F. James Rohlf

F. James Rohlf
State University of New York | SUNY · Anthropology dept. and Ecology & Evolution dept.

Ph.D.

About

252
Publications
228,711
Reads
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Introduction
F. James Rohlf currently is in the Ecology & Evolution dept. and Anthropology dept., State University of New York. He does research in Biostatistics. His recent project was 'Random skewers - what do they estimate?.' He is now on to other topics.
Additional affiliations
October 2014 - present
Stony Brook University
Position
  • Research Professor
January 2014 - present
Stony Brook University
Position
  • Distinguished Professor, Emeritus
September 2011 - December 2013
Stony Brook University
Position
  • John S. Toll Professor

Publications

Publications (252)
Article
Full-text available
Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relat...
Article
Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relat...
Article
Full-text available
Recent papers by Cardini et al. (Evolutionary Biology 46:307–316, 2019) and Bookstein (Evolutionary Biology 46:271–302, 2019) show that, when there are many variables and when sample sizes are small, scatterplots made using the between-groups principal components analysis method can appear to indicate clear group differences with little or no overl...
Article
Full-text available
Using sampling experiments, we found that, when there are fewer groups than variables, between-groups PCA (bgPCA) may suggest surprisingly distinct differences among groups for data in which none exist. While apparently not noticed before, the reasons for this problem are easy to understand. A bgPCA captures the g − 1 dimensions of variation among...
Article
Morphometric assessments of the dentition have played significant roles in hypotheses relating to taxonomic diversity among extinct hominins. In this regard, emphasis has been placed on the statistical appraisal of intraspecific variation to identify morphological criteria that convey maximum discriminatory power. Three-dimensional geometric morpho...
Article
Full-text available
Ecological and evolutionary studies are often concerned with the properties of covariance matrices. The method of random skewers (RS method) has been used compare a matrix to an a priori vector or to compare two matrices. The method involves multiplying a matrix by many random vectors drawn from a uniform distribution over all possible vector direc...
Article
Full-text available
Phylogenetic generalized least squares (PGLS) has become one of the most commonly used phylogenetic comparative methods. Despite its common use, descriptions and applications of methods to test for species' deviations from allometric predictions using phylogenetic regression have been piecemeal. We simplify previous computational descriptions of PG...
Article
Batoids (Chondrichthyes: Batoidea) are a diverse group of cartilaginous fishes which comprise a monophyletic sister lineage to all neoselachians or modern sharks. All species in this group possess anteroposteriorly expanded-pectoral fins, giving them a unique disc-like body form. Reliance on pectoral fins for propulsion ranges from minimal (sawfish...
Article
Instances of sexual dimorphism occur in a great variety of forms and manifestations. Most skates (Batoidea: Rajoidei) display some level of body shape dimorphism in which the pectoral fins of mature males develop to create a distinct bell-shaped body not found in females. This particular form of dimorphism is present in each of the sister species L...
Article
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The development and the present state of the “tps” series of software for use in geometric morphometrics on Windows-based computers are described. These programs have been used in hundreds of studies in mammals and other organisms.
Article
Full-text available
Purpose:To analyze the deformations of the peripapillary retinal pigment epithelial basement-membrane (ppRPE/BM)-layer in response to procedures that lower intracranial pressure(ICP). Second, to demonstrate how shape changes may complement the mean retinal nerve fiber layer(RNFL)-thickness as a measure of intracranial hypertension(ICH) and papilled...
Article
Full-text available
Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences...
Chapter
The term phenetics is defined and contrasted to cladistics.
Chapter
The conditions necessary for a dissimilarity coefficient called a 'metric' are described.
Chapter
Glossary Monothetic classification A classification in which all members of a group must share at least one trait. Polythetic classification A classification in which members of a group are very similar but need not have any single trait in common with the other members. Numerical taxonomy is the use of statistical and mathematical methods to group...
