Diet of stoats at Okarito Kiwi Sanctuary, South Westland, New Zealand

The diet of 871 stoats (Mustela erminea) caught within the Okarito Kiwi Sanctuary, South Westland, New Zealand, between 2001 and 2004 was studied by assessment of gut contents. Stoat and ship rat (Rattus rattus) captures were used as a measure of relative abundance over time, and rat and mouse (Mus musculus) abundance was indexed using tracking tunnels between spring 2002 and winter 2004. There were major increases in rat captures in spring of 2002 and again in spring of 2003. Stoat captures peaked in the following summers, as rat captures declined. Rats and invertebrates were major components of stoat diet, occurring in 41% and 52% of guts respectively; birds were found in 19%. Changes in these percentages with time indicated that stoats shifted their diet from rats to birds and invertebrates as rat abundance (as indexed by tracking tunnels) decreased. The greatest impact on native species is therefore likely to be when rat abundance is declining after major irruptions, as the increased consumption of birds and invertebrates overlaps with the periods of highest stoat abundance.     

Measuring stoat (

Comparisons were made of density indices of free-living populations of ship rats (Rattus rattus) in mixed forest in New Zealand by using footprint tracking tunnels and two kill-trapping methods. Tracking tunnels and snap-trap removal indices of rat densities showed similar trends when run on a 9 ha trapping grid, although immigration onto the grid occurred, thus violating one of the assumptions of the analysis. Tracking rates and snaptrap capture rates were not significantly correlated when run along a trapping line for a 12 month period, although tracking rates and the total number of rats caught in a trapping session were significantly correlated. Time series analysis showed that rat density indices from tracking tunnels and Fenn traps were significantly correlated when run for 27 consecutive months in a rat population with moderate density, but were not correlated in a low density rat population. The findings highlight the importance of habitat, sample size and target species behaviour in influencing relative density indices obtained from tracking tunnels, snap-traps and Fenn traps. Given the widespread use of rodent tracking tunnels in New Zealand, we suggest that tracking tunnels should only be used to compare relative abundance within similar habitat types, and should always be complemented with a second density index. The relationship between the commonly used density indices and true rodent population density requires urgent attention.     

Early colonisation population structure of a Norway rat island invasion

Colonists undergo non-equilibrium processes such as founder effects, inbreeding and changing population size which influence the mating system and demography of a population. Understanding these processes in colonising populations informs management and helps prevent further invasions. We sampled and genotyped most individuals of a Norway rat (Rattus norvegicus) reinvasion on Moturemu island (5 ha) in New Zealand. Population size was most likely between 30 and 33 rats. Genetic methods detected a clear bottleneck signal from the founding population. Parentage assignment revealed promiscuous mating dominated by a few individuals with increasing inbreeding, both putatively a result of small island size. Combining ecological and genetic data from a single sample allowed inferences on population structure and functioning. Invading Norway rats rapidly achieve population structure similar to established island populations despite a small number of colonists and associated inbreeding. Overcoming these initial obstacles to population establishment contributes to the global success of invasive rats.     

Genetic Diversity in Introduced Populations with an Allee Effect

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations.     

Managing an invasive predator pre-adapted to a pulsed resource: a model of stoat (Mustela erminea) irruptions in New Zealand beech forests

The stoat (Mustela erminea) is a specialist predator that evolved to exploit the unstable populations of northern voles and lemmings. It was introduced to New Zealand, where it is pre-adapted to respond with a population irruption to the resource pulses that follow a heavy seedfall of southern beech (Nothofagus spp.). Culling stoats during an irruption is necessary to reduce damaging predation on nesting endemic birds. Culling might not reduce the stoat population long term, however, if high natural mortality exceeds culling mortality in peak years. During other phases of the beech-mast cycle, culling might have a greater effect on a smaller stoat population, whether or not damage prevention is critical. We developed a 4-matrix model to predict the effects of culling on λ, the annual rate of change in the size of the stoat population, through the four annual phases of an average masting cycle, explicitly distinguishing between apparent and real culling. In the Post-seedfall phase of the cycle, large numbers of stoats are killed, but little of this extra mortality is additive; in other phases, culling removes larger proportions of smaller total numbers of stoats that would otherwise have lived. Culling throughout all phases is most effective at reducing stoat populations, but is also the most expensive option. Culling in Post-seedfall plus Seed or Crash years is somewhat less effective but better than culling in one phase only. Culling has different short-term effects on stoat age distribution depending on the phase of the cycle when culling begins.     

Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data

Dense genotype data can be used to detect chromosome fragments inherited from a common ancestor in apparently unrelated individuals. A disease-causing mutation inherited from a common founder may thus be detected by searching for a common haplotype signature in a sample population of patients. We present here FounderTracker, a computational method for the genome-wide detection of founder mutations in cancer using dense tumor SNP profiles. Our method is based on two assumptions. First, the wild-type allele frequently undergoes loss of heterozygosity (LOH) in the tumors of germline mutation carriers. Second, the overlap between the ancestral chromosome fragments inherited from a common founder will define a minimal haplotype conserved in each patient carrying the founder mutation. Our approach thus relies on the detection of haplotypes with significant identity by descent (IBD) sharing within recurrent regions of LOH to highlight genomic loci likely to harbor a founder mutation. We validated this approach by analyzing two real cancer data sets in which we successfully identified founder mutations of well-characterized tumor suppressor genes. We then used simulated data to evaluate the ability of our method to detect IBD tracts as a function of their size and frequency. We show that FounderTracker can detect haplotypes of low prevalence with high power and specificity, significantly outperforming existing methods. FounderTracker is thus a powerful tool for discovering unknown founder mutations that may explain part of the "missing" heritability in cancer. This method is freely available and can be used online at the FounderTracker website.     

Why do European stoats Mustela erminea not follow Bergmann's rule?

Stoat Mustela erminea body size shows remarkably great variation over the species' European range. The pattern of this variation is opposite to that suggested by Bergmann's rule, i.e., stoats in central Europe are significantly larger than those in southern Sweden which, in turn are considerably larger than their conspecifics in northern Sweden. Neither winter temperature nor the length of snow cover shows any consistent correlation with stoat body size variation, and the larger body size of the southern populations could not be related to a widening of the stoat's feeding niche. A positive correlation was found between the frequency distribution, by size, of available prey and stoat body size in the different areas examined. This supports the hypothesis that body size variation in the stoat, especially females, is an adjustment to regional variations in the sizes of their available prey.     

Characterizing Uncertainty in High-Density Maps from Multiparental Populations

Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B.     

Tracking tunnels: a novel method for detecting a threatened New Zealand giant weta (Orthoptera: Anostostomatidae)

Several species of giant weta, including wetapunga (Deinacrida heteracantha, Orthoptera: Anostostomatidae), New Zealand?s largest terrestrial invertebrate, have high conservation value, yet no methods for detecting and monitoring them have been developed. Here we show that rodent tracking tunnels set over three consecutive nights can be used to detect wetapunga on Little Barrier Island. Adult wetapunga footprints had significantly longer tarsal pad lengths than subadult wetapunga and Auckland tree weta, but tarsal pad length does not distinguish between subadult wetapunga and adult Auckland tree weta. Results suggest that setting tunnels on the ground is more effective than setting them on tree branches and that peanut butter as an attractant bait increases the detection rate of adult wetapunga. Future research is required to determine if the footprints of ground weta, tree weta and giant weta of different ages can be distinguished and to determine how tracking rates of giant weta relate to the population density.     

Latitudinal variation in the competition‐colonisation trade‐off reveals rate‐mediated mechanisms of coexistence

Theories of species coexistence often describe a trade‐off between colonising and competitive abilities. In sessile marine invertebrates, this trade‐off can manifest as trends in species distributions relative to the size of isolated patches of substrate. Based on their abilities to find available substrate and competitively exclude neighbours, good colonisers tend to dominate smaller patches, whereas better competitors tend to monopolise larger patches. In theory, species with equivalent colonising and competitive abilities should display similar distributions across patch sizes. We used patch size to observe this manifestation of the competition‐colonisation trade‐off over 20° of latitude. The trade‐off was more readily observed at lower latitudes and was proportional to the ‘ecological age’ of communities (i.e. the degree of resource acquisition and likelihood of species interactions). Results suggest that ecological age may mediate the prominence of stochastic or deterministic coexistence mechanisms and will depend on the rate of ecological processes.     

