Journal of Heredity 2007:98(6):594–602
doi:10.1093/jhered/esm064
Advance Access publication September 13, 2007
Published by Oxford University Press 2007.
Genetic Diversity in a Feral Horse
Population from Sable Island, Canada
YVES PLANTE, JOSE LUIS VEGA-PLA, ZOE LUCAS, DAVE COLLING, BRIGITTE
FIONA BUCHANAN
DE
MARCH,
AND
From the Agriculture and Agri-Food Canada, Canadian Animal Genetic Resource Program, Room 6D62, College of
Agriculture and Bioresources, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada (Plante); the Laboratorio de Genética
Molecular, FESCCR, Apartado Oficial Sucursal 2, Cordoba 14071, Spain (Vega-Pla); the Sable Island Green Horse Society,
PO Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada (Lucas); the Research and Innovation Branch, Ontario Ministry of
Agriculture and Food, Guelph, ON N1G 4Y2, Canada (Colling); 467 Churchill Drive, Winnipeg, MB R3L 1W3, Canada
(March); and the Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
(Buchanan and Plante).
Address correspondence to Y. Plante at the address above, or e-mail: [email protected].
Abstract
The present-day Sable Island horse population, inhabiting an island off the eastern coast of Canada, is believed to have
originated mainly from horses confiscated from the early French settlers in Nova Scotia in the latter half of the 18th century.
In 1960, the Sable Island horses were given legal protected status and no human interference has since been allowed. The
objective of this study was to characterize the current genetic diversity in Sable Island horses in comparison to 15 other
horse breeds commonly found in Canada and 5 Spanish breeds. A total of 145 alleles from 12 microsatellite loci were
detected in 1093 horses and 40 donkeys. The average number of alleles per locus ranged from 4.67 in the Sable Island horse
population to 8.25 in Appaloosas, whereas the mean observed heterozygosity ranged from 0.626 in the Sable Island
population to 0.787 in Asturcons. Various genetic distance estimates and clustering methods did not permit to support that
the Sable Island horses originated from shipwrecked Spanish horses, according to a popular anecdote, but closely resemble
light draft and multipurpose breeds commonly found in eastern Canada. Based on the Weitzman approach, the loss of the
Sable Island horse population to the overall diversity in Canada is comparable or higher than any other horse breed. The Sable
Island horse population has diverged enough from other breeds to deserve special attention by conservation interest groups.
The Sable Island horses are an isolated and protected
population living on a sand bar located approximately 200
km off the east coast of Nova Scotia, Canada (Figure 1). The
island is 42 km in length, with a maximum width of less than
1.5 km, with a total surface area of approximately 3400 ha
(Catling et al. 1985). The present-day population is believed
to descend from horses confiscated from the French settlers
and placed on Sable Island after the Acadian Expulsion
of 1755 (Christie 1995). The horses were left largely
unattended until 1801 when the first permanent life-saving
station was established on the island. From 1801 to 1940,
various breeding mares and stallions, likely Thoroughbred,
Morgan, and Clydesdale, were introduced to the island and
selected progeny were brought back to the mainland for sale
(Christie 1995). Although popular accounts often suggest
that the Sable Island population is descended from shipwrecked Spanish horses in the 1700s, this is not supported by
historical research (Campbell 1974; Christie 1995).
594
In 1960, the horses of Sable Island were given legal
protected status in the Sable Island Regulations of the
Canada Shipping Act. Since then the horses have been
protected from human interference. All observation and
research activities are noninvasive, and no veterinary care or
supplementary feed is provided.
Long-term studies have been underway since the mid1980s, and life history has been recorded for most horses.
The population generally ranges between 250 and 400
horses with severe weather and harsh winters being
significant mortality factors (Lucas et al. 1991). The horses
live in breeding groups of 2–10 males and females of varying
ages and in all-male groups comprised mostly of immature
individuals. Whereas the home ranges of family bands tend
to be well defined, those of all-male groups are variable.
