Download Wildlife Genetics Proficiency Testing Program – Test # 022608 Results

Wildlife Genetics Proficiency Testing Program – Test # 022608
Results
Test Start Date
Test Due Date
-02/26/2008
-05/02/2008
This document reports the results of the Wildlife Genetics Proficiency Testing Program. The
National Fish and Wildlife Forensic Laboratory was the duty Lab and was responsible for sample
preparation, sample verification, distribution, and gathering and reporting the results.
The results are self explanatory and are divided into three sections:
1. Results of Test for Species Origin
2. Results of Determination of Gender Origin
3. Results of Individual Identification
Each section contains the following:
1. The species source that you identified for Items 1, 2 and 3.
2. The methods used to make these identifications.
Scenario
A Wildlife Agent is investigating a poaching incident involving elk. The suspect claims the meat
in his freezer is coming from one elk. All three tissue samples were recovered from the suspect’s
freezer.
The Agent requests that the species and gender origins of all submitted evidence be determined.
She is also interested in knowing whether the three submitted evidence items are from the same
individual animal. It is not known where the poaching incident occurred.
Items Submitted
Item 1: Tissue from suspect’s freezer.
Item 2: Tissue from suspect’s freezer.
Item 3: Tissue from suspect’s freezer.
Wildlife Genetics Proficiency Testing Program Answers:
Species
Origin
Gender
Origin
Accession
No.
Provider
Original
ID
Item 1
Mule Deer (Odocoileus
hemionus)
Male
Item 2
Elk
(Cervus elaphus)
Male
Item 3
Mule Deer (Odocoileus
hemionus
Male
QA2L56-QA2M24
QA2M25-QA2M74
QA2L56-QA2M24
WY Game and Fish
WY Game and Fish
WY Game and Fish
HA81/82, Platte River
Wilderness Area
Elk#1 HA#10
HA81/82, Platte River
Wilderness Area
Items 1 and 3 are from the same individual
I) Compilation of Species Origin Results
1
Lab
Species Source
Item 1
RR01
RR03-A
Odocoileus sp.
Odocoileus hemionus
RR03-B
RR03-C
RR03-D
RR03-E
RR03-F
RR03-G
RR05
RR06
RR08
Odocoileus hemionus
Odocoileus hemionus
Odocoileus hemionus
Deer, Genus Odocoileus
Odocoileus hemionus
Odocoileus hemionus
Mule Deer
Mule Deer
Odocoileus sp (White-tailed
Deer/ Mule Deer)
Mule Deer
Mule Deer
Mule Deer
(Odocoileus hemionus)
Odocoileus hemionus
Mule Deer
(Odocoileus hemionus)
Deer (Odocoileus sp.),
possibly Odocoileus
hemionus
White-tailed Deer
Odocoileus sp.
Mule Deer
RR09
RR10
RR11
RR12
RR13
RR14
RR15
RR16
RR17
Item 2
Item 3
Cervus elaphus
Cervus elaphus
Likely NA elk-but can’t
exclude Red Deer
(European)
Cervus elaphus
Elk (Cervus elaphus)
Cervus elaphus
Cervus elaphus
Cervus elaphus
Cervus elaphus
Elk
Elk
Cervus elaphus (Elk)
Odocoileus sp.
Odocoileus hemionus
Elk
Elk
Elk (Cervus elaphus)
Cervus elaphus
Elk (Cervus elaphus)
Elk (Cervus canadensis)
Elk
Inconclusive
Elk
Odocoileus hemionus
Odocoileus hemionus
Odocoileus hemionus
Deer, Genus Odocoileus
Odocoileus hemionus
Odocoileus hemionus
Mule Deer
Mule Deer
Odocoileus sp (White-tailed
Deer/ Mule Deer)
Mule Deer
Mule Deer
Mule Deer
(Odocoileus hemionus)
Odocoileus hemionus
Mule Deer
(Odocoileus hemionus)
Deer (Odocoileus sp.),
possibly Odocoileus
hemionus
White-tailed Deer
Odocoileus sp.
