Genetic Diversity in a Feral Horse Population from Sable Island, Canada

Influence of Sires on Population Substructure in Dülmen Wild Horses

The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185 male foals sired by nine stallions. As females could not be sampled, we could not make inferences on all yearlings and test whether there are differences in the genetic population parameters between both sexes. The mean number of progeny was 19.92 with a range of 2-32, caused by the length of the service period per stallion. The average observed and unbiased expected heterozygosity was 0.688 and 0.631, the mean number of alleles was 4.448, and Wright's FIS was -0.173. Pairwise genetic distances (FST and Nei's unbiased genetic distances) were significant and varied between 0.038 to 0.091 and 0.085 to 0.290, respectively. Neighbor-joining dendrogram plots clustered a large proportion of the paternal progeny groups in different branches. Posterior Bayesian analyses using seven paternal half-sib groups with 10-74 members supported a maximum of six clusters, with two paternal progeny groups not differing, and a median of five clusters, with two groups of two sires each falling into the same clusters. When sires were employed in non-consecutive years, progeny from these different years of the same sires were grouped in the same cluster, whereas the progeny of one sire from two consecutive years were in different clusters. We were able to distinguish male progeny from Dülmen wild horse stallions and to show the effects of stallion use on the genetic substructure in the Dülmen wild horse herd. In conclusion, the analyses showed the genetic potential of the Dülmen wild horse stallions to maintain a high genetic diversity and also the effects in which breeding seasons and for how long stallions are used to sire foals. The selection of stallions may be sensitive for the further development of genetic diversity and preserve this closed population as a valuable resource for further studies on the evolution of the horse.

Genetic Diversity and Population Structure of Dülmen Wild, Liebenthal and Polish Konik Horses in Comparison with Przewalski, Sorraia, German Draught and Riding Horses

The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of -0.035. Pairwise genetic distances (FST, Nei's standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski's horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication.

The stable isotope hydrology of Sable Island, Nova Scotia, Canada with implications for evaluating the water budget of wild horses

We investigated the stable isotope hydrology of Sable Island, Nova Scotia, Canada over a five year period from September, 2017 to August, 2022. The δ2H and δ18O values of integrated monthly precipitation were weakly seasonal and ranged from -66 to -15 ‰ and from -9.7 to -1.9 ‰, respectively. Fitting these monthly precipitation data resulted in a local meteoric water line (LMWL) defined by: δ2H = 7.22 ± 0.21 · δ18O + 7.50 ± 1.22 ‰. Amount-weighted annual precipitation had δ2H and δ18O values of -36 ± 11 ‰ and -6.1 ± 1.4 ‰, respectively. Deep groundwater had more negative δ2H and δ18O values than mean annual precipitation, suggesting recharge occurs mainly in the winter, while shallow groundwater had δ2H and δ18O values more consistent with mean annual precipitation or mixing of freshwater with local seawater. Surface waters had more positive values and showed evidence of isolation from the groundwater system. The stable isotopic compositions of plant (leaf) water, on the other hand, indicate plants use groundwater as their source. Fog had δ2H and δ18O values that were significantly more positive than those of local precipitation, yet had similar 17O-excess values. δ2H values of horsehair from 4 individuals lacked seasonality, but had variations typical to those of precipitation on the island. Differences in mean δ2H values of horsehair were statistically significant and suggest variations in water use may exist between spatially disparate horse communities. Our results establish an important initial framework for ongoing isotope studies of feral horses and other wildlife on Sable Island.

An Estimation of Lameness in Sable Island Horses Using Radiographic Evaluation of the Distal Phalanx and Hoof Capsule

Laminitis is a painful condition that causes lameness in horses. However, monitoring this condition in feral horses is logistically difficult. Laminitis can be detected postmortem, as inflammation of the sensitive laminae of the hoof changes the relative location of the bony structures within the hoof capsule. Thus, evaluation of cadavers may be used to estimate laminitis prevalence in feral populations of horses. The objective of this study was to estimate the prevalence of laminitis in feral horses inhabiting the Sable Island National Park Reserve, Canada, using radiographic imagery on the hooves of naturally deceased horses. Radiographic indicators evaluated included coronary band extensor process distance (CE), capsular rotation (CR), palmar angle (PA), ratio of the dorsal hoof wall thickness to the length of the distal phalanx (DHWT:P3) and sole depth (SLD). Each value measured indicated the following prevalence of laminitis: CE 0% (97.5% Confidence Interval (CI) 0-4.51%), 8.75% CR (95%CI 3.59-17.2%), PA 25% (95% CI 15.99-35.94%), DHWT:P3 6.25% (95%CI 2.06-14.0%) and 65% SLD (95% CI 53.52-75.33%). The majority of indices measured for laminitis were low. These findings suggest that laminitis is fairly infrequent in the Sable Island horses evaluated in this study.

