Animal diet quantification using high-throughput DNA sequencing: Moving from precision to accuracy
Presentation Abstract
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer’s diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing, and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals’ diet to generate Tissue Correction Factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected), to 14 ± 9% (TCF corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate Digestion Correction Factors (DCFs). The DCFs were compared to possible proxies for differential digestion (e.g., fish % protein, % lipid, % moisture) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
Session Title
Session S-05D: Marine Birds and Mammals of the Salish Sea: Identifying Patterns and Causes of Change - II
Conference Track
Species and Food Webs
Conference Name
Salish Sea Ecosystem Conference (2014 : Seattle, Wash.)
Document Type
Event
Start Date
1-5-2014 5:00 PM
End Date
1-5-2014 6:30 PM
Location
Room 6C
Genre/Form
conference proceedings; presentations (communicative events)
Contributing Repository
Digital content made available by University Archives, Heritage Resources, Western Libraries, Western Washington University.
Subjects – Topical (LCSH)
Harbor seal--Food--Salish Sea (B.C. and Wash.); Feces--Examination--Salish Sea (B.C. and Wash.)
Geographic Coverage
Salish Sea (B.C. and Wash.)
Rights
This resource is displayed for educational purposes only and may be subject to U.S. and international copyright laws. For more information about rights or obtaining copies of this resource, please contact University Archives, Heritage Resources, Western Libraries, Western Washington University, Bellingham, WA 98225-9103, USA (360-650-7534; heritage.resources@wwu.edu) and refer to the collection name and identifier. Any materials cited must be attributed to the Salish Sea Ecosystem Conference Records, University Archives, Heritage Resources, Western Libraries, Western Washington University.
Type
Text
Language
English
Format
application/pdf
Animal diet quantification using high-throughput DNA sequencing: Moving from precision to accuracy
Room 6C
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer’s diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing, and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals’ diet to generate Tissue Correction Factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected), to 14 ± 9% (TCF corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate Digestion Correction Factors (DCFs). The DCFs were compared to possible proxies for differential digestion (e.g., fish % protein, % lipid, % moisture) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
