Source populations in carnivore management: cougar demography and emigration in a lightly hunted population

Wildlife agencies typically attempt to manage carnivore numbers in localized game management units through hunting, and do not always consider the potential influences of immigration and emigration on the outcome of those hunting practices. However, such a closed population structure may not be an appropriate model for management of carnivore populations where immigration and emigration are important population parameters. The closed population hypothesis predicts that high hunting mortality will reduce numbers and densities of carnivores and that low hunting mortality will increase numbers and densities. By contrast, the open population hypothesis predicts that high hunting mortality may not reduce carnivore densities because of compensatory immigration, and low hunting mortality may not result in more carnivores because of compensatory emigration. Previous research supported the open population hypothesis with high immigration rates in a heavily hunted (hunting mortality rate=0.24) cougar population in northern Washington. We test the open population hypothesis and high emigration rates in a lightly hunted (hunting mortality rate=0.11) cougar population in central Washington by monitoring demography from 2002 to 2007. We used a dual sex survival/fecundity Leslie matrix to estimate closed population growth and annual census counts to estimate open population growth. The observed open population growth rate of 0.98 was lower than the closed survival/fecundity growth rates of 1.13 (deterministic) and 1.10 (stochastic), and suggests a 12–15% annual emigration rate. Our data support the open population hypothesis for lightly hunted populations of carnivores. Low hunting mortality did not result in increased numbers and densities of cougars, as commonly believed because of compensatory emigration.     

Spatial and temporal genetic variation in Tunisian field populations of Macrosiphum euphorbiae (Thomas)

The potato aphid Macrosiphum euphorbiae (Thomas) is a major pest of several economic crops in Tunisia. Using 10 microsatellites, we analyzed five populations of M. euphorbiae sampled during the 2004-2005 solanaceous and cucurbit season (April through September) from five geographic origins. From 235 aphids, 61 different multilocus genotypes were identified of which three genotypes MLG1, MLG2, and MLG42 were predominant on all host plants and regions. MLG1 and MLG2 genotypes were detected in 2004 and did not reappear in spring 2005, while the genotype MLG42 was detected only in 2005. All populations showed significant deviation from Hardy-Weinberg equilibrium even in data sets including one individual per genotype. χ(2) independence tests and analysis of molecular variance showed no significant differentiation among populations collected on different host plant and from different geographic origin, but differences between populations from two successive years were significant. Factorial component analysis corroborates these results. The probable causes of this seasonal variation were discussed.     

Quantitative genetic variation in Daphnia: temporal changes in genetic architecture

Nonadditive genetic variation and genetic disequilibrium are two important factors that influence the evolutionary trajectory of natural populations. We assayed quantitative genetic variation in a temporary-pond-dwelling population of Daphnia pulex over a full season to examine the role of nonadditive genetic variation and genetic disequilibrium in determining the short-term evolutionary trajectory of a cyclic parthenogen. Quantitative traits were influenced by three factors: (1) clonal selection significantly changed the population mean phenotype during the course of the growing season; (2) sexual reproduction and recombination led to significant changes in life-history trait means and the levels of expressed genetic variation, implying the presence of substantial nonadditive genetic variation and genetic disequilibrium; and (3) Egg-bank effects were found to be an important component of the realized year-to-year change. Additionally, we examined the impact of genetic disequilibria induced by clonal selection on the genetic (co)variance structure with a common principal components model. Clonal selection caused significant changes in the (co)variance structure that were eliminated by a single bout of random mating, suggesting that a build-up of disequilibria was the primary source of changes in the (co)variance structure. The results of this study highlight the complexity of natural selection operating on populations that undergo alternating phases of sexual and asexual reproduction.     