Phenotypic and genetic diversity of the Anjian chicken in China

The Anjian chicken is a local breed in Hotan, Xinjiang, China. Herein, we studied the morphological characteristics and genetic diversity of the Anjian chicken population. The findings of this study could inform the genetic improvement strategy of this breed. Phenotypic characteristics investigated included the diversity in the general appearance, feather color, and crowing length of the Anjian cocks. The population structure of the Anjian chicken and its relationship with other chicken breeds were also assessed based on mitochondrial DNA (mtDNA) D-loop sequence analysis. Phenotypically, the feather color of the Anjian chicken varied considerably. The sequence diversity analysis revealed the following: nucleotide diversity (Pi) was 0.00618, haplotype diversity (Hd) was 0.776, the average number of nucleotide differences (k) was 7.631, and Tajima’s (D) was −0.00407, indicating that Anjian chicken is moderately genetically diverse. Further phylogenetic analysis revealed that the Anjian chicken breed has 10 haplotypes clustered into two branches. Genetic distance and median network analysis showed that the mtDNA D-loop sequence of the Anjian chicken was distributed in many different clusters of the tree. These data demonstrate that even though the Anjian chicken mainly originated from red jungle fowl, it has multiple maternal origins. In conclusion, the Anjian chicken is highly genetically diverse.

A paleolimnological context of ecological vulnerability for the freshwater ecosystems of Sable Island National Park Reserve, Canada

Protected areas require long-term monitoring to understand the influence and extent of ecosystem stress to inform management and conservation decisions. As long-term data are not always available, paleolimnological methods offer a way of extending our knowledge of past environmental conditions necessary to use as context for remediation. Here, we examine four sediment cores and additional surface sediments from 14 ponds located on Sable Island National Park Reserve Canada (SINPR), where long-term ecological changes and vulnerability to disturbance are not well defined. We develop a paleolimnological approach to assessing environmental vulnerability through the use of biological indicators (Diptera: Chironomidae), where shifts in the environment are inferred by shifts in chironomid assemblages over time. Analysis of surface sediments show four distinct assemblage types reflecting four different habitat conditions; primarily represented by the presence of Glyptotendipes, Chironomus, Microtendipes, and Dicrotendipes. Differences in habitat conditions through time based on these results are then compared to biostratigraphic analysis of sediment cores from four of the ponds. We found that two ponds had large shifts in chironomids assemblages that were associated with changes in habitat over time, while two others that were not as exposed to the influence of erosion and influx of sand dunes did not. Our findings established a baseline of historical change in SINPR, broadening the scope of long-term monitoring, which is essential for defining goals for management and conservation of the ecological integrity of Sable Island.

Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds

BACKGROUND

Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood species like the horse could provide information on the genetic health of those populations and offer insight into how such metrics compare between managed and unmanaged populations. Here we characterized ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable Island, Canada, using ~41 000 SNPs and contrasted results with those from 33 domestic breeds to assess the impacts of isolation on ROH abundance, length, distribution, and ROH islands.

RESULTS

ROH number, length, and ROH-based inbreeding coefficients (F_ROH) in Sable Island horses were generally greater than in domestic breeds. Short runs, which typically coalesce many generations prior, were more abundant than long runs in all populations, but run length distributions indicated more recent population bottlenecks in Sable Island horses. Nine ROH islands were detected in Sable Island horses, exhibiting very little overlap with those found in domestic breeds. Gene ontology (GO) enrichment analysis for Sable Island ROH islands revealed enrichment for genes associated with 3 clusters of biological pathways largely associated with metabolism and immune function.

CONCLUSIONS

This study indicates that Sable Island horses tend to be more inbred than their domestic counterparts and that most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift and highlight the value of this population as a reservoir of equine genetic variation. This research illustrates how ROH analyses can be applied to gain insights into the population history, genetic health, and divergence of wild or feral populations of conservation concern.

