Outlier-Robust Evidence for the Expectation Hypothesis

The test for homogeneity, on the other hand, is designed to test the null hypothesis that two or more , according to some criterion of classification applied to the samples.

Outlier-Robust Evidence for the Expectation Hypothesis …

“The Expectation Hypothesis of the Term ..

Author Page for Christina V. Atanasova :: SSRN

Smith and Kronforst proposed that the alternative explanations of introgression or ancestral polymorphism could be distinguished by considering absolute divergence within and outside of the loci of interest. Both hypotheses predict an excess of shared derived alleles at affected loci, but introgression should lead to reduced absolute divergence due to more recent coalescence at these loci, whereas the locus-specific population structure hypothesis predicts no reduction in absolute divergence at these loci compared with other loci in the genome. Loci with an excess of shared derived alleles, and therefore showing evidence of shared ancestry, were located by calculating the D statistic in nonoverlapping 5-kb windows across genomic regions of interest, and identifying outliers using an arbitrary cutoff (the 10% of windows with the highest D values). The mean absolute genetic divergence (dXY) was then compared between the outliers and nonoutliers, and found to be significantly lower in outlier windows, consistent with recent introgression (). This method makes two assumptions. First, that the D statistic can accurately identify regions that carry a significant excess of shared variation, and second, that D outliers do not have inherent biases leading to their cooccurrence with regions of low absolute divergence. These assumptions, which extend the use of D beyond its original definition, may be made by other researchers for similar purposes, but they remain to be tested.

A Random Thought on Outliers and Science | …

This analysis indicates that rejection of the null hypothesis is appropriate because the p-value is lower than 0.05. The probability values for the test of homogeneity of variances indicates that there is not enough information to reject the null hypothesis of equality of variances. No pattern or outlier data are apparent in either the “residuals versus order of the data” or “residuals versus fitted values .” The normal probability plot and histogram indicate that the residuals may not be normally distributed. Perhaps a transformation of the data could improve this fit; however, it is doubtful that any difference would be large enough to be of practical importance .

SMOOTH TRANSITION AUTOREGRESSIVE MODELS — A SURVEY OF ..

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and Phi(ST) under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (= Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements Phi(ST)/F(ST), SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

Outlier-robust convex segmentation

Severe declines in megafauna worldwide illuminate the role of top predators in ecosystem structure. In the Antarctic, the Krill Surplus Hypothesis posits that the killing of more than 2 million large whales led to competitive release for smaller krill-eating species like the Antarctic minke whale. If true, the current size of the Antarctic minke whale population may be unusually high as an indirect result of whaling. Here, we estimate the long-term population size of the Antarctic minke whale prior to whaling by sequencing 11 nuclear genetic markers from 52 modern samples purchased in Japanese meat markets. We use coalescent simulations to explore the potential influence of population substructure and find that even though our samples are drawn from a limited geographic area, our estimate reflects ocean-wide genetic diversity. Using Bayesian estimates of the mutation rate and coalescent-based analyses of genetic diversity across loci, we calculate the long-term population size of the Antarctic minke whale to be 670,000 individuals (95% confidence interval: 374,000-1,150,000). Our estimate of long-term abundance is similar to, or greater than, contemporary abundance estimates, suggesting that managing Antarctic ecosystems under the assumption that Antarctic minke whales are unusually abundant is not warranted.

Eletronic Proceedings of Neural Information Processing Systems ..

Understanding which species are most vulnerable to human impacts is a prerequisite for designing effective conservation strategies. Surveys of terrestrial species have suggested that large-bodied species and top predators are the most at risk, and it is commonly assumed that such patterns also apply in the ocean. However, there has been no global test of this hypothesis in the sea. We analyzed two fisheries datasets (stock assessments and landings) to determine the life-history traits of species that have suffered dramatic population collapses. Contrary to expectations, our data suggest that up to twice as many fisheries for small, low trophic-level species have collapsed compared with those for large predators. These patterns contrast with those on land, suggesting fundamental differences in the ways that industrial fisheries and land conversion affect natural communities. Even temporary collapses of small, low trophic-level fishes can have ecosystem-wide impacts by reducing food supply to larger fish, seabirds, and marine mammals.