Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)

Background: Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results: Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion: Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics

Premating behavioral tactics of Columbian ground squirrels

In polygynous and polygynandrous mating systems males possess a variety of behavioral tactics that increase their access to reproductive females. In addition to overt combat or defending resources that attract mates, males use premating tactics that provide them with subsequent opportunities to copulate with receptive females. For Columbian ground squirrels, Urocitellus columbianus, we report that co-occupation of a burrow system by a reproductive male and a female on the night before the female exhibits diurnal estrus is an example of such a tactic. Our hypothesis was that nocturnal underground association results in successful consortships and therefore constitutes a mating tactic that is complementary to other mating behaviors exhibited during a female's estrus. Under this hypothesis appropriate predictions are that: males co-occupying a burrow system with a female at night should mate first with that female; males co-occupying a burrow system with a female overnight should sire more of her offspring than her subsequent mates; and the reproductive success of males co-occupying a burrow system with females should be higher than the reproductive success of mates that do not. To test our predictions we used a combination of field observations on nocturnal underground consortships (NUCs) and microsatellite DNA analyses of paternity. Males copulated with females during NUCs, as evidenced by inseminations. These males sired more offspring than males that did not participate in NUCs. Males ≥3 years old participated in more NUCs than sexually mature 2-year-old males. Our results supported the hypothesis that entrance into NUCs with a female before she exhibits estrus was a premating tactic that increased male reproductive success when exhibited in concert with other mating tactics such as territorial defens

Indirect effects on fitness between individuals that have never met via an extended phenotype

Interactions between organisms are ubiquitous and have important consequences for phenotypes and fitness. Individuals can even influence those they never meet, if they have extended phenotypes that alter the environments others experience. North American red squirrels (Tamiasciurus hudsonicus) guard food hoards, an extended phenotype that typically outlives the individual and is usually subsequently acquired by non‐relatives. Hoarding by previous owners can, therefore, influence subsequent owners. We found that red squirrels breed earlier and had higher lifetime fitness if the previous hoard owner was a male. This was driven by hoarding behaviour, as males and mid‐aged squirrels had the largest hoards, and these effects persisted across owners, such that if the previous owner was male or died in mid‐age, subsequent occupants had larger hoards. Individuals can, therefore, influence each other’s resource‐dependent traits and fitness without ever meeting, such that the past can influence contemporary population dynamics through extended phenotypes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148423/1/ele13230.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148423/2/ele13230_am.pd

Mating order and reproductive success in male Columbian ground squirrels (Urocitellus columbianus)

Multiple mating by females is common in many mammalian species, often resulting in mixed paternity litters. In such mating systems, mating order, male age, and male body mass frequently play an important role in determining male reproductive success. We tested for these effects on male reproductive success in Columbian ground squirrels (Urocitellus columbianus). The mating activity of estrous females was observed, and the occurrence of sperm precedence was tested using microsatellites to determine paternity in a total of 147 litters (434 offspring), including 110 litters (334 offspring) where the mating position of individual males was determined. Females mated with up to 8 males per litter, whereas paternity analyses revealed that only the first 5 males to mate actually sired offspring. The number of offspring sired significantly decreased with position in the mating sequence, showing a strong first male advantage. The extent of this advantage diminished with an increasing number of male mating partners, indicating that sperm competition plays an important role. A male's position in the females' mating sequences was not consistent within and across seasons, suggesting that individual males did not follow distinct reproductive strategies. Rather, males of intermediate age were more successful than young and old males, when corrected for age effects; heavier males were more likely to mate first. We conclude that males gain the largest part of their seasonal reproductive output from mating first with a female due to a pronounced first male advantage but gain considerable additional fitness from mating with additional, already mated female

Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep

<p>Abstract</p> <p>Background</p> <p>The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corresponding sets of molecular markers that are sufficiently large. We took advantage of two long-term field studies of pedigreed individuals and genomic resources originally developed for domestic sheep (<it>Ovis aries</it>) to construct a linkage map for bighorn sheep, <it>Ovis canadensis</it>. We then assessed variability in genomic structure and recombination rates between bighorn sheep populations and sheep species.</p> <p>Results</p> <p>Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals.</p> <p>Conclusions</p> <p>We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the elevated mean recombination rate observed in domestic sheep, our results suggest that it is a characteristic of <it>Ovis </it>species. However, domestication may have played a role in altering patterns of heterochiasmy. Finally, we found that interval-specific patterns of sexual dimorphism were preserved among closely related <it>Ovis </it>species, possibly due to the conserved position of these intervals relative to the centromeres and telomeres. This study exemplifies how transferring genomic resources from domesticated species to close wild relative can benefit evolutionary ecologists while providing insights into the evolution of genomic structure and recombination rates of domesticated species.</p

Social effects of territorial neighbours on the timing of spring breeding in North American red squirrels

