Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera)

This study has as its primary aim the robust resolution of higher‐level relationships within the lepidopteran superfamily Bombycoidea. Our study builds on an earlier analysis of five genes (～6.6 kbp) sequenced for 50 taxa from Bombycoidea and its sister group Lasiocampidae, plus representatives of other macrolepidoteran superfamilies. The earlier study failed to yield strong support for the monophyly of and basal splits within Bombycoidea, among others. Therefore, in an effort to increase support specifically for higher‐level nodes, we generated 11.7 kbp of additional data from 20 genes for 24 of 50 bombycoid and lasiocampid taxa. The data from the genes are all derived from protein‐coding nuclear genes previously used to resolve other lepidopteran relationships. With these additional data, all but a few higher‐level nodes are strongly supported. Given our decision to minimize project costs by augmenting genes for only 24 of the 50 taxa, we explored whether the resulting pattern of missing data in the combined‐gene matrix introduced a nonphylogenetic bias, a possibility reported by others. This was achieved by comparing node support values (i.e. nonparametric bootstrap values) based on likelihood and parsimony analyses of three datasets that differ in their number of taxa and level of missing data: 50 taxa/5 genes (dataset A), 50 taxa/25 genes (dataset B) and 24 taxa/25 genes (dataset C). Whereas datasets B and C provided similar results for common nodes, both frequently yielded higher node support relative to dataset A, arguing that: (i) more data yield increased node support and (ii) partial gene augmentation does not introduce an obvious nonphylogenetic bias. A comparison of single‐gene bootstrap analyses identified four nodes for which one or two of the 25 genes provided modest to strong support for a grouping not recovered by the combined‐gene result. As a summary proposal, two of these four groupings (one each within Bombycoidea and Lasiocampidae) were deemed sufficiently problematic to regard them as unresolved trichotomies. Since the alternative groupings were always highly localized on the tree, we did not judge a combined‐gene analysis to present a problem outside those regions. Based on our robustly resolved results, we have revised the classification of Bombycoidea: the family Bombycidae is restricted to its nominate subfamily, and its tribe Epiini is elevated to subfamily rank (Epiinae stat.rev. ), whereas the bombycid subfamily Phiditiinae is reinstated as a separate family (Phiditiidae stat.rev. ). The bombycid subfamilies Oberthueriinae Kuznetzov & Stekolnikov, 1985, syn.nov. and Prismostictinae Forbes, 1955, syn.nov. , and the family Mirinidae Kozlov, 1985, syn.nov. are established as subjective junior synonyms of Endromidae Boisduval, 1828. The family Anthelidae (Lasiocampoidea) is reincluded in the superfamily Bombycoidea.     

Molecular support for morphology‐based family‐rank taxa: The contrasting cases of two families of Proseriata (Platyhelminthes)

Representatives of the Meidiamidae and Otomesostomidae (Platyhelminthes: Proseriata) are seldom encountered, and the monophyly and phylogenetic relationships of these families have never been assessed on molecular basis. Here, we present the first exhaustive molecular study of Proseriata at the family level, including species belonging to the genera Meidiama and Yorknia (Meidiamidae), and Otomesostoma auditivum (Otomesostomidae), using 18S and 28S genes as markers. We performed phylogenetic analyses (Maximum Likelihood [ML] and Bayesian Inference [BI] methods) and species delimitation methods (Single/Multiple Threshold‐Generalized Mixed Yule Coalescent [ST/MT‐GMYC] and Poisson Tree Processes [PTP/bPTP]). The taxon Meidiamidae was not supported, since the type species (Meidiama lutheri) and Meidiama etrusca sp. n. are nested within the Archimonocelididae, formerly restricted to specialized cnidarian feeders. Species belonging to the genus Yorknia resulted genetically well separated from species of Meidiama and from the rest of Archimonocelididae. The new family‐level taxon Yorkniidae fam. n. is thus here introduced, to include the type species of Yorknia (Yorknia aprostatica), and six new species, five of which are formally described here. Otomesostoma auditivum, representative of Otomesostomidae, the only exclusively freshwater taxon of the Proseriata, is the sister taxon of the predominantly marine Apingospermata. This result is not conflictual with the family level attributed to Otomesostomidae on morphological grounds, but it raises speculations on the marine versus freshwater origin of Apingospermata.     

