New Pub: Tamarin helminth survey

Primates, due to their longevity, take a great deal of time to understand. The same could be done within a matter of months for rodents, but to get baseline data on a wild primate, you have to really clock some hours. One of the neatest outcomes, therefore, is when all of that work pays off in the form of some interesting discoveries. And this is what happened on this particular publication, primarily led by the research of Gideon Erkenswick.

Parasites are ubiquitous within all wild primates, and simply hosting a parasite doesn’t actually make them ill. Our goal here was to establish what “normal” looked like for a wild tamarin. We worked for 30 group-years (a span of 3 calendar years) to examine 105 individuals (71 saddleback and 34 emperor tamarins) across a magnificent total of 288 hard-earned fecal samples.

Screen Shot 2019-11-11 at 10.29.37 AM

Within these, we identified 10 parasite taxa by light microscopy after standard sedimentation/flotation techniques.

Here is a summary of our findings, as an excerpt from the paper:

“Of these taxa, none were host‐specific, Dicrocoeliidae and Cestoda prevalences differed between host species, Prosthenorchis and Strongylida were the most prevalent. Host age was positively associated with Prosthenorchis ova and filariform larva, but negatively with cestode and the Rhabditoidea ova. We detected no differences between expected and observed levels of co‐infection, nor between group size and parasite species richness over 30 group‐years. Logistic models of individual infection status did not identify a sex bias; however, age and species predicted the presence of four and three parasite taxa, respectively, with saddleback tamarins exhibiting higher PSR. Now that we have reliable baseline data for future monitoring of these populations, next steps involve the molecular characterization of these parasites, and exploration of linkages with health parameters.”

Reference:

Erkenswick G., Watsa M, Gozalo A.S., A.S., Dudaie, S., Bailey, L., Muranda, K.S., Kuziez, A. and Parker, P.G. (2019). A multiyear survey of helminths from wild saddleback (Leontocebus weddelli) and emperor (Saguinus imperator) tamarins. Amer. J. Primatol. DOI: 10.1002/ajp.23063 

New Pub: Titi terrestriality

Every so often, you see a paper that appears to be put together by all the scientists in the world at once – and this felt a lot like one of those instances. This conglomeration of researchers has worked diligently on this manuscript for several years, coordinating across a large group efficiently and with nary a off-note in the entire process. Just that deserves applause!

We collaborated to collect data from 86 studies conducted in 65 different sites where the Callicebinae were found to be terrestrial (upon occasion). Within the group, terrestrial activity was recorded frequently for Callicebus and Plecturocebus spp., but rarely for Cheracebus spp. Across the board, these arboreal primates came to the ground to rest, as an anti-predator strategy, to eat soil (geophagy), to play and forage on terrestrial invertebrates and soil. The longer a researcher studied these animals, the more likely it was that they would observe terrestriality. Although it was difficult to identify patterns across so many disconnected studies, while keeping scientific rigor high, we did discover that unlike the other pitheciids, titi monkeys hit the floor rather a lot more than expected!

But, they’re not alone in this behavior – lots of other primates come to the ground despite being primarily arboreal:

Screen Shot 2019-11-11 at 11.00.10 AM.png

Please see the full paper for a lot more avenues of research! We also made the cover of this volume:)

Screen Shot 2019-11-11 at 11.03.26 AM

Reference:

Souza-Alves JP, Watsa, M, 62 other authors & Barnett AA. (2019) Terrestrial behavior in titi monkeys (Callicebus, Cheracebus and Plecturocebus): Potential correlates, patterns and differences between genera. International Journal of Primatology. pp1-20. https://doi.org/10.1007/s10764-019-00105-x

#wildlifegenomics Lab #2

In November, we wrapped up the installation of a small but exciting laboratory for domestic samples obtained from the areas in and around Guadalajara, in the Jalisco district of Mexico. A little different than the previous efforts at field laboratories by FPI (which is actually a thing now!), this laboratory is miniature but extremely focused. The company that owns it does a large amount of screening for disease vectors for domestic animals and some human samples, but they have never ventured into the world of DNA testing.

We were tasked with taking a small portable setup into a temporary lab space to run the first tests for Leptospira, Babesia and Ehrlichia on some known positive samples. In these circumstances, a variety of things could go wrong – the primers could be uncooperative, the extraction procedure could yield low amounts of DNA, or the positives themselves could be finicky or undependable. But to our utter delight, we were able to successfully get positives to amplify for leptospira and babesia infected animals. The test was simple – a quick extraction, PCR and gel electrophoresis, but the sheer number of doors that opens for the area is by no means unremarkable.

Future foci include making the setup and tests entirely portable, so vets can take it with them to sample animals directly in the field during field visits. Real-time results can completely streamline the process for regulating outbreaks of diseases in domestic animals in the area.

We are also helping them choose more disease-causing agents to test for in the area, and helping them officially launch the laboratory.

The possibilities, as always, are endless.

And we didn’t even have to sequence any DNA!

When they are ready to launch officially, I’ll be happy to rave a little more about them.

 


Terms of Note:

Leptospirosis is a bacterial disease that affects humans and animals. It is caused by bacteria of the genus Leptospira. In humans, it can cause a wide range of symptoms, some of which may be mistaken for other diseases. Some infected persons, however, may have no symptoms at all. Without treatment, Leptospirosis can lead to kidney damage, meningitis (inflammation of the membrane around the brain and spinal cord), liver failure, respiratory distress, and even death. Source: CDC
Babesiosis is a malaria-like parasitic disease caused by infection with Babesia, a type of Apicomplexa.[1] Human babesiosis transmission via tick bite is most common in the Northeastern and Midwestern United States and parts of Europe, and sporadic throughout the rest of the world. It occurs in warm weather.[2] People can get infected with Babesia parasites by the bite of an infected tick, by getting a blood transfusion from an infected donor of blood products, or by congenital transmission (an infected mother to her baby). Source: Wikipedia
Ehrlichia is a genus of rickettsiales bacteria that is transmitted to vertebrates by ticks. These bacteria cause the Ehrlichiosis infection, which is considered zoonotic, because the main reservoirs for the disease are animals. Source: Wikipedia

Can you #Genomicsinthejungle?

