Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats

We tested for cross‐species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one of two study populations) and 149 in mountain goats (≥ 2 alleles in a single study population) using 648 and 576 primer pairs, respectively. Our efforts increased the number of available polymorphic microsatellite markers to 327 for bighorn sheep and 180 for mountain goats. The average distance between successive polymorphic bighorn sheep and mountain goat markers inferred from the Australian domestic sheep genome linkage map (mean ± 1 SD) was 11.9 ± 9.2 and 15.8 ± 13.8 centimorgans, respectively. The development of genomic resources in these wildlife species enables future studies of the genetic architecture of trait variation.     

Restoration of a bighorn sheep population impeded by Mycoplasma ovipneumoniae exposure

Bighorn sheep (Ovis canadensis) were once extirpated from the Black Hills region of South Dakota, U.S.A., mirroring declining populations throughout North America. Since the 1960s, several reintroductions have occurred in the Black Hills to reestablish populations, with varying success. We translocated 26 bighorn sheep from Alberta, Canada, to the Black Hills (February 2015) to restore bighorn sheep to their historic range. Due to prior examinations of cause‐specific survival, subsequent genetic diversity and disease prevalence analyses were required to evaluate success of the restoration effort. We measured a mean allelic diversity of 5.23 (SE = 0.44 [mean number of alleles]) and an observed heterozygosity of 0.71 (SE = 0.06; expected = 0.64 ± 0.05) in the translocated individuals. Translocated bighorn sheep tested negative for Mycoplasma ovipneumoniae at capture. An autogenous vaccine was administered prior to release in an attempt to safeguard the translocated bighorn sheep from infection with a strain known to be resident in adjacent bighorn sheep populations. However, the year following the translocation, a different strain of M. ovipneumoniae was associated with a pneumonia outbreak that resulted in 57.9% mortality. Our results suggest that allelic diversity and heterozygosity were sufficient for long‐term herd establishment, reducing the potential for founder effects. However, the overwhelming mortality associated with pneumonia, via the transfer of M. ovipneumoniae from an unknown source, limited the success or our reintroduction efforts. Successful attempts to restore bighorn sheep to their historic ranges must consider and mitigate potential routes for M. ovipneumoniae transmission pre‐ and post‐reintroduction.     

Testing marker-based estimates of heritability in the wild

Marker-based estimates of heritability are an attractive alternative to pedigree-based methods for estimating quantitative genetic parameters in field studies where it is difficult or impossible to determine relationships and pedigrees. Here I test the ability of the marker-based method to estimate heritability of a suite of traits in a wild population of bighorn sheep (Ovis canadensis) using marker data from 32 microsatellite loci. I compared marker-based estimates with estimates obtained using a pedigree and the animal model. Marker-based estimates of heritability were imprecise and downwardly biased. The high degree of uncertainty in marker-based estimates suggests that the method may be sufficient to detect the presence of genetic variance for highly heritable traits, but not sufficiently reliable to estimate genetic parameters.     

Genetic diversity in Iranian indigenous sheep vis-à-vis selected exogenous sheep breeds and wild mouflon

The heterogeneity of climate and different agro-ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon (Ovis orientalis) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management. Based on 50K SNP genotype data, we studied the genetic diversity of five indigenous Iranian sheep breeds: Afshari (n = 37), Moghani (n = 34), Qezel (n = 35), Zel (n = 46) and Lori-Bakhtiari (n = 46), and Asiatic mouflon (n = 8) sampled from Iran. Furthermore, genetic diversity and the breed admixture of Iranian sheep were assessed on a larger geographic scale using a reference panel comprising: three indigenous Afghan breeds – Arabi (n = 15), Balouchi (n = 15) and Gadik (n = 15); three indigenous breeds from Turkey and Cyprus – Cyprus Fat Tail (n = 30), Karakas (n = 18) and Norduz (n = 20); and three commercial European breeds – Suffolk (n = 19), Comisana (n = 24) and Engadine Red Sheep (n = 24). The results revealed that the investigated breeds are divided into five genetically distinct clusters according to their geographic origin. Afshari was closest to the local mouflon population and showed signs of mouflon admixture. Qezel was identified as a hybrid sheep breed. Much evidence supported the Afghan breeds being identical. Inbreeding values, which were estimated based on ROHs, were highest for Suffolk (F_ROH = 0.0544) and lowest for Balouchi (F_ROH = 0.0078). In conclusion, analysis of selected breeds from neighboring countries along with Asiatic mouflon gave a deeper insight into the evolutionary history and origin of Iranian sheep with important implications for future breed management.     