Causes and consequences of an unusually male-biased adult sex ratio in an unmanaged feral horse population

The adult sex ratio (ASR) is important within ecology due to its predicted effects on behaviour, demography and evolution, but research examining the causes and consequences of ASR bias have lagged behind the studies of sex ratios at earlier life stages. Although ungulate ASR is relatively well-studied, exceptions to the usual female-biased ASR challenge our understanding of the underlying drivers of biased ASR and provide an opportunity to better understand its consequences. Some feral ungulate populations, including multiple horse populations, exhibit unusually male-biased ASR. For example, research suggests that the feral horse Equus ferus caballus population on Sable Island, Nova Scotia, Canada may exhibit a male-biased ASR. Such exceptions to the rule provide a valuable opportunity to reveal the contributions of environmental context and trait differences to ASR bias. We aimed to test for bias in Sable Island horse ASR, identify the demographic drivers of bias, and explore its demographic and social consequences. To do this, we used life history, movement and group membership information for hundreds of horses followed through a long-term individual-based study between 2007 and 2018. Sable Island horse ASR is male biased and this skew has increased over time, reaching 62% male in 2018. Our life table response experiment suggested that ASR skew was driven predominantly by male-biased adult survival. Further analyses pointed to sex-biased survival being driven by reduced female survival post-reproduction. Male-biased ASR was associated with reduced harem sizes, an increase in the number of social groups on the island, and reduced reproduction in young females. Our results support the idea that male-biased ASR in feral ungulate populations may be caused by a combination of high population density and high reproductive output. We suggest that female-biased mortality may be caused by females continuing to reproduce at high density, and thus being more susceptible to resource shortages. Thus, our results highlight the strong context dependence of ASR. Furthermore, our work indicates the potential for ASR to substantially alter a population's social organisation. Such changes in social structure could have knock-on consequences for demography by altering the formation/stability of social relationships, or competition for matings.

Genetic Diversity and Population Structure of Arabian Horse Populations Using Microsatellite Markers

Understanding the genetic diversity and the relationships among the show Arabian horse populations is a current issue for breeders and professionals. This study aimed to define the relationship among the Desert breed, the Straight Egyptian, and the Polish Arabian populations by considering the historical background of their origin and to verify their genetic diversity. All selected samples were related to Arabian show activities. One hundred forty four hair samples were collected from horses at stud farms having notoriety in the breeding of Arabians from different geographic regions. A set of 17 microsatellites markers for parentage control were used for genotyping. Genetic diversity among and between these populations were evaluated using several statistical methods. All the microsatellites were informative and the marker set analyzed provided 145 alleles. The average number of alleles per locus was 6.52, 6.35, and 7 for the Desert breed, Straight Egyptian, and Polish Arabian, respectively. The high genetic diversity observed within the three populations (0.63-0.71) was associated with a high number of effective alleles. Desert breed and Polish Arabian populations appeared the closest, whereas the Egyptian population was more distant. The significant positive inbreeding coefficient F_IS found in Desert breed, Straight Egyptian, and Polish Arabian horses (0.09, 0.14, and 0.11, respectively) confirmed the deficit of heterozygosity observed in these populations. These results suggested that the three populations have high levels of gene flow or share the same origin and have a recent divergence. This study may highlight the risk of the loss of gene diversity in these populations and help to implement appropriate breeding programs to preserve genetic diversity.

Not playing by the rules: Unusual patterns in the epidemiology of parasites in a natural population of feral horses (Equus caballus) on Sable Island, Canada