Power analysis to determine sample size for monitoring vegetation change in salt marsh habitats

Numerous initiatives are underway throughout New England and elsewhere to quantify salt marsh vegetation change, mostly in response to habitat restoration, sea level rise, and nutrient enrichment. To detect temporal changes in vegetation at a marsh or to compare vegetation among different marshes with a degree of statistical certainty an adequate sample size is required. Based on sampling 1 m² vegetation plots from 11 New England salt marsh data sets, we conducted a power analysis to determine the minimum number of samples that were necessary to detect change between vegetation communities. Statistical power was determined for sample sizes of 5, 10, 15, and 20 vegetation plots at an alpha level of 0.05. Detection of subtle differences between vegetation data sets (e.g., comparing vegetation in the same marsh over two consecutive years) can be accomplished using a sample size of 20 plots with a reasonable probability of detecting a difference when one truly exists. With a lower sample size, and thus lower power, there is an increased probability of not detecting a difference when one exists (e.g., Type II error). However, if investigators expect to detect major changes in vegetation (e.g., such as those between an un-impacted and a highly impacted marsh) then a sample size of 5, 10, or 15 plots may be appropriate while still maintaining adequate power. Due to the relative ease of collecting vegetation data, we suggest a minimum sample size of 20 randomly located 1 m² plots when developing monitoring designs to detect vegetation community change of salt marshes. The sample size of 20 plots per New England salt marsh is appropriate regardless of marsh size or permanency (permanent or non-permanent) of the plots.     

Markov Model of Haploid Random Mating with Given Distribution of Population Size

An exact Markov chain model is formulated and computed for random mating in a haploid gamete pool. There are two versions of the gamete, and there is a finite number of diploid monoecious organisms. The founder population is given, and the subsequent generations allow a prescribed statistical distribution over different population sizes. The non-homogeneous Markov chain works on the haploid gamete level provided the probability of self-fertilization is 1/n, where n is the number of diploid individuals. Standard deviations of gamete frequencies and fixation probabilities are calculated. Effective population sizes for different population size distributions are estimated, including periodic bottlenecks.     

Responses of stoats to scent lures in tracking tunnels

Abstract

Scent lures made from the anal sac secretions of stoats (Mustela ermined) in a long‐life formulation increased the number of visits by stoats to footprint tracking tunnels set near the shoreline of Lake Waikaremoana. Lures derived from female stoats received a similar number of visits to those derived from males. Blank lures with no active ingredient did not attract stoats. Most of the lures remained intact and active for about seven weeks in summer. Rodents were unaffected by the lures, being neither repelled by the scent of stoats, nor attracted to the edible casein‐based carrier compound. Our results suggest that scent lures could be useful for indexing stoat populations. Trials are needed to compare the effectiveness of lures and bait, and to determine seasonal changes in lure attractiveness. Problems of supply of the active ingredients will need to be overcome.     

Capacity of large-scale, long-term biodiversity monitoring programmes to detect trends in species prevalence

There is a critical need for monitoring programmes to assess change or trends in species status to inform conservation. A key aspect in developing such programmes is evaluating their statistical power—the ability to detect a real change. Here we examine the capacity of a broad-scale biodiversity monitoring programme in Alberta, Canada to measure changes in species prevalence. Using observed variation in detectability and prevalence for 252 species monitored at 85 sites, we simulated 3% annual declines and evaluated sample size (6 different sizes) and length of monitoring (5 different durations) necessary to detect change with a 90% certainty (power) at an α of 0.1. Our results suggest that after four monitoring cycles (e.g., 20 years for a 5-year cycle) a power of 90% can be expected for 99% of species when monitoring 1,625 sites, 65% of species for 300 sites, 27% of species for 75 sites, and 8% of species for 25 sites. We found that 66% detectability and 50% prevalence were needed to ensure that 3% annual change is detected at 50 sites over a 20-year period. Our results demonstrate that broad-scale monitoring programmes cannot effectively detect trends in all species at all spatial scales. The time period and spatial scale necessary to detect a real change at a specified level needs to be provided to stakeholders to ensure the short-term success of biodiversity monitoring programmes and to ensure that the most robust indicators of biodiversity are selected.     

Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents

The concepts of “founder equivalent” and “founder genome equivalent” are introduced to facilitate analysis of the founding stocks of captive or other populations for which pedigrees are available. The founder equivalents of a population are the number of equally contributing founders that would be expected to produce the same genetic diversity as in the population under study. Unequal genetic contributions by founders decrease the founder equivalents, portend greater inbreeding in future generations than would be necessary, and reflect a greater loss of the genetic diversity initially present in the founders. The number of founder genome equivalents of a population is that number of equally contributing founders with no random loss of founder alleles in descendants that would be expected to produce the same genetic diversity as in the population under study. The number of founder genome equivalents is approximately that number of wild-caught animals that would be needed to obtain the same amount of genetic diversity as is in the descendant captive population. Founder equivalents and founder genome equivalents allow comparison of the genetic merits of adding new wild-caught stock vs. further equalizing founder representations in a captive population.     

Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community.     

The Coalescent Process with Selfing

A method for estimating the selfing rate using DNA sequence data was recently proposed by Milligan. Unfortunately, a number of errors make interpretation of his results problematic. In the present paper we first show how the usual coalescent process can be adapted to models that include selfing, and then use this result to find moment estimators as well as the likelihood surface for the selfing rate, s, and the scaled mutation rate, θ. We conclude that, regardless of the method used, large sample sizes are necessary to estimate s with any degree of certainty, and that the estimate is always highly sensitive to recent changes in the true value.     

SIR dynamics in random networks with heterogeneous connectivity

Random networks with specified degree distributions have been proposed as realistic models of population structure, yet the problem of dynamically modeling SIR-type epidemics in random networks remains complex. I resolve this dilemma by showing how the SIR dynamics can be modeled with a system of three nonlinear ODE’s. The method makes use of the probability generating function (PGF) formalism for representing the degree distribution of a random network and makes use of network-centric quantities such as the number of edges in a well-defined category rather than node-centric quantities such as the number of infecteds or susceptibles. The PGF provides a simple means of translating between network and node-centric variables and determining the epidemic incidence at any time. The theory also provides a simple means of tracking the evolution of the degree distribution among susceptibles or infecteds. The equations are used to demonstrate the dramatic effects that the degree distribution plays on the final size of an epidemic as well as the speed with which it spreads through the population. Power law degree distributions are observed to generate an almost immediate expansion phase yet have a smaller final size compared to homogeneous degree distributions such as the Poisson. The equations are compared to stochastic simulations, which show good agreement with the theory. Finally, the dynamic equations provide an alternative way of determining the epidemic threshold where large-scale epidemics are expected to occur, and below which epidemic behavior is limited to finite-sized outbreaks.      

Inbreeding trends and genetic diversity in purebred sheep populations

Monitoring the rate of change in inbreeding and genetic diversity within a population is important to guide breeding programmes. Such interest stems from the impact of loss in genetic diversity on sustainable genetic gain but also the impact on performance (i.e. inbreeding depression). The objective of the present study was to evaluate trends in inbreeding and genetic diversity in 43 066 Belclare, 120 753 Charollais, 22 652 Galway, 78 925 Suffolk, 187 395 Texel, and 19 821 Vendeen purebred sheep. The effective population size for each of the six breeds was between 116.0 (Belclare population) and 314.8 (Charollais population). The Charollais population was the most genetically diverse with the greatest number of effective founders, effective ancestors, and effective founder genomes; conversely, the Belclare was the least genetically diverse population with the fewest number of effective founders, effective ancestors, and effective founder genomes for each of the six breeds investigated. Overall, the effective population sizes and the total genetic diversity within each of the six breeds were above the minimum thresholds generally considered to be required for the long-term viability of a population.     

Serial founder effects during range expansion: a spatial analog of genetic drift

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1-1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population.