Biomedical subjects

Robin S Waples

Publications and source records attributed to Robin S Waples.

10 recordsLinked to original sources

PubMed2006

Temporal estimates of effective population size in species with overlapping generations.

The standard temporal method for estimating effective population size (N(e)) assumes that generations are discrete, but it is routinely applied to species with overlapping generations. We evaluated bias in the estimates N(e) caused by violation of this assumption, using simulated data for three model species: humans (type I survival), sparrow (type II), and barnacle (type III). We verify a previous proposal by Felsenstein that weighting individuals by reproductive value is the correct way to calculate parametric population allele frequencies, in which case the rate of change in age-structured populations conforms to that predicted by discrete-generation models. When the standard temporal method is applied to age-structured species, typical sampling regimes (sampling only newborns or adults; randomly sampling the entire population) do not yield properly weighted allele frequencies and result in biased N(e). The direction and magnitude of the bias are shown to depend on the sampling method and the species' life history. Results for populations that grow (or decline) at a constant rate paralleled those for populations of constant size. If sufficient demographic data are available and certain sampling restrictions are met, the Jorde-Ryman modification of the temporal method can be applied to any species with overlapping generations. Alternatively, spacing the temporal samples many generations apart maximizes the drift signal compared to sampling biases associated with age structure.

Adult↗

PubMed2006

Genetic monitoring as a promising tool for conservation and management.

In response to ever-increasing anthropogenic changes to natural ecosystems, regional, national and international organizations have established guidelines for monitoring biological diversity. Most monitoring programs, however, do not take full advantage of the potential afforded by molecular genetic markers, which can provide information relevant to both ecological and evolutionary time frames, while costing less and being more sensitive and reliable than traditional monitoring approaches. As several molecular and computational approaches are relatively new, many technical and theoretical issues remain to be resolved. Here, we illustrate how DNA and population genetic data can provide valuable information, often unattainable via other approaches, for monitoring species of management, conservation and ecological interest.

Animals↗

PubMed2006

What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity.

We review commonly used population definitions under both the ecological paradigm (which emphasizes demographic cohesion) and the evolutionary paradigm (which emphasizes reproductive cohesion) and find that none are truly operational. We suggest several quantitative criteria that might be used to determine when groups of individuals are different enough to be considered 'populations'. Units for these criteria are migration rate (m) for the ecological paradigm and migrants per generation (Nm) for the evolutionary paradigm. These criteria are then evaluated by applying analytical methods to simulated genetic data for a finite island model. Under the standard parameter set that includes L = 20 High mutation (microsatellite-like) loci and samples of S = 50 individuals from each of n = 4 subpopulations, power to detect departures from panmixia was very high ( approximately 100%; P < 0.001) even with high gene flow (Nm = 25). A new method, comparing the number of correct population assignments with the random expectation, performed as well as a multilocus contingency test and warrants further consideration. Use of Low mutation (allozyme-like) markers reduced power more than did halving S or L. Under the standard parameter set, power to detect restricted gene flow below a certain level X (H(0): Nm < X) can also be high, provided that true Nm < or = 0.5X. Developing the appropriate test criterion, however, requires assumptions about several key parameters that are difficult to estimate in most natural populations. Methods that cluster individuals without using a priori sampling information detected the true number of populations only under conditions of moderate or low gene flow (Nm < or = 5), and power dropped sharply with smaller samples of loci and individuals. A simple algorithm based on a multilocus contingency test of allele frequencies in pairs of samples has high power to detect the true number of populations even with Nm = 25 but requires more rigorous statistical evaluation. The ecological paradigm remains challenging for evaluations using genetic markers, because the transition from demographic dependence to independence occurs in a region of high migration where genetic methods have relatively little power. Some recent theoretical developments and continued advances in computational power provide hope that this situation may change in the future.

Biological Evolution↗

PubMed2005

Seed banks, salmon, and sleeping genes: effective population size in semelparous, age-structured species with fluctuating abundance.

