Discovery of pathways using multiple genome-scale data sets

AbstractParmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

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JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

Journal of Biological Rhythms ◽

10.1177/0748730410379711 ◽

2010 ◽

Vol 25 (5) ◽

pp. 372-380 ◽

Cited By ~ 485

Author(s):

Michael E. Hughes ◽

John B. Hogenesch ◽

Karl Kornacker

Keyword(s):

Data Sets ◽

Nonparametric Algorithm ◽

Genome Scale ◽

Scale Data

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MODELING CANCER: INTEGRATION OF "OMICS" INFORMATION IN DYNAMIC SYSTEMS

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720007002990 ◽

2007 ◽

Vol 05 (04) ◽

pp. 977-986 ◽

Cited By ~ 9

Author(s):

BEATRIZ STRANSKY ◽

JUNIOR BARRERA ◽

LUCILA OHNO-MACHADO ◽

SANDRO J. DE SOUZA

Keyword(s):

Dynamic Systems ◽

Research Community ◽

Theoretical Knowledge ◽

Data Sets ◽

Detailed Mechanism ◽

Multi Scale ◽

Scale Models ◽

Genome Scale ◽

Effective Integration ◽

Scale Data

The last 10 years have seen the rise of many technologies that produce an unprecedented amount of genome-scale data from many organisms. Although the research community has been successful in exploring these data, many challenges still persist. One of them is the effective integration of such data sets directly into approaches based on mathematical modeling of biological systems. Applications in cancer are a good example. The bridge between information and modeling in cancer can be achieved by two major types of complementary strategies. First, there is a bottom–up approach, in which data generates information about structure and relationship between components of a given system. In addition, there is a top–down approach, where cybernetic and systems–theoretical knowledge are used to create models that describe mechanisms and dynamics of the system. These approaches can also be linked to yield multi-scale models combining detailed mechanism and wide biological scope. Here we give an overall picture of this field and discuss possible strategies to approach the major challenges ahead.

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Supertree Bootstrapping Methods for Assessing Phylogenetic Variation among Genes in Genome-Scale Data Sets

Systematic Biology ◽

10.1080/10635150500541722 ◽

2006 ◽

Vol 55 (3) ◽

pp. 426-440 ◽

Cited By ~ 32

Author(s):

J. Gordon Burleigh ◽

Amy C. Driskell ◽

Michael J. Sanderson

Keyword(s):

Data Sets ◽

Genome Scale ◽

Scale Data

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Reconstructing evolutionary timescales using phylogenomics

10.7287/peerj.preprints.2403v1 ◽

2016 ◽

Author(s):

K. Jun Tong ◽

Nathan Lo ◽

Simon Y W Ho

Keyword(s):

High Throughput ◽

Molecular Clock ◽

Evolutionary Biology ◽

High Throughput Sequencing ◽

Genetic Data ◽

Biological Information ◽

Data Sets ◽

Sequencing Technology ◽

Genome Scale ◽

Scale Data

Reconstructing the timescale of the Tree of Life is one of the principal aims of evolutionary biology. This has been greatly aided by the development of the molecular clock, which enables evolutionary timescales to be estimated from genetic data. In recent years, high-throughput sequencing technology has led to an increase in the feasibility and availability of genome-scale data sets. These represent a rich source of biological information, but they also bring a set of analytical challenges. In this review, we provide an overview of phylogenomic dating and describe the challenges associated with analysing genome-scale data. We also report on recent phylogenomic estimates of the evolutionary timescales of mammals, birds, and insects.

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Reconstructing evolutionary timescales using phylogenomics

10.7287/peerj.preprints.2403 ◽

2016 ◽

Author(s):

K. Jun Tong ◽

Nathan Lo ◽

Simon Y W Ho

Keyword(s):

High Throughput ◽

Molecular Clock ◽

Evolutionary Biology ◽

High Throughput Sequencing ◽

Genetic Data ◽

Biological Information ◽

Data Sets ◽

Sequencing Technology ◽

Genome Scale ◽

Scale Data

Reconstructing the timescale of the Tree of Life is one of the principal aims of evolutionary biology. This has been greatly aided by the development of the molecular clock, which enables evolutionary timescales to be estimated from genetic data. In recent years, high-throughput sequencing technology has led to an increase in the feasibility and availability of genome-scale data sets. These represent a rich source of biological information, but they also bring a set of analytical challenges. In this review, we provide an overview of phylogenomic dating and describe the challenges associated with analysing genome-scale data. We also report on recent phylogenomic estimates of the evolutionary timescales of mammals, birds, and insects.

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Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence

10.1101/168526 ◽

2017 ◽

Cited By ~ 8

Author(s):

Xiaofan Zhou ◽

Sarah Lutteropp ◽

Lucas Czech ◽

Alexandros Stamatakis ◽

Moritz von Looz ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Phylogenetic Signal ◽

Simulated Data ◽

Data Sets ◽

Gene Trees ◽

Branch Support ◽

Robust Measures ◽

Genome Scale ◽

Scale Data

AbstractIncongruence, or topological conflict, is prevalent in genome-scale data sets but relatively few measures have been developed to quantify it. Internode Certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internode (or internal branch) among a set of phylogenetic trees and complement regular branch support statistics in assessing the confidence of the inferred phylogenetic relationships. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of bipartitions (or splits) on a set of trees, the calculation of IC scores requires adjusting the frequencies of bipartitions from these partial gene trees. However, when the proportion of missing data is high, current approaches that adjust bipartition frequencies in partial gene trees tend to overestimate IC scores and alternative adjustment approaches differ substantially from each other in their scores. To overcome these issues, we developed three new measures for calculating internode certainty that are based on the frequencies of quartets, which naturally apply to both comprehensive and partial trees. Our comparison of these new quartet-based measures to previous bipartition-based measures on simulated data shows that: 1) on comprehensive trees, both types of measures yield highly similar IC scores; 2) on partial trees, quartet-based measures generate more accurate IC scores; and 3) quartet-based measures are more robust to the absence of phylogenetic signal and errors in the phylogenetic relationships to be assessed. Additionally, analysis of 15 empirical phylogenomic data sets using our quartet-based measures suggests that numerous relationships remain unresolved despite the availability of genome-scale data. Finally, we provide an efficient open-source implementation of these quartet-based measures in the program QuartetScores, which is freely available at https://github.com/algomaus/QuartetScores.

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Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

Systematic Biology ◽

10.1093/sysbio/syaa054 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sonal Singhal ◽

Timothy J Colston ◽

Maggie R Grundler ◽

Stephen A Smith ◽

Gabriel C Costa ◽

...

Keyword(s):

Evolutionary History ◽

Gene Tree ◽

Data Sets ◽

Gene Trees ◽

Squamate Reptiles ◽

Statistical Confidence ◽

Target Capture ◽

Anchored Hybrid Enrichment ◽

Genome Scale ◽

Scale Data

Abstract Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).]

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