Mule Deer
2
Lab
RR01
RR03-A
Methods Used
Methods/ Genetic Marker(s)
RR14
DNA Sequence Analysis/ d-loop of mtDNA
STR Analysis/ Species character proximal to BM1225 allele range
Comparative Restriction Analysis/ RsaI restriction analysis of species characteristic sites in
mtDNA control region
STR Analysis/ Co-amplified fragment Cer-1FAM/BM4107
Comparative Restriction Analysis/ CRA portion of Cyt b & Dloop; Cut w/ (RsaI)
STR Analysis/ MD/WTD STR Analysis
Comparative Restriction Analysis/ CRA w/ RsaI
STR Analysis/ DNA020C-STR PCR, Coamplified BM4107/ Cervid 1-FAM product
Comparative Restriction Analysis/ PCR of portion of Cyt.B/ D-loop cut w/ RsaI
DNA Sequence Analysis
STR Analysis/ WTD/ MD STR Analysis
Comparative Restriction Analysis/ CRA w/ RSAT
Mass Spectrometry/ CRM-010 Hgb Analysis by MALDI
Immunodiffusion/ DID, Isoelectric Focusing/ SOD, EAP
Immunodiffusion/ Deer Antiserum/ Ouchterlony
Isoelectric Focusing/ PGI, Albumine, Esterase
DNA Sequence Analysis/ Cytochrome B - mtDNA
Immunodiffusion/ Deer
Isoelectric Focusing/ PGI, SOD, EAP
Counter Immunoelectrophoresis
Isoelectric Focusing/ Phosphoglucose Isomerase and Albumin
Immunodiffusion/ Ouchterlony Deer anti-sera
Isoelectric Focusing/ PGI (IEF3-9); EAP(IEF5-8)
DNA Sequence Analysis/ Cytochrome b
STR Analysis/ FCB193, BL42, BM4208, BM6438, CELJP15
Immunodiffusion/ Ouchterlony
Isozyme Analysis/ PGI, EAP
STR Analysis/ CDFG deer suite
DNA Sequence Analysis/ 12s rRNA
RR15
Comparative Restriction Analysis
RR16
DNA Sequence Analysis/ Cytochrome B
RR17
Comparative Restriction Analysis/ D-loop digest with RsaI, MspI, HhaI
RR03-B
RR03-C
RR03-D
RR03-E
RR03-F
RR03-G
RR05
RR06
RR08
RR09
RR10
RR11
RR12
RR13
II) Compilation of Gender Origin Results
1
Lab
RR01
RR03-A
RR03-B
RR03-C
RR03-D
RR03-E
RR03-F
RR03-G
RR05
RR06
RR08
RR09
RR10
RR11
RR12
RR13
RR14
RR15
RR16
RR17
Gender Origin
Item 1
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Item 2
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Item 3
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
Male
2
Lab
RR01
RR03-A
RR03-B
Methods Used
Methods/ Genetic Marker(s)
RR12
SRY and ZFX/Y amplimers
PCR amplification of ZFX/Y + SRY markers on X + Y chromosomes
PCR amplifications of portions of SRY locus (characteristic of male mammals), fragment
analysis by capillary electrophoresis
Gender Test ZFX/Y and TDF
PCR of a portion of the ZFX/ ZFY and SRY (TDF) genes linked to mammalian sex
chromosomes. Fragment analysis w/ capillary electrophoresis
Amplification of sex chromosome markers, visualized by polyacrylamide gel electrophoresis
PCR Amplification of a portion of ZFX/ ZFY & SRY genes and visualized via gel
electrophoresis
PCR Analysis to amplify portions of the ZFX/Y and SRY genes linked to X and Y
chromosomes
Amplifications with two primers sets: the first specific to the ZFX/ ZFY genes located on the Xand Y- chromosomes respectively (Fain and Lemay 1995) and the second pair targets the sry
