Genetic Testing of Feral Horses - American Wild Horse Preservation

Report
E. Gus Cothran
Dept. Veterinary Integrated Biosciences
College of Veterinary Medicine and Biomedical
Science
Texas A&M University
 Testing began in early 1990s.
 Usually at the request of an individual from a specific
HMA or a private individual.
 Used blood group and biochemical polymorphisms.
 This required taking two blood samples from every
horse.
 Information supplied by the BLM ranged from none to
herd management plans. Usually just a form like the
following.
 17 loci were routinely tested.
 Sample sizes varied but were usually between 25 to 75
animals.
 Standard measures of genetic variability were
calculated for each herd.
 The values were compared to those of domestic horse
breeds and to other feral herds.
Genetic variability measures.
15 Mile Herd 2000
15 Mile Herd 1991
White Mountain
McCullough Peaks
Green Mountain
Muskrat Basin
N
29
47
40
41
40
38
Ho
0.431
0.379
0.340
0.405
0.380
0.374
He
0.416
0.365
0.368
0.431
0.339
0.352
Fis
-0.037
-0.038
0.077
0.060
-0.120
-0.061
Ae
2.128
1.847
2.249
2.205
1.883
1.876
TNV
33
34
37
34
27
30
Thoroughbred
Arabian
Andalusian
Shetland Pony
Welsh Pony
American Saddlebred
Peruvian Paso
Belgian Draft
265
117
140
50
42
259
141
82
0.294
0.307
0.348
0.368
0.388
0.404
0.451
0.427
0.288
0.327
0.362
0.407
0.387
0.409
0.445
0.415
-0.019
0.061
0.039
0.095
-0.002
0.013
-0.014
-0.028
1.780
1.846
1.993
2.210
2.127
2.354
2.506
2.279
34
38
44
38
47
54
46
35
Feral Horse Mean
Standard Deviation
Domestic Horse Mean
Standard Deviation
54
0.360
0.051
0.371
0.049
0.351
0.053
0.365
0.043
-0.035
0.118
-0.014
0.065
1.913
0.246
2.076
0.240
30.0
6.72
36.4
7.37
118
 Genetic similarity and distance measures also are
calculated.
 These are compared to the major domestic breed
groups.
 Depending upon the State comparisons to other herds
from the area or State may be done.
 Dendrograms are given showing similarity to domestic
breeds or other feral herds from the state.
Rogers’ genetic similarity of the McCullough Peaks feral horse herd to major groups of domestic horses.
Mean S
Std
Minimum
Maximum
Light Racing and Riding Breeds
0.792
0.024
0.744
0.822
Oriental and Arabian Breeds
0.800
0.023
0.765
0.844
Old World Iberian Breeds
0.797
0.024
0.775
0.816
New World Iberian Breeds
0.805
0.023
0.754
0.833
North American Gaited Breeds
0.808
0.023
0.771
0.835
Heavy Draft Breeds
0.813
0.021
0.751
0.867
True Pony Breeds
0.785
0.025
0.743
0.845
-
+--MORGAN HORSE
+----|
|
|
+----STANDARDBRED PACER
|
+------|
+--|
+------STANDARDBRED TROTTER
| |
| |
+----AMERICAN SADDLEBRED
| | +---|
| +--|
+-------ROCKY MOUNTAIN HORSE
|
|
|
+-------TENNESSEE WALKER
|
+--|
+--QUARTER HORSE
| |
|
| | +--| +----HANOVARIAN
| | | | |
| | | | |
+--------TRAKEHNER
| | | +--| +--|
| | |
| | | +-----------HOLSTEIN
| | |
| | +--|
| | |
+--|
| +-----THOROUGHBRED
| +--|
|
+--|
|
|
|
+----WIELKOPOLSKI
+--|
|
|
| |
|
+-------SELLA FRANCAIS
| |
|
| |
|
+-----KHUZESTAN ARABIAN
| |
|
+--|
| |
|
| | +ARABIAN
| |
+---| +--|
| |
|
+---------SHAGYA ARABIAN
--| |
|
| |
+----------KURD
| |
| | +---------------AKHAL TEKE
| +--|
|
| +-----------CASPIAN PONY
|
+--|
|
+-----TURKOMAN
|
+---------MCCULLOUGH PEAKS
SIMILARITY
.76
.80
.84
.88
.92
.96
1.00
----+----+----+----+----+----+----+----+----+----+----+---+
+-------------------------- Stewart Creek
+-----|
|
+-------------------------- Eagles Nest
+----|
|
|
+----------------------- Cooper Creek
+-|
+--------|
| |
+----------------------- Green Mountain
+--------| |
|
| +------------------------------------- White Mountain
+--|
|
| |
+--------------------------------------- Happy Creek Springs
+-| |
| | +------------------------------------------------ 15 Mile Herd
+-| |
| | +--------------------------------------------------- Cedar Ridge Trap
| |
+| +----------------------------------------------------- Tilley Creek
||
||
+-------------------------- McCullough Peaks
||
+-|
+|+--------------------------| +-------------------------- Whistle Creek
||
|
||
+---------------------------- Dry Creek
||
|+-------------------------------------------------------- Cold Springs Trap
|
+--------------------------------------------------------- Muskrat Basin
----+----+----+----+----+----+----+----+----+----+----+---+
.76
.80
.84
.88
.92
.96
1.00
 All genetic testing is now done by DNA microsatellite
loci.