In the late summer of 2018, I had the very great pleasure of conducting the first ever field course on genomics in the Amazon rainforest. We used rugged, field-friendly technology based at the Green Lab at IGFS in Peru, and Oxford Nanopore’s tiny sequencer – the MinION – to get from sample to sequence in a remarkably short period of time.

In total, we ran four experiments focused on 16s metagenomics, 18s metagenomics, ddRADSeq digests, and DNA barcoding. Our samples ranged from everything from primates to batflies, spanning all major terrestrial taxonomic orders. We worked with feces, blood, whole ectoparasites, and other insects, and plant samples.

The resulting publications will be co-written by all the students in this field course. See below, for a summary of one of the most rewarding teaching experiences of my lifetime.

I will be teaching this course again – once in India this winter, and again in Peru in the summer of 2019. Please see here for details!

(If the imagery below doesn’t display in your browser, click the link to explore).https://embed.wakelet.com/wakes/8651396b-e4c7-40dd-90da-e75b45da9235/grid

New Pub: Classification of producer characteristics in primate long calls using neural networks

Her findings are both methodologically and analytically intriguing. She used a novel machine learning model called an artificial neural network to condense the large number of measures taken on each vocalisation into a meaningful set that could then be used to see if each call encoded information about the call’s producer – either sex, age, or even individual identity.
Here is the paper’s abstract:
Primate long calls are high-amplitude vocalizations that can be critical in maintaining intragroup contact and intergroup spacing, and can encode abundant information about a call’s producer, such as age, sex, and individual identity. Long calls of the wild emperor (Saguinus imperator) and saddleback (Leontocebus weddelli) tamarins were tested for these identity signals using artificial neural networks, machine-learning models that reduce subjectivity in vocalization classification. To assess whether modelling could be streamlined by using only factors which were responsible for the majority of variation within networks, each series of networks was re-trained after implementing two methods of feature selection. First, networks were trained and run using only the subset of variables whose weights accounted for ≥50% of each original network’s variation, as identified by the networks themselves. In the second, only variables implemented by decision trees in predicting outcomes were used. Networks predicted dependent variables above chance (≥58.7% for sex, ≥69.2 for age class, and ≥38.8% for seven to eight individuals), but classification accuracy was not markedly improved by feature selection. Findings are discussed with regard to implications for future studies on identity signaling in vocalizations and streamlining of data analysis.
Screen Shot 2018-10-17 at 5.04.36 PM
Screen Shot 2018-10-17 at 5.04.49 PM.png
Robakis, E., Watsa, M. and Erkenswick, G., 2018. Classification of producer characteristics in primate long calls using neural networks. The Journal of the Acoustical Society of America144(1), pp.344-353.

The Green Lab

What if you could collect a sample from an animal, bring it back to camp, and be looking at the entirety of its genome by the same time the next day? Well, we think you can at the Green Lab. We are proud to collaborate with Field Projects International and the Inkaterra Association in the creation of the Amazon’s first in-situ molecular genetics field laboratory that can go from sample to sequence in just 24 hours.

The lab is located at the Inkaterra Guides Field Station, about an hour downriver from Puerto Maldonado on the Madre de Dios River in southeastern Peru. The Green Lab is set to launch in July 2018 with the following capabilities:

Biological sample preparation and storage, including but not limited to hair, nail, blood, faeces, serum, tissues and urine.

 

Kit-based DNA extraction from faeces, hair, blood (FTA cards), nail, and other tissues.

 

PCR-based DNA amplification with primers of your choice. We can procure these for you.

 

Agarose gel electrophoresis for presence/absence screening. Real-time visualisation and photography of gel results.

 

DNA quantification using fluorometer assays with a Quantiflor system.

 

Real-time portable genetic sequencing with ultra-long read lengths using MinION technology. Multiplexing possible.

 

Access the laboratory to perform analyses yourself, or leave it to our on-site experts.

 

Export of samples to an external provider for short turnaround Sanger sequencing

 

Winter field courses

 

screenshot-2016-10-03-12-08-03Several of our research team alumni are involved in teaching field courses in Peru and India this winter.

Liz Maciag, a research assistant alumn from 2011, will be teaching mammalogy with a focus on primatology in Peru. Tim Paine, long-time board member and veteran instructor will be co-teaching a module on herpetology in Peru. Ben Lybarger, a former research assistant, will be the lead TA on this course. For more details or to apply, please see here.

Lab PI Dr. Watsa and senior researcher Gideon Erkenswick will be teaching a course on primates and predators in the Western Ghats of India. They are joined by 2012 research assistant KC Hill, who is an expert on carnivore ecology and training to be a wildlife veterinarian today. For more details or to apply, please see here.

For a full listing of course offerings by FPI, please see here.

A new publication

_dsc7987

Our capture protocol is finally out! The journal Neotropical Primates has published our paper on novel handling methods of small arboreal primates. This was a collaborative effort including students who participated in our research program from its very inception in 2009. We are grateful for their perseverance, dedication and patience through this process!

For a photoessay on our mark-recapture program, or to participate in our global survey of primate protocols used in the last 20 years, please visit this page.