gene located on the Y chromosome of mammals (Aasen and Medrano 1990, Wasser et al.1997)
STR analysis; ZFX, ZFY and SRY markers on PAGE
Amplification of the zinc finger protein of the X- chromosome and the testes determining factor
of the Y- chromosome (if present) using PCR
PCR amplification and analysis of ZFX and ZFY using PAGE, and SRY markers analysis using
ABI 310
Amplification with dye-labeled SRY primers and separation by capillary electrophoresis
RR13
PCR – based ZFX/ SRY gender typing
RR14
RR15
Zinc finger (X positive control)
Sex determining region Y- chromosome (SRY)
PCR for Zinc Finger (control) and Y chromosome (SRY)
RR16
PCR Method using ZFX/XFY and SRY genes
RR17
Polymerase Chain Reaction of zinc finger (ZFX) on X chromosome, sex determining region
(SRY) on Y chromosome
RR03-C
RR03-D
RR03-E
RR03-F
RR03-G
RR05
RR06
RR08
RR09
RR10
RR11
III) Compilation of Individual Identification Results
Lab
Individual typing is not
1) What could be the
2) Which samples have
RR01
RR03-A
RR03-B
RR03-C
RR03-D
RR03-E
RR03-F
RR03-G
RR05
RR06
RR08
RR09
RR10
RR11
RR12
RR13
RR14
RR15
RR16
RR17
performed on the
following species
identified in this
proficiency test
minimum number of
animals represented in
these 3 samples?
the same genetic profile?
Cervus elaphus
Cervus elaphus Item 2
Item 2
Item 2
Cervus elaphus Item 2
Elk
Item 2
Item 2 Elk
Item 2
Elk
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
Item 1 and Item 3
3
Lab
RR01
RR03-A
RR03-B
RR03-C
RR03-D
RR03-E
RR03-F
RR03-G
RR05
RR06
RR08
RR09
RR10
RR11
RR12
Methods Used
Methods/ Genetic Marker(s)
STR Analysis/ RT7, RT24, BM1225, D, N
STR Analysis/ Cervid 1, BM1225, BM4107, RT24, BM4208, T7, T159S, RT7
STR Analysis/ Cervid 1, BM4107, RT7, RT24, T159S, BM4208, T7
STR Analysis/ Cervid 1, BM1225, BM4107, RT24, BM4208, T7, T159S, RT7
STR Analysis/ DNA020C-Cer1, BM4107, RT7, RT24, BM4208, T7 and T159S
STR Analysis/ Cervid 1, BM1225, RT7, RT24, T159S, BM4208, T7, BM4107
STR Analysis/ BM4107, T7, ovirA, Rt30, Rt7, Rt5, BM1225, OheN, BM4208, OheQ
STR Analysis/ BM4107, BM4208, BM1225, Cerv 1, RT7, T7, T159S, RT24
STR Analysis/ Map2C, BM1225, IgF, RT24, RT9
STR Analysis/ CDFG’s suite of 8 nuclear loci:P,M,Q,D,N,K,R,O
STR Analysis/ RT5, RT13, INRA040, RT24, RT30, Cerv 1, ETH152, BM1225, BM4107 and
BM4208
STR Analysis/ Protocol DNA020C/ Cervid1, BM1225, BM4107, RT24, BM4208, T7, T159S,
RT7 and SRY
STR Analysis/ ADCYC, AGLA226, BL42, BM203, BM4107, BM4208, BM6438, BM6506,
CELB9, CELJP15, CERVID1, CERVID2, ETH152, FCB193, GNZ204, RM006, SRCRSP1,
TGLA94
RR13
STR Analysis/ CDFG suite of 8 deer STR loci
RR14
STR Analysis/ Cervid1, RT24, BM1225, BM4107, RT7, C89, T159, T7, Texan4, CRSP1,
RT5
RR15
STR Analysis/ P/D and N/Q (CA DNR primer sets)
RR16
RR17
STR Analysis/ BM4107, T7, OvirA, Rt30, Rt7, Rt5, BM1225, OheN, BM4208, OheQ
STR Analysis/ BM1225, BM4107, BM4208, CERV1, ETH152, INRA040, RT1, RT5, RT9,
RT13, RT24, RT30, T7