With a generation interval of approximately 4 years, the
Sable Island horse population has been isolated from
possible introgression for about 11–12 generations. The
Plante et al. Genetic Diversity in Sable Island Horses
Figure 1. Geographic location of the Sable Island off the coast of Nova Scotia, Canada. Representatives of the Sable Island
horse population (inset).
current genetic structure of the Sable Island horse population
is likely the result of natural selection and genetic drift. As
with any other minor horse breeds with declining registrations in Canada, the Sable Island population could be facing
genetic erosion. Although not recognized as a horse breed
under the Canadian Animal Pedigree Act, the Sable Island
horse may represent a valuable genetic resource. Within the
context of horse population and breed conservation, genetic
characterization is the first step in developing proper
management strategies. Microsatellite markers are widely
used to estimate genetic diversity within and among horse
breeds (Aberle et al. 2004; Glowatzki-Mullis et al. 2005; Solis
et al. 2005), and large databases of genotypes for most
Canadian horse breeds are available. Microsatellites are also
particularly well suited for the estimation of genetic structure
(Pritchard et al. 2000), differentiation among populations
(Corander et al. 2003), and individual assignments to
predefined groups or clusters (Paetkau et al. 2004).
In this study, we estimated the genetic diversity and
divergence in Sable Island horses in relation to other isolated
breeds, draft and multipurpose breeds, and Spanish breeds.
We applied 3 different approaches to describe the distribution
of genetic diversity and to estimate the relative contribution of
each breed to the overall genetic variability in Canadian horses.
Material and Methods
Breed and Sampling
For the Sable Island population (Figure 1), 57 samples were
selected from a bank of frozen tissues collected from horses
that died of natural causes between 1987 and 2000. Those
selected were young animals that died before producing
offspring and were considered to be the least related.
Because it was possible to ensure that none of the sampled
horses shared a mother and to reduce the chance of shared
paternity, individuals were selected spatially; in addition to
this, they were also selected temporally, horses born before
1989 or after 1993. In total, 1093 individuals representing 15
horse breeds found in Canada: Appaloosa, Arabian, Belgian,
Canadian, Fjord, Hackney, Hannoverian, Icelandic, Morgan,
Newfoundland, Peruvian, Percheron, Saddlebred, Thoroughbred, Standardbred, and the Sable Island population;
along with 5 Spanish breeds: Asturcon, Malloquin, Menorquin, Pottok, and Andalusian were analyzed (Table 1). An
additional 40 donkeys were also included for comparison
and as an outgroup for phylogenetic purposes.
Microsatellite Typing
Twelve fluorescently labeled microsatellites were genotyped
in the horse breeds, the donkey, and the Sable Island
population: ASB2, ASB23 (Breen et al. 1997), AHT4, AHT5
(Binns et al. 1995), HTG4, HTG7, HTG10 (Marklund et al.
1994), HMS3, HMS6, HMS7 (Guerin et al. 1994), LEX33
(Coogle et al. 1996), and VHL20 (Van Haeringen et al.
1994). Microsatellite alleles were amplified in different
multiplexes by the polymerase chain reaction (PCR). All
microsatellite allele sizes were adjusted to the reference
samples provided by the International Society for Animal
Genetics. Estimated allele sizes in nucleotides were used
throughout this study.
