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Isle Royale National Park, Michigan. The island is approximately 80 km long and 12 km wide and is located in the northwestern portion of Lake Superior. At its shortest Euclidean distance, the island is 24 km off the southern coast of Canada.
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Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alc...
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... valuable information, finding naturally isolated wild populations with sufficient demographic and genetic data to evaluate change in genetic variation over time is difficult. Isle Royale is a small isolated island, approximately 80 km long, 12 km wide, and located, at its shortest Euclidean distance, 24 km off the southern coast of Canada ( Fig. 1) providing an opportunity to study genetic change under naturally isolated conditions. While Lake Superior has made colonization of the island difficult for many mammalian species, it is currently home to nearly twenty mammal species, including the North American moose, Alces alces, and gray wolves, Canis ...
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Kenyan indigenous goat populations are not fully characterized, and this can result in erosion of their unique genotypes through indiscriminate cross breeding. Kenyan goat breeds are morphologically classified as Small East African goats (SEA), Galla goats and their crosses. This study aimed at genetic characterization of Kenyan regional goat breed...
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... Nevertheless, a swift population decline could occur due to the small population size associated with habitat fragmentation. A similar scenario has been observed in the cases of historically widespread mammal populations where habitat fragmentation occurred recently (Sattler et al. 2017;Salado et al. 2023). In Taiwan, anthropogenic exploitation and environmental changes have led to the reduction of pristine forest habitats in recent history (Chen et al. 2019), and this habitat fragmentation has been hypothesized as the cause for the decrease in the effective population size of forest-dwelling beetles (De Vivo et al. 2023). ...
... We argue that the observed significant inbreeding pattern in the Formosan Long-Arm Scarab beetle, despite its geographically connected moderate population size, may have resulted from a similar process. To test this hypothesis, however, requires genetic data from historical samples (Sattler et al. 2017;Salado et al. 2023), which is beyond the scope of the current study. ...
Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately-sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies.
... During the period of the wolf population's decline from 2010 to 2019, the moose population increased from ∼500 moose to ∼2000 moose . The Isle Royale moose population was founded around 1900 likely by a small number of individuals, however the exact circumstances of this founding, and specifically whether it occurred naturally or by humans, remains unknown (Murie 1934;Mech 1966;Sattler et al. 2017). Thus, the Isle Royale moose population has endured in isolation for nearly twice as long as the wolf population and, although some evidence suggests that moose may be able to swim the 24 km distance between the island and nearby mainland, previous genetic studies suggest that the population is genetically isolated from the mainland and has low genetic diversity (Wilson et al. 2003;Sattler et al. 2017). ...
... The Isle Royale moose population was founded around 1900 likely by a small number of individuals, however the exact circumstances of this founding, and specifically whether it occurred naturally or by humans, remains unknown (Murie 1934;Mech 1966;Sattler et al. 2017). Thus, the Isle Royale moose population has endured in isolation for nearly twice as long as the wolf population and, although some evidence suggests that moose may be able to swim the 24 km distance between the island and nearby mainland, previous genetic studies suggest that the population is genetically isolated from the mainland and has low genetic diversity (Wilson et al. 2003;Sattler et al. 2017). However, despite this long-term isolation and reduced genetic diversity, the moose population appears to be free of obvious signs of inbreeding depression and has similar population growth rates to mainland populations (Hoy, MacNulty, et al. 2020). ...
... Finally, we also estimated kinship for all North American samples, and found that the mainland samples are not closely related to one another . In summary, these findings suggest that the Isle Royale population has been isolated from nearby mainland moose populations as suggested by previous work (Wilson et al. 2003;Sattler et al. 2017) and provide a general characterization of moose population structure in North America. ...
Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.
... The forecasted patterns of moose occurrence in 2060 under various climate and human development scenarios by Pearman-Gillman et al. (2020a) predicted that moose occurrence in New England may be reduced drastically, with only northern areas of New England maintaining high probabilities of moose occurrence. Increasing barriers to gene flow, combined with potential population reductions due to climate mediated Minnesota, Idaho, Montana, and Wyoming (Ferrante et al. 2021), in contrast with isolated moose populations in Michigan's Isle Royale experiencing decreasing heterozygosity and increasing inbreeding (Sattler et al. 2017). Nonetheless, high IBS values documented in this study indicated that moose shared similar genetic material. ...
... These contrasting results may be influenced by the unbalanced sampling in this study, but we note that this discrepancy existed in all sampled areas regardless of collection method and the number of moose sampled. Key to this contrast is the previously suggested idea that low levels of genetic variation in moose populations are the consequence of population bottlenecks (Cronin et al. 2001;Broders et al. 2002, Sattler et al. 2017. Low levels of heterozygosity may have resulted from genetic drift over the series of population founder events from the expansion of moose into eastern North America, and bottlenecks including the near extirpation of moose in the 19 th century and recent population declines due to parasitic disease and associated epizootics. ...
