The supermatrix approach to systematics

Recent reviews of the construction of large phylogenies have focused on supertree methods that involve separate analyses of data sets and subsequent integration of the resulting trees. Here, we consider the alternative method of analyzing all character data simultaneously. Such 'supermatrix' analyses use information from each character directly and enable straightforward incorporation of diverse kinds of data, including characters from fossils. The approach has been extended by the development of new methods, including model-based techniques for analyzing heterogeneous data and hierarchical methods for constructing extremely large trees. Recent work also suggests that the problem of missing data in supermatrix analyses has been overstated. Although the supermatrix approach is not suited for all cases, we suggest that its inherent strengths will ensure that it will continue to have a central role in inferring large phylogenetic trees from diverse data.     

Phylogeny and systematics of Old World serotine bats (genus Eptesicus,Vespertilionidae, Chiroptera): an integrative approach

Integrative taxonomy aims to document biodiversity by incorporating all useful characters to increase confidence in hypotheses about phylogenetic relationships. In this study, we combine data obtained independently from morphology, two maternally inherited mtDNA genes and two biparentally inherited nuDNA genes to make phylogenetic and taxonomic hypotheses about the Palaearctic members of the bat genus Eptesicus (Vespertilionidae). This genus is distributed worldwide (except for Antarctica) and is highly diversified, presenting one of the most entangled taxonomic puzzles among all mammals. Our results support restoring the genus Rhyneptesicus and separating E. isabellinus and E. pachyomus from E. serotinus and E. ognevi and E. anatolicus from E. bottae. Differences in the phylogenetic hypotheses from mtDNA and nuDNA data suggest the occurrence within E. serotinus of evolutionary processes such as mtDNA capture and secondary contacts between partially differentiated ecomorphs. These two evolutionary processes deserve more in‐depth studies within the group.     

Psychoimmune neuroendocrine integrative mechanisms revisited

This review analyzes recent publications on the topic of psycho-immune-neuroendocrine integrative mechanisms. Results on the role of cytokines in cognitive processes and in a major neuroendocrine event, i.e. the release of gonadotropin-releasing hormone, are discussed, as are the effects of cytokines on central neurotransmission. The control of immune responses by local sympathetic nerves, a major pathway in neuroimmune communication, is discussed. This review also updates information indicating that melatonin is a circulating signal affecting the periodic organization of the immune response.     

Advances in Ecological Speciation: an integrative approach

The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference ‘Advances in Ecological Speciation’ organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation.     

Protein complex prediction using an integrative bioinformatics approach

Since protein complexes play a crucial role in biological cells, one of the major goals in bioinformatics is the elucidation of protein complexes. A general approach is to build a prediction rule based on multiple data sources, e.g. gene expression data and protein interaction data, to assess the likelihood of two proteins having complex association. We critically revisit the step of predictor construction, i.e. the determination of a proper training set, an optimal classifier, and, most importantly, an optimal feature set. We use an exhaustive set of features, which includes the 2hop-feature as introduced by Wong et al. for predicting synthetic sick or lethal interactions. Post-processing of the likelihoods of protein interaction is then required to extract protein complexes. We propose a new protocol for combining these likelihood estimates. The protocol interprets the probabilities of complex association as output by the prediction rule as distances and employs hierarchical clustering to find groups of interacting proteins. In contrast to the computationally expensive search-and-score approach of Sharan et al., this protocol is very fast and can be applied to fully connected graphs. The protocol identifies trusted protein complexes with high confidence. We show that the 2hop-feature is relevant for predicting protein complexes. Furthermore, several interesting hypotheses about new protein complexes have been generated. For example, our approach linked the protein FYV4 to the mitochondrial ribosomal subunit. Interestingly, it is known that this protein is located in the mitochondrion, but its biological role is unknown. Vid22 and YGR071C were also linked, which corresponds to the new TAP data of Krogan et al.     

