Building the Foundation for International Conservation Planning for Breeding Ducks across the U.S. and Canadian Border

We used publically available data on duck breeding distribution and recently compiled geospatial data on upland habitat and environmental conditions to develop a spatially explicit model of breeding duck populations across the entire Prairie Pothole Region (PPR). Our spatial population models were able to identify key areas for duck conservation across the PPR and predict between 62.1 – 79.1% (68.4% avg.) of the variation in duck counts by year from 2002 – 2010. The median difference in observed vs. predicted duck counts at a transect segment level was 4.6 ducks. Our models are the first seamless spatially explicit models of waterfowl abundance across the entire PPR and represent an initial step toward joint conservation planning between Prairie Pothole and Prairie Habitat Joint Ventures. Our work demonstrates that when spatial and temporal variation for highly mobile birds is incorporated into conservation planning it will likely increase the habitat area required to support defined population goals. A major goal of the current North American Waterfowl Management Plan and subsequent action plan is the linking of harvest and habitat management. We contend incorporation of spatial aspects will increase the likelihood of coherent joint harvest and habitat management decisions. Our results show at a minimum, it is possible to produce spatially explicit waterfowl abundance models that when summed across survey strata will produce similar strata level population estimates as the design-based Waterfowl Breeding Pair and Habitat Survey (r² = 0.977). This is important because these design-based population estimates are currently used to set duck harvest regulations and to set duck population and habitat goals for the North American Waterfowl Management Plan. We hope this effort generates discussion on the important linkages between spatial and temporal variation in population size, and distribution relative to habitat quantity and quality when linking habitat and population goals across this important region.     

The relationships between net primary productivity, human population density and species conservation

Aim In this study, I determine the relationships between net primary productivity (NPP), human population density, species richness and land use. I also examine the implications of human settlement patterns for species conservation. Location Australia. Methods I document the associations between NPP, human population density and the species richness of birds, butterflies and mammals using correlations and spatial regressions. I also assess changes in land‐use with NPP and population density, focussing particularly on protected areas. An initial exploration into the implications of the NPP‐population density relationship for regional conservation strategies is provided. Results Human population density increases with NPP suggesting that available energy may be a key driving force of human settlement patterns. The species richness of each taxonomic group and geographically restricted species also increases with NPP leading to substantial overlap between species diversity and populated regions. The percentage of land designated as minimal use decreases considerably with increasing human population density and NPP, while intensive agriculture is confined entirely to areas of high NPP. There are strong negative relationships between the size of Australia's National Parks and human population density and NPP. Small parks are often surrounded by relatively dense settlements, but have high average NPP, while large parks are mostly isolated and characterized by low productivity. There are no areas in the highest quartile of NPP that also occur in the most sparsely populated regions, presenting challenges for conservation strategies wanting to protect productive areas under the least threat of human development. Main conclusions Human population density and species richness respond similarly to variation in NPP, leading to spatial congruence between human settlements and productive, species rich regions. Planning strategies are required that minimize the potential threat posed by human development to diverse ecosystems and maximize the underlying productivity of protected areas. Reducing the level of threat may require stabilizing the size of the human population, while capturing larger areas of relatively high productivity in the conservation reserve system would lead to greater protection of local diversity.     

Natural selection, fitness entropy, and the dynamics of coevolution

The coevolutionary dynamics of interacting populations were studied by combining continuous time Lotka-Volterra models of population growth with single-locus genetic models of weak selection. The effects of natural selection on population growth were evaluated using Ginzburg's fitness entropy function as a measure of the deviation of a population's initial allele frequencies from their polymorphic equilibrium values. This entropy measure was used to relate the dynamics of a community composed of evolving populations to the dynamics of a "reference community" whose populations are initially in genetic equilibrium. Specifically, a quantity called the "selective difference area" was defined as the total difference between the population size trajectories of a reference and evolving population. The selective difference area represents the amount of extra life a species would realize if the entire community were at genetic equilibrium. It was shown that this selective difference area is a simple linear function of the initial fitness entropies of each species. This prediction is independent of the strength of selection and holds for any arbitrary set of initial population densities. Numerical examples were presented to illustrate the results. Under the assumption of weak selection, a generalization for arbitrary population growth models was outlined.     

Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat

Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations.     

Restoration Biology: A Population Biology Perspective

A major goal of population biologists involved in restoration work is to restore populations to a level that will allow them to persist over the long term within a dynamic landscape and include the ability to undergo adaptive evolutionary change. We discuss five research areas of particular importance to restoration biology that offer potentially unique opportunities to couple basic research with the practical needs of restorationists. The five research areas are: (1) the influence of numbers of individuals and genetic variation in the initial population on population colonization, establishment, growth, and evolutionary potential; (2) the role of local adaptation and life history traits in the success of restored populations; (3) the influence of the spatial arrangement of landscape elements on metapopulation dynamics and population processes such as migration; (4) the effects of genetic drift, gene flow, and selection on population persistence within an often accelerated, successional time frame; and (5) the influence of interspecific interactions on population dynamics and community development. We also provide a sample of practical problems faced by practitioners, each of which encompasses one or more of the research areas discussed, and that may be solved by addressing fundamental research questions.     

