Matthew B. Hamilton

Tropical tree gene flow and seed dispersal

In tropical forests, trees provide habitats and environmental conditions that support thousands of species. However, deforestation creates a mosaic landscape of cleared areas and forest fragments, which become the source of future tree populations. Fragmentation changes the movement of pollen and seed dispersal, modifying the gene flow and altering historical patterns of genetic subdivision. Paternity studies in tropical figs and trees have shown that pollen is dispersed over long distances, maintaining gene flow among widely spaced forest fragments, but gene movement by seed dispersal has not been studied in tropical trees. I have estimated chloroplast genome subdivision in the Amazonian canopy tree Corythophora alta, and here I show that seed dispersal is limited, with forest fragments as large as ten hectares being founded by a single maternal lineage.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross‐tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis)

Microsatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical tree Corythophora alta and 11 loci in the anadromous fish Morone saxatilis by sequencing 14–23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy for M. saxatilis loci. Seven C. alta loci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy in C. alta generally produced little or no change in single‐locus estimates of RST, except for two loci in which some additional differentiation among populations was revealed. Twelve‐locus estimates of RST (including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% for C. alta and M. saxatilis, respectively. Simulations showed that the increase in RST produced by homoplasy correction was only slightly larger than variation in RST estimates expected to be caused by methodological errors.

FST and QST Under Neutrality

A commonly used test for natural selection has been to compare population differentiation for neutral molecular loci estimated by FST and for the additive genetic component of quantitative traits estimated by QST. Past analytical and empirical studies have led to the conclusion that when averaged over replicate evolutionary histories, QST = FST under neutrality. We used analytical and simulation techniques to study the impact of stochastic fluctuation among replicate outcomes of an evolutionary process, or the evolutionary variance, of QST and FST for a neutral quantitative trait determined by n unlinked diallelic loci with additive gene action. We studied analytical models of two scenarios. In one, a pair of demes has recently been formed through subdivision of a panmictic population; in the other, a pair of demes has been evolving in allopatry for a long time. A rigorous analysis of these two models showed that in general, it is not necessarily true that mean QST = FST (across evolutionary replicates) for a neutral, additive quantitative trait. In addition, we used finite-island model simulations to show there is a strong positive correlation between QST and the difference QST − FST because the evolutionary variance of QST is much larger than that of FST. If traits with relatively large QST values are preferentially sampled for study, the difference between QST and FST will also be large and positive because of this correlation. Many recent studies have used tests of the null hypothesis QST = FST to identify diversifying or uniform selection among subpopulations for quantitative traits. Our findings suggest that the distributions of QST and FST under the null hypothesis of neutrality will depend on species-specific biology such as the number of subpopulations and the history of subpopulation divergence. In addition, the manner in which researchers select quantitative traits for study may introduce bias into the tests. As a result, researchers must be cautious before concluding that selection is occurring when QST ≠ FST.

Hierarchical components of genetic variation at a species boundary: population structure in two sympatric varieties of Lupinus microcarpus (Leguminosae)

Lupinus microcarpus is a self‐compatible annual plant that forms a species complex of morphologically variable but indeterminate varieties. In order to examine the hypothesis that varieties of L. microcarpus comprise genetically differentiated and reproductively isolated species, populations of L. microcarpus var. horizontalis and var. densiflorus were sampled from an area of sympatry in central California and genotyped using six microsatellite loci. Bayesian clustering divided the total sample into two groups corresponding to the named varieties with extremely low levels of inferred coancestry. Similarly, maximum likelihood and distance methods for genetic assignment placed individuals in two nonoverlapping groups. Evidence for isolation by distance (IBD) within each variety was found at shorter distance classes, but varieties remained differentiated in sympatry. Furthermore, coalescent estimates of divergence time indicate separation within the past 950–5050 generations, with minimal gene flow after divergence. A four‐level hierarchical analysis of molecular variance (amova) found significant levels of genetic differentiation among varieties (θP = 0.292), populations within varieties (θS = 0.449), subpopulations within populations (θSS = 0.623), and individuals within subpopulations (f = 0.421); but the greatest degree of differentiation was at the subpopulation level. Although it is sometimes assumed that the magnitude of genetic differences (e.g. FST) should be greater between species than among populations or subpopulations of the same species, shared ancestral polymorphism may lead to relatively low levels of differentiation at the species level, even as the stochastic effects of genetic drift generate higher levels of differentiation at lower hierarchical levels. These results suggest that L. microcarpus var. horizontalis and var. densiflorus are recently diverged yet reproductively isolated species, with high levels of inbreeding resulting from the combined effects of limited gene flow, demographic bottlenecks, and partial selfing in finite, geographically structured populations.

Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms

BackgroundDifferences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (ITS1 and ITS2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial ITS divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences.ResultsRelative rate tests employing ITS sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for ITS. Relative rates of three nuclear loci and two chloroplast regions for the annual Arabidopsis thaliana compared with two closely related Arabidopsis perennials indicated that divergence was faster for the annual. In contrast, A. thaliana ITS divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of ITS1 and ITS2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference.ConclusionAlthough rate homogeneity was not rejected in many comparisons, in cases of significant rate heterogeneity annuals frequently exhibited faster substitution rates. Our results suggest that annual taxa may exhibit a less than 2-fold rate acceleration at ITS. Since the rate difference is small and ITS lacks statistical power to reject rate homogeneity, further studies with greater power will be required to adequately test the hypothesis that annual and perennial plants have heterogeneous substitution rates. Arabidopsis sequence data suggest that relative rate tests based on multiple loci may be able to distinguish a weak acceleration in annual plants. The failure to detect rate heterogeneity with ITS in past studies may be largely a product of low statistical power.

Properties of Weir and Cockerham's Fst estimators and associated bootstrap confidence intervals

Weir and Cockerham introduced single locus and multiloci F(st) estimators for the parameter θ. These estimators are commonly used, but little beyond their bias and variance is known. In this work, we develop formulas that allow us to describe how the underlying value of θ and the genetic diversity of sampled loci affect the distributions of these estimators. We show that in certain settings, these estimators are close to normal, while in others they are far from normal. We use these results to analyze confidence interval construction for θ, showing that the percentile-t bootstrap works well while the BCa bootstrap works poorly. Our results are derived using a novel coalescent based method.

speed-ne: Software to simulate and estimate genetic effective population size (N e ) from linkage disequilibrium observed in single samples

The genetic effective population size, Ne, can be estimated from the average gametic disequilibrium ( r2^ ) between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed‐ne is a suite of matlab computer code functions to estimate Ne^ from r2^ with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of Ne^ estimators under various population genetic scenarios. speed‐ne was validated with data simulated under both time‐forward and time‐backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on Ne^, how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact Ne^ . Estimators differed greatly in precision in the scenarios examined, and a widely employed Ne^ estimator exhibited the largest variances among replicate data sets. speed‐ne implements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies. speed‐ne provides an open‐source extensible tool for estimation of Ne^ from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare Ne^ estimators.