Demographic factors and genetic variation influence population persistence under environmental change

Population persistence has been studied in a conservation context to predict the fate of small or declining populations. Persistence models have explored effects on extinction of random demographic and environmental fluctuations, but in the face of directional environmental change they should also integrate factors affecting whether a population can adapt. Here, we examine the population‐size dependence of demographic and genetic factors and their likely contributions to extinction time under scenarios of environmental change. Parameter estimates were derived from experimental populations of the rainforest species, Drosophila birchii, held in the lab for 10 generations at census sizes of 20, 100 and 1000, and later exposed to five generations of heat‐knockdown selection. Under a model of directional change in the thermal environment, rapid extinction of populations of size 20 was caused by a combination of low growth rate (r) and high stochasticity in r. Populations of 100 had significantly higher reproductive output, lower stochasticity in r and more additive genetic variance (V_A) than populations of 20, but they were predicted to persist less well than the largest size class. Even populations of 1000 persisted only a few hundred generations under realistic estimates of environmental change because of low V_A for heat‐knockdown resistance. The experimental results document population‐size dependence of demographic and adaptability factors. The simulations illustrate a threshold influence of demographic factors on population persistence, while genetic variance has a more elastic impact on persistence under environmental change.     

Spatial and temporal variation in harvest probabilities for American black duck

Assessing spatial variation in waterfowl harvest probabilities from banding data is challenging because reporting and recovery probabilities have distinct spatial patterns that covary temporally with harvesting regulations, hunter effort, and reporting methods. We analyzed direct band recovery data from American black ducks banded on the Canadian breeding grounds from 1970 through 2010. Data were registered to a 1‐degree grid and analyzed using hierarchical logistic regression models with spatially correlated errors to estimate the annual probabilities of band recovery and the proportion of individuals recovered in Canada. Probability of harvest was estimated from these values, in combination with independent estimates of reporting probabilities in Canada and the USA. Model covariates included estimates of hunting effort and factors for harvest regulation and band reporting methods. Both the band recovery processes and the proportion of individuals recovered in Canada had significant spatial structure. Recovery probabilities were highest in southern Ontario, along the Saint Lawrence River in Quebec, and in Nova Scotia. Black ducks breeding in Nova Scotia and southern Quebec were harvested predominantly in Canada. Recovery probabilities for juveniles were correlated with hunter effort, while the adult recoveries were weakly correlated with the implementation of stricter harvest regulations in the early 1980s. Mean harvest probability decreased in the northern portion of the survey area but remained stable or even increased in the south. Harvest probabilities for juveniles in 2010 exceeded 20% in southern Quebec and the Atlantic provinces. Our results demonstrate fine‐scale variation in harvest probabilities for black duck on the Canadian breeding ground. In particular, harvest probabilities should be closely monitored along the Saint Lawrence River system and in the Atlantic provinces to avoid overexploitation.     

Sexual selection and temporal phenotypic variation in a damselfly population

Temporal variation in selection can be generated by temporal variation in either the fitness surface or phenotypic distributions around a static fitness surface, or both concurrently. Here, we use within- and between-generation sampling of fitness surfaces and phenotypic distributions over 2 years to investigate the causes of temporal variation in the form of sexual selection on body size in the damselfly Enallagma aspersum. Within a year, when the average female body size differed substantially from the average male body size, male body size experienced directional selection. In contrast, when male and female size distributions overlapped, male body size experienced stabilizing selection when variances in body size were large, but no appreciable selection when the variances in body size were small. The causes of temporal variation in the form of selection can only be inferred by accounting for changes in both the fitness surface and changes in the distribution of phenotypes.     

Using soil seed banks to assess temporal patterns of genetic variation in invasive plant populations

Most research on the genetics of invasive plant species has focused on analyzing spatial differences among existing populations. Using a long‐established Gunnera tinctoria population from Ireland, we evaluated the potential of using plants derived from seeds associated with different soil layers to track genetic variation through time. This species and site were chosen because (1) G. tinctoria produces a large and persistent seed bank; (2) it has been present in this locality, Sraheens, for ~90 years; (3) the soil is largely undisturbed; and (4) the soil's age can be reliably determined radiometrically at different depths. Amplified fragment length polymorphic markers (AFLPs) were used to assess differences in the genetic structure of 75 individuals sampled from both the standing population and from four soil layers, which spanned 18 cm (estimated at ~90 years based on ²¹⁰Pb and ¹³⁷Cs dating). While there are difficulties in interpreting such data, including accounting for the effects of selection, seed loss, and seed migration, a clear pattern of lower total allele counts, percentage polymorphic loci, and genetic diversity was observed in deeper soils. The greatest percentage increase in the measured genetic variables occurred prior to the shift from the lag to the exponential range expansion phases and may be of adaptive significance. These findings highlight that seed banks in areas with long‐established invasive populations can contain valuable genetic information relating to invasion processes and as such, should not be overlooked.     

