Facial patterns in Cercopithecoidea and Hominoidea: a geometric approach

The maxillofacial and orbital compartments of the primate skull contribute to the ontogenetic and phylogenetic variability of the viscerocranium and are of crucial evolutionary relevance. As the form of organisms changes depending on endo- and exogenous factors, metrical evaluation of specific adaptations and incorporation of the results into a biological framework could be helpful in identifying valid characters for separation of taxa (e.g. family, genus, and species) and in understanding divergence and convergence. During the last two decades a morphometric "revolution" heralded by Rohlf & Marcus (1993), Adams et al. (2004) and Oxnard (2004) brought about a synthesis of traditional quantitative-morphometrical with modern methods. This approach is called "Geometric Morphometrics (GM)" and constitutes the coremethod applied here. Based on standardized photographs (in Norma frontalis), landmarks (LM) were set and two-dimensional coordinates (X, Y) recorded for the facial cranium in selected representatives of the superfamilies Cercopithecoidea and Hominoidea. The comparison of two datasets by means of factor analysis and distance computation for the complete maxillofacial complex on the one hand, and circumorbital and orbital features on the other, indicate that morphological differences between super-families and genera are valid for separating them even in a heterogeneous sample like the one presented here. Including more landmarks and therewith capturing the morph in a more complex way optimizes separation within the sample.     

A robust approach based on Weibull distribution for clustering gene expression data

Background

Clustering is a widely used technique for analysis of gene expression data. Most clustering methods group genes based on the distances, while few methods group genes according to the similarities of the distributions of the gene expression levels. Furthermore, as the biological annotation resources accumulated, an increasing number of genes have been annotated into functional categories. As a result, evaluating the performance of clustering methods in terms of the functional consistency of the resulting clusters is of great interest.

Results

In this paper, we proposed the WDCM (Weibull Distribution-based Clustering Method), a robust approach for clustering gene expression data, in which the gene expressions of individual genes are considered as the random variables following unique Weibull distributions. Our WDCM is based on the concept that the genes with similar expression profiles have similar distribution parameters, and thus the genes are clustered via the Weibull distribution parameters. We used the WDCM to cluster three cancer gene expression data sets from the lung cancer, B-cell follicular lymphoma and bladder carcinoma and obtained well-clustered results. We compared the performance of WDCM with k-means and Self Organizing Map (SOM) using functional annotation information given by the Gene Ontology (GO). The results showed that the functional annotation ratios of WDCM are higher than those of the other methods. We also utilized the external measure Adjusted Rand Index to validate the performance of the WDCM. The comparative results demonstrate that the WDCM provides the better clustering performance compared to k-means and SOM algorithms. The merit of the proposed WDCM is that it can be applied to cluster incomplete gene expression data without imputing the missing values. Moreover, the robustness of WDCM is also evaluated on the incomplete data sets.

Conclusions

The results demonstrate that our WDCM produces clusters with more consistent functional annotations than the other methods. The WDCM is also verified to be robust and is capable of clustering gene expression data containing a small quantity of missing values.     

MartiTracks: a geometrical approach for identifying geographical patterns of distribution

Panbiogeography represents an evolutionary approach to biogeography, using rational cost-efficient methods to reduce initial complexity to locality data, and depict general distribution patterns. However, few quantitative, and automated panbiogeographic methods exist. In this study, we propose a new algorithm, within a quantitative, geometrical framework, to perform panbiogeographical analyses as an alternative to more traditional methods. The algorithm first calculates a minimum spanning tree, an individual track for each species in a panbiogeographic context. Then the spatial congruence among segments of the minimum spanning trees is calculated using five congruence parameters, producing a general distribution pattern. In addition, the algorithm removes the ambiguity, and subjectivity often present in a manual panbiogeographic analysis. Results from two empirical examples using 61 species of the genus Bomarea (2340 records), and 1031 genera of both plants and animals (100118 records) distributed across the Northern Andes, demonstrated that a geometrical approach to panbiogeography is a feasible quantitative method to determine general distribution patterns for taxa, reducing complexity, and the time needed for managing large data sets.     

