scholarly journals The impact of incongruence and exogenous gene fragments on estimates of the eukaryote root

2021 ◽  
Author(s):  
Caesar Al Jewari ◽  
Sandra L Baldauf
Keyword(s):  
Phylogenetic Analyses ◽  
Single Gene ◽  
Evolutionary Model ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Full Data ◽  
Data Set ◽  
Gene Level ◽  
The Impact ◽  
Exogenous Gene

Phylogenomics uses multiple genetic loci to reconstruct evolutionary trees, under the stipulation that all combined loci share a common phylogenetic history, i.e., they are congruent. Congruence is primarily evaluated via single-gene trees, but these trees invariably lack sufficient signal to resolve deep nodes making it difficult to assess congruence at these levels. Two methods were developed to systematically assess congruence in multi-locus data. Protocol 1 uses gene jackknifing to measure deviation from a central mean to identify taxon-specific incongruencies in the form of persistent outliers. Protocol_2 assesses congruence at the sub-gene level using a sliding window. Both protocols were tested on a controversial data set of 76 mitochondrial proteins previously used in various combinations to assess the eukaryote root. Protocol_1 showed a concentration of outliers in under-sampled taxa, including the pivotal taxon Discoba. Further analysis of Discoba using Protocol_2 detected a surprising number of apparently exogenous gene fragments, some of which overlap with Protocol_1 outliers and others that do not. Phylogenetic analyses of the full data using the static LG-gamma evolutionary model support a neozoan-excavate root for eukaryotes (Discoba sister), which rises to 99-100% bootstrap support with data masked according to either Protocol_1 or Protocol_2. In contrast, site-heterogeneous (mixture) models perform inconsistently with these data, yielding all three possible roots depending on presence/absence/type of masking and/or extent of missing data. The neozoan-excavate root places Amorphea (including animals and fungi) and Diaphoretickes (including plants) as more closely related to each other than either is to Discoba (Jakobida, Heterolobosea, and Euglenozoa), regardless of the presence/absence of additional taxa.

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

scholarly journals Genomic characterization and curation of UCEs improves species tree reconstruction

2019 ◽  
Author(s):  
Matthew H. Van Dam ◽  
James B. Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction ◽  
Phylogenomic Analyses

ABSTRACTUltraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 12 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including; birds, mammals, fish, Hymenoptera (ants, wasps and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees were significantly improved across all datasets. Increased loci length appears to drive this increase in bootstrap support. Additionally, we found that gene trees generated from merged UCEs were more accurate than those generated by unmerged and randomly merged UCEs, based on our simulation study. This modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.

The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1760-1777 ◽  
Author(s):  
LAURA M. McDONAGH ◽  
JAMIE R. STEVENS
Keyword(s):  
Sequence Data ◽  
Single Gene ◽  
Nuclear Gene ◽  
Evolutionary Status ◽  
28S Rrna ◽  
Gene Trees ◽  
Data Set ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

scholarly journals Terraces in Gene Tree Reconciliation-Based Species Tree Inference

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Michelle M. McMahon ◽  
Mike Steel
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Solution Space ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Tree Reconciliation ◽  
The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

scholarly journals Pilot Study of a Bayesian Approach To Estimate Vancomycin Exposure in Obese Patients with Limited Pharmacokinetic Sampling

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Joseph J. Carreno ◽  
Ben Lomaestro ◽  
John Tietjan ◽  
Thomas P. Lodise
Keyword(s):  
Medical Center ◽  
Estimation Method ◽  
Area Under The Curve ◽  
Predictive Performance ◽  
Good Precision ◽  
Obese Patients ◽  
Full Data ◽  
Data Set ◽  
The Best Approximation ◽  
The Impact

ABSTRACT This study evaluated the predictive performance of a Bayesian PK estimation method (ADAPT V) to estimate the 24-h vancomycin area under the curve (AUC) with limited pharmacokinetic (PK) sampling in adult obese patients receiving vancomycin for suspected or confirmed Gram-positive infections. This was an Albany Medical Center Institutional Review Board-approved prospective evaluation of 12 patients. Patients had a median (95% confidence interval) age of 61 years (39 to 71 years), a median creatinine clearance of 86 ml/min (75 to 120 ml/min), and a median body mass index of 45 kg/m2 (40 to 52 kg/m2). For each patient, five PK concentrations were measured, and four different vancomycin population PK models were used as Bayesian priors to estimate the vancomycin AUC (AUCFULL). Using each PK model as a prior, data-depleted PK subsets were used to estimate the 24-h AUC (i.e., peak and trough data [AUCPT], midpoint and trough data [AUCMT], and trough-only data [AUCT]). The 24-h AUC derived from the full data set (AUCFULL) was compared to the AUC derived from data-depleted subsets (AUCPT, AUCMT, and AUCT) for each model. For the four sets of analyses, AUCFULL estimates ranged from 437 to 489 mg·h/liter. The AUCPT provided the best approximation of the AUCFULL; AUCMT and AUCT tended to overestimate AUCFULL. Further prospective studies are needed to evaluate the impact of AUC monitoring in clinical practice, but the findings from this study suggest that the vancomycin AUC can be estimated with good precision and accuracy with limited PK sampling using Bayesian PK estimation software.