Disease,population viability,and recovery of endangered Sierra Nevada bighorn sheep

Sierra Nevada bighorn sheep (Ovis canadensis sierrae) experienced a severe population decline after European settlement from which they have never recovered; this subspecies was listed as endangered under the United States Endangered Species Act (ESA) in 1999. Recovery of a listed species is accomplished via federally mandated recovery plans with specific population goals. Our main objective was to evaluate the potential impact of disease on the probability of meeting specific population size and persistence goals, as outlined in the Sierra Nevada bighorn sheep recovery plan. We also sought to heuristically evaluate the efficacy of management strategies aimed at reducing disease risk to or impact on modeled bighorn populations. To do this, we constructed a stochastic population projection model incorporating disease dynamics for 3 populations (Langley, Mono, Wheeler) based on data collected from 1980 to 2007. We modeled the dynamics of female bighorns in 4 age classes (lamb, yearling, adult, senescent) under 2 disease scenarios: 5% lower survival across the latter 3 age classes and persistent 65% lower lamb survival (i.e., mild) or 65% reduced survival across all age classes followed by persistent 65% lower lamb survival (i.e., severe). We simulated management strategies designed to mitigate disease risk: reducing the probability of a disease outbreak (to represent a strategy like domestic sheep grazing management) and reducing mortality rate (to represent a strategy that improved survival in the face of introduced disease). Results from our projection model indicated that management strategies need to be population specific. The population with the highest growth rate ( ; Langley; = 1.13) was more robust to the effects of disease. By contrast, the population with the lowest growth rate (Mono; = 1.00) would require management intervention beyond disease management alone, and the population with a moderate growth rate (Wheeler; = 1.07) would require management sufficient to prevent severe disease outbreaks. Because severe outbreaks increased adult mortality, disease can directly reduce the probability of meeting recovery plan goals. Although mild disease outbreaks had minimal direct effects on the populations, they reduced recruitment and the number of individuals available for translocation to other populations, which can indirectly reduce the probability of meeting overall, range-wide minimum population size goals. Based on simulation results, we recommend reducing the probability of outbreak by continuing efforts to manage high-risk (i.e., spatially close) allotments through restricted grazing regimes and stray management to ensure recovery for Wheeler and Mono. Managing bighorn and domestic sheep for geographic separation until Sierra Nevada bighorn sheep achieve recovery objectives would enhance the likelihood of population recovery. © 2011 The Wildlife Society.     

Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs

Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r ²?≥?0.25) across the whole genome was observed at short distances of 0–10 kb. Further, the ancestral effective population size (N _e ) was analyzed by extent of LD and found that N _e increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, N _e only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.     

Harvest regulations and artificial selection on horn size in male bighorn sheep

Wild sheep in North America are highly prized by hunters and most harvest regulations restrict legal harvest to males with a specified minimum horn curl. Because reproductive success is skewed toward larger males that are socially dominant, these regulations may select against high-quality, fast-growing males. To evaluate potential selective effects of alternative management strategies, we analyzed horn increment measures of males harvested over 28 yr (1975–2003) in 2 bighorn sheep (Ovis canadensis) ecotypes in British Columbia, Canada. Using mixed-effect models we examined variation in hunter selection for horn size, early horn growth, and male age under different harvest regulations (Full Curl, Three Quarter Curl, Any Ram). Under all regulations, males with the greatest early horn growth were harvested at the youngest ages, before the age at which large horns influence reproductive success. Early growth decreased with harvest age and until ≥7 yr of age it was greatest in males harvested under Full Curl regulation. Permit type (General vs. Limited Entry Hunt) and hunter origin (British Columbia Resident vs. Non-Resident) had little effect on horn size of harvested males. Full Curl regulations increased the average age of harvested males by <1 yr relative to Three-Quarter Curl regulations. Age-specific horn measures in the California ecotype harvested under Three-Quarter Curl regulations declined over time but we observed no temporal declines in the Rocky Mountain ecotype, primarily harvested under Full Curl regulations. Management strategies that protect some males with greater early horn growth or provide harvest refuges to maintain genetic diversity are likely to reduce potential for negative effects of artificial selection. © 2010 The Wildlife Society     

