Diet and locomotion, but not body size, differentiate mammal communities in worldwide tropical ecosystems

Aim To test whether tropical habitat groups across the world can be differentiated by using taxon-free mammalian community structures and to discuss the implications of this analysis for palaeoecological community studies. Materials and methods We used mammalian community data for 169 localities, which were assigned a priori to hierarchical Olson (1983) vegetation categories. Species over 500 g were classified into dietary, locomotion, and body mass groups and the resulting group structures were analysed using community structure analyses (NPMANOVA, CAP, SIMPER). Results The test results show that the mammalian community structures are significantly different between all of Olson's categories. These differences are highest at Olson's major and minor ecosystem levels, and require the least number of variable categories. At the vegetation level, the number of variable categories required to distinguish between them becomes higher. Of the dietary groups, the number of frugivore–granivores, frugivore–omnivores, grazers and mixed feeders contribute most to these differences, while the number of arboreal, arboreal–terrestrial and subterranean–terrestrial species are the key locomotor groups. Body mass was not a good discriminator. Main conclusions As general ecosystem categories are broken down into more precisely defined habitats, it requires more detailed knowledge of the species adaptations to distinguish between them. Many of Olson's vegetation groups represent a continuum of cover that are, at least at the worldwide comparison, too detailed to differentiate when broad generalities are sought. We suggest using three worldwide tropical major ecosystems in mammalian community structure analyses: “Humid, closed forests”, “Seasonal or interrupted forests and grasslands”, and “Seasonal, open drylands”. Our results also demonstrate that community structures defined by both dietary and locomotor adaptations are powerful discriminators of tropical ecosystems and habitats across the continents we examined, but body mass should be interpreted with caution when the research question pertains to multiple continents

Exploration of the taxonomy of some Pleistocene Cervini (Mammalia, Artiodactyla, Cervidae) from Java and Sumatra (Indonesia): a geometric- and linear morphometric approach

Third molars of extant- and fossil Southeast Asian deer were metrically compared using a linear- and geometric morphometric approach and discussed in relation to known taxonomic information from the literature. Our analysis suggests the presence of medium sized deer of the genus Axis and large sized taxa of the genus Cervus s. l. in Java. Axis lydekkeri and Axis javanicus are considered valid taxa, with A. lydekkeri probably related to the subgenus Hyelaphus. The large deer, such as Cervus kendengensis, Cervus stehlini and Cervus problematicus are most likely of the subgenus Rusa, the former two closely related to extant Cervus timorensis. The Sumatran fossils are members of the subgenus Rusa, but not necessarily conspecific with extant Cervus (Rusa) unicolor

On the misidentification of species: sampling error in primates and other mammals using geometric morphometrics in more than 4,000 individuals

An accurate classification is the basis for research in biology. Morphometrics and morphospecies play an important role in modern taxonomy, with geometric morphometrics increasingly applied as a favourite analytical tool. Yet, really large samples are seldom available for modern species and even less common in palaeontology, where morphospecies are often identified, described and compared using just one or a very few specimens. The impact of sampling error and how large a sample must be to mitigate the inaccuracy are important questions for morphometrics and taxonomy. Using more than 4000 crania of adult mammals and taxa representing each of the four placental superorders, we assess the impacts of sampling error on estimates of species means, variances and covariances in Procrustes shape data using resampling experiments. In each group of closely related species (mostly congeneric), we found that a species can be identified fairly accurately even when means are based on relatively small samples, although errors are frequent with fewer specimens and primates more prone to inaccuracies. A precise reconstruction of similarity relationships, in contrast, sometimes requires very large samples (> 100), but this varies widely depending on the study group. Medium-sized samples are necessary to accurately estimate standard errors of mean shapes or intraspecific variance covariance structure, but in this case minimum sample sizes are broadly similar across all groups (≈ 20-50 individuals). Overall, thus, the minimum sample sized required for a study varies across taxa and depends on what is being assessed, but about 25-40 specimens (for each sex, if a species is sexually dimorphic) may be on average an adequate and attainable minimum sample size for estimating the most commonly used shape parameters. As expected, the best predictor of the effects of sampling error is the ratio of between- to within-species variation: the larger the ratio, the smaller the sample size needed to obtain the same level of accuracy. Even though ours is the largest study to date of the uncertainties in estimates of means, variances and covariances in geometric morphometrics, and despite its generally high congruence with previous analyses, we feel it would be premature to generalize. Clearly, there is no a priori answer for what minimum sample size is required for a particular study and no universal recipe to control for sampling error. Exploratory analyses using resampling experiments are thus desirable, easy to perform and yield powerful preliminary clues about the effect of sampling on parameter estimates in comparative studies of morphospecies, and in a variety of other morphometric applications in biology and medicine. Morphospecies descriptions are indeed a small piece of provisional evidence in a much more complex evolutionary puzzle. However, they are crucial in palaeontology, and provide important complimentary evidence in modern integrative taxonomy. Thus, if taxonomy provides the bricks for accurate research in biology, understanding the robustness of these bricks is the first fundamental step to build scientific knowledge on sound, stable and long-lasting foundations

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature