Abstract Residual randomization in permutation procedures (RRPP) is an appropriate means of generating empirical sampling distributions for ANOVA statistics and linear model coefficients, using ordinary or generalized least‐squares estimation. This especially useful approach high‐dimensional (multivariate) data. Here, we present r package that provides a comprehensive suite tools applying RRPP to models. Important available features include choices OLS GLS coefficient estimation, data...

Abstract Geometric morphometric (GM) tools are essential for meaningfully quantifying and understanding patterns of variation in complex traits like shape. In this field, the breadth answerable questions has grown dramatically recent years through development new analyses increased computational efficiency. note, we describe ways which geomorph , a widely used R package analysing GM data, with field. We present v4.0 version improved upon previous versions. also graphical user interface easy...

Many evolutionary studies require an understanding of phenotypic change. However, while analyses variation across pairs levels (populations or time steps) are well established, methods for testing hypotheses that compare sequences multiple less developed. Here we describe a general analytical procedure quantifying and comparing patterns evolution. The evolution lineage is defined as trajectory set in multivariate phenotype space. Attributes these trajectories (their size, direction, shape),...

Analyses of two-state phenotypic change are common in ecological research. Some examples include changes due to plasticity between two environments, predator/non-predator character shifts, displacement via competitive interactions, and patterns sexual dimorphism. However, methods for analyzing multivariate data have not been rigorously developed. Here we outline a method testing vectors terms important attributes: the magnitude (vector length) direction described by trait covariation...

We propose a framework for hypothesis-testing of stable isotope ratios in ecological studies. Statistical procedures are based on analysis nested linear models and residual permutation procedure (RPP) that is employed to evaluate probabilities associated with test statistics. used simulated examples real data set illustrate the utility generality method. First, we developed differences centroid location dispersion delta13C delta15N values within among groups isotopic data. Second, evaluated...

Research using shape data from geometric morphometric (GM) methods in ecology and evolutionary biology is typically comparative, analyzing shapes change over different points along ecological or gradients. Whereas standard multivariate statistics procedures are fine for static variation - testing location differences of groups spaces they limited dynamic specific the ways locations associated with changes state ecological, developmental In this paper, we show that continuous phenotypic can...

Phylogenetic regression is frequently used in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, the conditions leading to incorrect biological inferences when comparing multivariate phenotypes among groups remain underexplored. Here, we propose a refined method of randomizing residuals permutation procedure (RRPP) for evaluating phenotypic differences while conditioning data on...

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. trends are derived from distances directions between species a phenotype space. For these patterns be interpretable, should characterized by traits commensurate units scale. Visualizing such trends, as achieved with phylomorphospaces, continue play prominent role macroevolutionary analyses. Evaluating generalized least squares (PGLS) models...

The study of modularity is paramount for understanding trends phenotypic evolution, and determining the extent to which covariation patterns are conserved across taxa levels biological organization. However, biologists currently lack quantitative methods statistically comparing strength modular signal datasets, a robust approach evaluating alternative hypotheses same dataset. As solution these challenges, we propose an effect size measure ( ZCR ) derived from covariance ratio, develop...

Character displacement is typically identified by comparing phenotypic differences in sympatry and allopatry. Recently, however, Goldberg Lande (2006) pointed out that when characters vary along an environmental gradient, the standard approach may fail to identify sympatric character divergence. Here we present a general analytical procedure for identifying divergence while accounting changes covary with variables. Our uses residual randomization from generalized linear model, allows...

Evaluating statistical trends in high-dimensional phenotypes poses challenges for comparative biologists, because the high-dimensionality of trait data relative to number species can prohibit parametric tests from being computed. Recently, two methods were proposed circumvent this difficulty. One obtains phylogenetic independent contrasts all variables, and statistically evaluates linear model by permuting phylogenetically (PICs) response data. The other uses a distance-based approach obtain...

Abstract It has become common in evolutionary biology to characterize phenotypes multivariately. However, visualizing macroevolutionary trends multivariate datasets requires appropriate ordination methods. In this paper we describe phylogenetically aligned component analysis (PACA): a new approach that aligns phenotypic data with phylogenetic signal. Unlike principal (Phy‐PCA), which finds an alignment of eigenvector is independent signal, PACA maximizes variation directions while...

Abstract In organisms encountering predictable environments, fixed development is expected, whereas in that cannot predict their future environment, phenotypic plasticity would be optimal to increase local adaptation. To test this prediction we experimentally compared two rocky-shore snail species; Littorina saxatilis releasing miniature snails on the shore, and littorea drifting larvae settling various shores, expecting L. show more than saxatilis. We magnitude direction of vectors...

The differences in phenotypic plasticity between invasive (North American) and native (German) provenances of the plant Lythrum salicaria (purple loosestrife) were examined using a multivariate reaction norm approach testing two important attributes norms described by vectors change: magnitude direction mean trait environments. Data collected for six life history traits from plants split-plot design with experimentally manipulated water nutrient levels. We found significant comparisons low...

1. The competitive interactions of closely related species have long been considered important determinants community composition and a major cause phenotypic diversification. However, while patterns such as character displacement are well documented, less is known about how local adaptation influences diversifying selection from interspecific competition. 2. We examined body size head shape variation among allopatric sympatric populations two salamander species, the widespread Plethodon...

Abstract 1. Diversification of some highly host‐specific herbivorous insects may occur in allopatry, without shifts host use. Such allopatric divergence be accelerated by sexual selection operating on courtship displays. Wing size and shape affect visual vibrational displays tephritid fruit flies. Geometric morphometric methods were used to examine wings six sympatric cryptic species the neotropical genus Blepharoneura . All feed flowers same ( Gurania spinulosa ), a vine Cucurbitaceae....

Biodiversity elements with narrow niches and restricted distributions (i.e., 'short range endemics,' SREs) are particularly vulnerable to climate change. The New Mexico Ridge-nosed Rattlesnake (Crotalus willardi obscurus, CWO), an SRE listed under the U.S. Endangered Species Act within three sky islands of southwestern North America, is constrained at low elevation by drought high wildfire. We combined long-term recapture molecular data demographic niche modeling gauge its climate-driven...

Morphological data are a conduit for the recognition and description of species, their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join collection digital with exploratory 'big data' analytics. We employed this approach to dissect Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned mitochondrial (mt)DNA analyses into eastern western lineages (two seven subspecies, respectively). The GM (i.e., 33 dorsal...

<i>Ichthyology & Herpetology</i> (formerly <i>Copeia</i>) publishes work on the biology of fishes, amphibians, and reptiles, or using those organisms as models for testing hypotheses broad significance.