Planting designs in ecological restoration: Insights from the Button Wrinklewort

Summary   The re-establishment of threatened (and common) plant species populations is an important conservation activity in the agricultural landscapes of Australia where habitat fragmentation has destroyed much of their former range. The initial design of restoration plantings, including the number of individuals planted and their spatial configuration, is likely to affect long-term persistence of the re-introduced populations because of its potential effects on pollination and gene flow, but this topic has received little attention in the restoration literature. This study examined how population size and population density of experimental arrays of the grassland daisy Button Wrinklewort affected percentage seed set, a measure of reproductive success. We found strong evidence that population density, but not population size, affected seed set in this species. Seed set increased by, on average, 275% when plants were placed at high-density relative to low-density populations. The low seed set observed may occur because pollinator visitation rates decline in sparse populations or, alternatively, because pollinators are less efficient at pollen transfer when individuals are at low density. Hence, planting designs appear to be an important facet of restoration works that deserve far greater theoretical and practical attention than they have previously received.     

Estimating the effect of continual disturbances on discrete-time population models

In this paper, methods for estimating the effect of continual (but bounded) disturbances on ecosystems modelled by difference equations are discussed. The approach adopted is to estimate the region of state space (called a reachable set) which can be reached by the disturbed system from an initial healthy state in a given time period. Liapunov stability methods for estimating these reachable sets are presented and applied to two specific population models.     

Determining colony densities in wild honeybee populations (<Emphasis Type="Italic">Apis mellifera</Emphasis>) with linked microsatellite DNA markers

Estimating the population size of social bee colonies in the wild is often difficult because nests are highly cryptic. Because of the honeybee (Apis mellifera) mating behaviour, which is characterized by multiple mating of queens at drone congregation areas (DCA), it is possible to use genotypes of drones caught at these areas to infer the number of colonies in a given region. However, DCAs are difficult to locate and we assess the effectiveness of an alternative sampling technique to determine colony density based on inferring male genotypes from queen offspring. We compare these methods in the same population of wild honeybees, Apis mellifera scutellata. A set of linked microsatellite loci is used to decrease the frequency of recombination among marker loci and therefore increase the precision of the estimates. Estimates of population size obtained through sampling of queen offspring is significantly larger than that obtained by sampling drones at DCAs. This difference may be due to the more extensive flying range of queens compared with drones on mating flights. We estimate that the population size sampled through queen offspring is about double that sampled through drones.     

Descent measures for two loci with some applications

For any four genes, two at each of two loci, in a population, a 15 component descent measure has been introduced. These components are the probabilities of the 15 possible arrangements on a set of initial gametes of those genes of which the four of interest are copies. Since identity by descent of genes is equivalent to their being copies of a single gene on an initial gamete, descent measures have inbreeding coefficients as special cases. The individual descent measure, defined for four genes on two uniting gametes can be evaluated for any pedigree by means of an algorithm developed here. If initial gametic frequencies are specified, descent measures allow genotypic frequencies and disequilibria functions at one and two loci to be found. The procedures are illustrated for selfing and for sib mating. Several applications of the descent measures are discussed.     

Modelling the distribution of Bonelli's eagle in Spain: implications for conservation planning

Bonelli's eagle, Hieraaetus fasciatus, has recently suffered a severe population decline and is currently endangered. Spain supports about 70% of the European population. We used stepwise logistic regression on a set of environmental, spatial and human variables to model Bonelli's eagle distribution in the 5167 UTM 10 × 10 km quadrats of peninsular Spain. We obtained a model based on 16 variables, which allowed us to identify favourable and unfavourable areas for this species in Spain, as well as intermediate favourability areas. We assessed the stepwise progression of the model by comparing the model's predictions in each step with those of the final model, and selected a parsimonious explanatory model based on three variables — slope, July temperature and precipitation — comprising 76% of the predictive capacity of the final model. The reported presences in favourable and unfavourable areas suggest a source–sink dynamics in Bonelli's eagle populations. The fragmented spatial structure of the favourable areas suggests the existence of a superimposed metapopulation dynamics. Previous LIFE (The Financial Instrument of the European Union for the Environment and Nature) projects for the conservation of this species have focused mainly on the northern limit of its range, where the sharpest population decline has been recorded. In these areas, favourability is low and Bonelli's eagle populations are probably maintained by the immigration of juveniles produced in more favourable zones. However, southern populations, although stable, show signs of reduction in productivity, which could menace the population sizes in the whole study area. We suggest that conservation efforts should focus also on known favourable areas, which might favour population persistence in unfavourable areas through dispersal.     