Chapter
The meaning of similarity in numerical taxonomy is described.
Chapter
A phenogram is a diagram depicting taxonomic relationships among organisms based on overall similarity of many characteristics without regard to evolutionary 'history' or assumed significance of specific characters.
Chapter
The conditions necessary for a dissimilarity or distance coefficient to be called an ultrametric are described.
Article
[1] state that they are ‘biostatisticianswith a primary responsibility for collaborative research in a major medical school’. They do not illustratetheir article with any real data, however, and appear largely to ignore the context in which log transfor-mations are applied. Notably, log transformations are typically applied to data which are expect...
Article
Synurophytes, also known as scaled chrysophytes, are ecologically important algae that produce an array of siliceous structures upon which their taxonomy is based. Despite occupying a key position within the photosynthetic heterokonts, the evolutionary history of synurophytes remains poorly constrained. Here, modern and Middle Eocene siliceous scal...
Article
Full-text available
Twenty years ago, Rohlf and Marcus proclaimed that a "revolution in morphometrics" was underway, where classic analyses based on sets of linear distances were being supplanted by geometric approaches making use of the coordinates of anatomical landmarks. Since that time the field of geometric morphometrics has matured into a rich and cohesive disci...
Conference Paper
Little and winter skate are sister species with largely overlapping geographic distributions. Both are important components of northeast Atlantic coastal marine communities. Their juveniles are visually indistinguishable up to a total length of roughly 30 cm, however above this they diverge substantially with respect to body size and morphology. Pr...
Article
Study of morphological form is fundamental to the discipline of paleoanthropology. The size and shape of our ancestors' anatomical features have long been the focus of research on hominin systematics, phylogeny, functional morphology, ontogeny, variation, and evolutionary change. Early physical anthropologists relied on both qualitative description...
Article
Full-text available
We tested the hypothesis that Crohn's disease (CD)-related genetic polymorphisms involved in host innate immunity are associated with shifts in human ileum-associated microbial composition in a cross-sectional analysis of human ileal samples. Sanger sequencing of the bacterial 16S ribosomal RNA (rRNA) gene and 454 sequencing of 16S rRNA gene hyperv...
Article
Full-text available
The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn's disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD). Ex-vi...
Data
Permutation-based MANCOVA with stepwise variable selection results for Sanger, 454 V1–V3 and 454 V3–V5 sequencing. Samples with Crohn’s colitis and indeterminate colitis were excluded in this analysis. The dependent variable was the vector generated by the centered log ratio of the relative frequencies of six phyla/subphyla categories (see text). T...
Data
Distribution of the three common NOD2 genotypes in ileal CD, colitis and non-IBD control subjects. The three major NOD2 risk alleles that account for 80% of the NOD2 variants, are Leu1007fs (SNP13, rs2066847), R702W (SNP8, rs2066844), and G908W (SNP12, rs2066845). (DOCX)
Data
Permutation-based MANCOVA with stepwise variable selection results for Caucasian patients. Because NOD2 risk alleles are rarely observed in subjects of Asian and African descent, the analysis was repeated for the 150 Caucasian subjects in the study (48 ileal CD, 52 colitis, 50 non-IBD control subjects). The dependent variable was the vector generat...
Data
Permutation based ANCOVA with stepwise variable selection results for each of the six individual phyla/subphyla categories. Permutation based ANCOVA with step wise variable selection was carried out for the individual phyla/subphyla categories. in parallel for each of the datasets. A total of 164 samples were analyzed for the Sanger and the 454 V1–...
Data
A. Relative frequencies of the six phyla/subphyla categories selected to represent overall microbial composition based on the Sanger dataset. The mean value ± standard deviation is shown for each of the three disease phenotypes, ileal CD, colitis and control non-IBD. B. Relative frequencies of the six phyla/subphyla categories selected to represent...
