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Phylogenetic signal dissection identifies the root of starfishes.

ABSTRACT: Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.

SUBMITTER: Feuda R

PROVIDER: S-EPMC4425436 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca).

Project description:It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.

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Root/valve preservation in aortic dissection.

Project description:Role of root/valve preservation in aortic dissection and the relative merits and demerits of David procedure over Yacoub's remodeling operation have been discussed in a one on one discussion with Dr. O.P. Yadava, Editor-in-Chief, IJTC and Dr. P Davierwala of Heart Center, Leipzig.

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Phylogenetic signal in floral temperature patterns.

Project description:ObjectivesFloral structures may be warmer than their environment, and can show thermal patterning, where individual floral structures show different temperatures across their surface. Pollinators can differentiate between artificial flowers that mimic both naturally warmed and thermally patterned ones, but it has yet to be demonstrated that these patterns are biologically meaningful. To explore the relationship between pollinators and temperature patterning, we need to know whether there is diversity in patterning, and that these patterns are not simply a by-product of floral architecture constrained by ancestry. We analysed a dataset of 97 species to explore whether intrafloral temperature differences were correlated within clades (phylogenetic signal), or whether the variation seen was diverse enough to suggest that floral temperature patterns are influenced by the abiotic or pollinator-related niches to which plant species are adapted.ResultsSome phylogenetic signal was observed, with both the Asteraceae and species of Pelargonium being more similar than expected by chance, but with other species surveyed not showing signal. The Asteraceae tend to have large temperature differences across the floral surface, which may be due to floral architecture constraints within the family. Other families show no correlation, suggesting that patterning is influenced by pollinators and the environment.

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Phylogenetic Signal and Bias in Paleontology.

Project description:An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data sets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological data sets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA data sets usually increases congruence of resulting topologies to the well-corroborated tree, but this varies among morphological data sets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artifacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. [Concatenation; fossilization; morphology; parsimony; systematics; taphonomy; total-evidence.].

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Genomic repeat abundances contain phylogenetic signal.

Project description:A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

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Project description: Not available

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Phylogenetic signal of sub-arctic beetle communities.

Project description:Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.

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Phylogenetic signal in plant pathogen-host range.

Project description:What determines which plant species are susceptible to a given plant pathogen is poorly understood. Experimental inoculations with fungal pathogens of plant leaves in a tropical rain forest show that most fungal pathogens are polyphagous but that most plant species in a local community are resistant to any given pathogen. The likelihood that a pathogen can infect two plant species decreases continuously with phylogenetic distance between the plants, even to ancient evolutionary distances. This phylogenetic signal in host range allows us to predict the likely host range of plant pathogens in a local community, providing an important tool for plant ecology, design of agronomic systems, quarantine regulations in international trade, and risk analysis of biological control agents. In particular, the results suggest that the rate of spread and ecological impacts of a disease through a natural plant community will depend strongly on the phylogenetic structure of the community itself and that current regulatory approaches strongly underestimate the local risks of global movement of plant pathogens or their hosts.

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Transcriptional dissection of lateral root primordium cells

Project description:To specifically profile early stages of lateral root formation we used the marker pHB53:NLS-3xmCherry, which is only expressed in lateral root primordium cells. We isolated ~2,000 lateral root primordium cells from stages I to IV through Fluorescent Activated Cell Sorting, and profiled the transcriptome of 573 of these cells. As a LR primordium has ~6-10 cells at stage I and ~30-40 cells at stage IV, the number of sequenced cells would approximately cover 5-6 fold the total number of cells in the stages profiled.

2021-08-05 | GSE161970 | GEO

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Project description:Breeding new crop cultivars with efficient root systems carries great potential to enhance resource use efficiency and plant adaptation to unstable climates. Here, we evaluated the natural variation of root system architectural traits in a diverse spring barley association panel and conducted genome-wide association mapping to identify genomic regions associated with root traits. For six studied traits, root system depth, root spreading angle, seminal root number, total seminal root length, and average seminal root length 1.9- to 4.2-fold variations were recorded. Using a mixed linear model, 55 QTLs were identified cumulatively explaining between 12.1% of the phenotypic variance for seminal root number to 48.1% of the variance for root system depth. Three major QTLs controlling root system depth, root spreading angle and total seminal root length were found on Chr 2H (56.52 cM), Chr 3H (67.92 cM), and Chr 2H (76.20 cM) and explained 12.4%, 18.4%, and 22.2% of the phenotypic variation, respectively. Meta-analysis and allele combination analysis indicated that root system depth and root spreading angle are valuable candidate traits for improving grain yield by pyramiding of favorable alleles.

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