Midpoint attractors and species richness: Modelling the interaction between environmental drivers and geometric constraints

We introduce a novel framework for conceptualising, quantifying and unifying discordant patterns of species richness along geographical gradients. While not itself explicitly mechanistic, this approach offers a path towards understanding mechanisms. In this study, we focused on the diverse patterns of species richness on mountainsides. We conjectured that elevational range midpoints of species may be drawn towards a single midpoint attractor – a unimodal gradient of environmental favourability. The midpoint attractor interacts with geometric constraints imposed by sea level and the mountaintop to produce taxon‐specific patterns of species richness. We developed a Bayesian simulation model to estimate the location and strength of the midpoint attractor from species occurrence data sampled along mountainsides. We also constructed midpoint predictor models to test whether environmental variables could directly account for the observed patterns of species range midpoints. We challenged these models with 16 elevational data sets, comprising 4500 species of insects, vertebrates and plants. The midpoint predictor models generally failed to predict the pattern of species midpoints. In contrast, the midpoint attractor model closely reproduced empirical spatial patterns of species richness and range midpoints. Gradients of environmental favourability, subject to geometric constraints, may parsimoniously account for elevational and other patterns of species richness.     

A method of factor analysis for shape coordinates

Currently the most common reporting style for a geometric morphometric (GMM) analysis of anthropological data begins with the principal components of the shape coordinates to which the original landmark data have been converted. But this focus often frustrates the organismal biologist, mainly because principal component analysis (PCA) is not aimed at scientific interpretability of the loading patterns actually uncovered. The difficulty of making biological sense of a PCA is heightened by aspects of the shape coordinate setting that further diverge from our intuitive expectations of how morphometric measurements ought to combine. More than 50 years ago one of our sister disciplines, psychometrics, managed to build an algorithmic route from principal component analysis to scientific understanding via the toolkit generally known as factor analysis. This article introduces a modification of one standard factor‐analysis approach, Henry Kaiser's varimax rotation of 1958, that accommodates two of the major differences between the GMM context and the psychometric context for these approaches: the coexistence of “general” and “special” factors of form as adumbrated by Sewall Wright, and the typical loglinearity of partial warp variance as a function of bending energy. I briefly explain the history of principal components in biometrics and the contrast with factor analysis, introduce the modified varimax algorithm I am recommending, and work three examples that are reanalyses of previously published cranial data sets. A closing discussion emphasizes the desirability of superseding PCA by algorithms aimed at anthropological understanding rather than classification or ordination.     

Shallow genetic and morphological divergence among seaperches in the South Pacific (family Scorpaenidae; genus Helicolenus)

The phylogenetic relationships among populations of seaperch, Helicolenus spp., in the south-west Pacific were examined with mtDNA markers. Parts of the cytochrome b gene [459 base pair (bp)] and the control region (448 bp) were sequenced in 58 specimens from the south-west Pacific and four specimens of Helicolenus lengerichi from Chile. Only one clade was recognized in New Zealand coastal waters, despite a wide range of colour morphs. This clade also occurred in the mid Tasman Sea on the Norfolk Ridge and around Tasmania and Victoria. A second sympatric clade was identified around Tasmania and Victoria and to the west of New Zealand. A third allopatric clade was identified to the north of New Zealand and in deep water on the Chatham Rise and a fourth clade on the Foundation Seamounts and the Louisville Ridge. Helicolenus lengerichi from Chile formed a fifth clade. Assuming a molecular clock, the clades were estimated to have diverged c. 0·7–2·6 million years ago. Only two clades, around Tasmania and Victoria, were separated using morphology, colour (in live) and dorsal-fin soft ray counts and were confirmed as Helicolenus percoides and Helicolenus barathri . Two characters, orbit diameter and colour variation, previously used to identify two species in New Zealand waters were unreliable characters for species discrimination. Principle component analyses of 11 morphological measures from 67 individuals did not delineate the clades. A canonical discriminant analysis was able to separate four of the five clades, but mean discriminate probabilities were low (77·6%), except for the five Chilean specimens of H. lengerichi (100%).     

