in villages. And that is not an easy task.

Sampling sites in the Adamawan Highlands. This region is the transition zone from forest to savanna habitats, harboring high diversity of inversion polymorphism.

En route
As the transition area from forest to savanna ecozones, Adamawa is one of the least developed provinces in Cameroon. Road condition is really poor in the majority of the area so that a jeep or a truck is a must to move around. Starting from Yaoundé, we drove up north through the west province. Paved road stopped right after Foumban, which is near the border of Adamawa. And soon I found myself jolting on the muddy road, moving less than 30km per hour, without knowing that the rest of the journey would be pretty much like this or even worse. Bankim is our first site. Located near the reservoir Bankim, it enjoys the last bit of forest habitat before transition to wet savanna. The reservoir also serves as a good breeding site for mosquito larva.

Bankim

forest nearby

Reservoir Bankim

As a cheaper alternative to paved road, mud road functions well in dry seasons here. However, after one or two months of heavy rains, the road will soon be damaged by over-loaded trucks. Driving through uneven grounds with big rocks and ponds, my driver Elvis had to constantly swerve from one side to another. We can occasionally find Anopheles larva at the temporary ponds at the road side. When we reached the second site, Mbakaou, at the reservoir Mbakaou, our truck had a major repair to fix the brake, the battery and change the bearing of a tire. On the road to the province capital, Ngaoundéré, the LCD of my laptop got broken and the truck went to the garage for repair again. Bad road severely impairs the development. On the whole way of driving through the province, we rarely see any private cars or trucks. We were stuck for about two hours because the truck sank into the mud once. And surprisingly, there were only three trucks waiting behind us. It didn't cause a traffic jam or anything because there were simply no vehicles. Most people prefer to travel by train on the single railway from Ngaoundere to Yaounde. The demand way passes the supply. People were queuing for a standing ticket for hours because seat or sleeper class tickets will be sold out very very quickly. Despite the bad road, the best time en route was when occasionally we met a section of uphill paved road. Overlooking the savanna valley, we felt like we were the only beholder of the vast land. And then there came thatch-roofed huts, cattle herds and people.


on the way from Bankim to Tibati, Mbakaou; Wet savanna habitat


our truck got over-heated after Elvis managed to pull it out of a pile of mud


Reservoir Mbakaou provides a good amount of fish for the local people, as well as Anopheles mosquitoes


Cattle herds; Unlike deers in North America, cows here don't move when seeing vehicles. They only move aside when our truck almost hit them.

Originated in Asia, the humped zebu cattle are everywhere now in Africa. They are the major meat source in Northern Cameroon, especially among Muslims.

North of the Mount Ngaoundere starts the dry savanna. Mbe belongs to the North province and we could feel the increase in the temperature instantly.

Catching mosquitoes
How much communication with local people has to be done before we can get the permission to catch a mosquito inside a village house? I would say a lot. Upon reaching each town, we had to visit the administrative chief of the district, explain our purpose, show the order mission and get his signature. Then we would stop by the health center of the region, notifying the doctor and asking him to help us find local volunteers. Local guides then lead us to different villages in the district and explain to local people about our purpose in either French or local language. Since I don't speak French, these communications are done by my field assistant, Seraphin. Most of the time I had no idea what they said, and Seraphin was used to translate a twenty minute conversation into two sentences. Quite the same experience as that in the movie, "Lost in Translation". When people in the villages got to know exactly what we were going to do, they would be very cooperative. After greeting me with "Bonjour, Madame", they would say "entre, entre" when I intended to take off my shoes if they have floor mats on the ground. People in the villages are nice and honest. They might or might not lock the doors when they leave to work in the farm, but no one will enter the house without the host's permission. It's common to see shops wide open without the shopkeepers, who come back half an hour later. But nothing will be stolen. After finishing the mosquito catch in a village, we sometimes find a big sac of peanuts at the back of our truck as a gift from local people.

We usually do catching twice a day. In mornings from 8-12, we search for mosquitoes inside people's houses, especially bedrooms, using torches. Mosquitoes like dark areas. And they take big advantages on the holes on bed nets. Newly treated bed nets prevent us from catching a single female even using insecticide, but worn bed nets with big holes typically trap 1-20 blood fed mosquitoes. Unfortunately, it was usually old women or men who were using those old bed nets and got bitten terribly. I wish I could speak their local language and say "I'm sorry for the living condition, but thank you for contributing to my study". Mosquitoes are not a quick flyer. We use aspirators to suck them inside a tube when we spot them and blow them into a vial. Typical walls are bricks and mud, rarely concrete. Thatch roof is common. It blocks the sun, so inside it's always cool regardless of the temperature outside. But people are starting to switch to zinc roof for its fire resistance. Mosquitoes love hanging on the thatch roofs. Those that are caught in over-heated zinc houses are usually more fragile. Painted walls ease our search because otherwise their dark body hides well on mud walls.