595
Journal of Heredity 2007:98(6)
Table 1. Estimates of average and effective number of alleles per locus, and heterozygosity in horse breeds from Canada and Spain,
including the Sable Island horse population and the donkey. Identified breed-specific alleles (excluding the donkey)
Heterozygosity
Breeds
N
Average
number of
alleles per
locus, NA (SE)
Appaloosa (AP)
Arabian (AR)
Belgian (BE)
Canadian (CN)
Fjord (FJ)
Hackney (HA)
Hannoverian (HN)
Icelandic (IC)
Morgan (MO)
Newfoundland (NE)
Peruvian (PE)
Percheron (PH)
Saddlebred (SA)
Sable Island (SI)
Thoroughbred (TH)
Standardbred (ST)
Asturcon (AST)
Mallorquin (MAL)
Menorquin (MEN)
Pottok (POT)
Andalusian (AND)
Donkey (DO)
56
50
37
57
59
49
48
53
54
54
55
41
60
57
50
59
45
44
52
45
68
40
8.25
6.41
6.92
6.83
6.17
7.17
7.00
6.75
7.92
8.00
6.83
7.92
7.08
4.67
5.50
6.33
7.08
7.17
7.08
8.08
7.42
5.17
(0.57)
(0.29)
(0.53)
(0.41)
(0.44)
(0.44)
(0.49)
(0.49)
(0.47)
(0.70)
(0.32)
(0.47)
(0.50)
(0.51)
(0.42)
(0.36)
(0.66)
(0.44)
(0.34)
(0.54)
(0.48)
(0.65)
Effective
number of
alleles per
locus, NE (SE)
Observed
(SE)
Expected
(SE)
4.70
3.57
4.24
3.99
3.55
3.67
4.44
4.03
4.23
5.11
3.95
4.45
4.14
3.21
3.87
3.69
4.19
4.12
3.94
4.98
4.06
2.88
0.78
0.66
0.70
0.76
0.71
0.71
0.77
0.72
0.76
0.75
0.74
0.78
0.73
0.63
0.75
0.71
0.79
0.78
0.75
0.78
0.74
0.55
0.78
0.72
0.75
0.73
0.70
0.72
0.77
0.74
0.76
0.78
0.73
0.78
0.75
0.65
0.73
0.73
0.74
0.74
0.74
0.78
0.75
0.59
(0.33)
(0.33)
(0.38)
(0.38)
(0.26)
(0.25)
(0.29)
(0.27)
(0.31)
(0.59)
(0.29)
(0.27)
(0.30)
(0.36)
(0.28)
(0.21)
(0.37)
(0.35)
(0.26)
(0.47)
(0.25)
(0.38)
Statistical Analysis
The average (NA) and effective (NE) number of alleles, allele
frequency per locus, observed (HO) and expected (HE)
heterozygosity, fixation index (FIT, FST), detection of breedspecific alleles, and the analysis of molecular variance
(AMOVA) were estimated using the GENEALEX 6
program (Peakall and Smouse 2006). The test for deviation
from Hardy–Weinberg equilibrium was performed with the
software Arlequin version 3.01 (Excoffier et al. 2005).
Genetic divergence among the horse breeds and the
Sable Island population was estimated from the actual
genotypes and allele frequencies. Different model-specific
distance estimators can be used for microsatellite data, and
the natural logarithm of the proportion of shared alleles
(POSA) (Bowcock et al. 1994) was calculated using the
Microsatellite Analyzer (Dieringer and Schlötterer 2002),
whereas the Reynold’s distances (Reynolds et al. 1983) were
estimated using the PHYLIP 3.66 package (Felsenstein
1989–2006). Finally, the Kullback–Leibler (KL) divergence
matrix (Corander et al. 2003) between identified clusters was
estimated with the Bayesian Analysis of Population Structure
software (BAPS) (Corander et al. 2004). The neighbor-joining
(NJ) method (Saitou and Nei 1987), as implemented in
PHYLIP 3.66, was used to build the phylogenetic trees from
the distance matrices, and the results were visualized using
Splitstree 4.0 (Huson and Bryant 2006).
Possible admixture between the Sable Island population
and the other horse breeds was estimated with the factorial
596
Breed-specific alleles
(0.02)
(0.02)
(0.03)
(0.03)
(0.04)
(0.03)
(0.02)
(0.02)
(0.03)
(0.03)
(0.03)
(0.02)
(0.03)
(0.03)
(0.03)
(0.03)
(0.04)
(0.03)
(0.02)
(0.03)
(0.03)
(0.06)
(0.02)
(0.02)
(0.02)
(0.03)
(0.03)
(0.02)
(0.02)
(0.02)
(0.02)
(0.03)
(0.03)
(0.01)
(0.02)
(0.04)
(0.02)
(0.02)
(0.03)
(0.02)
(0.02)
(0.03)
(0.02)
(0.06)
FIS
0.001
0.083
0.065
0.034
0.011
0.017
0.007
0.026
0.001
0.033
0.009
0.009
0.029
0.043
0.023
0.023
0.058
0.046
0.018
0.007
0.010
0.061
Breed
Locus
Allele
Frequency
AR
FJ
FJ
HA
IC
NE
TH
ST
AST
MAL
MEN
HMS3
HTG10
AHT4
HTG10
ASB2
ASB17
ASB23
HMS6
HMS3
HMS7
ASB23
158
95
168
117
224
123
192
139
154
171
213
0.030
0.051
0.059
0.010
0.009
0.009
0.010
0.008
0.011
0.011
0.048
correspondence analysis implemented in GENETIX version 4.05.2 (Belkhir et al. 2004). This method is not sensitive
to the different mutation models for microsatellite markers.