Spatial and temporal genetic heterogeneity in a natural Daphnia population

Temporal and spatial genetic changes in a Daphnia pulex populationinhabiting a permanent pond were examined for 2     

Reproductive fitness,population size and genetic variation in Muscari tenuiflorum (Hyacinthaceae): The role of temporal variation

In plant populations a positive correlation between population size, genetic variation and fitness components is often found, due to increased pollen limitation or reduced genetic variation and inbreeding depression in smaller populations. However, components of fitness also depend on environmental factors which can vary strongly between years. The dry grassland species Muscari tenuiflorum experiences long term habitat isolation and small population sizes. We analyzed seed production of M. tenuiflorum in four years and its dependence on population size and genetic variation. Genetic diversity within populations was high (AFLP: H_e = 0.245; allozymes: H_e = 0.348). An analysis of molecular variance revealed considerable population differentiation (AFLP: 26%; allozyme: 17%). An overall pattern of isolation by distance was found, which, however was not present at distances below 20 km, indicating stronger effects of genetic drift. Genetic diversity was positively correlated to population size. Self pollination reduced seed set by 24%, indicating inbreeding depression. Reproductive fitness was not correlated to genetic diversity and a positive correlation with population size was present in two of four study years. The absence of a general pattern stresses the importance for multi-year studies. Overall, the results show that despite long term habitat isolation M. tenuiflorum maintains seed production in many years independent of population size. The long term persistence of populations is thus expected to depend less on intrinsic genetic or demographic properties affecting seed production but on successful plant establishment and persistence, which latter are based on conservation and protection of suitable habitats.     

Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations

Currently, there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here, we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during 4 years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only 1 year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programmes into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.     

MtDNA of Fulani nomads and their genetic relationships to neighboring sedentary populations

Despite the large size of the contemporary nomadic Fulani population (roughly 13 million people), the genetic diversity and degree of differentiation of Fulanis compared to other sub-Saharan populations remain unknown. We sampled four Fulani nomad populations (n = 186) in three countries of sub-Saharan Africa (Chad, Cameroon, and Burkina Faso) and analyzed sequences of the first hypervariable segment of the mitochondrial DNA. Most of the haplotypes belong to haplogroups of West African origin, such as L1b, L3b, L3d, L2b, L2c, and L2d (79.6% in total), which are all well represented in each of the four geographically separated samples. The haplogroups of Western Eurasian origin, such as J1b, U5, H, and V, were also detected but in rather low frequencies (8.1% in total). As in African hunter-gatherers (Pygmies and Khoisan) and some populations from central Tunisia (Kesra and Zriba), three of the Fulani nomad samples do not reveal significant negative values of Fu's selective neutrality test. The multidimensional scaling of FST genetic distances of related sub-Saharan populations and the analysis of molecular variance (AMOVA) show clear and close relationships between all pairs of the four Fulani nomad samples, irrespective of their geographic origin. The only group of nomadic Fulani that manifests some similarities with geographically related agricultural populations (from Guinea-Bissau and Nigeria) comes from Tcheboua in northern Cameroon.     

MtDNA variation in the Altai-Kizhi population of southern Siberia: a synthesis of genetic variation

The native peoples of Gorno Altai in southern Siberia represent a genetically diverse population and have been of great interest to anthropological genetics. In particular, the southern Altaian population is argued to be the best candidate for the New World ancestral population. In this study we sampled Altai-Kizhi from the southern Altaian village of Mendur-Sokkon, analyzed mtDNA RFLP markers and HVS-I sequences, and compared the results to other published mtDNA data from Derenko et al. (2003) and Shields et al. (1993) encompassing the same region. Because each independent study uses different sampling techniques in characterizing gene pools, in this paper we explore the accuracy and reliability of evolutionary studies on human populations. All the major Native American haplogroups (A, B, C, and D) were identified in the Mendur-Sokkon sample, including a single individual belonging to haplogroup X. The most common mtDNA lineages are C (35.7%) and D (13.3%), which is consistent with the haplogroup profiles of neighboring Siberian groups. The Mendur-Sokkon sample exhibits depressed HVS-I diversity values and neutrality test scores, which starkly differs from the Derenko et al. (2003) data set and more closely resembles the results for neighboring south Siberian groups. Furthermore, the multidimensional scaling plot of DA genetic distances does not cluster the Altai samples, showing different genetic affinities with various Asian groups. The findings underscore the importance of sampling strategy in the reconstruction of evolutionary history at the population level.     