Darkling beetle communities in two geologically contrasting biotopes: testing biodiversity patterns by microsite comparisons

Studies at a microsite scale, where most of the environmental variation can be reduced to a few factors, may help to identify the actual contribution of a particular environmental factor to community organization. Climate is known to be an important factor for regulating animal diversity. However, for soil‐dwelling animals, the role of soil characteristics can hardly be extracted out because of the inter‐relationships between climate and soil. The community structure of soil‐dwelling darkling beetles inhabiting the two geologically highly contrasting west‐ and east‐facing slopes (WFS and EFS, respectively) of the Mediterranean island of Santorini (Greece) was investigated in a case study aiming to assess the separate influence of soil characteristics and climate. Eroded pumice soils of EFS allowed a higher abundance of darkling beetle individuals and biomass, hosting more productive vegetation and being more penetrable to fossorial larvae. Moreover, the two slopes differed significantly with respect to the abundance of certain species that are characterized by a peculiar morphological adaptation to different soil characteristics. Thus, local geological sharp divergence led to darkling beetle interslope community differences as a result of local selection towards certain species. However, the two communities are similar in terms of darkling beetle diversity, evenness, and species niche‐breadth. This demonstrates that sites sharing the same climatic conditions tend to have similarly structured darkling beetle communities, even if there are marked differences in soil characteristics that promote differences in species composition, thus suggesting that climate is the major factor for regulating species diversity. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 787–793.     

Mandibles and molars of the wood mouse, Apodemus sylvaticus (L.): integrated latitudinal pattern and mosaic insular evolution

Aim The distinct nature of island populations has traditionally been attributed either to adaptation to particular insular conditions or to random genetic effects. In order to assess the relative importance of these two disparate processes, insular effects were addressed in the European wood mouse, Apodemus sylvaticus (Linnaeus, 1758). Location Wood mice from 33 localities on both mainland and various Atlantic and western Mediterranean islands were considered. This sampling covers only part of the latitudinal range of A. sylvaticus but included the two main genetic clades identified by previous studies. Islands encompass a range of geographical conditions (e.g. small islands fringing the continent through large and isolated ones). Methods The insular syndrome primarily invokes variations in body size, but ecological factors such as release from competition, niche widening and food availability should also influence other characters related to diet. In the present study, the morphology of the wood mice was quantified based on two characters involved in feeding: the size and shape of the mandibles and first upper molars. The size of the mandible is also a proxy for the body size of the animal. Patterns of morphological differentiation of both features were estimated using two‐dimensional outline analysis based on Fourier methods. Results Significant differences between mainland and island populations were observed in most cases for both the mandibles and molars. However, molars and mandibles displayed divergent patterns. Mandible shape diverged mostly on islands of intermediate remoteness and competition levels, whereas molars exhibited the greatest shape differentiation on small islands, such as Port‐Cros and Porquerolles. A mosaic pattern was also displayed for size. Body and mandible size increased on Ibiza, but molar size remained similar to mainland populations. Mosaic patterns were, however, not apparent in the mainland populations. Congruent latitudinal variations were evident for the size and shape of both mandibles and molars. Main conclusions Mosaic evolution appears to characterize insular divergence. The molar seems to be more prone to change with reduced population size on small islands, whereas the mandible could be more sensitive to peculiar environmental conditions on large and remote islands.     

Relationship of cranial robusticity to cranial form,geography and climate in Homo sapiens

