Using Science to Improve the BLM Wild Horse and Burro Program A Way Forward (2013) / Chapter Skim
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5 Genetic Diversity in Free-Ranging Horse and Burro Populations
5 Genetic Diversity in Free-Ranging Horse and Burro Populations
Pages 143-174
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From page 143... ...
. In small populations or populations that suffer size bottlenecks,1 allelic diversity is lost relatively quickly through random genetic drift, but heterozygosity is less affected.
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From page 144... ...
in c managed populations. Genetic diversity in a population results from a number of evolutionary forces: mutation, natural selection, gene flow, and genetic drift.
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From page 145... ...
In some herds, management actions have included removals that had unknown effects on the levels and distribution of genetic diversity. Isolation and small population size, in combination with the effects of genetic drift, may reduce genetic diversity to the point where herds suffer from the reduced fitness often associated with inbreeding.
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From page 146... ...
In addition to diseases related to genetic mutations, a species may demonstrate conditions or abnormalities and reduced fitness due to inbreeding. Some of the evidence on inbreeding depression or correlations between low genetic diversity and fitness traits in ungulates is reviewed below.
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From page 147... ...
correlated positively with heterozygosity at nine microsatellite loci. Finally, in a study of 12 species of ungulates maintained in zoos, Ballou and Ralls (1982)
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From page 148... ...
Recording the occurrence of phenotypic data associated with diseases and clinical issues along with information on the age and sex of the affected animals would allow BLM to monitor the distribution and prevalence of a number of genetic conditions that have direct effects on herd health. Genetics and Population Viability The maintenance of genetic diversity in a population is a function of the genetic effective population size (Ne; Wright, 1931, 1938)
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From page 149... ...
It was originally thought that an effective population size of at least 50 was necessary to avoid short-term inbreeding depression, but empirical work suggests that if maintenance of fitness is important, effective population sizes much larger than 50 are necessary. Theoretical studies suggest that the figure could be closer to 5,000 for several reasons.
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From page 150... ...
TABLE 5-1 Estimates of Genetic Diversity of Free-Ranging and Domestic Horses Observed Population Allelic Diversity Heterozygosity Fis Reference Sable Island 5.60 ± 1.35 SD 0.647 ± 0.035 SD 0.070 Lucas et al., 2009 Sorraia 3.32 ± 0.95 SD 0.450 ± 0.212 SD –0.061 to 0.018 Luis et al., 2007 Domestic breeds from 5.50 ± 0.42 SE to 0.66 ± 0.02 SE to –0.046 to 0.083 Plante et al., 2007 Canada and Spain 8.25 ± 0.57 SE 0.79 ± 0.04 SE Southern European 5.75 ± 1.54 SD to 0.687 ± 0.170 SD to Not estimated Solis et al., 2005 native horse breeds 8.08 ± 1.93 SD 0.772 ± 0.099 SD Domestic breeds (10 3.6 ± 0.3 SE to 0.494 ± 0.057 SE to Not estimated Vilà et al., 2001 breeds, 191 individuals) 4.5 ± 0.4 SE 0.626 ± 0.058 SE Colonial Spanish horse 4.00 ± 1.27 SD to 0.54 ± 0.18 SD to –0.069 to 0.058 Conant et al., 2012 populations (five)
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From page 151... ...
The management goal, as stated in the BLM's Wild Horses and Burros Management Handbook (BLM, 2010) , is to keep the observed heterozygosity (Ho)
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From page 152... ...