Marker genotypes were also used to cluster individuals into
predefined populations and to inferred clusters with the
Bayesian approach implemented in STRUCTURE 2.1
(Pritchard et al. 2000) with 5 independent replicates each
using a burn-in period of 100 000 and 1 000 000 iterations.
The above approach was used to model 2–25 inferred
clusters. Similarly, BAPS was also used to estimate the
number of clusters under an admixture model. Individual
assignment to predefined populations was tested using the
Monte Carlo resampling approach (Paetkau et al. 2004)
implemented in GENECLASS 2 (Piry et al. 2004).
The final step in partitioning genetic diversity followed
the Weitzman’s (1993) diversity function with the 3 different
matrices of genetic distances computed above. The
Reynold’s and POSA distances used 22 predefined groups,
identified as breeds, and the KL allelic divergence relied on
20 inferred clusters. The distance matrices were used as
input for the WEITZPRO software (Derban et al. 2002).
Results
Microsatellite Loci
A total of 145 different alleles were detected in the horses
assayed at 12 microsatellites. Estimates of the mean
and expected number of alleles, observed and expected
Plante et al. Genetic Diversity in Sable Island Horses
heterozygosities, FIS, and breed-specific alleles are presented
in Table 1. The Sable Island population had the lowest
diversity (0.63), the smallest number of observed (4.67) and
expected (3.21) number of alleles, and a significant heterozygotes deficiency (P 5 0.0413).
The AMOVA indicated that 17% of the variation
originated among the horse breeds, whereas 83% of the
observed variation was coming from within the breeds
(UPT 5 0.174, P 5 0.010). Global FST (0.1115, P 5 0.0002)
over all loci and horse groups indicate that 11.2% of the
genetic variability is attributed to significant differences
between the horse breeds including the Sable Island horse
population. The distribution of the genetic differentiation
among breed pairs ranged from 1.3% for the Appaloosa–
Hanoverian pair to 19.2% for the Sable Island horse–
Thoroughbred pair. All horse group pair differentiations
(FST) were highly significant (P , 0.001). Of the 210
possible horse group pair comparisons, the 13 largest
estimates of genetic differentiation involved the Sable Island
horse population.
Breed Differentiation
Results of the factorial correspondence analysis (Figure 2)
clearly separated the Sable Island horse population from the
other breeds. The first axis, which accounted for 17.54% of
the total inertia, isolated the Sable Island horses and the
small multipurpose horses (Icelandic, Fjord, Newfoundland,
and Hackney). The second axis accounted for 14.33% of the
total inertia and separated the sport horse breeds from the
heavier and light draft horses.
NJ trees based on the POSA and Reynolds’ genetic
distance presented similar topologies, comparable to Nei’s
standard distance and FST (data not presented). Figure 3
presents the split graph using the KL divergence matrix
obtained from the Bayesian analysis of genetic differentiation between the horse breeds, the Sable Island horse
population, and the donkey (used as an outgroup) under an
admixture model (goodness-of-fit of 94.3%). This approach
has the advantage of reducing the complexity of the
topology and assigning breeds to inferred clusters based on
the frequency of multiloci genotypes. The NJ tree clearly
clusters the Sable Island population with light draft and
multipurpose breeds (Fjord, Icelandic, Newfoundland,
Canadian, and Hackney) commonly found in eastern
Canada. The admixture model clustered the Appaloosa
and Hanoverian together and the Pottok and Peruvian.