 DNA testing allows the use of pulled mane or tail hairs
as samples.
 DNA results are analyzed in essentially the same way
as blood protein data.
N
29
Ho
0.77
He
0.756
Fis
-0.018
Ae TNV MNA
4.28
79
6.58
Ra
16
%Ra
0.202
Cleveland Bay
American Saddlebred
Andalusian
Arabian
Exmoor Pony
Friesian
Irish Draught
Morgan Horse
Suffolk Punch
Tennessee Walker
Thoroughbred
47
576
52
47
98
304
135
64
57
60
1195
0.610
0.740
0.722
0.660
0.535
0.545
0.802
0.715
0.683
0.666
0.734
0.627
0.745
0.753
0.727
0.627
0.539
0.799
0.746
0.711
0.693
0.726
0.027
0.007
0.041
0.092
0.146
-0.011
-0.003
0.041
0.038
0.038
-0.011
2.93
4.25
4.26
3.81
2.87
2.56
5.19
4.19
3.88
3.66
3.92
59
102
79
86
66
70
102
92
71
87
69
4.92
8.50
6.58
7.17
5.50
5.83
8.50
7.67
5.92
7.25
5.75
16
42
21
30
21
28
28
33
13
34
18
0.271
0.412
0.266
0.349
0.318
0.400
0.275
0.359
0.183
0.391
0.261
Feral Horse Mean
Standard Deviation
Minimum
Maximum
Domestic Horse Mean
Standard Deviation
Minimum
Maximum
126
0.716
0.056
0.496
0.815
0.710
0.078
0.347
0.822
0.710
0.059
0.489
0.798
0.720
0.071
0.394
0.799
-0.012
0.071
-0.284
0.133
0.012
0.086
-0.312
0.211
3.87
0.66
2.15
5.25
4.01
0.74
1.78
5.30
72.68
13.02
37
96
80.88
16.79
26
119
6.06
1.09
3.08
8.00
6.74
1.40
2.17
9.92
17
7.98
0
33
23.8
10.1
0
55
0.222
0.088
0
0.400
0.283
0.082
0
0.462
Augusta Mountains NV
80
SELLE FRANCAIS
THOROUGHBRED
HOLSTEIN
HANOVARIAN
TRAKEHNER
QUARTER HORSE
MORGAN HORSE
STANDARDBRED
MOUNTAIN PLEASURE HORSE
ROCKY MOUNTAIN HORSE
AMERICAN SADDLEBRED
AUGUSTA MOUNTAIN
TENNESSEE WALKER
ARGENTINE CRIOLLO
BRAZILIAN CRIOLLO
CHILEAN CRIOLLO
VENEZUELAN CRIOLLO
CAMPOLINO
MANGALARGA MARCHADOR
PANTANEIRO
PUERTO RICAN PASO FINO
PERUVIAN PASO
COLOMBIAN PASO FINO
GARANNO
ARABIAN
KURD
TURKOMAN
CASPIAN PONY
ANDALUSIAN
AKHAL TEKE
LUSITANO
DALES PONY
FELL PONY
SHIRE
NEW FOREST PONY
HAFLINGER
PERCHERON
SUFFOLK PUNCH
ICELANDIC
NORWEGIAN
SHETLAND PONY
AMERICAN CREAM DRAFT
EXMOOR PONY
POLISH PRIMITIVE
SIMILARITY
.60
.64
.68
.72
.76
.80
.84
.88
.92
.96
1.00
+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+
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CALLAGHAN austin
HALL CREEK
CALLAGHAN east
GRASS VALLEY
BALD MOUNTAIN
RODEO CREEK
STONE CABIN
NELLIS
NEW PASS/RAVENSWOOD
SAULSBURY
BEATYS BUTTE OR
MILLER MTN SWC
SOUTH SHOSONE
SAND SPRINGS EAST
ROCKY HILLS
SHAWAVE MOUNTAINS
AUGUSTA MOUNTAINS
MARVEL GAP SWC
ROBERTS MOUNTAIN
VIRGINIA RANGE
FISH CREEK
LITTLE OWYHEE TWIN
GRANITE RANGE2
GRANITE RANGE1
SILVER PEAK
REVEILLE
BLACK ROCK WEST
BLACK ROCK EAST
WARM SPRINGS CANYON
CHIMNEY CREEK
JOHNNIE
WHEELER PASS
RED ROCKS
DOLLY VARDEN
ANTELOPE VALLEY
SPRUCE PEQUOP
GOSHUTE
LITTLE OWYHEE FAIRB
LITTLE OWYHEE LAKE
LITTLE FISH LAKE
SEVEN MILE
CALICO MOUNTAINS
CATNIP HERD
SNOW STORMS CASTLE
LITTLE HUMBOLT
BUFFALO HILLS
PAYMASTER
MONTEZUMA PEAK
STILLWATER
LAHANTON RESERVOIR
ROCK CREEK
PINENUT MOUNTAIN
DESATOYA MOUNTAIN
JAKES WASH
SNOW STORMS DRYHILL
+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+
.60
.64
.68
.72
.76
.80
.84
.88
.92
.96
1.00
 DNA loci give somewhat higher variability measures so
are not directly comparable to protein loci.