TABLE 5-2 Genetic Diversity in Free-Ranging Horses in Herd Management Areas Determined by Using 12 Microsatellite Loci 152 Year Herd Management Area State N Sampled AML Ho He Fis MNA Cothran Report Date -- Comments Cerbat Mountains AZ 90 Evidence of Spanish blood Cibola-Trigo AZ 24 2005 150 0.497 0.490 –0.014 4.17 04/15/08 Arizona mean value 0.497 0.490 –0.014 4.17 Bitner CA 21 2012 25 0.734 0.713 –0.029 5.92 05/15/12 Buckhorn CA 31 2010 85 0.806 0.749 –0.076 6.42 10/20/10 Carter Reservoir CA 60 2009 35 0.689 0.688 –0.001 6.33 10/04/10 Centennial CA 69 2001 168 0.665 0.709 0.062 6.92 11/19/01 Chicago Valley CA 12 Coppersmith CA 53 2009 75 0.708 0.703 –0.007 6.33 10/05/10 Fort Sage CA 29 Fox Hog CA 115 2012 220 0.717 0.730 0.018 7.42 05/18/12 High Rock Canyon CA 35 2012 120 0.774 0.773 –0.001 7.75 05/17/02 Massacre Lakes CA 35 New Ravendale CA 25 Nut Mountain CA 47 2011 55 0.770 0.752 –0.230 7.33 05/14/12 Piper Mountain CA 17 Red Rock Lakes CA 25 Round Mountain CA 10 Twin Peaks - Gilman CA 13 2011 758 0.724 0.764 0.052 6.67 04/28/11 Twin Peaks - S Observ CA 52 2011 758 0.710 0.754 0.058 7.67 04/28/11 Twin Peaks - Skedaddle/Dry Valley CA 28 2011 758 0.673 0.744 0.096 6.92 04/28/11 Wall Canyon CA 14 2012 25 0.708 0.709 0.001 6.00 05/23/12 California mean value 0.723 0.732 0.005 6.81
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From page 153... ...
Little Book Cliffs CO 29 2002 150 0.745 0.721 –0.034 6.25 05/28/03 Piceance-East Douglas Creek CO 32 2006 235 0.635 0.640 0.007 4.67 06/01/10 Sand Wash Basin CO 50 2001 362 0.730 0.723 –0.009 6.50 04/16/02 Spring Creek Basin CO 15 2007 65 0.689 0.702 0.018 5.08 06/21/10 Colorado mean value 0.700 0.696 –0.005 5.63 Black Mountain ID 25 2010 60 0.720 0.704 –0.023 6.42 03/03/11 Challis ID 46 2002 253 0.743 0.735 –0.010 6.42 09/15/03 Four Mile ID 25 2003 60 0.740 0.691 –0.071 5.75 06/14/04 Hard Trigger ID 30 2010 130 0.764 0.733 –0.042 6.50 03/01/11 Sand Basin ID 25 2003 64 0.782 0.726 –0.077 6.33 06/14/04 Saylor Creek ID 50 2010 50 0.767 0.748 –0.025 6.42 12/17/10 Idaho mean value 0.753 0.723 –0.041 6.31 Pryor Mountains MT 103 2009 120 0.757 0.762 0.007 6.58 09/02/10 Evidence of Spanish blood Montana mean value 0.757 0.762 0.007 6.58 Antelope NV 324 Antelope Valley NV 28 2011 259 0.765 0.756 –0.012 6.75 06/13/11 Augusta Mountains NV 29 2011 308 0.770 0.756 –0.018 6.58 04/26/11 Bald Mountain NV 97 2009 215 0.759 0.775 0.021 7.58 08/13/10 Black Rock East NV 31 2012 93 0.710 0.753 0.057 7.00 05/30/12 Black Rock West NV 19 2012 93 0.675 0.654 –0.032 5.67 05/30/12 Monitor closely and consider introducing two to four new mares Buffalo Hills NV 51 2009 314 0.724 0.729 0.008 7.00 08/05/10 Calico Mountains NV 40 2012 333 0.748 0.723 –0.035 6.92 05/24/12 Callaghan Austin Allot NV 40 2009 237 0.742 0.780 0.049 7.25 08/12/10 153 continued
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From page 154... ...
TABLE 5-2 Continued 154 Year Herd Management Area State N Sampled AML Ho He Fis MNA Cothran Report Date -- Comments Callaghan East Allot NV 40 2009 incl 0.765 0.791 0.033 7.75 08/11/10 Clan Alpine NV 979 Desatoya NV 25 2003 180 0.703 0.707 0.005 6.00 05/05/04 Diamond NV 151 Diamond Hills North NV 37 Diamond Hills South NV 22 Dogskin Mountains NV 15 Eagle NV 210 Fish Creek NV 23 2005 180 0.790 0.758 –0.042 7.00 06/03/08 Fish Lake Valley NV 54 Flanigan NV 125 Fort Sage NV 36 Fox Lake Range NV 204 Garfield Flat NV 125 Goshute NV 28 2011 123 0.765 0.748 –0.022 6.50 06/15/11 Granite Peak NV 18 Granite Range NV 40 2012 258 0.760 0.737 –0.032 7.08 05/24/12 Horse Mountain NV 95 Hot Creek NV 41 Jackson Mountains NV 217 Kamma Mountains NV 77 Lahontan NV 28 2004 10 0.595 0.687 0.133 5.50 07/01/04 Lava Beds NV 148 Little Fish Lake NV 40 2005 39 0.703 0.748 0.060 6.75 05/30/08
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From page 155... ...