Variation in cranial robusticity among modern human populations is widely acknowledged but not well‐understood. While the use of “robust” cranial traits in hominin systematics and phylogeny suggests that these characters are strongly heritable, this hypothesis has not been tested. Alternatively, cranial robusticity may be a response to differences in diet/mastication or it may be an adaptation to cold, harsh environments. This study quantifies the distribution of cranial robusticity in 14 geographically widespread human populations, and correlates this variation with climatic variables, neutral genetic distances, cranial size, and cranial shape. With the exception of the occipital torus region, all traits were positively correlated with each other, suggesting that they should not be treated as individual characters. While males are more robust than females within each of the populations, among the independent variables (cranial shape, size, climate, and neutral genetic distances), only shape is significantly correlated with inter‐population differences in robusticity. Two‐block partial least‐squares analysis was used to explore the relationship between cranial shape (captured by three‐dimensional landmark data) and robusticity across individuals. Weak support was found for the hypothesis that robusticity was related to mastication as the shape associated with greater robusticity was similar to that described for groups that ate harder‐to‐process diets. Specifically, crania with more prognathic faces, expanded glabellar and occipital regions, and (slightly) longer skulls were more robust than those with rounder vaults and more orthognathic faces. However, groups with more mechanically demanding diets (hunter‐gatherers) were not always more robust than groups practicing some form of agriculture. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Comparative 3D quantitative analyses of trapeziometacarpal joint surface curvatures among living catarrhines and fossil hominins

Comparisons of joint surface curvature at the base of the thumb have long been made to discern differences among living and fossil primates in functional capabilities of the hand. However, the complex shape of this joint makes it difficult to quantify differences among taxa. The purpose of this study is to determine whether significant differences in curvature exist among selected catarrhine genera and to compare these genera with hominin¹ fossils in trapeziometacarpal curvature. Two 3D approaches are used to quantify curvatures of the trapezial and metacarpal joint surfaces: (1) stereophotogrammetry with nonuniform rational B‐spline (NURBS) calculation of joint curvature to compare modern humans with captive chimpanzees and (2) laser scanning with a quadric‐based calculation of curvature to compare modern humans and wild‐caught Pan, Gorilla, Pongo, and Papio. Both approaches show that Homo has significantly lower curvature of the joint surfaces than does Pan. The second approach shows that Gorilla has significantly more curvature than modern humans, while Pongo overlaps with humans and African apes. The surfaces in Papio are more cylindrical and flatter than in Homo. Australopithecus afarensis resembles African apes more than modern humans in curvatures, whereas the Homo habilis trapezial metacarpal surface is flatter than in all genera except Papio. Neandertals fall at one end of the modern human range of variation, with smaller dorsovolar curvature. Modern human topography appears to be derived relative to great apes and Australopithecus and contributes to the distinctive human morphology that facilitates forceful precision and power gripping, fundamental to human manipulative activities. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc. ¹ The term “hominin” refers to members of the tribe Hominini, which includes modern humans and fossil species that are related more closely to modern humans than to extant species of chimpanzees, Wood and Lonergan (2008). Hominins are in the family Hominidae with great apes.     

Monte Carlo integration over stepping stone models for spatial genetic inference using approximate Bayesian computation

Approximate Bayesian computation (ABC) substitutes simulation for analytic models in Bayesian inference. Simulating evolutionary scenarios under Kimura’s stepping stone model (KSS) might therefore allow inference over spatial genetic process where analytical results are difficult to obtain. ABC first creates a reference set of simulations and would proceed by comparing summary statistics over KSS simulations to summary statistics from localities sampled in the field, but: comparison of which localities and stepping stones? Identical stepping stones can be arranged so two localities fall in the same stepping stone, nearest or diagonal neighbours, or without contact. None is intrinsically correct, yet some choice must be made and this affects inference. We explore a Bayesian strategy for mapping field observations onto discrete stepping stones. We make Sundial, for projecting field data onto the plane, available. We generalize KSS over regular tilings of the plane. We show Bayesian averaging over the mapping between a continuous field area and discrete stepping stones improves the fit between KSS and isolation by distance expectations. We make Tiler Durden available for carrying out this Bayesian averaging. We describe a novel parameterization of KSS based on Wright’s neighbourhood size, placing an upper bound on the geographic area represented by a stepping stone and make it available as m Vector. We generalize spatial coalescence recursions to continuous and discrete space cases and use these to numerically solve for KSS coalescence previously examined only using simulation. We thus provide applied and analytical resources for comparison of stepping stone simulations with field observations.     

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits — including body shape, colour, lips and jaws — is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high‐bodied benthic species (Amphilophus astorquii). A total of 453 genome‐wide informative SNPs were identified in 240 F₂ hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy‐two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL‐linked genomic regions, genes that might contribute to divergence in body shape along the benthic–limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.