运用稀疏法分析物种丰富度的海拔梯度分布格局:以样方实测乔木种数据为例

植物物种丰富度随山地海拔梯度的变化格局是生物多样性研究的热点之一.基于种-面积关系的任何模型对群落物种数目所作估计,其精度都依赖于样本的代表性、抽样尺度以及所涉及的分类群.作者以秦岭南坡森林群落样方实测的乔木种数据为例,借鉴群落最小面积(minimum area,MA)的概念及其确定方式,利用稀疏法(rarefacti...     

A statistical approach to estimate soil ciliate diversity and distribution based on data from five continents

A total of 359 soil samples collected from five continents (Africa, Asia, Australia, Europe and South America) were investigated for the presence/absence of soil ciliate species. Merging records by species identity, we have compiled a master data list (species by sample matrix). In the list, a total of 964 soil ciliate species (644 described and 320 undescribed) are recorded. The species distributions within the 359 samples and across the five continents are examined. The frequency distribution of the species over samples is used for global diversity estimation. A statistical ACE (abundance‐based coverage estimation) model which links observed data to unseen species is applied to assess regional and global soil ciliate species richness. The model, whose reliability was tested by its power to predict the number of new species in additional samples from Africa, may resolve the controversial issue on global species diversity of soil ciliates. Although an accurate point estimate is not feasible due to severe undersampling, the statistical model enables us to obtain a minimum regional diversity and global species diversity. A consistent finding over all five continents is that at least half of the species diversity is still undiscovered. Our model also yields a global soil ciliate diversity of at least 1900 species, that is, doubles the number of currently known species, and thus diversity is relatively high. This is consistent with the finding of Foissner, who used a probability‐based method. Soil ciliate distributions between continent pairs are analyzed by adjusted abundance‐based similarity/overlap indices. These new indices account for the effect of unseen species and also reduce the bias generated by undersampling. The adjusted abundance‐based Jaccard (or Sørensen) index shows that there is about 30% (18% for Sørensen) dis‐similarity between any two continents, supporting the moderate endemicity model. The results are discussed with respect to protist species distribution, that is, whether they are cosmopolitan or of restricted distribution.     

Modeling spatial distribution of amphibian populations: a GIS approach based on habitat matrix permeability

Predictions of occurrence of two amphibian species, the common toad and the alpine newt, were made using information on land use surrounding breeding ponds. A geographical information system (GIS) was used to compile a landuse map, from which permeability estimates (friction) were derived. Potential migration zones based on friction and maximum migration distance were then modeled. Contacts between several migration zones suggest the potential for migration between ponds by adult individuals. The ability of the migration zones to enhance predictions of species occurrence was tested using generalized additive models (GAMs), and several landscape variables were selected as determinants of amphibian presence. The area of a migration zone and the number of ponds within that zone were positively related to both toad and newt presence, suggesting the importance of buffer habitats around each pond in amphibian conservation. Toad presence declined with cultivated field area and newt presence declined with vineyard area, suggesting the negative effect of agricultural activity on amphibians. The friction-based modeling approach improved the prediction of toad presence when compared to a more classical analysis of habitat composition within a circular zone centered on the focal pond. Prediction of newt presence was, however, less accurate than prediction of toad presence. Despite its exploratory nature and the subjectivity of permeability estimates, this study shows the usefulness of GIS in the functional analysis of a landscape, with potential applications in biological conservation. It also highlights the need for improving our knowledge of habitat use by animals.     

The exceptionally diversified Neotropical genus Veturius Kaup: more new data on its phylogeny,taxonomy and distribution (Coleoptera: Passalidae)