Sable Island, Nova Scotia, Canada hosts one of few natural populations of feral horses (Equus caballus) never exposed to anthelmintics. Coproculture revealed cyathostomes, Strongylus equinus, S. edentatus, and S. vulgaris, with S. equinus (unusually) dominating in adult horses and cyathostomes dominating in young horses (<3 years of age). We examined 35 horses found dead in the springs of 2017 and 2018, as well as fecal samples from live horses in spring (n = 45) and summer 2018 (n = 236) using McMaster fecal flotation and Baermann larval sedimentation on fresh samples, and modified Wisconsin flotation and sucrose gradient immunofluorescent assay for Giardia and Cryptosporidium on frozen samples. Mean strongyle fecal egg counts were 666 eggs per gram (EPG) in dead horses, 689 EPG in live horses in spring, and 1105 EPG in summer; domestic horses are usually treated at counts exceeding 200 EPG. Adult horses (unusually) had patent infections with the lungworm Dictyocaulus arnfieldi and ascarids (Parascaris spp.), and in spring, dead horses had 5 times higher odds of having patent ascarid infections than live horses, likely due to malnutrition and corresponding immunodeficiency. Fecal prevalence and intensity of D. arnfieldi and Parascaris spp. were significantly higher in young horses, and in spring versus summer. A higher proportion of fecal samples were positive for strongyle and ascarid eggs using a centrifugal flotation technique on previously frozen feces, as compared to a passive flotation method on fresh feces. Eggs of the tapeworm Paranoplocephala mamillana were present in fecal samples from 28% of live, and 42% of dead, horses in spring. This research represents several new geographic records (S. edentatus, D. arnfieldi, and Eimeria leuckarti), provides insight into unusual patterns of parasite epidemiology in a nutrition-limited environment, and has conservation and biosecurity implications for this unique equine population, as well as for parasite management in domestic horses.

Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies

The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin. This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyze the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected (a total of 485 animals were used for mtDNA analysis and 450 for microsatellite analysis), and previously published data were used to place the British and Irish ponies in a global context. The native ponies of Britain and Ireland were found to have had a complex history, and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were maintained in native breeds, although some reduction was evident in small or isolated populations (Shetland, Carneddau, and Section C). Unusual mitochondrial diversity distribution patterns were apparent for the Carneddau and Dartmoor, although among breeds and global haplogroups there was a high degree of haplotype sharing evident, well-represented within British and Irish ponies. Ancestral maternal diversity was maintained by most populations, particularly the Fells and Welsh ponies, which exhibited rare and ancient lineages. The maternal and paternal histories of the breeds are distinct, with male-biased crossings between native breeds, and other shared influences, likely Arabs and Thoroughbreds, are apparent. The data generated herein provide valuable information to guide and implement the conservation of increasingly rare native genetic resources.

MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites

The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC haplotypes have been previously described in any other horse breed. Only one MHC homozygote was found in the entire population studied. These results indicate a very high level of MHC heterozygosity and haplotype diversity in the Icelandic horse. The environment in Iceland is remarkable for its lack of common agents of equine infectious disease, including equine herpesvirus type 1, influenza virus, and streptococcus equi. The driving forces for maintenance of MHC heterozygosity in Icelandic horses must thus be sought outside of these major horse pathogens. Based on our results, we propose that intra-MHC recombination may play a major role in the generation of novel haplotypes.

Environmental and demographic drivers of male mating success vary across sequential reproductive episodes in a polygynous breeder

Ecological and social factors underpinning the inequality of male mating success in animal societies can be related to sex ratio, sexual conflict between breeders, effects of nonbreeders, resource dispersion, climatic conditions, and the various sequential stages of mating competition that constitute the sexual selection process. Here, we conducted an individual-based study to investigate how local resource availability and demography interact with annual climate conditions to determine the degree of male mating inequality, and thus opportunity for sexual selection across two sequential reproductive episodes (harem and subsequent mate acquisition) in a naturally regulated (feral) horse population in Sable Island National Park Preserve, Canada. Using a 5-year, spatially explicit, mark-resight dataset and hierarchical mixed-effects linear modeling, we evaluated the influence of adult sex ratio (ASR) on mating success and then tested for effects of freshwater availability, density, unpaired male abundance, and precipitation during each breeding season. Unpaired male abundance, freshwater availability, and ASR differed in their effects on male mating success according to year and selection episode. Opportunity for sexual selection in males associated with harem acquisition increased with ASR, and unpaired male abundance further explained weather-related interannual variation after accounting for ASR. In contrast, once a harem was secured, ASR had little effect on male mating inequality in regard to acquiring additional females, while interannual variation in mating inequality increased with decreasing freshwater availability. Our findings show that local demography, resource availability, and weather effect opportunity for sexual selection in males differently depending on selection episode, and can attenuate or accentuate effects of ASR.

Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour

Gene mutations influencing melanocytes also impact on physiological and behavioural functions. In this study, we investigated their association with four different coat colours in the Pura Raza Español (PRE) horse using morphological traits and molecular datasets. Four different subpopulations were identified according to individual coat colour: grey, bay, chestnut and black. Coat colour significantly associated with morphological measurements. Observed and expected heterozygosity values were low in grey compared with the other three subpopulations, suggesting the presence of unique ancestral alleles probably arisen by genetic drift and selection mechanism effects. Nei's distance demonstrated a clear division among subpopulations, the grey being the most divergent group. Gene flow estimates were similar, showing the lowest values in grey. Divergence times among subpopulations assessed with the average square distance suggested that grey was the original PRE population which diverged from bay, chestnut and black. Our results also demonstrated a clear morphological differentiation according to coat colour. The close genetic structure of bay and chestnut PRE subpopulations and the clear differences in most morphological traits of grey and chestnut PRE mares would suggest the pleiotropic effect of genomic regions determining coat colour in horses. However, further analysis including genomic information would be necessary to elucidate the mechanisms involved.

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park

Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.

The legend of the Canadian horse: genetic diversity and breed origin

The Canadian breed of horse invokes a fascinating chapter of North American history and as such it is now a heritage breed and the national horse of Canada. The aims of this study were to determine the level of genetic diversity in the Canadian, investigate the possible foundation breeds and the role it had in the development of the US horse breeds, such as Morgan Horse. We tested a total of 981 horses by using 15 microsatellite markers. We found that Canadian horses have high values of genetic diversity indices and show no evidence of a serious loss of genetic diversity and the inbreeding coefficient was not significantly different from zero. Belgian, Percheron, Breton and Dales Pony, unlike the light French horses, may have common ancestries with the Canadian and could be important founders. However, the Shire and Clydesdale influenced the Canadian to a lesser extent than French and Belgian draft breeds. Furthermore, our finding indicated that there was no evidence of a clear relationship between Canadian and Oriental or Iberian breeds. Also, the Canadian likely contributed to the early development of the Morgan. Finally, these findings support the ancient legends of the Canadian Horse as North America’s first equine breed and the foundation bloodstock to many American breeds and may help in the management and breeding program of this outstanding breed in North America.

Small Ne of the Isolated and Unmanaged Horse Population on Sable Island

For small, isolated populations 2 common conservation concerns relate to genetic threats: inbreeding and negative consequences associated with loss of genetic diversity due to drift. Mitigating these threats often involves conservation actions that can be controversial, such as translocations or captive breeding programs. Although such actions have been successful in some situations, in others they have had undesirable outcomes. Here, we estimated the effective population size (N e ) of the Sable Island horses to assess the risk to this population of these genetic threats. We found surprising consistency of N e estimates across the 5 different methods used, with a mean of 48 effective individuals. This estimate falls below the 50 criterion of the "50/500 rule," below which inbreeding depression is a concern for population viability. However, simulations and knowledge of population history indicate that this population is still in its early stages of approaching equilibrium between mutation, drift, and genetic diversity; and no negative consequences have been identified that could be associated with inbreeding depression. Therefore, we do not recommend taking management action (such as translocations) at this stage. Rather, we propose continued monitoring of genetic diversity and fitness over time so that trends and any substantial changes can be detected. This represents one of the few unmanaged horse populations in the world, and therefore these data will not only alert us to serious concerns regarding their conservation status, but will also provide a wealth of information about how natural processes drive patterns of reproduction, mortality, and population growth over time.

Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations

As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K = 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.

Genetic structure and gene flows within horses: a genealogical study at the french population scale

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species F_IT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.

Genetic diversity and phylogenetic analysis of native mountain ponies of Britain and Ireland reveals a novel rare population

The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free-living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free-living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats.

Microsatellite analysis of genetic variability in Waler horses from Australia

The Waler horse breed is an integral part of Australian history. The purposes of this study were to analyse the genetic variability in Waler horses from Australia and to investigate genetic relationships with other horse breeds. We examined the genetic diversity of 70 Waler horses sampled from seven breeding stations in Australia. Also we analysed the relationships of these horses with 11 other horse breeds. Analysis of the genetic structure was carried out using 15 microsatellite loci, genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method. We found that the genetic diversity in the Waler was greater than the domestic horse mean and exceeded that of all endangered horse breeds. Our findings also revealed moderate population subdivision rather than inbreeding. All genetic similarity measures indicated that the Thoroughbred might be a key ancestor to the Waler. This study indicates that there is no immediate concern for loss of variation in Waler horses. Also, there clearly has been a strong input from the Thoroughbred into the Waler horse breed. However, the genetic evidence suggests that this input was not just direct but also came through other types of horses with a Thoroughbred cross background.