The role of solitary population waves in efficient suppression of adventive weeds by introduced phytophagous insects

Successful introduction and application of phytophagous insects to control invading weeds is a complex systemic process based on formation of solitary population waves (SPW) of phytophages. Consequently, each stage from selection to release of the biological control agent should pursue the objective of the wave formation. When selecting a biological control agent one should choose species among phylogenetically young “juvenile taxa,” which are capable of forming a solitary population wave upon introduction. The initial phytophage population increase, preceding the wave emergence, requires special conditions, in particular a high density of the weed in the release areas. The SPW restores the natural succession previously arrested by the weed, allowing the native plants to overgrow the weed completely.     

Assessing re-introductions of the African Wild dog (Lycaon pictus) in the Limpopo Valley Conservancy, South Africa, using the stochastic simulation program VORTEX

The African wild dog (Lycaon pictus) is one of Africa's most endangered species and therefore classified as endangered by IUCN. Earlier distributions included most of Africa but currently the African wild dog only has populations larger than 300 individuals in three countries (Botswana, Tanzania and South Africa). In 1998, a plan was launched in South Africa to manage sub-populations of the African wild dog in several small, geographically isolated, conservation areas. This management program involved the reintroduction of wild dogs into suitable conservation areas and periodic translocations among them. We used the stochastic population simulation model VORTEX to evaluate the Limpopo Valley Conservancy in the north of South Africa, as a possible reintroduction site for African wild dogs. The simulations showed that the size of the initial population released only had a small effect on the population dynamics. However, when individuals were supplemented and harvested over a longer period the probability of persistence increased. Number of females breeding, male mortality, and carrying capacity were key factors in the population dynamics, but according to VORTEX the severity of natural catastrophes had the greatest influence on the extinction risk and inbreeding. We suggest that the reintroduction program may be successful, if areas are properly secured, the dogs are held in a boma before release, wild animals or at least a mix of wild and captive animals are used for the release and the animals are vaccinated against rabies. It is, however, essential to continue monitoring followed by modelling efforts to re-evaluate the success of the reintroduction program.     

Geneland: a computer package for landscape genetics

Geneland is a computer package that allows to make use of georeferenced individual multilocus genotypes for the inference of the number of populations and of the spatial location of genetic discontinuities between those populations. Main assumptions of the method are: (i) the number of populations is unknown and all values are considered a priori equally likely, (ii) populations are spread over areas given by a union of some polygons of unknown location in the spatial domain, (iii) Hardy–Weinberg equilibrium is assumed within each population and (iv) allele frequencies in each population are unknown and treated as random variable either following the so‐called Dirichlet model or Falush model. Different algorithms implemented in Geneland to perform inferences are first briefly presented. Then major running steps and outputs (i.e. histogram of number of populations and map of posterior probabilities of population membership) are illustrated from the analysis of a simulated data set, which was also produced by Geneland.     

Pollen limitation and fruit abortion in a declining rare tree,the Eurasian yew (Taxus baccata L.): A reproductive cost of ecological marginality

Populations of rare tree species such as the dioecious and anemophilous yew (Taxus baccata) are especially prone to extinction if they occupy marginal habitats. This is the case of yew populations growing in Mediterranean mountains under dry climate and a severe anthropogenic disturbance regime, which show insufficient regeneration. We examined two of the likely mechanisms driving this population decline. The study was conducted in a central Spanish yew population in 2005 and 2006. On one hand, we tested for the effect of the amount of pollen received by female flowers by means of a pollen addition experiment. On the other hand, we tested for the effect of initial fruit set on abortion and mature fruit production. Finally, we evaluated the effect of the spatial arrangement of male and female yew trees on realized fecundity. The success of fertilization and fruiting in the experimental population was pollen-limited. Female trees aborted ca. 70% of the fruit set in both years and treatments. Fruit set was significantly influenced by the females' neighbourhood, with fecundity decreasing exponentially with distance to the nearest male in both years. Overall, our results indicate that factors associated with ecological marginality have a strong influence on yew performance.     

Models of an annual plant population with a seedbank

Two models are set up, in terms of difference equations, for a population of a species of annual plant, of which a proportion of the seeds remain dormant for at least one year. Analytical and numerical results are presented demonstrating the effect of the seedbank on the return to equilibrium of the plant population following an initial disturbance. The seedbank can exert both a damping (stabilising) effect, speeding up oscillatory return, and an inertial (destabilising) effect, slowing down exponential return to the equilibrium population.     