Comprehensive analysis of mRNA‐level and miRNA‐level subpathway activities for identifying robust ovarian cancer prognostic signatures

Ovarian cancer (OvCa) causes the highest mortality among all gynaecologic cancers. A large number of mRNA‐ or miRNA‐based signatures were identified for OvCa patient prognosis. However, the comprehensive analysis of function‐level prognostic signatures is currently not considered in OvCa. In the present study, we respectively inferred subpathway activities from mRNA and miRNA levels based on high‐throughput expression profiles and reconstructed subpathways. Firstly, the activities of two tumour pathways were calculated and the difference between normal and tumour samples were analysed using multiple tumour types. Then, we calculated subpathway activities for OvCa based on the expression profiles from both mRNA and miRNA levels. Furthermore, based on these subpathway activity matrices, we performed bootstrap analysis to obtain sub‐training sets and utilized univariate method to identify robust OvCa prognostic subpathways. A comprehensive comparison of subpathway results between these two levels was performed. As a result, we observed subpathway mutual exclusion trend between the levels of mRNA and miRNA, which indicated the necessary of combining mRNA‐miRNA levels. Finally, by using ICGC data as testing sets, we utilized two strategies to verify survival predictive power of the mRNA‐miRNA combined subpathway signatures and performed comparisons with results from individual levels. It was confirmed that our framework displayed application to identify robust and efficient prognostic signatures for OvCa, and the combined signatures indeed exhibited advantages over individual ones. In the study, we took a step forward in relevant novel integrated functional signatures for OvCa prognosis.     

Delayed dispersal and prolonged brood care in a family‐living beetle

Delayed juvenile dispersal is an important prerequisite for the evolution of family‐based social systems, such as cooperative breeding and eusociality. In general, young adults forego dispersal if there are substantial benefits to remaining in the natal nest and/or the likelihood of dispersing and breeding successfully is low. We investigate some general factors thought to drive delayed juvenile dispersal in the horned passalus beetle, a family‐living beetle in which young adults remain with their families in their natal nest for several months before dispersing. Fine‐scale population genetic structure indicated high gene flow between nest sites, suggesting that constraints on mobility are unlikely to explain philopatry. Young adults do not breed in their natal log and likely disperse before reaching breeding age, suggesting that they do not gain direct reproductive benefits from delayed dispersal. We also examined several ways in which parents might incentivize delayed dispersal by providing prolonged care to adult offspring. Although adult beetles inhibit fungal growth in the colony by manipulating both the nest site and deceased conspecifics, this is unlikely to be a major explanation for family living as both parents and adult offspring seem capable of controlling fungal growth. Adult offspring that stayed with their family groups also neither gained more mass nor experienced faster exoskeleton development than those experimentally removed from their families. The results of these experiments suggest that our current understanding of the factors underlying prolonged family living may be insufficient to explain delayed dispersal in at least some taxa, particularly insects.     

Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia)

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.     

Perceived stress is associated with increased rostral middle frontal gyrus cortical thickness: a family‐based and discordant‐sibling investigation

Elevated stress perception and depression commonly co‐occur, suggesting that they share a common neurobiology. Cortical thickness of the rostral middle frontal gyrus (RMFG), a region critical for executive function, has been associated with depression‐ and stress‐related phenotypes. Here, we examined whether RMFG cortical thickness is associated with these phenotypes in a large family‐based community sample. RMFG cortical thickness was estimated using FreeSurfer among participants (n = 879) who completed the ongoing Human Connectome Project. Depression‐related phenotypes (i.e. sadness, positive affect) and perceived stress were assessed via self‐report. After accounting for sex, age, ethnicity, average whole‐brain cortical thickness, twin status and familial structure, RMFG thickness was positively associated with perceived stress and sadness and negatively associated with positive affect at small effect sizes (accounting for 0.2–2.4% of variance; p‐fdr: 0.0051–0.1900). Perceived stress was uniquely associated with RMFG thickness after accounting for depression‐related phenotypes. Further, among siblings discordant for perceived stress, those reporting higher perceived stress had increased RMFG thickness (P = 4 × 10^?7). Lastly, RMFG thickness, perceived stress, depressive symptoms, and positive affect were all significantly heritable, with evidence of shared genetic and environmental contributions between self‐report measures. Stress perception and depression share common genetic, environmental, and neural correlates. Variability in RMFG cortical thickness may play a role in stress‐related depression, although effects may be small in magnitude. Prospective studies are required to examine whether variability in RMFG thickness may function as a risk factor for stress exposure and/or perception, and/or arises as a consequence of these phenotypes.     