Ulocladium systematics revisited: phylogeny and taxonomic status

The genus Ulocladium represents phaeodictyosporic Hyphomycetes that produce conidia that are essentially obovoid in shape. Previous molecular studies that included Ulocladium and related taxa in Alternaria, Embellisia, and Stemphylium revealed a conflict between morphology and phylogeny, and Ulocladium was supported as polyphyletic with a paraphyletic core group. Moreover, the genus consistently resolved within a larger Alternaria/Ulocladium clade, resulting in paraphyly of Alternaria and questions as to the taxonomic status of Ulocladium. In the present study, 13 Ulocladium species and three genetic loci were included for a more comprehensive systematic analysis of the genus than had previously been conducted. Total genomic DNA was extracted from representative taxa and sequences were determined for the nuclear internal transcribed spacer region, including the 5.8S rDNA gene, and the protein-coding genes glyceraldehyde-3-phosphate dehydrogenase and Alt a1. Subsequent phylogenetic analyses based on maximum parsimony and Bayesian methods included related Alternaria, Embellisia, and Stemphylium spp. Results supported previous findings of polyphyletic and paraphyletic relationships of Ulocladium among other taxa. Ten Ulocladium species clustered into a core Ulocladium clade and all taxa possessed the key diagnostic feature of Ulocladium, namely, conidia essentially obovoid in shape. However, A. cheiranthi and E. indefessa also clustered within this group with high bootstrap support but did not posses this diagnostic feature. This paraphyletic clade resolved basal to the core Alternaria clade with high bootstrap support, unlike previous studies in which its position was imbedded within the primary Alternaria clade. Thus, the status of the genus as an independent lineage and a unique taxon is strongly supported. As previously reported, U. alternariae and U. oudemansii, which posses the key conidium characteristics of Ulocladium, clustered as a separate clade sister to the core Ulocladium clade. Further studies are necessary to determine if these taxa represent an independent lineage or share a common ancestor with other Ulocladium species. Obovoid conidia were poorly represented in the isolate of U. lanuginosum that was included in these analyses (the only U. lanuginosum isolate currently available), and the isolate resolved as A. radicina based upon all three loci sequenced. Based upon these data and the origin of the isolate, which was originally deposited as A. malvae, a reassessment of its identity is supported.     

The systematics of Mantodea revisited: an updated classification incorporating multiple data sources (Insecta: Dictyoptera)

After a brief synopsis of the history of mantodean classification, a re-organized systematic arrangement of extant praying mantids is provided. To overcome past homoplasy problems, a phylogenetic framework based on male genital structure was used, supplemented by published morphological, chromosomal and molecular data. As already noticed by previous authors, external morphology is highly homoplastic and does not provide useful systematic tools above subfamily level. In contrast, the morphology of male external genitalia is largely congruent with the results of recent molecular phylogenies, but contradicts the most widely used past systems. Additionally, some genital structures widely used for taxonomic purposes could be shown to be not homologous, most notably the distal process. Evolutionary transitions of the distal process and the phalloid apophysis across the mantodean phylogenetic tree are identified and named. The phalloid apophysis of many derived mantodeans shows a tendency towards bifurcation into an anterior and a posterior lobe. This and other observed genital traits are hypothesized to be an adaptation of males towards a stable copulatory grasp in groups exhibiting increased sexual dimorphism, associated with an increased risk for the male to be cannibalized during copulation. Genital characters allowed most genera to be unambiguously assigned to the major clades (superfamilies) recovered by our genital and previous molecular data. The few exceptions concern genera with secondarily simplified genitalia lacking diagnostic structures. Taxonomic literature is very heterogeneous, and several subfamilies yet lacking any modern revisionary treatment will need further refinement. To account for phylogenetic constraints, i.e. correct for past polyphyletic groupings, the number of families was elevated to 29, and the number of subfamilies to 60. We establish the new family Leptomantellidae, the new subfamilies Brancsikiinae and Deiphobinae, the new tribes Leptomiopterygini, Hagiomantini, Gonypetellini, Bolbellini, Epsomantini, Neomantini, Amantini, Armenini, Danuriellini, Deiphobini, Cotigaonopsini, Didymocoryphini, Oxyelaeini, Heterochaetulini, Rhodomantini and Pseudoxyopsidini, and the new subtribes Amphecostephanina, Bolbina, Tricondylomimina, Gonypetyllina, Antistiina, Toxomantina and Tarachomantina. New morphological diagnoses are provided for the currently recognized families. Despite a few yet to be solved problems, this work offers the urgently needed working base for future studies in Mantodean systematics, life history and ecology.     

Microsampling: an alternative approach using sesquiterpene lactones for systematics

The localization of sesquiterpene lactones in glandular trichomes of numerous Asteraceae makes it possible to use a microtechnique to investigate their occurrence. General aspects of the utility and value of the method in comparison with standard procedures are discussed with special focus on the advantage of a quick, inexpensive and reproducible analytical technique in systematic and biochemical studies. Using analytical HPLC, it was possible to establish the sesquiterpene lactone profiles of all 64 known taxa of the genus Helianthus. Intraspecific variation of sesquiterpene lactones was found to be low in comparison to morphological characters. Hybrids were shown to possess the additive sesquiterpene lactone patterns of their parents. This suggests that the chemistry of these compounds could be a useful tool in taxonomy.     