Simulating Linkage Disequilibrium Structures in a Human Population for SNP Association Studies

Existing simulation methods usually simulate linkage disequilibrium (LD) structures starting with an initial population that is randomly generated according to specified allele frequencies. These at random based methods might be unstable because the LD level of the initial population is generally extremely low. This study presents a new algorithm, SIMLD, to simulate genome populations with real LD structures. SIMLD begins from an initial population with possibly the highest LD level, and then the LD decays to fit the desired level through processes of mating and recombination over generations. SIMLD can produce case-control samples according to various disease models. Using empirical SNP marker information from three populations of HapMap data, we implement the proposed algorithm and demonstrate a set of experimental results.     

A new multi-population artificial bee algorithm based on global and local optima for numerical optimization

Artificial Bee Colony (ABC) algorithm is a nature-inspired algorithm that showed its efficiency for optimizations. However, the ABC algorithm showed some imbalances between exploration and exploitation. In order to improve the exploitation and enhance the convergence speed, a multi-population ABC algorithm based on global and local optimum (namely MPGABC) is proposed in this paper. First, in MPGABC, the initial population is generated using both chaotic systems and opposition-based learning methods. The colony in MPGABC is divided into several sub-populations to increase diversity. Moreover, the solution search mechanism is modified by introducing global and local optima in the solution search equations of both employed and onlookers. The scout bees in the proposed algorithm are generated similarly to the initial population. Finally, the proposed algorithm is compared with several state-of-art ABC algorithm variants on a set of 13 classical benchmark functions. The experimental results show that MPGABC competes and outperforms other ABC algorithm variants.

     

Successful establishment of the invasive fire ant Solenopsis invicta in Taiwan: insights into interactions of alternate social forms

Aim Understanding the factors underlying the successful establishment of invasive ant species is critical for developing quarantine strategies to prevent additional invasions as well as for determining how such species overcome the selective pressures in invaded areas. Although several studies have revealed differences in the social organization and population genetics of invasive ants in their native and introduced ranges, few studies have considered the potential interactions between alternate social forms within newly‐invaded areas simply because many invasive ants are characterized as polygyne or unicolonial. Location Taoyuan and Chiayi County, Taiwan. Methods Both social forms (polygyne and monogyne) of the red imported fire ant, Solenopsis invicta, occur in two separately invaded areas in Taiwan (Taoyuan and Chiayi). We employed intensive sampling methods and diagnostic polymerase chain reaction assays to determine the distribution of these two social forms in both infested areas in Taiwan. Results The distribution of social forms differs dramatically between the two infested areas, consistent with different invasion histories regarding the original make‐up of individuals comprising the initial founder group. The Taoyuan population likely was colonized initially by ants of both social forms, with the subsequent spread characterized by continuous outward movement of the two forms, particularly the monogyne form. In contrast, the initial founders of the Chiayi population likely were of the polygyne social form only, suggesting the monogyne social form in this population appeared only recently and likely arose directly from polygyne queens converting to the alternate social form. Main conclusions Our results provide detailed insights into the invasion history of S. invicta in Taiwan and suggest that the distinct reproductive biology of the two social forms may have shaped the current distribution of S. invicta in these infested areas and that the dynamics of two forms may affect the long‐term persistence and potential for spread of this pest ant species.     

Variant evolutionary trees under phenotypic variance

Evolutionary branching, which is a coevolutionary phenomenon of the development of two or more distinctive traits from a single trait in a population, is the issue of recent studies on adaptive dynamics. In previous studies, it was revealed that trait variance is a minimum requirement for evolutionary branching, and that it does not play an important role in the formation of an evolutionary pattern of branching. Here we demonstrate that the trait evolution exhibits various evolutionary branching paths starting from an identical initial trait to different evolutional terminus traits as determined by only changing the assumption of trait variance. The key feature of this phenomenon is the topological configuration of equilibria and the initial point in the manifold of dimorphism from which dimorphic branches develop. This suggests that the existing monomorphic or polymorphic set in a population is not an unique inevitable consequence of an identical initial phenotype.     

Kinship and Deep History: Exploring Connections between Culture Areas, Genes, and Languages

Large-scale geographic variation in kinship systems may have deep roots. A number of authors now argue for an "emerging synthesis," with genetic, linguistic, and archeological findings coming together to paint a consistent picture of large-scale population spreads in prehistory. This article explores a social structural dimension of this synthesis: Major culture areas based on variation in kinship systems correspond closely—yet not perfectly—to genetic and linguistic clusters identified by other researchers. Thus it may be possible to reconstruct: (1) a set of "primary" culture areas corresponding to major population blocs and associated with ancient demic expansions and parallel transmission of genes and culture, and (2) a smaller set of overlying "secondary" culture areas of more recent origin that do not map onto genetic subdivisions and result from changes in subsistence or political economy independent of large-scale demic expansions. I also review latitudinal variation in kinship systems. [Keywords: culture areas, demic expansions, kinship (prehistory), protolanguages]