Little Humbolt NV 23 2010 80 0.743 0.742 –0.001 6.58 12/09/10 Little Owyhee Fairbanks NV 10 2004 298 0.775 0.704 –0.101 5.42 02/29/08 Little Owyhee Lake Creek NV 10 2004 298 0.764 0.713 –0.072 5.67 02/29/08 Little Owyhee Twin Valley NV 10 2004 298 0.760 0.737 –0.031 5.83 02/29/08 Maverick-Medicine NV 276 Montezuma Peak NV 46 2010 4 0.737 0.707 –0.043 6.33 12/16/10 Montgomery Pass NV 100 Nevada Wild Horse Range NV 500 New Pass/Ravenswood NV 52 2007 566 0.780 0.771 –0.013 7.42 07/07/10 Nightingale Mountains NV 126 North Monitor NV 8 North Stillwater NV 50 2008 205 0.670 0.722 0.072 6.75 07/07/10 Owyhee NV 231 Palmetto NV 76 Pancake NV 493 Paymaster NV 49 2010 38 0.748 0.702 –0.066 5.83 12/10/10 High incidence of club foot Pilot Mountain NV 415 Pine Nut Mountains NV 26 2003 179 0.670 0.687 0.026 6.08 04/27/04 Red Rock (Bird Springs) NV 23 2006 27 0.786 0.743 –0.059 6.08 06/18/09 Reveille NV 51 2010 138 0.753 0.715 –0.054 6.50 12/17/10 Roberts Mountain NV 29 2008 150 0.730 0.740 0.013 6.42 07/15/10 Rock Creek NV 28 2010 250 0.738 0.745 0.010 6.00 12/17/10 Rocky Hills NV 64 2009 143 0.759 0.774 0.019 7.33 08/06/10 Sand Springs West NV 49 Saulsbury NV 25 2007 40 0.773 0.768 –0.007 6.83 06/17/10 Seven Mile NV 27 2005 0.756 0.748 –0.011 6.58 06/03/08 Seven Troughs NV 156 155 continued
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From page 156... ...
TABLE 5-2 Continued 156 Year Herd Management Area State N Sampled AML Ho He Fis MNA Cothran Report Date -- Comments Shawave Mountains NV 28 2003 73 0.783 0.762 –0.027 6.50 06/04/04 Silver King NV 128 Snowstorm Castle Ridge NV 10 2004 140 0.659 0.718 0.082 5.42 02/29/08 Snowstorm Dryhill NV 9 2004 140 0.750 0.616 –0.218 4.25 02/29/08 South Shoshone NV 52 2008 100 0.761 0.770 0.012 7.33 07/21/10 South Stillwater NV 42 2003 16 0.705 0.716 0.015 5.58 04/07/04 Spruce-Pequop NV 26 2011 82 0.750 0.709 –0.058 5.75 06/16/11 Stone Cabin NV 50 2007 364 0.763 0.775 0.015 7.67 06/16/10 Some incidence of club foot Tobin Range NV 42 Triple B NV 518 Warm Springs Canyon NV 28 2010 175 0.729 0.719 –0.014 7.17 11/04/10 Wassuk NV 165 Wheeler Pass NV 26 2007 66 0.756 0.763 0.008 7.08 06/16/10 Whistler Mountain NV 24 Nevada mean value 0.739 0.734 –0.008 6.49 Bordo Atravesado NM 27 2011 60 0.787 0.749 –0.051 6.08 04/25/11 Carracas Mesa NM 23 New Mexico mean value 0.787 0.749 –0.051 6.08 Beaty's Butte OR 32 2010 250 0.747 0.763 0.020 6.67 11/04/10 Cold Springs OR 24 2010 150 0.806 0.754 –0.068 6.00 11/11/10 Coyote Lake/Tule Springs OR 50 2011 390 0.792 0.766 –0.034 7.33 05/09/12 Hog Creek OR 14 2003 50 0.815 0.739 –0.103 6.00 05/13/04
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From page 157... ...