Data
Comparison between nonIBD control subjects with primary colon adenocarcinoma with non-IBD subjects without primary colon adenocarcinoma. Continuous variables (e.g. age, BMI, relative frequency of bacterial groups) were compared using the Wilcoxon rank sum test and categorical variables (e.g. genotype, smoking, race) were compared using the chi-squa...
Article
Full-text available
Geometric morphometric techniques allow for the direct quantification and analysis of variation in biological shape and have been used in studies in systematic biology. However, these techniques have not been used for species discrimination in the gastropod genus Conus, a major taxon of significant tropical reef predators recognized for their pepti...
Book
Full-text available
The premier text in the field, Biometry provides both an elementary introduction to basic biostatistics as well as coverage of more advanced methods used in biological research. Students are shown how to think through research problems and understand the logic behind the different experimental situations. This book is designed to serve not only as...
Article
Full-text available
Geometric morphometrics (GM) was used to analyze the shape of the peripapillary retinal pigment epithelium-Bruch's membrane (RPE/BM) layer imaged on the SD-OCT 5-line raster in normal subjects and in patients with papilledema and ischemic optic neuropathy. Three groups of subjects were compared: 30 normals, 20 with anterior ischemic optic neuropath...
Article
Introduction: Recently, Gonza ´lez-Jose ´ et al. (2008) proposed that phylogeny estimation using principal components (PCs) from shape analyses of cranial ‘modules’ (modular cladistic approach: MCL) is an advance that could provide a benchmark for future studies of evolutionary relationships. Unfortunately, MCL ignores serious practical and theoret...
Article
Understanding the processes underlying morphological diversification is a central goal in ecology and evolutionary biology and requires the integration of information about phylogenetic divergence and ecological niche diversity. In the present study, we use geometric morphometrics and comparative methods to investigate morphological diversification...
Article
Full-text available
Updated harness designs are needed to accommodate diverse populations in the current workforce. This paper determined an improved fall-arrest harness sizing scheme and strap-length configurations for harness design. A 3-D elliptic Fourier analysis (EFA) procedure with 123 coefficients was developed to quantify torso-shape effect on harness fit, bas...
Article
Full-text available
The results of facial surgery are intuitively judged in terms of the visible changes in facial features or proportions. However, describing these morphologic outcomes objectively remains a challenge. Biometric morphing addresses this issue by merging statistical shape analysis and image processing. This study describes the implementation of biometr...
Article
The results of facial surgery are intuitively judged in terms of the visible changes in facial features or proportions. However, describing these morphologic outcomes objectively remains a challenge. Biometric morphing addresses this issue by merging statistical shape analysis and image processing. This study describes the implementation of biometr...
Article
The present study investigates the pattern of differentiation of cranial shape in three closely related delphinid cetacean species of the complex Delphinus-Stenella-Tursiops: Delphinus delphis, Stenella coeruleoalba and Tursiops truncatus. Dorsal and ventral aspects of the cranium were analysed using landmark-based geometric morphometric methods. W...
Article
Upward and downward arching of the body was observed during a study on redfishes Sebastes sp. population structure in the north-west Atlantic Ocean. The present study investigated the potential causes of this arching artefact. The results suggested that it is not related to biological factors (size or species) or to the preservation technique (free...
Article
Chromosomal races of the house mouse (Mus musculus domesticus) in Valtellina and Orobian Alps (Northern Italy) are known for their very fast raciation. Here we present a study using geometric morphometries on size and shape changes in the skull and the mandible of three races (Orobian, Upper Valtellina, Poschiavo) occurring in this area and forming...
Chapter
Full-text available
Fred Szalay is a polymath of evolutionary morphology. From the mid-1960s (Szalay, 1968) to at least the mid-1980s (Szalay et al., 1987), he was acknowledged as the leading researcher on non-anthropoid fossil primates, complementing the anthropoid expertise of Elwyn Simons who had just laid the foundations for paleoprimatology as a distinct field th...
Article
Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifact due to...
Article
Abstract Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifa...