Genetic diversity is critical to a population’s ability to overcome gradual environment change. Large-bodied wildlife existing in regions with relatively high human population density are vulnerable to isolation-induced genetic drift, population bottlenecks, and loss of genetic diversity. Moose ( Alces americanus americanus ) in eastern North America have a complex history of drastic population changes. Current and potential threats to moose populations in this region could be exacerbated by loss of genetic diversity and connectivity among subpopulations. Existing genetic diversity, gene flow, and population clustering and fragmentation of eastern North American moose are not well quantified, while physical and anthropogenic barriers to population connectivity already exist. Here, single nucleotide polymorphism (SNP) genotyping of 507 moose spanning five northeastern U.S. states and one southeastern Canadian province indicated low diversity, with a high proportion of the genomes sharing identity-by-state, with no consistent evidence of non-random mating. Gene flow estimates indicated bidirectionality between all pairs of sampled areas, with magnitudes reflecting clustering and differentiation patterns. A Discriminant Analysis of Principal Components analysis indicated that these genotypic data were best described with four clusters and indicated connectivity across the Saint Lawrence River and Seaway, a potential physical barrier to gene flow. Tests for genetic differentiation indicated restricted gene flow between populations across the Saint Lawrence River and Seaway, and between many sampled areas facing expanding human activity. These results document current genetic variation and connectivity of moose populations in eastern North America, highlight potential challenges to current population connectivity, and identify areas for future research and conservation.
... Additionally, this result may not apply to all moose subpopulations in the contiguous United States. For example, we see cases of geographically isolated moose having higher inbreeding values as expected, such as the A. a. andersoni population on Michigan's Isle Royale (not included in this study) whose F IS values have doubled between 1960-1965 (F IS = 0.08) and 2000-2005 (F IS = 0.16) due to lack of gene flow from neighboring populations (Sattler et al. 2017). ...
Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
... Thus, this population displays evidence that reduction in mean body and antler size can occur over the relatively short time period of 100 years. While moose on Isle Royale also show reduced genetic diversity relative to mainland populations (Wilson et al. 2003;Sattler et al. 2017), reductions in body and antler sizes have been attributed to nutrient limitation on the island caused by five to 10 times higher population densities relative to the mainland population (Peterson et al. 2011;Mills and Peterson 2013). For the purposes of understanding genetic and phenotypic differences of A. a. shirasi, the Isle Royale example supports the notions that: 1) observed differences in body and antler size seen in A. a. shirasi could be caused, at least in part, by differences in environmental conditions; and 2) that such differences can manifest over relatively short (100 years) time periods. ...
Subspecies designations within temperate species' ranges often reflect populations that were isolated by past continental glaciation, and glacial vicariance is believed to be a primary mechanism behind the diversification of several subspecies of North American cervids. We used genetics and the fossil record to study the phylogeography of three moose subspecies (Alces alces andersoni, A. a. gigas, and A. a. shirasi) in western North America. We sequenced the complete mitochondrial genome (16,341 base pairs; n = 60 moose) and genotyped 13 nuclear microsatellites (n = 253) to evaluate genetic variation among moose samples. We also reviewed the fossil record for detections of all North American cervids to comparatively assess the evidence for the existence of a southern refugial population of moose corresponding to A. a. shirasi during the last glacial maximum of the Pleistocene. Analysis of mtDNA molecular variance did not support distinct clades of moose corresponding to currently recognized subspecies, and mitogenomic haplotype phylogenies did not consistently distinguish individuals according to subspecies groupings. Analysis of population structure using microsatellite loci showed support for two to five clusters of moose, including the consistent distinction of a southern group of moose within the range of A. a. shirasi. We hypothesize that these microsatellite results reflect recent, not deep, divergence and may be confounded by a significant effect of geographic distance on gene flow across the region. Review of the fossil record showed no evidence of moose south of the Wisconsin ice age glaciers ≥ 15,000 years ago. We encourage the integration of our results with complementary analyses of phenotype data, such as morphometrics, originally used to delineate moose subspecies, for further evaluation of subspecies designations for North American moose.
... It is possible if an ice bridge forms between Isle Royale and the continental mainland, however this is increasingly rare. Even when an ice bridge has formed, moose departure from the mainland is undocumented [60]. The island was likely colonized by moose that swam from the mainland [61], but genetic analyses have reported no evidence of recent immigration [60] Balsam fir is an important component of winter diet; twigs from other woody vascular plants and arboreal lichens compose the remainder [62]. ...
... Even when an ice bridge has formed, moose departure from the mainland is undocumented [60]. The island was likely colonized by moose that swam from the mainland [61], but genetic analyses have reported no evidence of recent immigration [60] Balsam fir is an important component of winter diet; twigs from other woody vascular plants and arboreal lichens compose the remainder [62]. The spring diet of moose includes newly emergent leaves and the summer diet is largely composed of current annual leaf growth of deciduous plants as well as aquatic macrophytes [63,64]. ...