scholarly journals Decomposing variation in dairy profitability: the impact of output, inputs, prices, labour and management

2011 ◽  
Vol 149 (4) ◽  
pp. 507-517 ◽  
Author(s):  
P. WILSON
Keyword(s):  
Structural Change ◽  
Holistic Approach ◽  
Herd Size ◽  
Full Data ◽  
Price Variation ◽  
Data Set ◽  
Economic Return ◽  
Net Margin ◽  
The Uk ◽  
The Impact

SUMMARYThe UK dairy sector has undergone considerable structural change in recent years, with a decrease in the number of producers accompanied by an increased average herd size and increased concentrate use and milk yields. One of the key drivers to producers remaining in the industry is the profitability of their herds. The current paper adopts a holistic approach to decomposing the variation in dairy profitability through an analysis of net margin data explained by physical input–output measures, milk price variation, labour utilization and managerial behaviours and characteristics. Data are drawn from the Farm Business Survey (FBS) for England in 2007/08 for 228 dairy enterprises. Average yields are 7100 litres/cow/yr, from a herd size of 110 cows that use 0·56 forage ha/cow/yr and 43·2 labour h/cow/yr. An average milk price of 22·57 pence per litre (ppl) produced milk output of £1602/cow/yr, which after accounting for calf sales, herd replacements and quota leasing costs, gave an average dairy output of £1516/cow/yr. After total costs of £1464/cow/yr this left an economic return of £52/cow/yr (0·73 ppl) net margin profit. There is wide variation in performance, with the most profitable (as measured by net margin per cow) quartile of producers achieving 2000 litres/cow/yr more than the least profitable quartile, returning a net margin of £335/cow/yr compared to a loss of £361/cow/yr for the least profitable. The most profitable producers operate larger, higher yielding herds and achieve a greater milk price for their output. In addition, a significantly greater number of the most profitable producers undertake financial benchmarking within their businesses and operate specialist dairy farms. When examining the full data set, the most profitable enterprises included significantly greater numbers of organic producers. The most profitable tend to have a greater reliance on independent technical advice, but this finding is not statistically significant. Decomposing the variation in net margin performance between the most and least profitable groups, an approximate ratio of 65:23:12 is observed for higher yields: lower costs: higher milk price. This result indicates that yield differentials are the key performance driver in dairy profitability. Lower costs per cow are dominated by the significantly lower cost of farmer and spouse labour per cow of the most profitable group, flowing directly from the upper quartile expending 37·7 labour h/cow/yr in comparison with 58·8 h/cow/yr for the lower quartile. The upper quartile's greater milk price is argued to be achieved through contract negotiations and higher milk quality, and this accounts for 0·12 of the variation in net margin performance. The average economic return to the sample of dairy enterprises in this survey year was less than £6000/farm/yr. However, the most profitable quartile returned an average economic return of approximately £50 000 per farm/yr. Structural change in the UK dairy sector is likely to continue with the least profitable and typically smaller dairy enterprises being replaced by a smaller number of expanding dairy production units.

Application of Fitts' Law to Individuals with Cerebral Palsy

2002 ◽  
Vol 94 (3) ◽  
pp. 883-895 ◽  
Author(s):  
Alison Gump ◽  
Miriam Legare ◽  
Deborah L. Hunt
Keyword(s):  
Cerebral Palsy ◽  
Linear Models ◽  
Motor Behavior ◽  
Error Rates ◽  
Subject Group ◽  
Full Data ◽  
Data Set ◽  
Fitts Law ◽  
The Impact ◽  
Speed Accuracy

Cerebral palsy is a condition that results in motor abnormalities as a direct consequence of injury to the developing brain. Fitts' law, which describes a speed-accuracy tradeoff in visually guided movements, has been shown to characterize the motor behavior of normal subjects during aiming tasks. To assess whether Fitts' law can also describe the aimed movements of persons with cerebral palsy, eight cerebral palsied adults participated in an aimed movement study. 12 targets were used with Indices of Difficulty ranging from 2.19 to 6.00 bits. The impact of Gan and Hoffmann's 1988 ballistic movement factor, A, and Fitts' 1954 Index of Difficulty on subject's movement and reaction times was examined using multivariate linear models. The analysis of the full data set yielded a significant effect of A on movement times and no significant adherence to Fitts' law. However, high error rates that could be the result of oculomotor problems among the subject group were noted, and the method of handling errors had a large effect on the results. Tracking eye position during a Fitts' law task would provide information regarding the effect of oculomotor difficulties on aiming tasks in the cerebral palsied subject group.

scholarly journals Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas

2019 ◽  
Author(s):  
Angie M. Macias ◽  
David M. Geiser ◽  
Jason E. Stajich ◽  
Piotr Łukasik ◽  
Claudio Veloso ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Single Gene ◽  
Elongation Factor ◽  
Phylogenetic Inference ◽  
Monophyletic Group ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Trees ◽  
Morphological Studies