Previous studies reached contrasting conclusions regarding how fluctuations in abundance affect Ne in semelparous species with variable age at maturity: that Ne is determined by the arithmetic mean N among the T years within a generation (Ne approximately = T(N)t; monocarpic plants with seed banks) or the harmonic mean (Ne approximately T[symbol: see text]; Pacific salmon). I show that these conclusions arise from different model assumptions rather than inherent differences between the species. Sequentially applying standard, discrete-generation formulas for inbreeding Ne to a series of nominal generations accurately predicts the multigenerational rate of increase in inbreeding. Variability in mean realized reproductive success across years (kt) is the most important factor determining Ne and Ne/N. When abundance is driven by random variation in kt, Ne < or = T[symbol: see text] < T(N)t. With random variation in Nt and constant per capita seed production (C), variation in kt is low and Ne approximately T[symbol: see text]; however, if C varies among years, Ne can be closer to T[symbol: see text]. Because population regulation affects the genetic contribution of entire cohorts of monocarpic perennials, Ne for these species may be more closely approximated by T[symbol: see text] than by T(N)t. With density-dependent compensation, Cov(kt, Nt) < 0, and Ne is further reduced because relatively few breeders make a disproportionate contribution to the next generation.

Aging↗

PubMed2005

Assignment methods: matching biological questions with appropriate techniques.

Assignment methods, which use genetic information to ascertain population membership of individuals or groups of individuals, have been used in recent years to study a wide range of evolutionary and ecological processes. In applied studies, the first step of articulating the biological question(s) to be addressed should be followed by selection of the method(s) best suited for the analysis. However, this first step often receives less attention than it should, and the recent proliferation of assignment methods has made the selection step challenging. Here, we review assignment methods and discuss how to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation (assessing population structure; measuring dispersal and hybridization; and forensics and mixture analysis). We also identify several topics for future research that should ensure that this field remains dynamic and productive.

Journal Article↗

PubMed2005

Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?

Although most genetic estimates of contemporary effective population size (Ne) are based on models that assume Ne is constant, in real populations Ne changes (often dramatically) over time, and estimates (Ne) will be influenced by Ne in specific generations. In such cases, it is important to properly match Ne to the appropriate time periods (for example, in computing Ne/N ratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity--the 'salmon' model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following. Discrete generations: (i) Temporal samples from generations 0 and t estimate the harmonic mean Ne in generations 0 through t - 1 but do not provide information about Ne in generation t; (ii) Single samples provide an estimate of Ne in the parental generation, not the generation sampled; (iii) single-sample and temporal estimates never provide information about Ne in exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations. Salmon model: (i) A pair of single-cohort (typically juvenile) samples from years 0 and t provide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (N b(0) and N b(t)), but adult samples are more difficult to interpret because they are influenced by Nb in a number of previous years; (ii) For single-cohort samples, both one-sample and temporal methods provide estimates of Nb in the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single-sample estimates of Nb as much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates of Ne in iteroparous species with overlapping generations and identify areas in need of further research.

Animals↗

PubMed2004

The alluring simplicity and complex reality of genetic rescue.

A series of important new theoretical, experimental and observational studies demonstrate that just a few immigrants can have positive immediate impacts on the evolutionary trajectory of local populations. In many cases, a low level of immigration into small populations has produced fitness benefits that are greater than those predicted by theoretical models, resulting in what has been termed 'genetic rescue'. However, the opposite result (reduced fitness) can also be associated with immigration of genetically divergent individuals. Central to our understanding of genetic rescue are complex interactions among fundamental concepts in evolutionary and population biology, including both genetic and non-genetic (environmental, behavioral and demographic) factors. Developing testable models to predict when genetic rescue is likely to occur is a daunting challenge that will require carefully controlled, multi-generation experiments as well as creative use of information from natural 'experiments'.