Early development, adult mass, and reproductive success in bighorn sheep

Despite considerable empirical and theoretical work on the individualand population consequences of early development, little isknown about the correlations between early mass and adult sizeor lifetime reproductive success of free-ranging mammals. Usinga 26-year study of bighorn sheep (Ovis canadensis), we examinedhow mass as a lamb and mass gain as a yearling affected adultmass for both sexes, horn length of males and lifetime reproductivesuccess of females at different population densities. Mass asa 3-week-old lamb was either weakly or not correlated withadult mass, horn length of adult males, or the number of lambsweaned over a ewe's lifetime. Weaning mass was correlated withmost of these variables when the number of ewes in the populationwas taken into account. When weaning mass was controlled throughpartial correlation, mass as a yearling was correlated with adult mass of ewes but not with ewe reproductive success orwith adult mass or horn length of rams. Lamb mass and numberof ewes explained more of the variance in adult characteristicsfor males than for females. Our results suggest that mass gainduring lactation, possibly but not necessarily related to theamount of maternal care received, affects adult mass and reproductive success. Females appear better able than males to compensatefor poor early development, likely by postponing their firstreproduction. Mass gain over several years and the number ofewes in the population strongly affect adult mass of both sexesand therefore can have profound effects on reproductive successof this long-lived species with a multi-year growth period.     

Genome‐wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)

Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1,121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar‐Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographic pattern. Pairwise F_ST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor‐Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population—TIK, and maximum values were observed in the most southern population—SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH, and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the Late Pleistocene glaciations of Verkhoyansk Range.     

Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing

The objectives of this study were to develop breed-specific single nucleotide polymorphisms (SNPs) in five pig breeds sequenced with Illumina's Genome Analyzer and to investigate their usefulness for breed assignment purposes. DNA pools were prepared for Duroc, Landrace, Large White, Pietrain and Wild Boar. The total number of animals used for sequencing was 153. SNP discovery was performed by aligning the filtered reads against Build 7 of the pig genome. A total of 313,964 high confidence SNPs were identified and analysed for the presence of breed-specific SNPs (defined in this context as SNPs for which one of the alleles was detected in only one breed). There were 29,146 putative breed-specific SNPs identified, of which 4441 were included in the PorcineSNP60 beadchip. Upon re-examining the genotypes obtained using the beadchip, 193 SNPs were confirmed as being breed specific. These 193 SNPs were subsequently used to assign an additional 490 individuals from the same breeds, using the sequenced individuals as reference populations. In total, four breed assignment tests were performed. Results showed that for all methods tested 99% of the animals were correctly assigned, with an average probability of assignment of at least 99.2%, indicating the high utility of breed-specific markers for breed assignment and traceability. This study provides a blueprint for the way next-generation sequencing technologies can be used for the identification of breed-specific SNPs, as well as evidence that these SNPs may be a powerful tool for breed assignment and traceability of animal products to their breeds of origin.     

A framework for power and sensitivity analyses for quantitative genetic studies of natural populations, and case studies in Soay sheep (Ovis aries)

Studies of the quantitative genetics of natural populations have contributed greatly to evolutionary biology in recent years. However, while pedigree data required are often uncertain (i.e. incomplete and partly erroneous) and limited, means to evaluate the effects of such uncertainties have not been developed. We have therefore developed a general framework for power and sensitivity analyses of such studies. We propose that researchers first generate a set of pedigree data that they wish to use in a quantitative genetic study, as well as data regarding errors that occur in that pedigree. This pedigree is then permuted using the data regarding errors to generate hypothetical 'true' and 'assumed' pedigrees that differ so as to mimic pedigree errors that might occur in the study system under consideration. Phenotypic data are then simulated across the true pedigree (according to user-defined genetic and environmental covariance structures), before being analysed with standard quantitative genetic techniques in conjunction with the 'assumed' pedigree data. To illustrate this approach, we conducted power and sensitivity analyses in a well-known study of Soay sheep (Ovis aries). We found that, although the estimation of simple genetic (co)variance structures is fairly robust to pedigree errors, some potentially serious biases were detected under more complex scenarios involving maternal effects. Power analyses also showed that this study system provides high power to detect heritabilities as low as about 0.09. Given this range of results, we suggest that such power and sensitivity analyses could greatly complement empirical studies, and we provide the computer program PEDANTICS to aid in their application.