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

An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

/pdf/experimental-design-and-data-analysis-for-biologists-8ybva8d53x.pdf

Experimental Design and Data Analysis for Biologists

Hybrid zones are, roughly speaking, narrow regions in which genetically distinct populations meet, mate, and produce hybrids. They are often only a few hundred meters wide and yet may be several hundred kilometers long. They are found in a wide variety of organisms: Tables 1 and 2 list about 150 reasonably clear examples, in which there is a spatial transition between two hybridizing forms. Such a widespread and striking phenomenon requires explanation; more importantly, it offers us several ways of understanding the nature and origin of species. First, hybrid zones pose interesting questions for the taxonomist, for they contrast two views of the species: as a set of populations delimited by genetic barriers to gene exchange; and as a set of populations maintained in a particular stable equilibrium by selection. Second, the wide range of genotypes found in a hybrid zone can be used to analyze the genetic differences and selective forces that separate the taxa involved. This may allow some inferences about the way these differences evolved and, by extrapolation, about the way fully isolated species diverge from each other. Finally, models of parapatric speciation, and of Wright's "shifting balance," involve the formation, move­ ment, and modification of hybrid zones. Hybrid zones must be understood before the plausibility of these models can be judged. After clarifying our terminology, we will summarize the relevant theory and then see how this can be used to make inferences from field data. A notable increase in the number of detailed genetic studies of hybrid zones occurred over

Analysis of Hybrid Zones

▪ Abstract Nonindigenous species can bring about a form of extinction of native flora and fauna by hybridization and introgression either through purposeful introduction by humans or through habitat modification, bringing previously isolated species into contact. These phenomena can be especially problematic for rare species coming into contact with more abundant ones. Increased use of molecular techniques focuses attention on the extent of this underappreciated problem that is not always apparent from morphological observations alone. Some degree of gene flow is a normal, evolutionarily constructive process, and all constellations of genes and genotypes cannot be preserved. However, hybridization with or without introgression may, nevertheless, threaten a rare species' existence.

https://www.jstor.org/stable/pdfplus/2097230.pdf

Extinction by hybridization and introgression

It is often necessary in population biology to compare two sets of distance measures. These measures can be based on genetic markers, morphological traits, geographic separation, ecological divergence, and so on. The distance measures can take various forms and frequently have unknown distributional properties. Many different procedures have been developed to compare the correspondence of one set of distances with another set. Prominent among them are the: (1) matrix correlation techniques of Sokal and Rohlf (1962), and Sneath and Sokal (1973); (2) networkmatching techniques of Spielman (1973); (3) matrix dilation and rotation techniques of Gower (1971) and of Schonemann and Carrol (1970); and (4) smallest-space techniques of Lingoes (1965) and Guttman (1968). Each of these strategies has strong points, but all suffer from a difficulty in assessing the statistical significance of attained correspondence. The problem is that a set of all possible pairwise distances between k units (populations, taxa, habitats, etc.) cannot be independent. More recently, a test of matrix correspondence-originally developed by Mantel (1967) and widely applied in geography (Hubert and Golledge, 1982) and psychometrics (Hubert, 1979a, b)-has caught the attention of population biologists (Sokal, 1979; Sokal et al., 1980; Douglas and Endler, 1982; Dow and Cheverud, 1985; Schnell et al., 1985, 1986; Sokal et al., 1986, 1987; O'Brien, 1987; Smouse and Wood, 1987). Attractions of the Mantel procedure are its wide applicability and computational simplicity. Mantel (1967) presented a formal analysis of matrix correspondence based on the assumption of asymptotic normality for a particular test criterion. Later workers (Mielke et al., 1981) developed more general procedures for Mantel statistics that assume a Pearson Type III distributional form. The most widely used evaluation procedure, however, involves the construction of a null distribution by Monte Carlo randomization, whereby one of the matrices is held rigid and the other has its rows and corresponding columns randomly permuted (Cliff and Ord, 1981). Dietz (1983) evaluated the Mantel test as one of several permutational tests for association between distance matrices. When dimensions of two matrices are small (say K ' 7), it is customary to evaluate the Mantel test criterion for all K! equally likely permutations. If K is large, then a large number of random permutations are sampled with replacement. Although the test has been useful in its present form, there are some simple modifications and extensions that would encourage even wider deployment in population work. Our purpose here is to sketch these changes and to illustrate them with an example drawn from the Yanomama Indians of lowland South America.

http://www.pelagicos.net/MARS6300/readings/Smouse_et_al._1986.pdf

Multiple regression and correlation extensions of the mantel test of matrix correspondence

Biotic homogenization, the gradual replacement of native biotas by locally expanding non-natives, is a global process that diminishes floral and faunal distinctions among regions. Although patterns of homogenization have been well studied, their specific ecological and evolutionary consequences remain unexplored. We argue that our current perspective on biotic homogenization should be expanded beyond a simple recognition of species diversity loss, towards a synthesis of higher order effects. Here, we explore three distinct forms of homogenization (genetic, taxonomic and functional), and discuss their immediate and future impacts on ecological and evolutionary processes. Our goal is to initiate future research that investigates the broader conservation implications of homogenization and to promote a proactive style of adaptive management that engages the human component of the anthropogenic blender that is currently mixing the biota on Earth.

http://depts.washington.edu/oldenlab/wordpress/wp-content/uploads/2013/03/TrendsEcolEvol_2004.pdf

Ecological and evolutionary consequences of biotic homogenization.

Biology of the vipers.

in gut analyses; and (c) 34 head, fin, and body measurements. Ecological data were arcsine transformed, while morphological data were converted first into common logarithms, then into canonical variate scores and scores from a sheared principal components analysis. A taxonomic matrix based on accepted phylogenetic relationships amongst species of the assemblage was also constructed. Microhabitat, trophic, morphological, and taxonomic matrices were then compared against one another using pair-wise Mantel tests, matrix correlation analyses, and three-way Mantel tests. In analyses across families, two-way Mantel tests revealed that taxonomy and body shape (based on sheared principal component scores) were each significantly related to one another, and to the trophic matrix. Yet, three-way Mantel comparisons indicated that body shapes of constituent species were significantly correlated only with taxonomy, and not with diet. To circumvent the confounding effects of taxonomy, the largest family in the study (Cyprinidae, 8 species represented) was then evaluated separately. The same analyses were performed as before, using trophic, microhabitat, and morphological matrices adjusted for numbers of species. In these analyses, morphology (represented by canonical variate and sheared principal component scores) was significantly related to the microhabitat matrix, and to no others. Previous field studies have indicated that cyprinids segregate along habitat rather than trophic dimensions. Ecomorphological analyses thus appear to be a valid assay for structure within fish assemblages only when limited to within-family comparisons (where the effects of history appear less significant). When many different families are involved in the analysis, historical influences predominate.

Michael E. Douglas

Papers

Ecological and evolutionary consequences of biotic homogenization.

Biology of the vipers.

Does morphology predict ecology? Hypothesis testing within a freshwater stream fish assemblage

Quantitative Matrix Comparisons in Ecological and Evolutionary Investigations

Statistical comparison of proximity matrices: applications in animal behaviour