Seraphin took out tools and gave them to local volunteers

Culex and Anopheles are the two genera that would be commonly found inside houses. Anopheles, however, prefer rural areas much more. The species I'm interested in, An.gambiae, dominates the catch in most sites except for Bankim. At the end of rainy season there, An. funestus is more common. Both of them are notorious severe malaria vectors. Mosquitoes caught in the morning would be reared in vials and fed sugar water to make sure that they digest the blood properly and develop big ovaries.

a good catch

In the afternoon, we do spray catching by directly killing mosquitoes using insecticide and let them fall on white sheets spread on the ground because that's the time when most of the female are half-gravid (i.e., blood is half digested and ovaries have accumulated a lot of eggs). We then kill the morning batch and dissect ovaries out. That can last forever depending on the quantity we catch. We celebrated a good catch with a good meal late in the evening. If it was a bad one, obviously we would have more time eating and drinking!


Dr. Atangana adjusting the microscope for dissection.

Sadou, the best mosquito catcher from the whole trip. He can literally see mosquitoes that I would otherwise never notice.


Life in the villages
Work is highly divided between men and women here. Men go to farms, rear cattle, ride motorcycle taxis, or sit together drinking Sha-y (a kind of sweet herbal tea) for the whole day. Women prepare food, take care of kids, wash clothes and give birth. Violation of the common division of work is considered bad. Usually, when we visit people's houses in the morning, there are only women, pre-school kids and old people. Polygamy is prevalent here. As explained by Seraphin and a local volunteer, Sadou, it is partly because girls over number boys and it's usually difficult for a girl to find a reliable husband. Sadou, a typical Muslim living near Ngaoundere, has two wives in the villages and one in the city. He's only 35 and already has eight kids. He said he should have another wife and at least another two kids. Interestingly, he got a chance to get a fourth wife in Mbe. One afternoon, we sprayed a house and caught a lot of blood-fed mosquitoes. The old woman was so grateful for our work as she thought she'd have peaceful sleep for three weeks. She told Sadou she's willing to give her daughter to him. When I heard Seraphin's translation, they saw my mouth wide open and laughed, saying that that's how people behave here, that's how people regard marriage here. The whole thing is about finding a hard-working guy with means or finding a well-behaved girl who can give birth.


a woman carrying stuff on her head, with a child on her back and probably pregnant


A typical bedroom


a lot of kids have huge tummies. I don't know if that was because of schistosoma in the pond.

Despite the poor living conditions, people are content with life here. It's hard to see people with miserable expressions. There is no electricity or water in most villages. They still lift water from wells, use bush light in the night and firewood for cooking. As a good habit of most tropical countries, they take baths every day at least once using collected rain or well water. Despite the muddy road, they still wash their motorcycles everyday, with a bucket of water. The town of Mbe only has three and half hours of electricity: 6:30-10pm. Nevertheless, Cameroonians cannot live without bars. People continue to drink in the darkness without lights or music in bars.

women selling peanuts

two grades in a single class

Children selling water and food to passengers

moto taxi drivers

I ate local food and drank local boisson for the whole journey. Although I was concerned about the cleanliness, especially about eating with hands, I didn't get diarrhea even once. I guess the fact that I grew up in China gave me a pretty strong stomach. Although the variety, taste and quantity of the food here correlates exactly with the economic status of the place, I think most of the food here is super healthy and organic. Because crops are all naturally farmed with less chemicals added. cattle eat fresh grass and walk long distances every day. I'm wondering how long can this natural way of farming last? When will cattle raising factories start to show up?

a typical meal in Muslim region: tomato soup with beef stew and a huge pile of rice

a woman cutting cassava

a typical Cameroonian meal: Foufou (maize flour made buns), Njamo Njamo (a leafy veggie) and beef stew

Then I sometimes wish the road would never be paved and industries will never come to destroy the beautiful land. But I know that's a too selfish idea. And I know their life has already been permanently influenced by manufactured goods. The most obvious example is the garbage. No recycling, no waste management whatsoever. You'll find piles of trash at a corner here or there in villages or towns. Organic matters go away very quickly, so only plastic bags, bottles, batteries lie there, probably forever. I wish these villages would never become as trashy as some of the Chinese villages. Sustainable development, that's possible, right?

smart usage of the roof


I'm looking forward to my sampling in the west province soon. Wait for my blog about new experience in three weeks!