Transfer of bovine microsatellites to the cervine (Cervus elaphus)

Bovine microsatellites were used to amplify DNA of red deer ( Cervus elaphus ). Fourteen of 27 bovine systems (52%) displayed polymorphism, while no (CA)_n-repeat was detected in seven systems and six systems gave no amplificates in red deer. The allele number ranged from 2 to 7, the polymorphism information content between 0.24 and 0.76. The results demonstrate that transfer of microsatellite systems between families of the same order (artiodactyla) is possible. Molecular genetic research will help to clarify the differentiation and ecology of wild animals and will contribute to define criteria needed for the preservation of endangered species.     

Characterization of 11 polymorphic tetranucleotide microsatellites for forensic applications in California elk (Cervus elaphus canadensis)

Eleven polymorphic tetranucleotide microsatellite loci have been developed for forensic use in the protection of California elk. Based on a reference sample of elk taken from three races throughout California, the loci consist of 4–9 alleles (average 6.125). Probabilities of identity ( Paetkau et al. 1995 ) range from 0.079 to 0.288, with an overall probability of identity of 1.3 × 10^?9 (one in 7.8 × 10⁸).     

Population viability analysis to identify management priorities for reintroduced Elk in the Cumberland Mountains,Tennessee

We used an individual-based population model to perform a viability analysis to simulate population growth (λ) of 167 elk (Cervus elaphus manitobensis; 71 male and 96 female) released in the Cumberland Mountains, Tennessee, to estimate sustainability (i.e., λ > 1.0) and identify the most appropriate options for managing elk restoration. We transported elk from Elk Island National Park, Alberta, Canada, and from Land Between the Lakes, Kentucky, and reintroduced them beginning in December 2000 and ending in February 2003. We estimated annual survival rates for 156 radio-collared elk from December 2000 until November 2004. We used data from a nearby elk herd in Great Smoky Mountains National Park to simulate pessimistic and optimistic recruitment and performed population viability analyses to evaluate sustainability over a 25-year period. Annual survival averaged 0.799 (Total SE = 0.023). The primary identifiable sources of mortality were poaching, disease from meningeal worm (Parelaphostrongylus tenuis), and accidents (environmental causes and unintentional harvest). Population growth given pessimistic recruitment rates averaged 0.895 over 25 years (0.955 in year 1 to 0.880 in year 25); population growth was not sustainable in 100% of the runs. With the most optimistic estimates of recruitment, mean λ increased to 0.967 (1.038 in year 1 to 0.956 in year 25) with 99.6% of the runs failing to be sustainable. We suggest that further translocation efforts to increase herd size will be ineffective unless survival rates are increased in the Cumberland Mountains. © 2011 The Wildlife Society.     

Rapidly declining fine-scale spatial genetic structure in female red deer

A growing literature now documents the presence of fine-scale genetic structure in wild vertebrate populations. Breeding population size, levels of dispersal and polygyny--all hypothesized to affect population genetic structure--are known to be influenced by ecological conditions experienced by populations. However the possibility of temporal or spatial variation in fine-scale genetic structure as a result of ecological change is rarely considered or explored. Here we investigate temporal variation in fine-scale genetic structure in a red deer population on the Isle or Rum, Scotland. We document extremely fine-scale spatial genetic structure (< 100 m) amongst females but not males across a 24-year study period during which resource competition has intensified and the population has reached habitat carrying capacity. Based on census data, adult deer were allocated to one of three subpopulations in each year of the study. Global F(ST) estimates for females generated using these subpopulations decreased over the study period, indicating a rapid decline in fine-scale genetic structure of the population. Global F(ST) estimates for males were not different from zero across the study period. Using census and genetic data, we illustrate that, as a consequence of a release from culling early in the study period, the number of breeding females has increased while levels of polygyny have decreased in this population. We found little evidence for increasing dispersal between subpopulations over time in either sex. We argue that both increasing female population size and decreasing polygyny could explain the decline in female population genetic structure.     

Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations

Genetic diversity is low in natural populations of red pine, Pinus resinosa, a species that has a vast range across north-eastern North America. In this study, we examined 10 chloroplast microsatellite or simple sequence repeats (cpSSR) loci in 136 individuals from 10 widespread populations. Substantial variation for the cpSSR loci was observed in the study populations. The contrast with red pine's lack of variation for other types of loci is likely to be due to the higher mutation rates typical of SSR loci. The amount of variation is lower than that generally found for cpSSR loci in other pine species. In addition, the variation exhibits a striking geographical pattern. Most of the genetic diversity is among populations, with little within populations, indicating substantial isolation of and genetic drift within many populations in the southern half of the species distribution. The greatest diversity now occurs in the north-eastern part of New England, which is especially intriguing because this entire area was glaciated. Thus the centre of diversity cannot be the origin of postglacial populations, rather it is likely caused by admixture, most probably because of influences from two separate refugia. Furthermore, the pattern indicates that the spread of red pine since the last glaciation is rather more complex than usually described, and it likely includes more than one refugia, complex migration routes, and postglacial-retreat isolation and genetic drift among shrinking populations in regions of the present southern range.     

Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 × 87 km), significant population structure was found using F -statistics ( F _ST = 0.019) and the program structure , with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.     

Mark-resight and sightability modeling of a western Washington elk population

The North Cascades (Nooksack) elk (Cervus elaphus) population declined during the 1980s, prompting a closure to state and tribal hunting in 1997 and an effort to restore the herd to former abundance. In 2005, we began a study to assess the size of the elk population, judge the effectiveness of restoration efforts, and develop a practical monitoring strategy. We concurrently evaluated 2 monitoring approaches: sightability correction modeling and mark-resight modeling. We collected data during February–April helicopter surveys and fit logistic regression models to predict the sightability of elk groups based on group and environmental variables. We used an information-theoretic criterion to compare 9 models of varying complexity; the best model predicted sightability of elk groups based on 1) transformed (log₂) group size, 2) forest canopy cover (%), and 3) a categorical activity variable (active vs. bedded). The sightability model indicated relatively steady and modest herd growth during 2006–2011, but estimates were less than minimum-known-alive counts. We also used the logit-normal mixed effects (LNME) mark-resight model to generate estimates of total elk population size and the sizes of the adult female and branch-antlered male subpopulations. We explored 15 LNME models to predict total population size and 12 models to predict subpopulations. Our results indicated individual heterogeneity in resighting probabilities and variation in resighting probabilities across sexes and some years. Model-averaged estimates of total population size increased from 639 (95% CI = 570–706) in spring 2006 to 1,248 (95% CI = 1,094–1,401) in 2011. We estimated the adult female subpopulation increased from 381 (95% CI = 338–424) in spring 2006 to 573 (95% CI = 507–639) by 2011. The branch-antlered male subpopulation estimates increased from 87 (95% CI = 54–119) to 180 (95% CI = 118–241) from spring 2006 to spring 2011. The LNME model estimates were greater than sightability model estimates and minimum-known-alive counts. We concluded that mark-resight performed better and was a viable approach for monitoring this small elk population and possibly others with similar characteristics (i.e., small population and landscape scales), but this approach requires periodic marking of elk; we estimated mark-resight costs would be about 40% greater than sightability model application costs. The utility of sightability-correction modeling was limited by a high proportion of groups with low detectability on our densely forested landscape. © 2012 The Wildlife Society.     

Microsatellite variation and assessment of genetic structure in tea tree (Melaleuca alternifolia– Myrtaceae)

Analysis of five microsatellite loci in 500 Melaleuca alternifolia individuals produced 98 alleles that were useful for population genetic studies. Considerable levels of observed heterozygosity were recorded (HO = 0.724), with approximately 90% of the variability being detected within populations. A low level of selfing (14%) was suggested to be the principal cause of excess homozygosity in a number of populations (overall FIS = 0.073). This study showed low levels of inbreeding in certain populations as well as a significant isolation-by-distance model. Only two groups of populations (Queensland and New South Wales) constituted different genetic provenances as a result of geographical isolation. The M. alternifolia data suggest that microsatellite loci did not always arise by a stepwise mutation process but that larger jumps in allele size may be involved in their evolution.     

Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas

The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations.     

Variations in elk aggregation patterns across a range of elk population sizes at Wall Creek,Montana

In the Greater Yellowstone Ecosystem, growing concern over increasing rates of brucellosis seroprevalence in wildlife has challenged wildlife managers to develop strategies for minimizing the potential for pathogen exchange within and between wildlife populations. Recent evidence suggests that increases in elk seroprevalence may be associated with increasing elk densities and/or increasing size of elk aggregations. However, the interactions between elk population density, landscape factors, and elk aggregation patterns are not well-understood, making appropriate management responses challenging. Using a unique, long-term elk aggregation dataset collected across a wide range of elk population sizes, we investigated relationships between elk population size, landscape factors, and elk aggregation responses (group size and group density) with goals of clarifying how changes in elk population size may affect elk aggregation patterns. Overall, landscape attributes and weather had a stronger influence on elk aggregation patterns than factors such as elk population size that are within management control. We found little evidence that elk population size affected mean elk group sizes, but we did find evidence that the size and density of the largest elk aggregations increased as elk population size increased. We also found some evidence that group densities increased following the establishment of wolves. However, across the relatively wide range of elk population sizes observed in this study, only modest changes in elk group density were observed, suggesting that dramatic reductions in population sizes would be necessary to produce measureable reductions in elk group density to affect frequency-dependent transmission. Management actions designed to lower disease transmission are likely to negatively affect other objectives related to elk management and conservation. We therefore suggest that a first step in managing disease transmission risk is agreement among stakeholders interested in elk management of all objectives related to elk management, including acknowledgment that disease transmission is undesirable. © 2011 The Wildlife Society.     

Microsatellite loci for the Chinese bamboo rat Rhizomus sinensis

We describe 19 polymorphic microsatellite loci for the bamboo rat Rhizomus sinensis. When tested with 20 samples from a single population, these loci exhibited a mean of 4.5 alleles per locus and a mean expected heterozygosity of 0.612. All loci were in Hardy-Weinberg equilibrium and no evidence for linkage disequilibrium was detected between any loci. These loci will be useful for studying population genetic diversity and differentiation in the Chinese bamboo rat.     

Microsatellite variation and population genetic structure of the red throat emperor on the Great Barrier Reef

Analysis (using three analytical approaches) of eight microsatellite markers from six locations in three geographic regions of the Great Barrier Reef (GBR), including populations that differed in demographic characteristics, showed no evidence of genetic stock structure in the red throat emperor Lethrinus miniatus. Measures of inter‐population differentiation were non‐significant (P ≥ 0·67). Using a Bayesian clustering approach, ‘admixture’ was detected (mean alpha values >1) with allele frequencies for each of the locations sampled being correlated equally with allele frequencies from all locations sampled. The number of populations (K) identified was one, based on the estimates of the probability of the data at various K values (K = 1, 2, 3, … 6). Additionally, alpha values did not stabilize to relatively constant values in any of the Bayesian analyses performed, indicating that there was no real genetic structure between locations. Analysis of genetic variation as detected by analysis of molecular variance (AMOVA) indicated that almost all of the variance in the data (99·74%, P ≤ 0·023) was within populations, rather than among populations (0·15%, P ≤ 0·176) or amongst regions sampled (0·10%, P ≤ 0·247) on the GBR. F_st statistics identified four individual loci having statistically significant differentiation among populations, but these were only related to one out of 12 pair‐wise comparisons where populations differed demographically. Given these results (albeit using neutral markers), together with the capacity of adults and larvae to be mobile between reefs on the inter‐connected GBR, it is considered unlikely that L. miniatus populations exist as distinct genetic stocks in the GBR. It is therefore not possible, using neutral markers, to reject the null hypothesis that the fishery be managed as a single panmictic stock.     

