genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/

genalex 6: genetic analysis in Excel. Population genetic software for teaching and research

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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Modern Applied Statistics With S

spag e d i version 1.0 is a software primarily designed to characterize the spatial genetic structure of mapped individuals or populations using genotype data of codominant markers. It computes various statistics describing genetic relatedness or differentiation between individuals or populations by pairwise comparisons and tests their significance by appropriate numerical resampling. spag e d i is useful for: (i) detecting isolation by distance within or among populations and estimating gene dispersal parameters; (ii) assessing genetic relatedness between individuals and its actual variance, a parameter of interest for marker based inferences of quantitative inheritance; (iii) assessing genetic differentiation among populations, including the case of haploids or autopolyploids.

spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels

As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping.

A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

Spatial genetic structure of a tropical understory shrub, PSYCHOTRIA OFFICINALIS (RuBIACEAE)

▪ Abstract For many years biologists have debated whether mast seeding (the synchronous intermittent production of large seed crops in perennial plants) results from weather conditions or is an evolved plant reproductive strategy. In this review, we analyze the evidence for the underlying causes of masting. In the absence of selection for higher or lower variability, plants will vary in tandem with the environment (resource matching). Two selective factors often favor the evolution of masting: increased pollination efficiency in wind-pollinated species, and satiation of seed predators. Other factors select against masting, including animal pollination and frugivore dispersal. A survey of 570 masting datasets shows that wind-pollinated species had higher seed production coefficients of variation (CVs) than biotically pollinated ones. Frugivore-dispersed species had low CVs whereas predator-dispersed plants had high CVs, consistent with gaining benefits from predator satiation rather than dispersal. The glo...

MAST SEEDING IN PERENNIAL PLANTS: Why, How, Where?

We conducted an 8—yr study of flower and acorn production in three species of oak in east—central Missouri: white oak (Quercus alba), red oak (Q. rubra), and Black oak (Q. velutina). The goal was to evaluate whether mast—fruiting, the synchronous production of large seed crops followed by small seed crops, is simply a response to weather conditions or is actually an evolved reproductive strategy. In this paper, we address four specific questions: (1) Are annual fluctuations in acorn crop size the result of synchronous production of acorns by individuals? (2) Are large acorn crops the result of large flower crops and/or high survival of those flowers to mature fruit? (3) To what extent do weather variables account for variation in acorn production among years? (4) Does acorn crop size correlate negatively with prior acorn production? Red oak and white oak showed a greater degree of mast—fruiting than did black oak. Within a species, individuals tended to produce large acorn crops in the same years, but each species differed in which years they produced large crops. The size of a given acorn crop was determined by both flower abundance and survival of flowers to fruit. Principal components and multiple—regression analyses were used to describe the relationship between weather variables and acorn production. The first principal component explained the largest amount of the variation in black oak (R2 = 0.55) and the red oak (R2 = 0.89). In white oak, two principal components combined to explain 77% of the variation in acorn production. The weather variables that were associated with these principal components included spring temperature (positive effect) and summer drought (negative effect). Past acorn production had a major impact on the size of the current acorn crop, with each species showing a different pattern. In black oak, the current acorn crop was negatively correlated with the crop 3 yr prior but positively correlated with the crop 2 yr prior. In red oak, acorn crop size 1, 2, and 3 yr prior had negative correlations with current acorn crop, while acorn crop size 4 yr prior was positively correlated. In white oak, there were negative correlations between acorn crop size and crop size 1, 2, and 4 yr prior but a positive correlation with the acorn crop size 3 yr prior. These data are consistent with the hypothesis that mast—fruiting species must store resources during some years in order to produce a mast crop. We discuss the possibility that these three species may have inherent cycles of reproduction that are modified by the impact of weather conditions, black oak with 2—yr cycles, white oak with 3—yr cycles, and red oak with 4—yr cycles. We conclude that the patterns of acorn production for black oak, red oak, and white oak are not simply responses to weather events but are also a function of prior reproductive events. This suggests that masting is an evolved reproductive strategy.

Ecology of mast-fruiting in three species of North American deciduous oaks.

Growing interest in metapopulation dynamics and dispersal at a landscape level is promoting new approaches to the study of contemporary gene flow. These approaches have been fostered by the development of new genetic markers and statistical methods, as well as an awareness that contemporary gene flow cannot be reliably estimated by conventional methods based on genetic structure. Estimation of the spatial and temporal dynamics of pollen and seed movement with respect to extant landscape features can aid evolutionary and conservation biologists in predicting the demographic and genetic responses of species to naturally occurring or human-mediated population subdivision.

Landscape approaches to historical and contemporary gene flow in plants.

Genetic connectivity in plant populations is determined by gene movement within and among populations. When populations become genetically isolated, they are at risk of loss of genetic diversity that is critical to the long-term survival of populations. Anthropogenic landscape change and habitat fragmentation have become so pervasive that they may threaten the genetic connectivity of many plant species. The theoretical consequences of such changes are generally understood, but it is not immediately apparent how concerned we should be for real organisms, distributed across real landscapes. Our goals here are to describe how one can study gene movement of both pollen and seeds in the context of changing landscapes and to explain what we have learned so far. In the first part, we will cover methods of describing pollen movement and then review evidence for the impact of fragmentation in terms of both the level of pollen flow into populations and the genetic diversity of the resulting progeny. In the second part, we will describe methods for contemporary seed movement, and describe findings about gene flow and genetic diversity resulting from seed movement. Evidence for pollen flow suggests high connectivity, but it appears that seed dispersal into fragments may create genetic bottlenecks due to limited seed sources. Future work should address the interaction of pollen and seed flow and attention needs to be paid to both gene flow and the diversity of the incoming gene pool. Moreover, if future work is to model the impact of changing landscapes on propagule movement, with all of its ensuing consequences for genetic connectivity and demographic processes, we will need an effective integration of population genetics and landscape ecology.

Victoria L. Sork

Papers

Spatial genetic structure of a tropical understory shrub, PSYCHOTRIA OFFICINALIS (RuBIACEAE)

MAST SEEDING IN PERENNIAL PLANTS: Why, How, Where?

Ecology of mast-fruiting in three species of North American deciduous oaks.

Landscape approaches to historical and contemporary gene flow in plants.

Genetic analysis of landscape connectivity in tree populations