Economic context and pigeons' risk-taking: an integrative approach

The present work tested pigeons' (Columba livia) risk sensitivity to changes in resource availability in the concurrent-chains choice procedure. Subjects were provided choices, generally between variable-ratio (VR) and fixed-ratio (FR) outcome schedules with equal or different mean values. Predictions from ecology's risk sensitivity, behavioral economic's rate maximization, and psychology's delay-reduction theory were contrasted under settings where budget was adversely affected by one of three manipulations in seven experiments: (1) session length was dramatically reduced; (2) choice-phase duration was substantially increased by increasing the response requirements in the choice phase, or (3) outcome duration was significantly increased by increasing the response requirements in the outcome phase while holding session length constant. Although preference measures were sensitive to every budget manipulation, the nature of the changes observed were dependent upon the manner in which resource availability was manipulated and the choice alternatives offered. For example, choice was affected in an opposite manner when budget was adversely altered by lengthening choice duration ("search time") as opposed to lengthening outcome duration ("handling time"). Findings revealed partial support for pigeons' sensitivity both to changes in budget and to changes in conditioned reinforcer value. The overall pattern of results thus favors an integrative approach to describing the effect of economic context on general risk sensitivity.     

Comparative phylogeography as an integrative approach to historical biogeography

Phylogeography has become a powerful approach for elucidating contemporary geographical patterns of evolutionary subdivision within species and species complexes. A recent extension of this approach is the comparison of phylogeographic patterns of multiple co-distributed taxonomic groups, or 'comparative phylogeography.' Recent comparative phylogeographic studies have revealed pervasive and previously unrecognized biogeographic patterns which suggest that vicariance has played a more important role in the historical development of modern biotic assemblages than current taxonomy would indicate. Despite the utility of comparative phylogeography for uncovering such 'cryptic vicariance', this approach has yet to be embraced by some researchers as a valuable complement to other approaches to historical biogeography. We address here some of the common misconceptions surrounding comparative phylogeography, provide an example of this approach based on the boreal mammal fauna of North America, and argue that together with other approaches, comparative phylogeography can contribute importantly to our understanding of the relationship between earth history and biotic diversification.     

Neuromechanics: an integrative approach for understanding motor control

Neuromechanics seeks to understand how muscles, sense organs,motor pattern generators, and brain interact to produce coordinatedmovement, not only in complex terrain but also when confrontedwith unexpected perturbations. Applications of neuromechanicsinclude ameliorating human health problems (including prosthesisdesign and restoration of movement following brain or spinalcord injury), as well as the design, actuation and control ofmobile robots. In animals, coordinated movement emerges fromthe interplay among descending output from the central nervoussystem, sensory input from body and environment, muscle dynamics,and the emergent dynamics of the whole animal. The inevitablecoupling between neural information processing and the emergentmechanical behavior of animals is a central theme of neuromechanics.Fundamentally, motor control involves a series of transformationsof information, from brain and spinal cord to muscles to body,and back to brain. The control problem revolves around the specifictransfer functions that describe each transformation. The transferfunctions depend on the rules of organization and operationthat determine the dynamic behavior of each subsystem (i.e.,central processing, force generation, emergent dynamics, andsensory processing). In this review, we (1) consider the contributionsof muscles, (2) sensory processing, and (3) central networksto motor control, (4) provide examples to illustrate the interplayamong brain, muscles, sense organs and the environment in thecontrol of movement, and (5) describe advances in both roboticsand neuromechanics that have emerged from application of biologicalprinciples in robotic design. Taken together, these studiesdemonstrate that (1) intrinsic properties of muscle contributeto dynamic stability and control of movement, particularly immediatelyafter perturbations; (2) proprioceptive feedback reinforcesthese intrinsic self-stabilizing properties of muscle; (3) controlsystems must contend with inevitable time delays that can simplifyor complicate control; and (4) like most animals under a varietyof circumstances, some robots use a trial and error processto tune central feedforward control to emergent body dynamics.     