New data are provided on 24 known and five new species in three subgenera of Veturius Kaup (Proculini), from Central and South America. Veturius s. str.: V. hincksi Boucher, 2006 (wing polymorphism, Colombia: Nariño), V. perecasi Boucher, 2006 (Colombia: Boyacá, Santander, perhaps Risaralda), V. montivagus Boucher, 2006 (first precise location, Colombia: Tolima), V. schusteri Boucher, 2006 (Costa Rica: Guanacaste, Cartago, Alajuela), V. platyrhinus (Hope & Westwood, 1845) (Colombia: Tolima), V. aspina Kuwert, 1898 (polymorphism, Colombia: Sucre, Cesar, Córdoba, Antioquia), V. yahua Boucher, 2006 (Colombia: Amazonas, Meta), V. ecuadoris Kuwert, 1898 (Colombia: Caquetá), V. muisca n. sp. (Colombia: Cundinamarca), V. nonuya Boucher & Salazar, n. sp. (Colombia: Amazonas), V. standfussi Kuwert, 1891 (polymorphism, Colombia: Caquetá; Peru: Piura), V. arawak Boucher, 2006 (Peru: Cuzco, Puno), V. fabieni Boucher & Salazar, n. sp. (Peru: Junín), V. dreuxi Boucher, 2006 (Bolivia). Publius Kaup: V. crassus (Smith, 1852) (Colombia: Cundinamarca, Boyacá, Meta, perhaps Tolima), V. rugifrons Boucher, 2006 (Colombia: Cundinamarca, Boyacá), V. concretus (Kaup, 1868) (Colombia: Cundinamarca, Boyacá, Meta), V. tectus Boucher, 2006 (second record, Colombia: Santander), V. dupuisi Boucher, 2006 (second record, Colombia: Cundinamarca), V. centralis Boucher, 2006 (second record, Colombia: Antioquia), V. taurus Boucher, 2006 (second record, Colombia: Norte de Santander), V. spinipes Zang, 1905 (topotype, Bolivia). Ouayana Boucher: V. paraensis Luederwaldt, 1927 (Brazil, Pará), V. negroensis Boucher, 2006 (Colombia: Vaupés; Brazil: Amazonas), V. amazonicus Boucher, 2006 (Colombia: Guainía), V. quaesitor Boucher & Salazar, n. sp. (Peru: Piura), V. uncinatus n. sp. (Colombia: no other indication), V. casalei Boucher, 2006 (Colombia: first precise location, Caldas, Antioquia), V. fanestus Boucher, 2006 (Colombia: Nariño). Veturius contains now 86 species, and is by far the most diversified recognized monophyletic genus in the Passalidae.     

Mining gene expression data using a novel approach based on hidden Markov models

In this work we have developed a new framework for microarray gene expression data analysis. This framework is based on hidden Markov models. We have benchmarked the performance of this probability model-based clustering algorithm on several gene expression datasets for which external evaluation criteria were available. The results showed that this approach could produce clusters of quality comparable to two prevalent clustering algorithms, but with the major advantage of determining the number of clusters. We have also applied this algorithm to analyze published data of yeast cell cycle gene expression and found it able to successfully dig out biologically meaningful gene groups. In addition, this algorithm can also find correlation between different functional groups and distinguish between function genes and regulation genes, which is helpful to construct a network describing particular biological associations. Currently, this method is limited to time series data. Supplementary materials are available at http://www.bioinfo.tsinghua.edu.cn/~rich/hmmgep_supp/.     

Phylogenetic tests of distribution patterns in South Asia: towards an integrative approach

The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we outline an integrative framework for studying taxon distribution patterns. While doing so, we pay particular attention to challenges posed by the complex geological and ecological history of the region, and the differences in distribution across taxonomic groups. We outline and compare three widely used phylogenetic biogeographic approaches: topology-based methods (TBMs), pattern-based methods (PBMs) and event-based methods (EBMs). TBMs lack a quantitative framework and utilize only part of the available phylogenetic information. Hence, they are mainly suited for preliminary enquiries. Both PBMs and EBMs have a quantitative framework, but we consider the latter to be particularly suited to the South Asian context since they consider multiple biogeographic processes explicitly, and can accommodate a reticulated history of areas. As an illustration, we present a biogeographic analysis of endemic Sri Lankan agamid lizards. The results provide insights into the relative importance of multiple processes and specific zones in the radiation of two speciose lizard clades.     

Mining DNA microarray data using a novel approach based on graph theory.

The recent demonstration that biochemical pathways from diverse organisms are arranged in scale-free, rather than random, systems [Jeong et al., Nature 407 (2000) 651-654], emphasizes the importance of developing methods for the identification of biochemical nexuses--the nodes within biochemical pathways that serve as the major input/output hubs, and therefore represent potentially important targets for modulation. Here we describe a bioinformatics approach that identifies candidate nexuses for biochemical pathways without requiring functional gene annotation; we also provide proof-of-principle experiments to support this technique. This approach, called Nexxus, may lead to the identification of new signal transduction pathways and targets for drug design.     