AbstractThe fungal genus Massospora (Zoopagomycota: Entomophthorales) includes more than a dozen obligate, sexually transmissible pathogenic species that infect cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection, which has garnered considerable interest for this enigmatic genus. As with many Entomophthorales, the evolutionary relationships and host associations of Massospora spp. are not well understood. The acquisition of M. diceroproctae from Arizona, M. tettigatis from Chile, and M. platypediae from California and Colorado provided an opportunity to conduct molecular phylogenetic analyses and morphological studies to investigate if these fungi represent a monophyletic group and delimit species boundaries. In a three-locus phylogenetic analysis including the D1–D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha-like (EFL), and beta-tubulin (BTUB), Massospora was resolved in a strongly supported monophyletic group containing four well-supported genealogically exclusive lineages, based on two of three methods of phylogenetic inference. There was incongruence among the single-gene trees: two methods of phylogenetic inference recovered trees with either the same topology as the 3-gene concatenated tree (EFL), or a basal polytomy (28S, BTUB). Massospora levispora and M. platypediae isolates formed a single lineage in all analyses and are synonymized here as M. levispora. Massospora diceroproctae was sister to M. cicadina in all three single-gene trees and on an extremely long branch relative to the other Massospora, and even the outgroup taxa, which may reflect an accelerated rate of molecular evolution and/or incomplete taxa sampling. The results of the morphological study presented here indicate that spore measurements may not be phylogenetically or diagnostically informative. Despite recent advances in understanding the ecology of Massospora, much about its host range and diversity remains unexplored. The emerging phylogenetic framework can provide a foundation for exploring co-evolutionary relationships with cicada hosts and the evolution of behavior-altering compounds.

scholarly journals SVhound: Detection of future Structural Variation hotspots

2021 ◽  
Author(s):  
Luis Felipe Paulin ◽  
Muthuswamy Raveendran ◽  
Ronald Alan Harris ◽  
Jeffrey Rogers ◽  
Arndt von Haeseler ◽  
...  
Keyword(s):  
Population Level ◽  
Model Organisms ◽  
Average Correlation ◽  
Full Data ◽  
Data Set ◽  
1000 Genomes ◽  
Unique Method ◽  
Project Data ◽  
The Impact

Recent population studies are ever growing in size of samples to investigate the diversity of a given population or species. These studies reveal ever new polymorphism that lead to important insights into the mechanisms of evolution, but are also important for the interpretation of these variations. Nevertheless, while the full catalog of variations across entire species remains unknown, we can predict which regions harbor additional variations that remain hidden and investigate their properties, thereby enhancing the analysis for potentially missed variants. To achieve this we implemented SVhound (https://github.com/lfpaulin/SVhound), which based on a population level SVs dataset can predict regions that harbor novel SV alleles. We tested SVhound using subsets of the 1000 genomes project data and showed that its correlation (average correlation of 2,800 tests r=0.7136) is high to the full data set. Next, we utilized SVhound to investigate potentially missed or understudied regions across 1KGP and CCDG that included multiple genes. Lastly we show the applicability for SVhound also on a small and novel SV call set for rhesus macaque (Macaca mulatta) and discuss the impact and choice of parameters for SVhound. Overall SVhound is a unique method to identify potential regions that harbor hidden diversity in model and non model organisms and can also be potentially used to ensure high quality of SV call sets.

Homortomyces tamaricis sp. nov. and convergent evolution of Homortomyces and Stilbospora

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 156 ◽  
Author(s):  
NALIN N. WIJAYAWARDENE ◽  
KEVIN D. HYDE ◽  
ERIO CAMPORESI ◽  
D. JAYARAMA BHAT ◽  
YU SONG ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Convergent Evolution ◽  
Phylogenetic Analyses ◽  
Bootstrap Support ◽  
Lsu Rdna ◽  
Maximum Likelihood Analysis ◽  
Data Set ◽  
Incertae Sedis ◽  
Rdna Sequences ◽  
Likelihood Analysis

A new species Homortomyces tamaricis is introduced from Cervia, Italy. It is distinct from H. combreti, the type species of this monotypic genus, in having smaller conidia, smaller paraphyses and shorter supporting cells. Morphologically Homortomyces is similar to Stilbospora, which groups in Diaporthales incertae sedis in maximum-likelihood analysis of LSU rDNA sequences. Maximum-likelihood analysis of the combined data set of LSU and ITS rDNA sequences indicates that Homortomyces species cluster with Tubeufiaceae with 77% bootstrap support, but group as a distinct clade with high bootstrap value (100%). These two genera show convergent evolution since both share very similar morphological characters, but have distinct phylogenetic lineages. Further phylogenetic analyses are needed, when more strains of Homortomyces and related genera are available, to resolve the genus familial placement. We maintain the genus in Dothideomycetes incertae sedis. No sexual state has yet been reported for this genus.

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