Explaining spatial heterogeneity in population dynamics and genetics from spatial variation in resources for a large herbivore

Fine-scale spatial variation in genetic relatedness and inbreeding occur across continuous distributions of several populations of vertebrates; however, the basis of observed variation is often left untested. Here we test the hypothesis that prior observations of spatial patterns in genetics for an island population of feral horses (Sable Island, Canada) were the result of spatial variation in population dynamics, itself based in spatial heterogeneity in underlying habitat quality. In order to assess how genetic and population structuring related to habitat, we used hierarchical cluster analysis of water sources and an indicator analysis of the availability of important forage species to identify a longitudinal gradient in habitat quality along the length of Sable Island. We quantify a west-east gradient in access to fresh water and availability of two important food species to horses: sandwort, Honckenya peploides, and beach pea, Lathyrus japonicas. Accordingly, the population clusters into three groups that occupy different island segments (west, central, and east) that vary markedly in their local dynamics. Density, body condition, and survival and reproduction of adult females were highest in the west, followed by central and east areas. These results mirror a previous analysis of genetics, which showed that inbreeding levels are highest in the west (with outbreeding in the east), and that there are significant differences in fixation indices among groups of horses along the length of Sable Island. Our results suggest that inbreeding depression is not an important limiting factor to the horse population. We conclude that where habitat gradients exist, we can anticipate fine-scale heterogeneity in population dynamics and hence genetics.

Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds

A 378-bp section of the mitochondrial displacement loop was used to estimate genetic diversity in the native Canadian equine populations. The inclusion of 10 Mountain and Moorland, 3 Nordic pony breeds, 2 feral populations, and 5 horse breeds were also investigated as they may have influenced the development (or rejuvenation) of the native Canadian populations. A total of 281 samples were sequenced, which produced 75 haplotypes derived from 54 informative sites. On further investigation, 36 of these 75 haplotypes were found to be previously unreported. Overall, total diversity was lowest in the feral Sable Island population with a haplotype diversity (0.27 ± 0.12), nucleotide diversity (0.0007 ± 0.0004), and pairwise difference of 0.286 ± 0.317. This is not surprising due to the geographic isolation of this population. Haplotype diversity was highest (1.00 ± 0.13) in the New Forest population, pairwise difference was highest (8.061 ± 4.028) in the Icelandic breed, whereas nucleotide diversity was highest in the Exmoor breed (0.0209 ± 0.0025). Within the Canadian populations, haplotype diversity was highest in the Newfoundland pony (0.96 ± 0.08), whereas pairwise difference and nucleotide diversity was highest in the Canadian horse (7.090 ± 3.581 and 0.0188 ± 0.0042, respectively). Three different estimates of genetic distances were used to examine the phylogenetic relationships amongst these populations. All 3 estimates produced similar topologies. In general, the native Canadian populations were highly represented in the D clade, with particular emphasis in the D1 and D2 clades. This is an important factor when considering the phylogenetic conservation of these Canadian equine populations.

Genetic structure and differentiation of the Italian catria horse

Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explained by the between-breed differences and the 3 approaches utilized gave similar results. Italian native breeds are clearly separated from the other examined breeds. However, by the correspondence analysis, the Catria appears closer to Maremmano and Murgese. The results of Bayesian approaches give further information showing for Catria a common origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.

Effects of a 10-year conservation programme on the genetic diversity of the Pottoka pony--new clues regarding their origin

Here, we present the results of a genetic analysis of 463 Pottoka ponies corresponding to four generations, using 17 microsatellite markers. Ten years after the beginning of the Pottoka conservation programme, the values for the genetic diversity of the breed are still high and stable, indicating the success of the programme. We found null alleles in Pottoka for the ASB23, HMS3 and HTG10 microsatellites. Together with information obtained from other pony breeds from the Iberian Peninsula, this finding indicates that these microsatellites should not be used for phylogenetic analyses or parentage tests, at least for these breeds. The high heterozygosity exhibited by this breed in comparison to other ponies, together with its genetic proximity to the centroid of the allele frequencies, suggest that Pottoka allele frequencies are close to those initially exhibited by the ancestors of current European ponies. The results obtained in the current work, together with results from previous studies of ponies and horses from the Iberian Peninsula, corroborate the idea of a unique origin of all ponies from the European Atlantic Area. In contrast, our results do not corroborate the idea that these are derived from a domestication event in the Iberian Peninsula, nor that they have incorporated ancient Iberian horse genes into their genetic pool to a larger extent than other horse breeds.