Non-linear PCA: a missing data approach

MOTIVATION: Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values. RESULTS: Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data.Application: We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress. CONTACT: scholz@mpimp-golm.mpg.de.     

Reassessing the spatial relationship between sponges and macroalgae in sublittoral rocky bottoms: a descriptive approach

Because sublittoral sponges of temperate areas are usually more abundant at sites with low algal abundance, there is the widespread notion that macroalgae out-compete and displace sponges to habitats less suitable for algal proliferation. In this study, based on 292 sampling quadrats, we collected a total of 87 demosponge species and examined the level at which sponge distribution pairs with a variety of alga-dominated and animal-dominated habitats occurring in three zones located across a marked in-bay/out-bay environmental gradient. We found significant differences in sponge biomass, richness and diversity between the 18 habitats considered in the three zones, with abundance, richness and diversity being significantly higher in caves, vertical surfaces and overhangs out of the bay than in the remaining habitats. The cluster analysis and the unconstrained ordination consistently reflected the in-bay/out-bay environmental gradient. These analyses also revealed that the taxonomic distribution of sponge abundance is independent of the algal occurrence in the habitat, being more related to between-zone differences than to between-habitat differences. This trend was corroborated when the role of depth, algal abundance and substratum inclination in explaining total sponge abundance and diversity was examined by canonical correspondence analysis, regression analysis and mean comparisons. These analyses pointed to substratum inclination, rather than to algal abundance, as the factor explaining most variation in distribution of sponge abundance. These results, when discussed in the context provided by the outcome of other studies concerned with the spatial distribution of the sessile benthos in rocky temperate communities, strongly suggest a need to re-examine the idea that spatial distribution of sublittoral sponges largely results from competition with macroalgae.     

Habitat use by a Neotropical desert marsupial (Thylamys pallidior): A multi-scale approach

In South America, most didelphid marsupials are associated with tropical and moist forests; however, a few species are adapted to more extreme environments such as desert systems. The desert mouse opossum, Thylamys pallidior, is a small marsupial which inhabits the arid regions of South America and has the broadest distribution of the genus. The objective of this research was to assess the habitat use and selection by the desert marsupial T. pallidior considering different scales and habitat levels of analysis, as well as seasonality. We considered two habitat levels (macro and microhabitat) and the microhabitat was analyzed at two spatial scales (1 ha and 4 m²). We recorded 95 captures of mouse opossums in 27,600 trap-nights. Our study showed that habitat type was not a significant factor for selection; instead mouse opossums selected areas with low complexity and high grass cover. The scale of analysis was also important since the selection was stronger in larger areas. Habitat selection by T. pallidior occurred mainly during the dry season. During the wet season, the species used all habitat areas and types indistinctly. The present study highlights the importance of performing analyses which include multiple spatial and temporal scales for a better understanding of the patterns involved in habitat use and species distribution.     

Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics

As systematists grapple with assembling the Tree of Life, recent studies have encouraged a genomic-scale approach, obtaining DNA sequence data for entire nuclear, plastid or mitochondrial genomes for a few exemplar taxa. Some have proclaimed that this comparative genomic strategy heralds the end of incongruence in phylogeny reconstruction. Although we applaud the use of many genes to resolve phylogenetic patterns, there is a significant caveat. In spite of, or even because of, the abundant data per taxon, whole-genome sequencing for a few exemplars can provide completely resolved and strongly supported, but incorrect, evolutionary reconstructions. We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor.     

