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

scientific article published on 05 February 2014

A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1111/1755-0998.12222
P698PubMed publication ID24410873

P50authorHernán López-FernándezQ21395294
P2093author name stringKatriina L Ilves
P2860cites workAnchored hybrid enrichment for massively high-throughput phylogenomicsQ34273260
Choosing among Partition Models in Bayesian PhylogeneticsQ34407757
Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant cladeQ35176069
STRAW: Species TRee Analysis Web serverQ36953964
Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary timeQ36976280
Visual pigment molecular evolution in the Trinidadian pike cichlid (Crenicichla frenata): a less colorful world for neotropical cichlids?Q39582392
A novel primer set for multilocus phylogenetic inference in East African cichlid fishesQ39582783
Cone opsin genes of african cichlid fishes: tuning spectral sensitivity by differential gene expression.Q43686332
Comparative phylogenetic analyses of the adaptive radiation of Lake Tanganyika cichlid fish: nuclear sequences are less homoplasious but also less informative than mitochondrial DNA.Q43947503
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescalesQ46198301
Natural selection of the rhodopsin gene during the adaptive radiation of East African Great Lakes cichlid fishesQ46739095
African cichlid fish: a model system in adaptive radiation research.Q51724184
Age and spread of the haplochromine cichlid fishes in Africa.Q51874364
Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae)Q54517642
Phylogeny, taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae)Q54520245
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciencesQ21092859
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogeneticsQ21093422
A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencingQ21133738
A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)Q21559620
MUSCLE: multiple sequence alignment with high accuracy and high throughputQ24613456
Basic local alignment search toolQ25938991
MrBayes 3: Bayesian phylogenetic inference under mixed modelsQ26778438
Fast gapped-read alignment with Bowtie 2Q27860699
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsQ27860746
The Sequence Alignment/Map format and SAMtoolsQ27860966
Ensembl 2013Q28280494
Manipulation of FASTQ data with GalaxyQ28285724
Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan riftingQ28680622
A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq)Q28710081
Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergencesQ28757499
Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae)Q29300654
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic AnalysesQ29546512
Galaxy: a platform for interactive large-scale genome analysisQ29547494
Quality control and preprocessing of metagenomic datasetsQ29615829
Distinguishing Homologous from Analogous ProteinsQ29617777
Adaptive evolution and explosive speciation: the cichlid fish modelQ29617928
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizardsQ29618642
Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiationQ30573040
The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.Q31120116
Calculating bootstrap probabilities of phylogeny using multilocus sequence dataQ31146938
Systematics and historical biogeography of Greater Antillean CichlidaeQ33234519
Age of cichlids: new dates for ancient lake fish radiationsQ33279264
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case studyQ33279467
Phylogenomics: gene duplication, unrecognized paralogy and outgroup choiceQ33411297
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levelsQ33534007
A maximum pseudo-likelihood approach for estimating species trees under the coalescent modelQ33714988
Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungiQ33886674
Applications of next-generation sequencing to phylogeography and phylogeneticsQ34111807
P433issue4
P921main subjectCichlidaeQ3406
phylogenomicsQ3381973
P304page(s)802-811
P577publication date2014-02-05
P1433published inMolecular Ecology ResourcesQ15760135
P1476titleA targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics
P478volume14

Reverse relations

cites work (P2860)
Q90176943A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
Q39730939A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese
Q46299515Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America.
Q39048580Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards
Q90115130Assexon: Assembling Exon Using Gene Capture Data
Q56636794Cichlid fishes as models of ecological diversification: patterns, mechanisms, and consequences
Q35804034Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes
Q47555686Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure.
Q30991103EAPhy: A Flexible Tool for High-throughput Quality Filtering of Exon-alignments and Data Processing for Phylogenetic Methods
Q35717326Exon capture phylogenomics: efficacy across scales of divergence.
Q46285707Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae).
Q64061955Gene markers for exon capture and phylogenomics in ray-finned fishes
Q35749247Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing
Q36320300Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes
Q60482586Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
Q36198052Resources for phylogenomic analyses of Australian terrestrial vertebrates.
Q64892034Sequence capture using AFLP-generated baits: A cost-effective method for high-throughput phylogenetic and phylogeographic analysis.
Q37738605Targeted Capture of Complete Coding Regions across Divergent Species
Q38650308Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"?
Q36771745Targeted capture in evolutionary and ecological genomics.
Q46262797Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems.

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