 Rank levels of variation are similar.
 Allelic measures of diversity are more important for
mSat loci.
 Overall DNA gives data that is as useful for population
genetic analysis as blood typing.
 Over 100 population analyses were made using blood
protein loci.
 Some herds were tested more than one time.
 DNA testing was done on some herds analyzed using
blood proteins during transitional period for lab.
 Have DNA data for ~180 herds, again, some tested
more than once.
 Burro testing is very similar to that for horses. The
same mSat loci are used although not all work for
burros.
 Only have four domestic breeds to compare to.
 Most burro herds show very low variability.
Genetic variation measures.
Population
Ho
He
Fis
Ae
TNV
Ar
Butte Valley
.422
.496
.148
2.369
31
.22
Panamints
.446
.465
.041
2.380
28
.27
Salin Valley
.479
.518
.074
2.504
34
.23
Poitou Donkey
.533
.515
-.036
2.501
42
37
Mammouth Jack
.585
0602
.028
2.602
35
.37
Miniature Donkey
.562
.623
.099
3.483
57
.40
Standard Donkey
.539
.565
.046
2.900
40.6
.30
Domestic Mean
.539
3565
.046
2.900
40.6
.30
Feral Mean
.397
.445
.104
2.198
30.7
.20
********************************* Poitou
*
*
*********************** Pannaments CA
* ****
**** * *********************** Butte Valley CA
* * *****
* * * * *********************** Saline Valley CA
* * * ****
* ****
*
*************** Slate Range CA
* * *********
********* *
*************** Centennial Ca
*
* *
*
* ****************************** Clark Mtn. CA
*
*
*
*
*********** Picacho CA
*
*
****************
*
*
*
*********** Chocolate Mule CA
*
***********
***
* *********************** Sinbad UT
**
****
**
*********************** Yuma 1 AZ
**
**
********************** Minniature
**
********
***** *
*****
********************** Standard
* **
* *
* * ************ ***************************** Ossabaw GA
* *
*
* *
********************************* Cibola/Trigo 1 AZ
****************************** *
*
* *
********************************* Mammoth Jack
*
* **************
*
*
********************************* Sardinian
**********
*
*
*
*
***************************** Chemehuevi CA
*
*
**********************
***
*
***************************** Park Moab CA
**
*
**
******************************************************************************* Blue Wing NV
** *
** **************************************************************************************** Wikieup AZ
**
************************************************************************************************ Kingman AZ
* *
* *
********************************************************************************** Seven Tanks NV
** **********
**
********************************************************************************** East Mohave CA
****
* ************************************************************************************************* Ed's Camp Az
*** *
* * ************************************************************************************************* Yuma 2 AZ
**
* *************************************************************************************************** Havasu AZ
*
***************************************************************************************************** Cibola/Trigo 2 AZ
 The majority of herds have moderate to high genetic
variability.
 This is probably due to the mixed origins of the herds.
 About 18% of herds have variation levels that are low
enough to be of concern. Most of these are just below
that level.
 Only about 3% have exceptionally low variation.
 Variation is usually correlated with population size.
 Sometimes variation is high is small populations but
this is due to recent reductions.
 Most herds have not shown changes in variation levels
between two or more sampling periods. This is
probably due to not enough time having elapsed for a
change to take place.
 No large changes in variation level have been seen in
any BLM herd to this point.

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