Conservation priority of Italian Alpine habitats: a floristic approach based on potential distribution of vascular plant species

In the European Union, the Directive 92/43/EEC defines a number of species and habitats of community interest that are worthy to be preserved because in danger to disappear or because they are representative of the different European bio-geographical regions. In the light of the limited economic resources generally allocated to conservation efforts, there is the necessity to prioritise conservation actions in order to avoid deterioration of protected areas. To this aim, in the present study the most representative habitats of the Italian Alps are compared on the basis of vascular plant biodiversity and a conservation priority index is proposed for each habitat taking into account the potential distribution of 252 threatened vascular plant species. Rocky slopes, screes and alpine grasslands resulted to have the greatest percentage of endemic plant species so reflecting the general distributional pattern of endemic plant species at high altitudes in Eurasian mountains. The relationship between the conservation priority index and the corresponding habitat extent within the Natura 2000 network suggests that peatlands, arid grasslands, wet meadows and freshwater habitats deserve a higher priority in conservation actions. Although vascular plant biodiversity is not necessarily a surrogate of overall biodiversity of Alpine habitats, the results here reported can be used as an initial reference framework for prioritising conservation actions, so as to accomplish the provisions of Article 6 of Habitats Directive.     

Metacommunity of a host metapopulation: explaining patterns and structures of a fish parasite metacommunity in a Neotropical floodplain basin

Host-parasite metacommunities are influenced by a myriad of factors, although little is known about which processes affect this relationship at different scales. Here, we tested how local habitat characteristics and host traits explained the parasite metacommunity of a migratory fish in a large Brazilian river floodplain. The parasite metacommunity structure showed a Clementsian pattern, which indicates a more deterministic assembly pattern, in accordance with partial Redundancy Analysis results. Results indicated that species filtering is the predominant mechanism driving community assembly. Patterns were clearer in the dry season of the floodplain. Environmental determinism seems to explain ectoparasite metacommunities in the dry season, in contrast with endoparasites that were more correlated to host traits. Overall, our results indicated that ectoparasitism is an interaction marked by opportunity, whereas endoparasitism is likely related to host features. Thus, we argue that metacommunity structuring of parasites depends on the infection strategy. Our results show that floodplain dynamics are central not only for free-living animal organizations but also for symbiotic interactions. Here, we highlight the importance of understanding the factors influencing the distribution of parasites to predict their transmission, as well as the importance of floodplain dynamics and its hydrological regime on the maintenance of ecological interactions.

     

Male differentiation patterns in two polyphenic sister species of the genus Onthophagus Latreille, 1802 (Coleoptera: Scarabaeidae): a geometric morphometric approach

This paper focuses on morphological (both shape and size ) differences that quite similar polyphenic sister species evolve during divergence processes. Traits were analysed using a geometrical morphometric approach, which has the ability to evidence also very subtle differences in shape. As a case study, we considered males of the dung beetle sister species pair Onthophagus taurus and Onthophagus illyricus (Coleoptera, Scarabaeidae); these species represent a typical example of polyphenic trait expression concerning the facultative development of horns and considerable body size differences. External shape morphology failed to discriminate O. taurus from O. illyricus , whereas the reproductive system shape showed significant interspecific discrimination power. However, the head of O. taurus was significantly larger than that of O. illyricus and the reverse was true for the elytra. The two species also showed different allometric values of the head with respect to body size. This complex pattern of interspecific morphological divergence is discussed in the light of the differential trait divergence rate hypothesis. In both species, differences between major and minor forms concern the overall shape of head and pronotum: we suggest that such different forms, which likely reflect morphological readjustment to accommodate horns of considerable bulk and disproportionate length, may be nevertheless advantageously used by the two male morphs in their alternative reproductive tactics. Male genitalia sizes were virtually constant with respect to body size; however, the ratio between phallotheca and body size was significantly higher in minor males, in keeping with the hypothesis of a higher investment in genitalia borne by this morph.     

Global patterns of isolation by distance based on genetic and morphological data

The isolation-by-distance model predicts that genetic similarity between populations will decrease exponentially as the geographic distance between them increases, because of the limiting effect of geographic distance on rates of gene flow. Many studies of human populations have applied the isolation-by-distance model to genetic variation between local populations in a limited geographic area, but few have done so on a global level, and these few used different models and analytical methods. I assess genetic variation between human populations across the world using data on red blood cell polymorphisms, microsatellite DNA markers, and craniometric traits. The isolation-by-distance model provides an excellent fit to average levels of genetic similarity within geographic distance classes for all three data sets, and the rate of distance decay is the same in all three. These results suggest that a common pattern of global gene flow mediated by geographic distance is detectable in diverse genetic and morphological data. An alternative explanation is that the correspondence between genetic similarity and geographic distance reflects the history of dispersal of the human species out of Africa.