An automated in‐gel digestion/iTRAQ‐labeling workflow for robust quantification of gel‐separated proteins

Simple protein separation by 1DE is a widely used method to reduce sample complexity and to prepare proteins for mass spectrometric identification via in‐gel digestion. While several automated solutions are available for in‐gel digestion particularly of small cylindric gel plugs derived from 2D gels, the processing of larger 1D gel‐derived gel bands with liquid handling work stations is less well established in the field. Here, we introduce a digestion device tailored to this purpose and validate its performance in comparison to manual in‐gel digestion. For relative quantification purposes, we extend the in‐gel digestion procedure by iTRAQ labeling of the tryptic peptides and show that automation of the entire workflow results in robust quantification of proteins from samples of different complexity and dynamic range. We conclude that automation improves accuracy and reproducibility of our iTRAQ workflow as it minimizes the variability in both, digestion and labeling efficiency, the two major causes of irreproducible results in chemical labeling approaches.     

SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi‐gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi‐gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases (“Ns”), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re‐split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near‐identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java‐based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/ . © The Willi Hennig Society 2010.     

Landscape‐level tree cover predicts species richness of large‐bodied frugivorous birds in forest fragments

Large‐bodied frugivorous birds play an important role in dispersing large‐sized seeds in Neotropical rain forests, thereby maintaining tree species richness and diversity. Conversion of contiguous forest land to forest fragments is thought to be driving population declines in large‐bodied frugivores, but the mechanistic drivers of this decline remain poorly understood. To assess the importance of fragment‐level versus local landscape attributes in influencing the species richness of large‐bodied (>100 g) frugivorous birds, we surveyed 15 focal species in 22 forest fragments (2.7 to 33.6 ha, avg. = 16.0 ha) in northwest Ecuador in 2014. Fragment habitat variables included density of large trees, canopy openness and height, and fragment size; landscape variables included elevation and the proportion of tree cover within a 1 km radius of each fragment. At both the individual species level, and across the community of 12 species of avian frugivore we detected, there was higher richness and probability of presence in fragments with more tree cover on surrounding land. This tendency was particularly pronounced among some endangered species. These findings corroborate the idea that partially forested land surrounding fragments may effectively increase the suitable habitat for forest‐dwelling frugivorous birds in fragmented landscapes. These results can help guide conservation priorities within fragmented landscapes, with particular reference to retaining trees and reforesting to attain high levels of tree cover in areas between forest patches.     

Evidence of a spatial auto‐correlation in the browsing level of four major European tree species

1. The contribution of spatial processes to the spatial patterns of ecological systems is widely recognized, but spatial patterns in the ecology of plant‐herbivore interactions have rarely been investigated quantitatively owing to limited budget and time associated with ecological research. Studies of the level of browsing on various tree species reported either no spatial auto‐correlation or a small effect size. Further, the effects of disturbance events, such as hurricanes, which create large forest openings on spatial patterns of herbivory are not well understood.
2. In this study, we used forest inventory data obtained from the federal state of Baden‐Württemberg (Southern Germany) between 2001 and 2009 (grid size: 100 × 200 m) and thus, after hurricane Lothar struck Southern Germany in 1999. We investigated whether the browsing level of trees (height ≤ 130 cm) in one location is independent of that of the neighborhood.
3. Our analyses of 1,758,622 saplings (187.632 sampling units) of oak (Quercus), fir (Abies), spruce (Picea), and beech (Fagus) revealed that the browsing level is characterized by a short distance spatial auto‐correlation.
4. The application of indicator variables based on browsed saplings should account for the spatial pattern as the latter may affect the results and therefore also the conclusions of the analysis.