A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States

The domestic horse (Equus caballus) was re-introduced to the Americas by Spanish explorers. Although horses from other parts of Europe were subsequently introduced, some New World populations maintain characteristics ascribed to their Spanish heritage. The southeastern United States has a history of Spanish invasion and settlement, and this influence on local feral horse populations includes two feral-recaptured breeds: the Florida Cracker and the Marsh Tacky, both of which are classified as Colonial Spanish horses. The feral Banker horses found on islands off the coast of North Carolina, which include, among others, the Shackleford Banks, the Corolla and the Ocracoke, are also Colonial Spanish horses. Herein we analyse 15 microsatellite loci from 532 feral and 2583 domestic horses in order to compare the genetic variation of these five Colonial Spanish Horse populations to 40 modern horse breeds. We find that the Corolla horse has very low heterozygosity and that both the Corolla and Ocracoke populations have a low mean number of alleles. We also find that the Florida Cracker population has a heterozygosity deficit. In addition, we find evidence of similarity of the Shackleford Banks, Marsh Tacky and Florida Cracker populations to New World Iberian horse breeds, while the origins of the other two populations are less clear.

Genotyping in the Brazilian Criollo Horse Stud Book: resources and perspectives

The goal of this research was to evaluate the ability of the genotyping information available in the Brazilian Criollo Horse Stud Book to describe the genetic variability of the breed and the exclusion probability determined in comparative tests. Altogether, two softwares were used in the analyses of the available genotypes: Cervus 3.0.3 and Genepop 4.0. Eight microsatellite markers totaled 109 alleles, with an average of 13.6 +/- 0.6 alleles per locus. Large differences between expected and observed heterozygosity were ubiquitous (0.821 +/- 0.07 and 0.470 +/- 0.17, respectively). Although the estimated null allele frequency caused initial concern (0.284 +/- 0.199), it is likely that it was a reflection of the inbreeding coefficients found (0.432 +/- 0.184). All loci showed significant deviation from Hardy-Weinberg equilibrium, with heterozygote deficit (P < 0.0001) and genotypic linkage disequilibrium with at least one marker. The high polymorphic information content (0.798 +/- 0.088) could not warrant exclusion power for three loci (HMS7, HMS6 and HTG4) above 50% (0.491 +/- 0.158). However, combined exclusion probability reached 99.61%, a level close to ideal. The results demonstrate the excellent performance of the markers assessed in describing the genetic status of the breed and suggest the considerable ability to establish parentage.

Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources

The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.

Multiscale analysis reveals restricted gene flow and a linear gradient in heterozygosity for an island population of feral horses

We studied the genetic (microsatellite) diversity of a feral population of horses ( Equus caballus L., 1758) on Sable Island, Nova Scotia, Canada (1983–2003), at two spatial scales: (1) for the island as a whole and (2) at the level of four equally sized subdivisions along the length of Sable Island, which is a long (42 km) and narrow (1.5 km) vegetated sand bar. At the island scale (n = 264 horses), observed heterozygosity over 10 loci was 0.647 ± 0.035 (mean ± 1 SE), while expected heterozygosity was 0.696 ± 0.029; we observed significant heterozygote deficiency with all loci considered (P < 0.0001). At the subdivision scale, observed heterozygosity ranged from 0.589 to 0.694 in a gradient from west to east. We observed a corresponding gradient in effective number of alleles and allelic richness. Pairwise values of FST were significant for most subdivision pairs, ranging as high as 0.067 from west to east. Western areas showed highest levels of inbreeding (FIS = 0.113) with outbreeding indicated in the east (FIS = –0.008). Our results suggest that for a large mammal that lives in polygynous social groups, like the feral horse, gene flow along linear habitats (corridors) may be restricted (relative to the dispersal capabilities of the species), even over short distances.

Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.