This study aimed to determine if migratory songbirds feed on key insect pests of coffee plants in southern Mexico by extracting and analyzing DNA from bird crop and fecal samples. The researchers tested two DNA extraction methods on 225 samples that had been stored for 10 years, finding that 17.5% yielded amplifiable insect DNA. Molecular analysis identified DNA from mosquitoes, moths and flies but not the target coffee pests. The results suggest that while migratory songbirds eat a variety of insects in coffee plantations, they may not be a major predator of the coffee berry borer, tortuguilla and chacuatete insects compared to bats.

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• If you want to extract DNA from bird crop and
fecal samples, don’t leave them sitting on a shelf
at room temperature in a tropical country for a
decade!
• Although migratory songbirds feed on a variety
of insects in coffee plantations, based on our
data set it appears that these birds rarely feed on
the key insect pests of coffee in our study area
(coffee berry borer, chacuatete, and tortuguilla)
• Assuming that these results are comparable to a
similar study done on bat fecal samples, it
appears that bats may play a more important role
than migratory songbirds in limiting populations
of these three insect pest species.
• Looking ahead, DNA sequencing can provide us
with evidence for future study of migratory bird
diets.
We are investigating the diets of migratory birds
that overwinter in shade coffee plantations in
southern Mexico. During the winter months, many
songbirds fly south to Central and South America,
resulting in an increased density of insect-eating
birds in these ecosystems.
Previous studies (Perfecto et al., 2004; Williams-
Guillén et al., 2008) have shown that birds play an
important role in limiting insect numbers in coffee
farms. However, in this system the degree to which
birds feed on particular insect pests of coffee is
unknown.
Study Objectives:
• Extract and amplify insect DNA from the crop
and fecal samples of migratory birds
• Determine if samples have DNA from three
insects that are pests of coffee in study area
Introduction
• Birds were captured in shade coffee plantations
in the Soconusco region of Chiapas, Mexico
Study Area and Species
Methods
Results
Conclusions
Acknowledgements
References Cited
Department of Biology, University of Washington, Bothell, WA
Hikmatullah Arif, Andrea Bedlington, Kylea Gleason, Parisa Monirzad, Nikita Nayudu
Using Molecular Scatology to Determine Migratory Birds Predation
impact on Coffee Plantation Pests
• We started with a collection of 225 samples of bird crop and fecal samples from 25 different species of
migratory songbirds
• Samples were collected between 2000 and 2012 as part of an investigation on diversity of migratory
songbirds in shade coffee plantations. These samples were not collected with a DNA study in mind;
therefore they have been stored at room temperature for 10 years, leading to DNA degradation!
• To extract DNA from the samples, we tried two different methods:
• Extraction using a spin-column kit (Qiagen DNEasy): fast, but low recovery of DNA
• Extraction using an Sodium Dodecyl (lauryl) Sulfate lysis buffer and phenol-chloroform protocol:
time consuming and laborious, but higher recovery rate of DNA
• Most samples had a small amount of tissue (less than 50 mg total material)
• After testing for the presence of amplifiable insect DNA using a universal arthropod primer (Zeale et al.,
2011), we then tested samples for the presence of DNA from the following three insect pests of coffee
using species-specific primers
We would like to thank the Science and Technology
Program of the University of Washington Bothell for
their support and the members of the Biology Research
Lab for generously sharing their space with us.
Funding for this research was provided by the National
Science Foundation, UW Bothell, and the University of
Michigan.
• Sample collection focused on migratory
songbirds, mainly species of warblers:
Coffee Berry Borer
(Hypothenemus hampei)
Tortuguilla
(Rhabdopterus sp.)
Chacuatete
(Idiarthron subquadratum)
This figure compares both of the methods of DNA extraction
performed in this investigation; blue indicates extractions that did
not produce PCR product (no amplifiable insect DNA) and red
indicates extractions with amplifiable insect DNA.
• We were able to produce amplifiable insect DNA from 46
of 263 extractions (17.5% of extractions); the SDS
method was better for samples with small tissue volume
(<10 mg tissue).
• Our samples did not return positive results for DNA of
the specific insect pests in question: the Coffee Berry
Borer, Tortuguilla, or Chacuatete.
• We have also used molecular cloning to characterize bird
diets in more detail (methods not shown); so far, we have
found the presence of DNA from mosquitoes, moths, and
flies in the bird fecal matter.
Nashville
Warbler
Rufus‐capped
warbler‐not migratory
Yellow green vireo
Tennessee warbler
Swainson’s
Thrush
• With one of the samples
that returned amplifiable
DNA we found that a
violet-sabre-wing
(pictured below) was
eating Culicidae
(mosquitoes),
Mimallonidae (moths) and
Tachnidae (flies that are
parasites of a caterpillars
mother). It is possible the
bird ate the caterpillar that
had a parasite.
Perfecto, I., J. H. Vandermeer, G. L. Bautista, G. Ibarra-Nunez, R. Greenberg, P. Bichier, and S.
Langridge. 2004. Greater predation in shaded coffee farms: the role of resident neotropical birds.
Ecology 85:2677–2681.
Williams-Guillen, Kimberly. "Bats and Birds: A Potent Team for Coffee Plantations." BATS. Bat
Conservation International, Inc., 2008. Web. 17 May 2012.
http://batcon.org/pdfs/BATSmag/BATSSummer08.pdf
Zeale, M.R., R.K. Butlin, G.L. Barker, D.C. Lees, and G. Jones. 2011. Taxon-specific PCR for DNA barcoding
arthropod prey in bat feces. Molecular Ecology Resources 11:236-244.