     

Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate + echinoderm clade

SUMMARY Hemichordates were traditionally allied to the chordates, but recent molecular analyses have suggested that hemichordates are a sister group to the echinoderms, a relationship that has important consequences for the interpretation of the evolution of deuterostome body plans. However, the molecular phylogenetic analyses to date have not provided robust support for the hemichordate + echinoderm clade. We use a maximum likelihood framework, including the parametric bootstrap, to reanalyze DNA data from complete mitochondrial genomes and nuclear 18S rRNA. This approach provides the first statistically significant support for the hemichordate + echinoderm clade from molecular data. This grouping implies that the ancestral deuterostome had features that included an adult with a pharynx and a dorsal nerve cord and an indirectly developing dipleurula-like larva.     

Plant‐soil feedbacks from 30‐year family‐specific soil cultures: phylogeny,soil chemistry and plant life stage

Intraspecific negative feedback effects, where performance is reduced on soils conditioned by conspecifics, are widely documented in plant communities. However, interspecific feedbacks are less well studied, and their direction, strength, causes, and consequences are poorly understood. If more closely related species share pathogens, or have similar soil resource requirements, plants may perform better on soils conditioned by more distant phylogenetic relatives. There have been few empirical tests of this prediction across plant life stages, and none of which attempt to account for soil chemistry. Here, we test the utility of phylogeny for predicting soil feedback effects on plant survival and performance (germination, seedling survival, growth rate, biomass). We implement a full factorial experiment growing species representing five families on five plant family‐specific soil sources. Our experiments exploit soils that have been cultured for over 30 years in plant family‐specific beds at Oxford University Botanic Gardens. Plant responses to soil source were idiosyncratic, and species did not perform better on soils cultured by phylogenetically more distant relatives. The magnitude and sign of feedback effects could, however, be explained by differences in the chemical properties of “home” and “away” soils. Furthermore, the direction of soil chemistry‐related plant‐soil feedbacks was dependent on plant life stage, with the effects of soil chemistry on germination success and accumulation of biomass inversely related. Our results (1) suggest that the phylogenetic distance between plant families cannot predict plant–soil feedbacks across multiple life stages, and (2) highlight the need to consider changes in soil chemistry as an important driver of population responses. The contrasting responses at plant life stages suggest that studies focusing on brief phases in plant demography (e.g., germination success) may not give a full picture of plant–soil feedback effects.     

MS2‐Deisotoper: A Tool for Deisotoping High‐Resolution MS/MS Spectra in Normal and Heavy Isotope‐Labelled Samples

High‐resolution MS/MS spectra of peptides can be deisotoped to identify monoisotopic masses of peptide fragments. The use of such masses should improve protein identification rates. However, deisotoping is not universally used and its benefits have not been fully explored. Here, MS2‐Deisotoper, a tool for use prior to database search, is used to identify monoisotopic peaks in centroided MS/MS spectra. MS2‐Deisotoper works by comparing the mass and relative intensity of each peptide fragment peak to every other peak of greater mass, and by applying a set of rules concerning mass and intensity differences. After comprehensive parameter optimization, it is shown that MS2‐Deisotoper can improve the number of peptide spectrum matches (PSMs) identified by up to 8.2% and proteins by up to 2.8%. It is effective with SILAC and non‐SILAC MS/MS data. The identification of unique peptide sequences is also improved, increasing the number of human proteoforms by 3.7%. Detailed investigation of results shows that deisotoping increases Mascot ion scores, improves FDR estimation for PSMs, and leads to greater protein sequence coverage. At a peptide level, it is found that the efficacy of deisotoping is affected by peptide mass and charge. MS2‐Deisotoper can be used via a user interface or as a command‐line tool.     

The how and why of branch support and partitioned branch support, with a new index to assess partition incongruence

An introduction and step‐by‐step guide to the calculation of branch support (BS) and partitioned branch support (PBS) is provided, along with a new summary measure of conflict among data partitions, the partition congruence index (PCI). Patterns of PCI vs. BS are compared for two data matrices from butterflies. PCI is a close mirror of BS unless BY is relatively low and there is a lot of conflict among data partitions, in which case PCI becomes negative. Some theoretical concerns relating to PBS are noted. © The Willi Hennig Society 2006.     