Moose (Alces alces) are generalist herbivores, but are important aquatic-terrestrial ecotone specialists. Aquatic macrophytes are a high-quality food source for moose during summer, but the importance of aquatic food sources to the moose diet is difficult to study. We used stable isotope analysis of carbon and nitrogen from moose hooves and forage (terrestrial plants, aquatic macrophytes, and arboreal lichen) to assess the diet of moose at Isle Royale National Park, Michigan, USA, using Bayesian mixing models. We also evaluated the isotopic variability along chronologies of serially sampled hooves. Overall, our mixing models indicate that 13%-27% of the summer moose diet was aquatic in origin. Among moose that died during winter, body condition was impaired and hoof δ 15 N was higher where aquatic habitats were sparse. Although isotope chronologies preserved in hooves could significantly enhance our understanding of ungulate foraging ecology, interpretation of such chronologies is presently limited by our lack of knowledge pertaining to hoof growth rate and seasonal growth variability related to age and health. Distinct isotopic values among terrestrial plants, aquatic macrophytes, and arboreal lichens indicate that continued methodological advances in stable isotope ecology will lead to more precise estimates of the contribution of aquatic feeding to moose population dynamics and other ungulates.
... For example, in case of diversity studies, they have been used in functional diversity (Acuña et al., 2012), ecological trait diversity assessment (van Tienderen et al., 2002). Molecular markers have been used in computation of important attributes of an ecological population (Putman and Carbone, 2014) like estimation of inbreeding (Al-Atiyat, 2016) and relatedness (Taylor, 2015), population viability and extinction rate estimation (Sattler et al., 2017), genealogical registrations and conservation decisions (Sereno et al., 2008). Designing conservation strategies based on Franklin's 50/500 rule of conservation (Franklin, 1980), such tool can be used to estimate effective population size and optimal census size to rationalize and optimize time and cost factor in a conservation program formulation. ...
Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.
... This form of testing first gained popularity with the development of microsatellite short tandem repeat (STR), and mitochondrial genome markers, concurrent with the development of DNA amplification and sequencing technologies. Approximately 5 to 11 microsatellite markers from cattle, sheep, and caribou (Rangifer tarandus) have been adapted for moose studies [17][18][19][20][21][22] . These studies form the basis of our current understanding of North American moose population structure and genetic diversity. ...
Background: Moose ( Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data.
Methods: WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively. Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs.
Results: Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively. The reads clustered at genomic segments, where sequence identity between these species was greater than 95%. In these segments, average mapped read depth was approximately 19-fold. Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species. Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east. A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design.
Conclusions: All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating relatedness in North American moose.
Species reintroductions have the potential to cause genetic bottleneck events resulting in increased genetic drift, increased inbreeding, and reduced genetic diversity creating negative fitness consequences for populations. Roosevelt elk (Cervus canadensis roosevelti Erxleben 1777) are ‘at risk’ in British Columbia (BC), Canada. Once widespread along the west coast, Roosevelt elk were likely extirpated from the mainland by 1900 and experienced a substantial population bottleneck on Vancouver Island at that time, and again in the 1950s. Reintroduced to the mainland from Vancouver Island in the 1980s, this re-established population became the source for subsequent mainland translocations. To understand the effects of reintroduction strategy on genetic diversity, we analyzed genetic variation in 355 Roosevelt elk from Vancouver Island and mainland BC. Using mitochondrial DNA and 10 microsatellite loci, molecular analyses showed overall reduced genetic diversity relative to other extant elk populations, genetic isolation of the southern Vancouver Island population, and increased genetic drift among reintroduced herds. Four reintroduced populations were found to have increased levels of inbreeding. Results of this study contribute to our knowledge of reintroduction biology and can be used to guide continued conservation and management of at-risk species.
Eastern Moose (Alces americanus americanus (Clinton, 1822)) on mainland Nova Scotia (MNS) are declining and experience limited immigration across the Isthmus of Chignecto from the larger population in neighbouring New Brunswick. Provincially Endangered, the recovery strategy for MNS Moose involves mitigating various threats that may lead to local extirpation. We examine genetic diversity of MNS Moose using microsatellite markers and mitochondrial (mtDNA) control region sequences. Genetic similarities with the Alces a. americana population in New Brunswick and the introduced Northwestern Moose (Alces americanus andersoni (= Alces alces andersoni) Peterson, 1952) population on Cape Breton Island are also analysed. Observed heterozygosity for microsatellites for MNS Moose was low and there was also evidence of limited gene flow between Nova Scotia and New Brunswick across the narrow Isthmus of Chignecto that connects these provinces. Consistent with relatively recent colonization of North America by Moose dispersing across the Bering Land Bridge <15 000 years ago, mtDNA haplotypes of MNS Moose were identical or extremely similar to haplotypes found across North America. However, mtDNA diversity was lower in Nova Scotia and New Brunswick than in more central regions of the species’ range. Active measures to maintain habitat that promote connectivity across the Isthmus of Chignecto would likely be valuable for Moose in terms of maintaining genetic variation in the region and reducing inbreeding.