After the factorial correspondence analysis, the KL divergence matrix also removed the potential relationship of
the Sable Island horses to the Spanish breeds (Asturcon,
Mallorquin, Menorquin, Pottok, and Andalusian).
Figure 2. Factorial correspondence analysis of the 12
microsatellite loci analyzed in the horse breeds registered in
Canada and the Sable Island horse population.
clusters (Table 2). Individual genotype membership to
inferred clusters varied from 0.95 for the donkeys (Cluster
XIV) and just more than 0.90 for the Sable Island horses
(Cluster XV). The individual memberships for the Appaloosa and Hanoverian indicated that these horses are highly
variable and difficult to assign to a unique cluster. The
probabilities of individual assignment to predefined breeds
or population showed similar trends. Within the Appaloosa
breed, 43 (77%) horses were properly assigned and the
remaining 13 could be assigned to other breeds including
the Hanoverian, Thoroughbred, Standardbred, Saddlebred,
Menorquin, Mallorquin, and Arabian. One hundred percent
of the Fjord, Sable Island, Icelandic, and Standardbred
horses, and as expected of the donkeys, were properly
assigned to the predefined population. For the remaining
Breed and Individual Assignment
Using the complete multiloci dataset, including the donkey,
2 different Bayesian approaches were used to infer the
number of likely clusters (2 K 25) under an admixture
model (Figure 4). Both approaches identified 20 possible
Figure 3. Split graphs for the 20 identified clusters based on
the KL allele divergence estimates. AP–HN and PE–POT are
the groups identified with the Bayesian approach.
597
Journal of Heredity 2007:98(6)
Discussion
Genetic Variation
Figure 4. Proportion of membership 1133 individuals from
Canadian horse breeds, the Sable island population, the Spanish
breeds, and the donkey for K 5 2, 5, 10, and 15–20.
breeds, more than 88% of the horses could be assigned to
the alleged breed of origin.
Breed Contribution to Diversity
Using different measures of isolation and genetic distances,
and following the Weitzman’s diversity function, Table 3
summarizes the marginal contribution and loss of genetic
diversity at the breed level. Regardless of the distance
estimate used, the biggest decrease in diversity would occur
from the hypothetical loss of the Sable Island horse
population. Considering the potential loss of the minor
light draft and multipurpose breeds registered in Canada
(Canadian, Morgan, Hackney, Newfoundland, Icelandic,
Fjord, Saddlebred, and Sable Island population), the
marginal loss of diversity from this group would be 40%
compared with 18% for the Spanish breeds and 28% for the
other more common horse breeds with higher numbers of
registrations.
598
This study presents an analysis of genetic diversity in a set
of 15 Canadian-registered horse breeds, 5 Spanish breeds,
and a feral horse population from Sable Island. The number
of alleles per locus (Table 1) is a simple and common
measure of genetic diversity and, in some cases, may
be more informative than genic heterozygosity, especially
when populations have gone through recent bottlenecks
(Maruyama and Fuerst 1985; Luikart et al. 1998). Because of
their recent breeding history and some introgression from
other breeds, the Appaloosa, Morgan, Newfoundland,
Hackney, and Saddlebred showed the largest average
number of alleles. For the other breeds commonly found
in Canada, the number of alleles and heterozygosities are
comparable to those previously reported for the Arabian,
Icelandic, Hanoverian, and Thoroughbred (Aberle et al.
2004; Glowatzki-Mullis et al. 2005). Our estimates for the
Spanish breeds are similar to those reported by Marletta
et al. (2006) and Vega-Pla et al. (2006) but slightly higher
than those presented by Cañon et al. (2000) and Solis et al.
(2005). These latter 2 studies collected relatively large
samples from different populations, whereas we collected
breed genotypes from an available database, irrespective of
localities.