Patterns of genetic variation in anthropogenically impacted populations

Genetic variation is considered critical for allowing natural populations to adapt to their changing environment, and yet the effects of human disturbance on genetic variation in the wild are poorly understood. Different types of human disturbances may genetically impact natural populations in a predictable manner and so the aim of this study was to provide an overview of these changes using a quantitative literature review approach. I examined both allozyme and microsatellite estimates of genetic variation from peer-reviewed journals, using the mean number of alleles per locus and expected heterozygosity as standardized metrics. Populations within each study were categorized according to the type of human disturbance experienced (“hunting/harvest”, “habitat fragmentation”, or “pollution”), and taxon-specific, as well as time- and context-dependent disturbance effects were considered. I found that human disturbances are associated with weak, but consistent changes in neutral genetic variation within natural populations. The direction of change was dependent on the type of human disturbance experienced, with some forms of anthropogenic challenges consistently decreasing genetic variation from background patterns (e.g., habitat fragmentation), whereas others had no effect (e.g., hunting/harvest) or even slightly increased genetic variation (e.g., pollution). These same measures appeared sensitive to both the time of origin and duration of the disturbance as well. This suggests that the presence or absence, strength, type, as well as the spatial and temporal scale of human disturbance experienced may warrant careful consideration when conservation management plans are formulated for natural populations, with particular attention paid to the effects of habitat fragmentation.     

Beyond race: towards a whole-genome perspective on human populations and genetic variation

The renewed emphasis on population-specific genetic variation, exemplified most prominently by the International HapMap Project, is complicated by a longstanding, uncritical reliance on existing population categories in genetic research. Race and other pre-existing population definitions (ethnicity, religion, language, nationality, culture and so on) tend to be contentious concepts that have polarized discussions about the ethics and science of research into population-specific human genetic variation. By contrast, a broader consideration of the multiple historical sources of genetic variation provides a whole-genome perspective on the ways i n which existing population definitions do, and do not, account for how genetic variation is distributed among individuals. Although genetics will continue to rely on analytical tools that make use of particular population histories, it is important to interpret findings in a broader genomic context.     

Habitat segregation and temporal variation in some tropical intertidal populations

Observations were made to document habitat segregation and seasonal changes in density for the most common intertidal organisms at a study site on the Pacific coast of Costa Rica. The pulmonate limpets Siphonaria gigas (Sowerby) and Siphonaria maura (Sowerby) were more abundant in the mid-high- and high-intertidal zone, whereas the keyhole limpet Fissurella virescens (Sowerby) was more abundant in the mid zone. Coiled gastropods were found in the mid- and mid-high-intertidal zone but were absent or scarce in the high zone. Barnacles and coralline algae were found throughout the intertidal zone and foliose algae were mostly present in the splash zone. Abundance of all species changed over the 2-yr period of the study. S. gigas and S. maura and the barnacle Chthamalus fissus Darwin exhibited well-defined fluctuations in density related to recruitment. No recruitment was observed for F. virescens or Tetraclita panamensis Pilsbry and populations of both species declined. Changes also occurred for coiled gastropods and were probably related to movement of adults. Coralline and foliose algae were more abundant during the rainy season than during the dry months. Far from being constant, populations on these tropical shores were highly dynamic with temporal changes rivaling those in the temperate zone.     

A study of temporal genetic variation in a natural population of Atlantic salmon in the River Bush, Northern Ireland

Temporal genetic variation in River Bush Atlantic salmon was low and much less than among geographically discrete samples reported from elsewhere.     

Comparing G: multivariate analysis of genetic variation in multiple populations

The additive genetic variance–covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design.