Article
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Article
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The Neighbor-Joining (NJ) method of Saitou and Nei is the most widely used distance based method in phylogenetic analysis. Central to the method is the selection criterion, the formula used to choose which pair of objects to amalgamate next. Here we ...
Article
Full-text available
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Conference Paper
We introduce a technique to visualize the gradual evolutionary change of the shapes of living things as a morph between known three-dimensional shapes. Given geometric computer models of anatomical shapes for some collection of specimens - here the skulls of the some of the extant members of a family of monkeys - an evolutionary tree for the group...
Article
Full-text available
Fall protection harnesses are commonly used to reduce the number and severity of injuries. Increasing the efficiency of harness design requires the size and shape variation of the user population to be assessed as detailed and as accurately as possible 3 . In light of the unsatisfactory performance of traditional anthropometry with respect to such...
Article
Full-text available
The analysis of shape is a fundamental part of much biological research. As the field of statistics developed, so have the sophistication of the analysis of these types of data. This lead to multivariate morphometrics in which suites of measurements were analyzed together using canonical variates analysis, principal components analysis, and related...
Article
Congruence between patterns of localized, hierarchical variation in cranial shape and topological, molecular phylogenetic structure was investigated in a monophyletic lineage of Neotropical spiny rats of the genus Trinomys. Levels of organizational complexity in shape were assessed from two-dimensional coordinates of anatomical landmarks for dorsal...
Article
Sampling experiments were performed to investigate mean square error and bias in estimates of mean shape produced by different geometric morphometric methods. The experiments use the isotropic error model, which assumes equal and independent variation at each landmark. The case of three landmarks in the plane (i.e., triangles) was emphasized becaus...
Article
Full-text available
Any change in shape of a configuration of landmark points in two or three dimensions includes a uniform component, a component that is a wholly linear (affine) transformation. The formulas for estimating this component have been standardized for two-dimensional data but not for three-dimensional data. We suggest estimating the component by way of t...
Article
Full-text available
This study is concerned with statistical methods used for the analysis of comparative data (in which observations are not expected to be independent because they are sampled across phylogenetically related species). The phylogenetically independent contrasts (PIC), phylogenetic generalized least-squares (PGLS), and phylogenetic autocorrelation (PA)...
Article
This paper is concerned with the problem of computing spanning tree (MST) for n points in a p-dimensional space where the "distance" between each pair of points i and j satisfies the relationship' dq max {Ixti - xtql} , where xki is the coordinate of object i along the ktti dimension. This relationship is clearly satisfied by all Minkowski metrics...
Article
Full-text available
The relatively new two-block partial least-squares method for analyzing the covariance between two sets of variables is described and contrasted with the well-known method of canonical correlation analysis. Their statistical properties, types of answers, and visualization techniques are discussed. Examples are given to show its usefulness in compar...
Article
: This study is concerned with statistical methods used for the analysis of comparative data (data in which observations are not expected to be independent because they are sampled across phylogenetically related species). The phylogenetically independent contrasts (PIC), phylogenetic generalized least-squares (PGLS), and phylogenetic autocorrelati...
Article
Previous reports indicate that brain structural abnormalities may be progressive in some patients with schizophrenia. Our study was designed to determine deviations in the shape of midline brain structures at the time of onset of symptoms of schizophrenia and 3-5 years later. Eleven landmarks were located on the midsagittal magnetic resonance image...
Article
Full-text available
Abstract Several methods have been proposed to use differences in configurations of landmark points to measure the amount of shape difference between two structures. Shape difference coefficients ignore differences in the configurations that could be due to the effects of translation, rotation, and scale. One way to understand the differences betwe...
Article
Full-text available
Ecological character displacement describes a pattern where morphological differences between sympatric species are enhanced through interspecific competition. Although widely considered a pervasive force in evolutionary ecology, few clear-cut examples have been documented. Here we report a case of ecological character displacement between two sala...