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 methods. In the 1980s, a fundamental change began in the nature of the data gathered and analyzed. This change focused on the coordinates of landmarks and the geometric information about their relative positions. As a by-product of such an approach, results of multivariate analyses could be visualized as configurations of landmarks back in the original space of the organism rather than only as statistical scatter plots. This new approach, called “geometric morphometrics”, had benefits that lead Rohlf and Marcus (1993) to proclaim a “revolution” in morphometrics. In this paper, we briefly update the discussion in that paper and summarize the advances in the ten years since the paper by Rohlf and Marcus. We also speculate on future directions in morphometric analysis.

Geometric morphometrics: Ten years of progress following the ‘revolution’

Introduction.- Data management and software.- Advice for teachers.- Exploration.- Linear regression.- Generalised linear modelling.- Additive and generalised additive modelling.- Introduction to mixed modelling.- Univariate tree models.- Measures of association.- Ordination--first encounter.- Principal component analysis and redundancy analysis.- Correspondence analysis and canonical correspondence analysis.- Introduction to discriminant analysis.- Principal coordinate analysis and non-metric multidimensional scaling.- Time series analysis--Introduction.- Common trends and sudden changes.- Analysis and modelling lattice data.- Spatially continuous data analysis and modelling.- Univariate methods to analyse abundance of decapod larvae.- Analysing presence and absence data for flatfish distribution in the Tagus estuary, Portugual.- Crop pollination by honeybees in an Argentinean pampas system using additive mixed modelling.- Investigating the effects of rice farming on aquatic birds with mixed modelling.- Classification trees and radar detection of birds for North Sea wind farms.- Fish stock identification through neural network analysis of parasite fauna.- Monitoring for change: using generalised least squares, nonmetric multidimensional scaling, and the Mantel test on western Montana grasslands.- Univariate and multivariate analysis applied on a Dutch sandy beach community.- Multivariate analyses of South-American zoobenthic species--spoilt for choice.- Principal component analysis applied to harbour porpoise fatty acid data.- Multivariate analysis of morphometric turtle data--size and shape.- Redundancy analysis and additive modelling applied on savanna tree data.- Canonical correspondence analysis of lowland pasture vegetation in the humid tropics of Mexico.- Estimating common trends in Portuguese fisheries landings.- Common trends in demersal communities on the Newfoundland-Labrador Shelf.- Sea level change and salt marshes in the Wadden Sea: a time series analysis.- Time series analysis of Hawaiian waterbirds.- Spatial modelling of forest community features in the Volzhsko-Kamsky reserve.

Analysing Ecological Data

The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.

https://science.sciencemag.org/content/sci/253/5027/1503.full.pdf

African populations and the evolution of human mitochondrial DNA

In 1967 the Kibish Formation in southern Ethiopia yielded hominid cranial remains identified as early anatomically modern humans, assigned to Homo sapiens. However, the provenance and age of the fossils have been much debated. Here we confirm that the Omo I and Omo II hominid fossils are from similar stratigraphic levels in Member I of the Kibish Formation, despite the view that Omo I is more modern in appearance than Omo II. 40Ar/39Ar ages on feldspar crystals from pumice clasts within a tuff in Member I below the hominid levels place an older limit of 198 +/- 14 kyr (weighted mean age 196 +/- 2 kyr) on the hominids. A younger age limit of 104 +/- 7 kyr is provided by feldspars from pumice clasts in a Member III tuff. Geological evidence indicates rapid deposition of each member of the Kibish Formation. Isotopic ages on the Kibish Formation correspond to ages of Mediterranean sapropels, which reflect increased flow of the Nile River, and necessarily increased flow of the Omo River. Thus the 40Ar/39Ar age measurements, together with the sapropel correlations, indicate that the hominid fossils have an age close to the older limit. Our preferred estimate of the age of the Kibish hominids is 195 +/- 5 kyr, making them the earliest well-dated anatomically modern humans yet described.

Stratigraphic placement and age of modern humans from Kibish, Ethiopia

Many problems in comparative biology and biological anthropology require meaningful definitions of “relative size” and “shape” Here we review the distinguishing features of ratios and residuals and their relationships to other methods of “size-adjustment” for continuous data Eleven statistical techniques are evaluated in reference to one broadly interspecific data set (craniometries of adult Old World monkeys) and one narrowly intraspecific data set (anthropometries of adult Native American males) Three different types of residuals are compared to three versions of shape ratios, and these are contrasted to “cscores,” Penrose shape, and multivariate adjustments based on the first principal component of the logged variance-covariance matrix; all methods are also compared to raw and logged raw data In order to help us identify appropriate; methods for size-adjustment, geometrically similar or “isometric” versions of the male vervet and the Inuit male were created by scalar multiplication of all variables The geometric mean of all variables is used as overall “size” throughout this investigation, but our conclusions would be the same for most other size variables