Organisms can affect one another’s phenotypes when they socially interact. Indirect genetic effects occur when an individual’s phenotype is affected by genes expressed in another individual. These heritable effects can enhance or reduce adaptive potential, thereby accelerating or reversing evolutionary change. Quantifying these social effects is therefore crucial for our understanding of evolution, yet estimates of indirect genetic effects in wild animals are limited to dyadic interactions. We estimated indirect phenotypic and genetic effects, and their covariance with direct effects, for the date of spring breeding in North American red squirrels (Tamiasciurus hudsonicus) living in an array of territories of varying spatial proximity. Additionally, we estimated indirect effects and the strength of selection at low and high population densities. Social effects of neighbours on the date of spring breeding were different from zero at high population densities but not at low population densities. Indirect phenotypic effects accounted for a larger amount of variation in the date of breeding than differences attributable to the among‐individual variance, suggesting social interactions are important for determining breeding dates. The genetic component to these indirect effects was however not statistically significant. We therefore showcase a powerful and flexible method that will allow researchers working in organisms with a range of social systems to estimate indirect phenotypic and genetic effects, and demonstrate the degree to which social interactions can influence phenotypes, even in a solitary species.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149549/1/jeb13437_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149549/2/jeb13437.pd

Using playback of territorial calls to investigate mechanisms of kin discrimination in red squirrels

Kin recognition can facilitate kin selection and may have played a role in the evolution of sociality. Red squirrels (Tamiasciurus hudsonicus) defend territories using vocalizations known as rattles. They use rattles to discriminate kin, though the mechanism underlying this ability is unknown. Our objective was to distinguish between the mechanisms of prior association, where animals learn the phenotypes of kin they associate with early in life, and phenotype matching/recognition alleles, where animals use a template to match phenotypes, thereby allowing them to recognize kin without an association early in life. We used audio playbacks to measure the responses of squirrels to rattles from familiar kin, unfamiliar kin, and non-kin. Initial analyses revealed that red squirrels did not discriminate between familiar and unfamiliar kin, but also did not discriminate between kin and non-kin, despite previous evidence indicating this capability. Post hoc analyses showed that a squirrel’s propensity to rattle in response to playback depended on an interaction between relatedness and how the playback stimuli had been recorded. Red squirrels discriminated between rattles from close kin (r = 0.5) and rattles from non-kin (r < 0.125) when the rattles were recorded from provoked squirrels. Squirrels did not exhibit kin discrimination in response to unsolicited rattles. Once we accounted for how the stimuli had been recorded, we found no difference in the responses to familiar and unfamiliar kin. Our study suggests that kin discrimination by red squirrels may be context dependent

Red squirrels use territorial vocalizations for kin discrimination

The ability to discriminate among individuals, or among classes of individuals, can provide animals with important fitness benefits. Although several mechanisms for discrimination are possible, most require animals to show stable phenotypic variation that reflects their identity or their membership in a particular class (e.g. sex, mate, kin). For territorial animals that rarely interact physically, vocalizations could serve as long-distance signals that facilitate discrimination. In this study, we tested whether the territorial rattle vocalizations of North American red squirrels, Tamiasciurus hudsonicus, are repeatable, and whether they could hence provide the basis for multiple types of discrimination. We measured four structural features from two rattles from each of 76 marked squirrels. All four features were repeatable, which is consistent with territorial rattles being individually distinctive. We then conducted a playback experiment to determine whether squirrels use rattles for discrimination. Specifically, we tested whether squirrels discriminate between the rattles of neighbours and non-neighbours, and kin (coefficient of relatedness, r ≥ 0.25) and non-kin (r < 0.125). Following a 2 × 2 factorial design, we broadcast a rattle from a non-neighbouring nonkin individual to 15 subjects, from a neighbouring nonkin individual to 14 subjects, from a non-neighbouring kin individual to 11 subjects, and from a neighbouring kin individual to 13 subjects. Subjects did not discriminate between the rattles of neighbours and non-neighbours, but did respond differently to the rattles of kin and nonkin. Specifically, squirrels were significantly more likely to produce a rattle of their own in response to the broadcasted rattles of nonkin versus the broadcasted rattles of kin. This result demonstrates that red squirrels can use territorial vocalizations for kin discrimination. It also suggests that they are more tolerant of territorial intrusions by kin

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels

Abstract Background Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota. Result For the first time, this study revealed significant spatial patterns of gut microbiota within a host population, suggesting limited dispersal could play a role in shaping and maintaining the structure of gut microbial communities. We also found a remarkable seasonal rhythm in red squirrel’s gut microbial composition manifested by a tradeoff between relative abundance of two genera Oscillospira and Corpococcus and clearly associated with seasonal variation in diet availability. Our results show that in nature, environmental factors exert a much stronger influence on gut microbiota than host-associated factors including age and sex. Despite strong environmental effects, we found clear evidence of individuality and maternal effects, but host genetics did not seem to be a significant driver of the gut microbial communities in red squirrels. Conclusion Taken together, the results of this study emphasize the importance of external ecological factors rather than host attributes in driving temporal and spatial patterns of gut microbiota in natural environment.https://deepblue.lib.umich.edu/bitstream/2027.42/140397/1/40168_2017_Article_382.pd

Sexually selected infanticide by male red squirrels in advance of a mast year

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143645/1/ecy2158-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143645/2/ecy2158-sup-0001-AppendixS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143645/3/ecy2158.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143645/4/ecy2158_am.pd