Jackies Butte OR 40 2011 150 0.750 0.742 –0.010 7.17 04/30/12 Kiger OR 40 2011 82 0.671 0.695 0.034 5.83 03/29/12 Morphologically unique Spanish blood not confirmed Liggett Table OR 17 2010 25 0.500 0.448 –0.115 2.58 11/12/10 Horse destroyed for unspecified defect Murderers Creek OR 71 2009 35 0.696 0.707 0.015 6.25 09/23/10 Paisley Desert No year 150 0.743 0.780 0.047 8.00 E.G. Cothran, Texas A&M University, email OR 83 communication, December 21, 2011 Palomino Buttes OR 64 Pokegama OR 50 Riddle Mountain OR 21 2011 56 0.679 0.657 –0.034 5.50 03/29/12 Sand Springs OR 15 2011 200 0.772 0.759 –0.017 6.67 05/08/12 Sheepshead/Heath Creek OR 48 2011 302 0.790 0.787 –0.004 7.25 05/09/12 South Steens OR 31 2010 304 0.758 0.741 –0.023 6.92 10/19/10 Stinkingwater OR 24 2010 80 0.726 0.680 –0.067 5.50 04/07/10 Three Fingers OR 50 2011 150 0.710 0.753 0.058 7.25 04/30/12 Warm Springs OR 83 2010 202 0.766 0.778 0.015 8.00 04/05/11 Oregon mean value 0.733 0.722 –0.018 6.43 Bible Spring UT 60 Cedar Mountain UT 20 2002 390 0.742 0.726 –0.021 6.08 09/23/03 Chloride Canyon UT 30 Low diversity and dwarfism per 2001 Blawn Wash HMA report Choke Cherry UT 30 Confusion UT 115 Conger UT 80 Four Mile UT 60 Frisco UT 60 157 continued
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From page 158... ...
TABLE 5-2 Continued 158 Year Herd Management Area State N Sampled AML Ho He Fis MNA Cothran Report Date -- Comments Kingtop UT 40 Mount Elinor UT 25 Muddy Creek UT 33 2001 125 0.619 0.638 0.029 5.33 01/03/02 North Hills UT 28 2002 36 0.807 0.710 –0.136 6.00 09/09/02 Onaqui Mountain UT 40 2005 210 0.298 0.282 –0.053 06/03/08 Values for blood groups Range Creek UT 26 No year 125 0.663 0.707 0.061 5.25 E.G. Cothran, Texas A&M University, email communication, December 21, 2011 Sulphur Herd N UT 53 2009 250 0.682 0.732 0.067 6.33 07/29/10 Evidence of Spanish blood Sulphur Herd S UT 41 2009 250 0.679 0.715 0.050 5.83 07/29/10 Evidence of Spanish blood Swasey UT 100 Tilly Creek UT 25 2002 50 0.609 0.617 0.013 5.08 04/29/03 Utah mean value 0.637 0.641 0.001 5.70 Adobe Town WY 103 2010 800 0.776 0.776 0.000 7.75 04/21/11 Antelope Hills WY 25 2004 82 0.747 0.733 –0.018 6.33 03/05/08 Conant Creek WY 22 2004 100 0.680 0.656 –0.035 5.50 03/06/08 Crooks Mountain WY 85 Dishpan Butte WY 30 2004 100 0.768 0.743 –0.034 6.33 03/06/08 Divide Basin WY 60 2011 600 0.785 0.787 0.003 7.75 05/15/12 Fifteenmile WY 160 Green Mountain WY 300 Little Colorado WY 45 2011 100 0.761 0.768 0.009 6.67 05/07/12 Lost Creek WY 30 2009 82 0.775 0.788 0.017 6.67 10/14/10 McCullough Peaks WY 50 2004 140 0.755 0.715 –0.055 6.33 07/06/06
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From page 159... ...
N = number of animals sampled, AML = appropriate management level, Ho = observed heterozygosity, He = expected heterozygosity under Hardy-Weinberg equilibrium, Fis = inbreeding coefficient, MNA = mean number of alleles per individual. For Herd Management Areas listed without genetic data, neither data nor reports were provided to the committee for review.
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From page 160... ...
All but one of the reports on burros provided to the committee involved samples collected during 2001-2005. Optimal Genetic Diversity in Herd Management Areas Although the BLM Wild Horses and Burros Management Handbook (2010)
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From page 161... ...