Residual adjustments failed to correctly identify individuals of the same shape in both sampkles Like residuals, cscores are also sample-specific and incorrectly attribute different shape values to individuals known to be identical in shape Multivariate “residuals” (eg, discarding the first principal component and Burnaby's method) are plagued by similar problems If one of the goals of an analysis is to identify individuals (OTUs) of the same shape after accounting for overalll size differences, then none of these methods can be recommended We also reject the assertion that size-adjusted variables should be unciorrelated with size of “size-free”; rather, whether or not shape covaries with size is an important empirical determination in any analysis Without explicit similarity criteria, “lines of subtraction” can be very misleading



Only variables in the Mosimann family of shape rations allowed us to identify sized individuals of the same shape (“Iso-OUTs”) Residuals from isometric lines in logarithmic space, projections of logged data to a plane orthogonal to an isometric vector, and Penrose shape distance based on logged data are also part of this shape family Shape defined in this manner can be significantly correlated with size in allometric data sets (eg, guenon craniometrics); ratio shape differences may be largely independent of size in narrowly intraspecific or intrasexual data sets (eg, Native American anthropometrics) Log-transformations of shape variables are not always necessary or desirable We hope our findings enciourage other workers to question the assumptions and utility of residuals as size-adjusted data and to explore shape and relative size within Mosimann's explicitly geometric framework © 1995 Wiley-Liss, Inc

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.1330380608

Shape, relative size, and size‐adjustments in morphometrics

During the past decade or so, considerable new data pertinent to the origin of modern humans have come to light. Based on these new data and reinterpretation of older information, three models have been offered to explain the development of modern people. These models—Brauer's Afro-European sapiens hypothesis, Stringer and Andrew's recent African evolution model, and Wolpoff, Wu, and Thorne's multiregional evolution model—have their roots in earlier models but differ from most by virtue of their worldwide perspective and integration of genetic and paleoanthropological data pertinent to modern human origins. This review presents a detailed discussion of these data in light of the three models. While convincing arguments can be offered for each of these models, it is concluded that none are unequivocally supported by the available data.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.1330320504

Modern human origins

Biological anthropology of the human skeleton

One of the greatest mysteries for most of the twentieth century was the fate of the Romanov family, the last Russian monarchy. Following the abdication of Tsar Nicholas II, he and his wife, Alexandra, and their five children were eventually exiled to the city of Yekaterinburg. The family, along with four loyal members of their staff, was held captive by members of the Ural Soviet. According to historical reports, in the early morning hours of July 17, 1918 the entire family along with four loyal members of their staff was executed by a firing squad. After a failed attempt to dispose of the remains in an abandoned mine shaft, the bodies were transported to an open field only a few kilometers from the mine shaft. Nine members of the group were buried in one mass grave while two of the children were buried in a separate grave. With the official discovery of the larger mass grave in 1991, and subsequent DNA testing to confirm the identities of the Tsar, the Tsarina, and three of their daughters – doubt persisted that these remains were in fact those of the Romanov family. In the summer of 2007, a group of amateur archeologists discovered a collection of remains from the second grave approximately 70 meters from the larger grave. We report forensic DNA testing on the remains discovered in 2007 using mitochondrial DNA (mtDNA), autosomal STR, and Y- STR testing. Combined with additional DNA testing of material from the 1991 grave, we have virtually irrefutable evidence that the two individuals recovered from the 2007 grave are the two missing children of the Romanov family: the Tsarevich Alexei and one of his sisters.

/pdf/mystery-solved-the-identification-of-the-two-missing-romanov-26ej38ly3e.pdf

Mystery solved: the identification of the two missing Romanov children using DNA analysis.

Mosimann and colleagues formulated a technique that distinguishes between size and shape, based on the concept of geometric similarity and the distinction between “log size-and-shape” and “log shape” variables. We extend these formulations in an examination of the forelimb of three callitrichid species (adultSaguinus oedipus, Saguinus fuscicollis, andCallithrix jacchus). We employ principal components analysis to explore the relationship between variance explained by size-and-shape versus shape alone. Independence of shape vectors is examined via correlation analysis. Then we use log shape data to construct intersample (species means) and total sample (between all paris of individuals) matrices of average taxonomic distances. These distance matrices are subjected to cluster analysis and principal coordinate ordinations. Results of principal components analysis suggest that after isometric size is removed, there remains sufficient shape information to discriminate among the three taxa. Careful examination and quantification of the relationships between shape and size suggest that size information (e.g., geometric mean) is fundamental for understanding shape differences within and among callitrichid species; in other words, most aspects of forelimb shape are significantly correlated with size. Contrary to conventional wisdom, we also demonstrate that such correlations are not “spurious”. Ordinations and clustering of log shape distance matrices (based on means and individuals) support the notion that, despite differences in size, the two tamarins are more similar in shape than either is toC. jacchus (despite size similarity betweenS. fuscicollis andC. jacchus). Although shape variation in the forelimb of calliirichids may have a functional component, the phylogenetic signal remains strong and serves to group individuals accordingly.

Anthony B. Falsetti

Papers

Shape, relative size, and size‐adjustments in morphometrics

Modern human origins

Biological anthropology of the human skeleton

Mystery solved: the identification of the two missing Romanov children using DNA analysis.

Morphometrics of the callitrichid forelimb: A case study in size and shape