FECAL PELLET GENOTYPING SERVICE FOR ABUNDANCE AND SEX RATIO ESTIMATION
(Draft date: 4/25/2014, update 2/27/2015)
Contact:
Ben Sacks, Director
Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory
School of Veterinary Medicine
University of California, Davis
(530)754-9088
bnsacks@ucdavis.edu
Background:
Estimates or indexes of abundance and sex ratio are essential to ungulate management and monitoring
programs, yet can be difficult to obtain through traditional approaches in certain circumstances (e.g.,
forested habitats that impede visibility for aerial surveys). Therefore, use of noninvasive capture-markrecapture (CMR) approaches that utilize individual genetic “fingerprints” gathered from fecal pellets
have been gaining popularity as an alternative. This approach has both advantages and disadvantages
to traditional approaches. For example, fecal CMR approaches have potential to provide precise,
unbiased estimates of abundance, density, and (if sex markers are included in genotyping) sex ratio that
are comparable across study sites and regions, regardless of visibility, enabling more reliable data with
which to monitor population trends, especially when conducted in a regional framework. The main
disadvantages are costs associated with intensive field collection activities and laboratory analysis. Thus,
fecal CMR approaches are likely to be most useful when strategically integrated with traditional
monitoring approaches.
Our services: We provide a range of services based on fecal pellets from deer or other ruminants
provided to us (see below for sample preservation protocols), including individual genotyping with 10
microsatellite markers and an SRY marker to determine sex as well as species-typing based on
mitochondrial sequencing (i.e., only necessary when species or origin is ambiguous). Analysis of
genotypic data to produce abundance estimates also can be arranged.
Pilot studies: Genotyping success can vary substantially based on the study area and time of year, due
to any number of factors, such as climate, precipitation, herbivore diet, etc. Therefore, we recommend
conducting pilot studies using ~100 pellet samples prior to finalizing plans for a project, as success can
range from 30 to 80%, which makes a significant difference with respect to numbers of samples required
to meet study objectives.
Field collection: Currently, the best way we have found to preserve DNA in pellets is to immerse them in
95-100% ethanol (e.g., Sigma-Aldrich, Product No.: 459844). (Because 100% ethanol is federally and
state-regulated, ordering requirements may vary by institution and region; see below for shipping
requirements.) We use polypropylene 15 ml conical tubes (e.g., Fisher Catalog No.: 14-959-49B).
Although it is possible to obtain DNA by swabbing pellets in the field (e.g., with a Q-tip), we have
performed sire-by-side experiments and found to perform poorly relative to preservation of pellets in
ethanol.
To reduce risk of contamination, pre-fill tubes with ethanol prior to collection of pellets. To the extent
possible, collect only fresh pellets (preferably <1 week) that have not been rained on.
(1) Record date, time, and GPS waypoint (and habitat type) of each collected sample (4-6 pellets
from each pile; others cleared)
(2) Put the 4-6 pellets in a 15 mL conical tube containing 8-10 ml of 95-100% ethanol.
(3) Label tube with unique number referenced to data above (label cap and tube and cover tube
label with scotch tape)
(4) Keep tubes upright as leakage of ethanol will erase label information (possibly even when
taped). Keep tubes in order so that samples can be renumbered if ethanol erases labeling.
IMPORTANT: We are in the process of research to improve sample preservation protocols, so please
contact us for the most up-to-date recommendations.
Costs: Costs will vary depending on project size. Please contact us for a quote.
Shipping samples in 100% ethanol: Because ethanol is flammable and hazardous, shipping of samples in
ethanol is also regulated by the International Air Transport Association (IATA) and U.S. Department of
Transportation (DOT) regulations. Individuals are legally required to have someone with IATA or DOT
training package samples for shipping. Samples in 100% ethanol can be shipped by courier (Fed Ex, DHL,
UPS) if the internal containers (i.e., your conical tubes) are <30 mL and the total volume of the combined
samples is <500 ml. Tubes must have space for liquid to expand (i.e., not be completely full), be sealed
and secured into a styrofoam or other rack or otherwise bound together and inside of a ziploc bag
containing sufficient absorbent material (e.g., newspaper) to absorb all ethanol were tubes to break,
and the Ziploc bag put into a cardboard shipping box. The entire package must be able to withstand
dropping from 6 feet and having similar sized boxes stacked upon it up to 10 feet high. Additionally,
packages must be marked with a “Dangerous Goods in Excepted Quantities” label at least 100 mm on a
side (e.g., http://www.cmarz.org/images/shiplabel_dangerousgoods.jpg ). Ethanol is a Class 3 substance
with UN No. 1170.