We have also observed a relatively large number of
breed-specific alleles (Table 1). Except for the ABS23 192
allele found in one Thoroughbred, which could be a single
nucleotide insertion/deletion or a PCR artifact, all other rare
alleles appear valid, albeit at very low frequencies. It is
surprising to find that such alleles are still segregating in
minor breeds such as the Fjord (with 2 rare alleles),
Icelandic, Newfoundland, and the Hackney. Drift alone may
not be severe enough to cause the loss of these particular
alleles in these breeds.
Our results for the donkey reference population sample
revealed less genetic variation (Table 1) than previously
reported for other breeds and populations (Jordana et al.
2001; Aranguren-Méndez et al. 2002). Our random sampling
of genotypes from an established database probably underestimated the average number of alleles and heterozygosities, and the latter 2 published studies better reflect genetic
variation in Spanish donkeys.
As previously reported by Behara, Colling, Cothran,
Gibson (1998) and Behara, Colling, Gibson (1998) and
confirmed in this study, rare and endangered horse breeds in
Canada such as the Canadian, Hackney, Morgan, Newfoundland, and Saddlebred show levels of genetic variability
comparable or even higher than any other breeds analyzed.
The status of these breeds for conservation efforts is based
on the small or declining number of breeding individuals
and annual registrations. However, our results show that
genetic diversity measured in these breeds has been
maintained to high levels and supports continued conservation efforts. On the other hand, the Sable Island horse
population sample analyzed in this study may not represent
Table 2.
Estimated membership to inferred clusters obtained by STRUCTURE and individual assignment results of each individual horse to its own predefined breed or to other breeds
Inferred Clusters
Assignment
II
III
IV
V
VI
VII
VIII
IX
X
XI
XII
XIII
XIV
XV
XVI
XVII
XVIII XIX
XX
To
To
self
other
group groups %
AP
AR
BE
CN
FJ
HA
HN
IC
MO
NE
PE
PH
SA
SI
TH
ST
AST
MAL
MEN
POT
AND
DO
0.030
0.011
0.048
0.737
0.007
0.025
0.017
0.008
0.016
0.021
0.035
0.014
0.011
0.005
0.008
0.007
0.012
0.007
0.037
0.060
0.017
0.002
0.126
0.032
0.007
0.018
0.007
0.010
0.199
0.007
0.019
0.017
0.009
0.030
0.029
0.006
0.406
0.012
0.055
0.012
0.015
0.030
0.018
0.002
0.029
0.007
0.015
0.011
0.842
0.021
0.036
0.022
0.012
0.022
0.015
0.016
0.016
0.005
0.008
0.008
0.010
0.025
0.010
0.024
0.012
0.002
0.099
0.018
0.009
0.015
0.008
0.011
0.064
0.008
0.064
0.017
0.007
0.019
0.027
0.005
0.015
0.765
0.011
0.025
0.023
0.021
0.014
0.003
0.047
0.011
0.010
0.012
0.008
0.070
0.036
0.012
0.033
0.038
0.015
0.024
0.027
0.005
0.012
0.017
0.013
0.689
0.037
0.060
0.015
0.003
0.019
0.010
0.023
0.020
0.008
0.013
0.027
0.019
0.022
0.577
0.011
0.033
0.016
0.006
0.011
0.008
0.009
0.015
0.015
0.020
0.021
0.003
0.038
0.020
0.009
0.021
0.007
0.019
0.050
0.011
0.033
0.041
0.017
0.545
0.024
0.007
0.008
0.013
0.022
0.018
0.033
0.187
0.019
0.003
0.024
0.010
0.068
0.024
0.011
0.016