Journal Article↗

PubMed2004

Life-history divergence in Chinook salmon: historic contingency and parallel evolution.

By jointly considering patterns of genetic and life-history diversity in over 100 populations of Chinook salmon from California to British Columbia, we demonstrate the importance of two different mechanisms for life-history evolution. Mapping adult run timing (the life-history trait most commonly used to characterize salmon populations) onto a tree based on the genetic data shows that the same run-time phenotypes exist in many different genetic lineages. In a hierarchical gene diversity analysis, differences among major geographic and ecological provinces explained the majority (62%) of the overall G(ST), whereas run-time differences explained only 10%. Collectively, these results indicate that run-timing diversity has developed independently by a process of parallel evolution in many different coastal areas. However, genetic differences between coastal populations with different run timing from the same basin are very modest (G(ST) < 0.02), indicating that evolutionary divergence of this trait linked to reproductive isolation has not led to parallel speciation, probably because of ongoing gene flow. A strikingly different pattern is seen in the interior Columbia River Basin, where run timing and other correlated life-history traits map cleanly onto two divergent genetic lineages (G(ST) approximately 0.15), indicating that some patterns of life-history diversity have a much older origin. Indeed, genetic data indicate that in the interior Columbia Basin, the two divergent lineages behave essentially as separate biological species, showing little evidence of genetic contact in spite of the fact that they comigrate through large areas of the river and ocean and in some locations spawn in nearly adjacent areas.

Animal Migration↗

PubMed2002

Evaluating the effect of stage-specific survivorship on the N(e)/N ratio.

Evaluating effective population size (Ne) and the effective size to census size ratio (Ne/N) in species with Type III survivorship curves is complicated when key demographic parameters [mean (k macro) and variance (V(k)) of family size] are measured during early life stages. The method of Crow & Morton (1955) for scaling demographic data collected at a juvenile stage to expected values at adulthood is extended to consider sequential episodes of random and family correlated survival. Results show the following: (i) The order in which the episodes of random and family-correlated survival occur does not affect N(e) or N(e)/N; (ii) If a population experiences an episode of family-correlated survival, N(e)/N scaled to its expected value in a population of constant size (k macro= 2) is simply the survival rate during the family-correlated stage. If multiple such stages occur, scaled N(e)/N is the product of the survivals during all family-correlated life stages; (iii) Under the assumption of random post-enumeration survival, adjusting the variance effective size to its expected value at k macro= 2 is equivalent to computing the inbreeding effective size at the earlier life stage. Application to experimental data for hatchery populations of Pacific salmon (Oncorhynchus spp.) indicates that nonrandom survival during the marine phase led to estimated reductions in effective size of 0-62 (mean 19) in 12 different cohorts. This approach can provide insights into N(e)/N in highly fecund species, including some marine species in which N(e) has been estimated to be several orders of magnitude less than N.

Animals↗

PubMed2002

Effective size of fluctuating salmon populations.

Pacific salmon are semelparous but have overlapping year classes, which presents special challenges for the application of standard population genetics theory to these species. This article examines the relationship between the effective number of breeders per year (N(b)) and single-generation and multigeneration effective population size (N(e)) in salmon populations that fluctuate in size. A simple analytical model is developed that allows calculation of N(e) on the basis of the number of spawners in individual years and their reproductive contribution (productivity) to the next generation. Application of the model to a 36-year time series of data for a threatened population of Snake River chinook salmon suggests that variation in population dynamic processes across years reduced the multigeneration N(e) by approximately 40-60%, and reductions may have been substantially greater within some generations. These reductions are comparable in magnitude to, and in addition to, reductions in N(b) within a year due to unequal sex ratio and nonrandom variation in reproductive success. Computer simulations suggest that the effects of variable population dynamics on N(e) observed in this dataset are not unexpected for species with a salmon life history, as random variation in productivity can lead to similar results.

Computer Simulation↗