Functional demands of dynamic biological adhesion: an integrative approach

Climbing organisms are constantly challenged to make their way rapidly and reliably across varied and often novel terrain. A diversity of morphologically and mechanically disparate attachment strategies have evolved across widely distributed phylogenetic groups to aid legged animals in scaling these surfaces, notable among them some very impressive adhesive pads. Despite the differences between, for example, the dry fibrillar pads of geckos and the smooth, secretion-aided pads of stick insects, I hypothesize that they face similar functional demands in their environment. I outline three broad criteria defining dynamic biological adhesion: reusability, reversibility, and substrate tolerance. Organismal adhesive pads must be able to attach repeatedly without significant decline in performance, detach easily at will, and adhere strongly to the broadest possible range of surfaces in their habitat. A survey of the literature suggests that evidence for these general principles can be found in existing research, but that many gaps remain to be filled. By taking a comparative, integrative approach to biological dynamic adhesion, rather than focusing on a few model organisms, investigators will continue to discover new and interesting attachment strategies in natural systems.     

An integrative approach elucidates the systematics of Sea Hayward and Cybdelis Boisduval (Lepidoptera: Nymphalidae: Biblidinae)

The systematics of the enigmatic and rather uncommon species of Sea Hayward and Cybdelis Boisduval is assessed through morphological and molecular analyses. The aim of this paper is three‐fold: (i) to ascertain the phylogenetic position of Sea and Cybdelis in Biblidinae; (ii) to determine the evolutionary relationships among species of Sea and Cybdelis; and (iii) to review the taxonomy of Sea and Cybdelis. The result of the molecular analysis recovers Sea sister to Cybdelis, and this clade sister to Eubagina (sensu Lamas, 2004 ), rendering Epicaliina (sensu Lamas, 2004 ) paraphyletic. A new tribe, Cybdelini trib.n. is erected to include Sea and Cybdelis; the other genera formerly included in Epicaliina (sensu Lamas, 2004 ), Eunica Hübner and Sevenia Koçak are assigned to Eunicini trib.rest. , and the remaining genera of Biblidinae to other previously recognized tribes, similar to those implicitly proposed by Wahlberg et al. ( 2009 ). The morphological analysis recovers similar results and the following relationships among species of Cybdelis: C. phaesyla (Hübner) (C. boliviana Salvin (C. mnasylus Doubleday (C. petronita Burmeister stat.rest. + C. thrasylla C. Felder & R. Felder stat.rest. ))). Sea and Cybdelis are recognized as distinct genera; a new subspecies, S. sophronia jenkinsi Dias, Siewert & Freitas ssp.n. , distributed from Venezuela to Bolivia along the Andes eastern foothills, is described; and C. petronita and C. thrasylla are accepted as valid species. Lectotypes for C. boliviana, C. peruviana Staudinger, C. mnasylus, C. thrasylla, C. petronita and C. mnasylus var. meridionalis Hall and a neotype for Vanessa sophronia Godart are designated. Additionally, dichotomous keys and distribution maps to all taxa are provided; male genitalia and hypandria are illustrated for all species; generic characters of the head, labial palpi and legs are illustrated; immature stages of some species also are figured. The published work has been registered on ZooBank: http://zoobank.org/urn:lsid:zoobank.org:pub:D8EBB649‐5E9D‐4218‐B1F1‐7A69DA775FD0 .     

The integrative taxonomic approach reveals host specific species in an encyrtid parasitoid species complex

Integrated taxonomy uses evidence from a number of different character types to delimit species and other natural groupings. While this approach has been advocated recently, and should be of particular utility in the case of diminutive insect parasitoids, there are relatively few examples of its application in these taxa. Here, we use an integrated framework to delimit independent lineages in Encyrtus sasakii (Hymenoptera: Chalcidoidea: Encyrtidae), a parasitoid morphospecies previously considered a host generalist. Sequence variation at the DNA barcode (cytochrome c oxidase I, COI) and nuclear 28S rDNA loci were compared to morphometric recordings and mating compatibility tests, among samples of this species complex collected from its four scale insect hosts, covering a broad geographic range of northern and central China. Our results reveal that Encyrtus sasakii comprises three lineages that, while sharing a similar morphology, are highly divergent at the molecular level. At the barcode locus, the median K2P molecular distance between individuals from three primary populations was found to be 11.3%, well outside the divergence usually observed between Chalcidoidea conspecifics (0.5%). Corroborative evidence that the genetic lineages represent independent species was found from mating tests, where compatibility was observed only within populations, and morphometric analysis, which found that despite apparent morphological homogeneity, populations clustered according to forewing shape. The independent lineages defined by the integrated analysis correspond to the three scale insect hosts, suggesting the presence of host specific cryptic species. The finding of hidden host specificity in this species complex demonstrates the critical role that DNA barcoding will increasingly play in revealing hidden biodiversity in taxa that present difficulties for traditional taxonomic approaches.