0.025
0.009
0.023
0.027
0.730
0.013
0.012
0.005
0.006
0.011
0.017
0.010
0.025
0.077
0.019
0.003
0.230
0.019
0.007
0.012
0.005
0.010
0.243
0.007
0.041
0.013
0.008
0.020
0.029
0.004
0.431
0.038
0.018
0.016
0.029
0.030
0.024
0.003
0.022
0.010
0.011
0.012
0.015
0.019
0.017
0.791
0.015
0.038
0.019
0.013
0.018
0.007
0.006
0.008
0.013
0.015
0.014
0.013
0.014
0.003
0.029
0.014
0.017
0.012
0.007
0.012
0.021
0.008
0.016
0.016
0.011
0.023
0.009
0.005
0.010
0.008
0.690
0.016
0.015
0.092
0.013
0.002
0.044
0.731
0.012
0.013
0.008
0.015
0.055
0.011
0.015
0.014
0.009
0.027
0.014
0.005
0.013
0.013
0.017
0.031
0.022
0.041
0.017
0.003
0.003
0.002
0.003
0.003
0.002
0.003
0.002
0.004
0.003
0.002
0.003
0.004
0.003
0.002
0.002
0.003
0.004
0.003
0.002
0.004
0.003
0.949
0.019
0.021
0.007
0.008
0.017
0.012
0.024
0.018
0.020
0.027
0.008
0.018
0.011
0.903
0.010
0.008
0.009
0.008
0.012
0.013
0.009
0.003
0.046
0.021
0.012
0.015
0.007
0.015
0.051
0.009
0.016
0.024
0.012
0.020
0.017
0.005
0.011
0.012
0.014
0.043
0.589
0.053
0.017
0.002
0.063
0.011
0.014
0.007
0.009
0.014
0.026
0.008
0.032
0.013
0.009
0.032
0.657
0.006
0.009
0.013
0.016
0.015
0.019
0.054
0.010
0.003
0.032
0.015
0.009
0.007
0.007
0.010
0.036
0.010
0.020
0.013
0.017
0.021
0.023
0.004
0.013
0.009
0.023
0.010
0.026
0.066
0.705
0.003
0.033
0.016
0.021
0.018
0.009
0.662
0.028
0.020
0.034
0.016
0.017
0.029
0.012
0.005
0.006
0.012
0.011
0.013
0.019
0.043
0.020
0.002
43
47
36
56
59
47
42
53
48
49
53
38
56
57
48
59
42
40
46
40
67
40
56
50
37
57
59
49
48
53
54
54
55
41
60
57
50
59
45
44
52
45
68
40
0.047
0.010
0.013
0.011
0.009
0.022
0.027
0.008
0.546
0.020
0.010
0.041
0.035
0.006
0.010
0.017
0.021
0.017
0.035
0.030
0.017
0.003
0.020
0.010
0.686
0.024
0.008
0.022
0.018
0.009
0.019
0.042
0.039
0.056
0.010
0.005
0.006
0.015
0.014
0.012
0.025
0.083
0.016
0.003
13
3
1
1
2
6
6
5
2
3
4
2
3
4
6
5
1
76.79
94.00
97.30
98.25
100.00
95.92
87.50
100.00
88.89
90.74
96.36
92.68
93.33
100.00
96.00
100.00
93.33
90.91
88.46
88.89
98.53
100.00
599
Plante et al. Genetic Diversity in Sable Island Horses
Number
Breed of
code individuals I
Journal of Heredity 2007:98(6)
Table 3.
Weitzman’s diversity and marginal loss (%) estimates
POSA
Reynold’s distance
Fixation index FST
KL divergence
Total
diversity
7.50
1.47
0.78
15.94
Breed
Diversity
Marginal
loss
Diversity
Marginal
loss
Diversity
Marginal
loss
AP
AR
BE
CN
FJ
HA
HN
IC
MO
NE
PE
PH
SA
SI
TH
ST
7.23
6.94
7.08
7.07
6.96
6.99
7.28
7.00
7.10
7.10
7.06
7.06
7.04
6.67
7.05
7.05
3.43
7.41
5.55
5.59
7.12
6.77
2.91
6.68
5.33
5.29
5.85
5.81
6.08
10.98
5.95
5.90
1.44
1.36
1.40
1.39
1.37
1.37
1.44
1.35
1.41
1.40
1.40
1.40
1.38
1.24
1.36
1.38
2.15
7.67
4.75
5.22
6.62
7.07
1.65
7.84
4.19
4.36
4.49
4.81
5.98
15.67
7.47
6.02
0.77
0.72
0.74
0.74
0.73
0.73
0.77
0.72
0.75
0.75
0.75
0.74
0.74
0.64
0.72
0.74
2.06
7.42
5.00
5.16
6.41
6.75
1.56
7.56
3.95
4.24
4.38
4.77
5.90
17.29
7.55
5.79
a truly random collection of animals. As such, our measures
of genetic diversity in this particular group may be biased
and better reflect the upper limit of estimated genetic
diversity.
