(Q36320300)

13 August 2017

title

Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes (English)

1 reference

13 August 2017

1 reference

Alex Dornburg

7

0 references

Michael E. Alfaro

Michael E Alfaro

12

0 references

Thomas J. Near

Thomas J Near

6

0 references

Brant C. Faircloth

2

Brant C Faircloth

1 reference

13 August 2017

11

Laurie Sorenson

1 reference

13 August 2017

Melanie L. J. Stiassny

10

Melanie L J Stiassny

0 references

William B Ludt

William B Ludt

4

0 references

Jairo Arroyave

Jairo Arroyave

9

0 references

Caleb D. McMahan

5

Caleb D McMahan

1 reference

13 August 2017

Prosanta Chakrabarty

1

1 reference

13 August 2017

Fernando Alda

3

1 reference

13 August 2017

James S Albert

8

1 reference

13 August 2017

publication date

27 February 2017

1 reference

13 August 2017

1 reference

ExaBayes: massively parallel bayesian tree inference for the whole-genome era.

13 August 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

TESTING HYPOTHESES OF NEURAL EVOLUTION IN GYMNOTIFORM ELECTRIC FISHES USING PHYLOGENETIC CHARACTER DATA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Oligosarcus amome (Ostariophysi: Characidae), a new species from the río Uruguay basin, Misiones, Argentina

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

State-of the art methodologies dictate new standards for phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Three new species of saddled loricariid catfishes, and a review of Hemiancistrus, Peckoltia, and allied genera (Siluriformes)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Are characiform fishes Gondwanan in origin? Insights from a time-scaled molecular phylogeny of the Citharinoidei (Ostariophysi: Characiformes)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Trimmomatic: a flexible trimmer for Illumina sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A New Species ofRhamphichthys(Gymnotiformes: Rhamphichthyidae) from the Amazon Basin

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Epidermal 'alarm substance' cells of fishes maintained by non-alarm functions: possible defence against pathogens, parasites and UVB radiation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Discordance of species trees with their most likely gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A framework for variation discovery and genotyping using next-generation DNA sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A molecular and morphological perspective on the phylogenetic relationships of the otophysan fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Is a new and general theory of molecular systematics emerging?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Five hundred million years of extinction and recovery: a phanerozoic survey of large-scale diversity patterns in fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Developmental origin of shark electrosensory organs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Full-length transcriptome assembly from RNA-Seq data without a reference genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Phylogenomics: the beginning of incongruence?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Selecting optimal partitioning schemes for phylogenomic datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

South American Weakly Electric Fish (Gymnotiformes) Are Long-Wavelength-Sensitive Cone Monochromats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Evolution of the immune system influences speciation rates in teleost fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Applications of next-generation sequencing to phylogeography and phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Bayesian phylogenetic analysis of combined data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Resolving difficult phylogenetic questions: why more sequences are not enough

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Phylogenetic models of molecular evolution: next-generation data, fit, and performance

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Discordance of species trees with their most likely gene trees: a unifying principle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The drivers of tropical speciation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The genome sequence of Atlantic cod reveals a unique immune system

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Resolving Cypriniformes relationships using an anchored enrichment approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

DendroPy: a Python library for phylogenetic computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Family-group names of Recent fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Origins, Innovations, and Diversification of Suction Feeding in Vertebrates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Multiple alignment by aligning alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Morphology should not be forgotten in the era of genomics–a phylogenetic perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX038

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYX038

1 reference

13 August 2017

1 reference