Title: A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes

Journal Article · · Molecular Phylogenetics and Evolution

Not Available

Sponsoring Organization:
USDOE Office of Electricity (OE), Advanced Grid Research & Development. Power Systems Engineering Research
OSTI ID:
1642281
Journal Information:
Molecular Phylogenetics and Evolution, Journal Name: Molecular Phylogenetics and Evolution Journal Issue: C Vol. 129; ISSN 1055-7903
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

References (53)

Identifiability and Reconstructibility of Species Phylogenies Under a Modified Coalescent journal June 2018
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites journal June 2015
New developments in museum-based informatics and applications in biodiversity analysis journal September 2004
Applications of next-generation sequencing to phylogeography and phylogenetics journal February 2013
Incongruence among different mitochondrial regions: A case study using complete mitogenomes journal September 2014
Building the avian tree of life using a large-scale, sparse supermatrix journal March 2015
Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences journal May 2016
Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences journal September 2016
Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data journal April 2017
Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds journal March 2018
Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea) journal October 2018
Bird sequencing project takes off journal June 2015
The global diversity of birds in space and time journal October 2012
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing journal October 2015
Full-length transcriptome assembly from RNA-Seq data without a reference genome journal May 2011
Fast gapped-read alignment with Bowtie 2 journal March 2012
Genome-wide genetic marker discovery and genotyping using next-generation sequencing journal June 2011
Drastic population fluctuations explain the rapid extinction of the passenger pigeon journal June 2014
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies journal January 2014
Trimmomatic: a flexible trimmer for Illumina sequence data journal April 2014
Quartet Inference from SNP Data Under the Coalescent Model journal August 2014
PHYLUCE is a software package for the analysis of conserved genomic loci journal November 2015
Prediction of missing sequences and branch lengths in phylogenomic data journal January 2016
Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences journal August 2017
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species journal November 2009
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) journal December 2015
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales journal January 2012
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics journal July 2012
Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods journal February 2016
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics journal June 2017
ABySS: A parallel assembler for short read sequence data journal February 2009
Sequence capture of ultraconserved elements from bird museum specimens journal October 2015
Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA journal March 2017
Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera journal March 2017
Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura) journal March 2015
Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens journal July 2011
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches journal September 2015
Unlocking the vault: next-generation museum population genomics journal October 2013
Revival of the genusTropicoperdix Blyth 1859 (Phasianidae, Aves) using multilocus sequence data journal May 2015
Whole-genome analyses resolve early branches in the tree of life of modern birds journal December 2014
Specimen collection: An essential tool journal May 2014
Natural selection shaped the rise and fall of passenger pigeon genomic diversity journal November 2017
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes journal January 2013
Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens journal April 2016
The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing journal February 2013
Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae journal May 2013
Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens journal July 2013
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement journal November 2014
Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing journal December 2015
Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens journal August 2016
Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives journal July 2010
Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics journal February 2012
Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix journal April 2014

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