Estimation of stem and tree level biomass models for Prosopis juliflora/pallida applicable to multi-stemmed tree species

The aim of this paper is to develop biomass models for commonly multi-stemmed Prosopis juliflora/pallida trees. The data were collected on three of the Cape Verde islands (Maio, Santiago and Santo Antao). The dataset covers 240 trees containing 1,882 stems with stem diameter at breast height over 2 cm; of that 255 individual tree stems were sampled destructively. These calibration data were used to construct stem and tree-level models for estimation of total aboveground biomass and its fine and course fractions with diameter threshold of 5 cm. A set of parameterized biomass models for multi-stemmed Prosopis spp. trees suited for biomass estimation at tree and stem levels using appropriate set of independent variables, commonly available in forest inventory programs, was created. The effect of site (island) on tree allometry was not detected. The two-phase construction of tree biomass models based on destructive sampling limited to individual stems combined with a routine field measurement of entire multi-stemmed tree specimen represents a practicable approach leading to biomass and carbon assessment that may be generally suited for tree species with complex multi-stemmed growth form similar to that of Prosopis spp.     

Association of the ROBO1 gene with reading disabilities in a family‐based analysis

Linkage studies have identified a locus on chromosome 3 as reading disabilities (RD) and speech and sound disorder (SSD) susceptibility region, with both RD and SSD sharing similar phonological processing and phonological memory difficulties. One gene in this region, roundabout homolog 1 (ROBO1), has been indicated as a RD candidate and has shown significant association with measures of phonological memory in a population‐based sample. In this study, we conducted a family‐based association analysis using two independent samples collected in Toronto and Calgary, Canada. Using the two samples, we tested for association between ROBO1 single nucleotide polymorphisms (SNPs) and RD, along with quantitative measures for reading, spelling and phonological memory. One SNP, rs331142, which was selected based on its correlation with ROBO1 expression in brain tissue, was found to be significantly associated with RD in the Toronto sample with over transmission of the minor C allele (P = 0.001), correlated with low expression. This SNP is located ～200 bp from a putative enhancer and results for a marker within the enhancer, rs12495133, showed evidence for association with the same allele in both the Toronto and Calgary samples (P = 0.005 and P = 0.007). These results support previous associations between ROBO1 and RD, as well as correlation with low gene expression, suggesting a possible mechanism of risk conferred by this gene.     

Oligarchies in Amazonian tree communities: a ten‐year review

This paper revisits various hypotheses about oligarchic patterns in Amazonian tree communities put forward by Pitman et al. (2001) . Together, these hypotheses predict that most lowland sites in the Amazon are located within large patches of relatively homogeneous edaphic and other environmental conditions, where an oligarchy of common, frequent tree species accounts for a majority of trees. To assess the degree to which these hypotheses have been corroborated or refuted over the last ten years, we reviewed > 200 studies published since 2001. We found overwhelming support for the hypo thesis that large‐scale oligarchies of common and frequent species are a common feature of Amazonian tree communities. At least 22 studies have documented oligarchies in Amazonian woody plant communities to date, and no studies have looked for oligarchies as defined by Pitman et al. (2001) and failed to find them. We argue that six publications that offer critiques of the oligarchy hypothesis do not constitute valid tests. The other hypotheses in Pitman et al. (2001) – one regarding the specific oligarchic taxa that dominate forests near the eastern base of the Andes and one that attempts to explain why oligarchic species exist – are less well supported by the literature, in large part because they have not been subjected to many tests. We discuss links between these hypotheses and other well‐known patterns and hypotheses in ecology (the abundance–occupancy relationship, the Janzen–Connell hypothesis, the niche‐environment hypothesis, and the niche breadth hypothesis), and provide additional detail to facilitate rigorous tests in the future. The paper concludes by presenting remote sensing evidence that large patches of relatively homogeneous environmental conditions account for most of the upland forest landscape across Amazonian Peru.