With a reduced effective number of alleles per locus and
a significant heterozygous deficiency, the Sable Island horse
population exhibits lower genetic diversity than other feral
horse populations (Ashley 2004; Morais et al. 2005; Vega-Pla
et al. 2006).
Breed Differentiation and Assignment
Different classical estimates of genetic distances were used
to illustrate genetic divergence between the horse breeds
and the Sable Island feral population and all resulted in very
similar topologies. Our results for the Spanish horse breeds
closely resemble those of Vega-Pla et al. (2006). Marletta
et al. (2006) elegantly used kinship distances and molecular
coancestry (Caballero and Toro 2002) along with a distance
estimate based on the average proportion qk(i) of the
genome of breed i that comes from an ancestral population
k (with k equal to the number of breeds), following the
Bayesian approach of Pritchard et al. (2000), to illustrate the
genetic relationships among western Mediterranean native
horse breeds. Here, we also used a Bayesian approach to
estimate the KL divergence matrix between underlying
clusters of multilocus genotypes as a measure of the relative
genetic distance between these clusters (Corander et al.
2003). Results from the analyses of horse breed differentiation and individual assignment to unique clusters clearly
define the Sable Island feral horse population and its close
phylogenetic relationships to sport and light draft horse
breeds commonly found in eastern Canada. Consequently,
600
Cluster
Diversity
Marginal
loss
AP–HN
TH
BE
PE
MO
PH
NE
CN
HA
AR
SA
ST
FJ
IC
SI
15.55
14.94
15.32
15.30
15.29
15.25
15.31
14.93
14.89
14.83
14.91
14.80
14.77
14.69
13.32
2.40
6.23
3.87
4.00
4.05
4.29
5.06
6.30
6.58
6.93
6.41
7.15
7.30
7.82
16.41
the popular anecdotal influence of Spanish breeds in the
Sable Island horse population could not be supported.
Within the cluster of eastern horse breeds found in Canada,
it remains difficult to assess the origin of the Sable Island
horse population; however, these horses share a common
ancestor with the Newfoundland, Icelandic, and Fjord
breeds.
Several Canadian horse breeds analyzed in this study are
considered as critical to endangered by Rare Breeds Canada
and other conservation interest groups. All these recognized
breeds exhibit levels of genetic diversity comparable to and
in some cases higher than more common and major horse
breeds. As such, in situ conservation efforts can still rely on
accessible genetic variability and thus should be able to
maintain genetic diversity through well-designed breeding
programs. Furthermore, the Weitzman’s diversity function
as applied to a different measure of differentiation clearly
illustrates the relevance of these breeds to the overall genetic
diversity of the Canadian horse population.
The Sable Island feral population represents a unique
group of individuals. Legally protected since 1960, this horse
population has significantly diverged from any other ancestral breeds. No introgression has occurred for at least
11 to 12 generations, and genetic drift and inbreeding likely
played a role in the observed loss of genetic diversity as
measured by the number of alleles per loci, heterozygous
deficiency, and the large genetic distances to other horse
breeds. All the measured genetic statistics, including the
marginal contribution to diversity under a hypothetical extinction, probably underestimate the true value of the Sable
Island horse as a genetic resource. Field observations on
body condition and reproduction (Lucas et al. 1991) indicate
Plante et al. Genetic Diversity in Sable Island Horses
that the Sable Island horse is well adapted to the local
conditions of a seasonally demanding environment with
limited resources and may be characterized by higher
frequencies of alleles associated with life-history traits.
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Received April 13, 2007
Accepted June 14, 2007
602
Corresponding Editor: Ernest Bailey