Microsatellite variation among diverging populations of Drosophila mojavensis

Divergence and speciation may occur by various means, depending on the particular history, selective environments, and genetic composition of populations. In Drosophila mojavensis, a good model of incipient speciation, understanding the population genetic structure within this group facilitates our ability to understand the context in which reproductive isolation among populations is developing. Here we report the genetic structure and relationships of D. mojavensis populations at nuclear loci. We surveyed 29 populations throughout the distribution of D. mojavensis for four microsatellite loci to differentiation among populations of this species. These loci reveal four distinct geographical regions of D. mojavensis populations in the south-western United States and north-western Mexico--(i) Baja California peninsula (Baja), (ii) Sonora, Mexico-southern Arizona, United States (Sonora), (iii) Mojave Desert and Grand Canyon (Mojave), and (iv) Santa Catalina Island (Catalina). While all regions show strong isolation, Mojave and Catalina are highly diverged from other regions. Within any region, populations are largely homogenous over broad geographical distances. Based on the population structure, we find clear geographical barriers to gene flow appear to have a strong effect in isolating populations across regions for this species.     

Genetic structure of red deer population in northeastern Poland in relation to the history of human interventions

We studied the genetic structure of a red deer (Cervus elaphus) population in 8 woodlands of northeastern Poland and 1 in western Belarus and compared it with the documented history of the population in the region. Red deer nearly went extinct in the region in the 18th and 19th centuries. In the mid-19th century, reintroductions began and continued until the mid-1960s. Animals were translocated from various sites in Poland and other European countries. We genotyped 303 individuals using 14 microsatellite loci and sequenced 253 individuals for a fragment of the control region (mitochondrial DNA [mtDNA]). The microsatellite analyses demonstrate that 3 genetically separate subpopulations exist, but 4 according to mtDNA. All haplotypes found in northeastern Poland are closely related to haplotypes from northern and northwestern Europe. The only individuals that could have originated from autochthonous red deer populations, rather than introductions, were found in Napiwoda Forest. The present regional genetic structure of the species is consistent with the known history of red deer translocations. Current patterns of genetic diversity in these populations are determined by the interaction of past human management and contemporary natural migrations. © 2012 The Wildlife Society.     

Density-dependent effects on physical condition and reproduction in North American elk: an experimental test

Density dependence plays a key role in life-history characteristics and population ecology of large, herbivorous mammals. We designed a manipulative experiment to test hypotheses relating effects of density-dependent mechanisms on physical condition and fecundity of North American elk (Cervus elaphus) by creating populations at low and high density. We hypothesized that if density-dependent effects were manifested principally through intraspecific competition, body condition and fecundity of females would be lower in an area of high population density than in a low-density area. Thus, we collected data on physical condition and rates of pregnancy in each experimental population. Our manipulative experiment indicated that density-dependent feedbacks affected physical condition and reproduction of adult female elk. Age-specific pregnancy rates were lower in the high-density area, although there were no differences in pregnancy of yearlings or in age at peak reproduction between areas. Age-specific rates of pregnancy began to diverge at 2 years of age between the two populations and peaked at 6 years old. Pregnancy rates were most affected by body condition and mass, although successful reproduction the previous year also reduced pregnancy rates during the current year. Our results indicated that while holding effects of winter constant, density-dependent mechanisms had a much greater effect on physical condition and fecundity than density-independent factors (e.g., precipitation and temperature). Moreover, our results demonstrated effects of differing nutrition resulting from population density during summer on body condition and reproduction. Thus, summer is a critical period for accumulation of body stores to buffer animals against winter; more emphasis should be placed on the role of spring and summer nutrition on population regulation in large, northern herbivores.