To maintain the free-ranging horse and burro HMAs at the prescribed AMLs with the genetic diversity needed for long-term genetic health, continued monitoring and active management will be required. MANAGEMENT ACTIONS TO ACHIEVE OPTIMAL GENETIC DIVERSITY The goal of genetic management is to maintain as much as possible of the standing genetic diversity of a population and thereby provide the raw material needed to respond to environmental changes.
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From page 162... ...
AZ 25 2004 478 0.551 0.553 0.003 4.111 10/30/08 Cibola-Trigo 2 AZ 28 2004 285 0.453 0.506 0.104 4.000 11/06/08 Havasu AZ 19 2004 166 0.487 0.498 0.021 3.889 11/06/08 Lake Pleasant AZ 208 Arizona mean value 0.495 0.517 0.042 3.917 Chemehuevi CA 52 2003 121 0.354 0.427 0.171 3.222 07/15/03 Chocolate Mule CA 55 2002 133 0.298 0.394 0.243 3.444 01/24/03 Lee Flats CA 2 No year 15 0.278 0.278 0.000 1.778 E.G. Cothran, Texas A&M University, email communication, December 21, 2011 Twin Peaks CA 39 2011 116 0.487 0.526 0.075 3.444 10/5/12 Waucoba-Hunter Mountain CA 11 California mean value 0.354 0.406 0.122 2.972 Blue Wing NV 28 2003 28 0.252 0.268 0.059 2.556 08/03/04 Bullfrog NV 49 No year 91 0.492 0.502 0.199 3.889 E.G.
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From page 163... ...
Cothran, Texas A&M University, email communication, December 21, 2011 Comparison with Cothran reports: Mean domestic burros 4 0.450 0.550 0.153 4.143 Standard deviation 0.094 0.120 0.195 1.386 Mean burro HMAs 12 0.408 0.441 0.093 3.333 Standard deviation 0.107 0.096 0.105 0.677 NOTE: Gray shading indicates observed heterozygosity or MNA values below the mean minus one standard deviation. N = number of animals sampled, AML = appropriate management level, Ho = observed heterozygosity, He = expected heterozygosity under Hardy-Weinberg equilibrium, Fis = inbreeding coefficient, MNA = mean number of alleles per individual.
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From page 164... ...
Second, any movement of the sex ratio of breeders from 1:1 will also decrease effective population size. That effect can be subtle in polygynous species, such as horses and burros, inasmuch as the number of breeding males is usually less than the number of breeding females.
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From page 165... ...
. Selection of Animals for Translocation As early as the 1930s, it was established that inbreeding depression in small, isolated populations could lead to loss of fitness and increased risk of extinction (Wright, 1931)
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From page 166... ...
extended the analyses by modeling variation in population fluctuation and suggested that more than 20 immigrants per generation may be necessary if high population fluctuation leads to drastically reduced effective population size. In addition to the number of animals to translocate, the interval for doing so must be determined.
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From page 167... ...
In most cases, pedigree information on free-ranging horse and burro populations will not be available, so absolute genetic relationships among individual animals will be unknown. The use of genetic information, however, will make it possible to choose individual animals that have moderate levels of differentiation from the target population.
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From page 168... ...
Thus, there would be fewer challenges in integrating new females into a burro population, so females would be the first choice for translocation of animals for genetic restoration of burro populations. Males would also be viable candidates for genetic restoration, but introduced males would have to compete with resident males for access to breeding females.
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From page 169... ...
The BLM Wild Horses and Burros Management Handbook does not clearly state which HMAs should be monitored and how often studies should be repeated. The committee recommends routine monitoring at all gathers and collection and analysis of a sufficient number of samples to detect losses of diversity.
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From page 170... ...
New laboratory and data-analysis tools promise to reduce costs while providing more powerful methods for monitoring genetic diversity and resolving breed relationships. The 12 nuclear microsatellite loci that are currently used for estimating genetic diversity and genetic differentiation among herds were chosen largely from those approved by the International Society of Animal Genetics for their informativeness in equine genotyping.
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From page 171... ...
1986. Wild Horses of the Great Basin: Social Competition and Population Size.
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From page 172... ...
1996. Inbreeding depression in an isolated population of adders (Vipera berus)
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From page 173... ...
1991. Wild Horse Populations: Field Studies in Genetics and Fertility.
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From page 174... ...
2000. Inbreeding depression influ ences lifetime breeding success in a wild population of red deer (Cervas elaphus)
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