Applications of next-generation sequencing to phylogeography and phylogenetics (Q34111807)

31 July 2017

Applications of next-generation sequencing to phylogeography and phylogenetics (English)

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31 July 2017

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31 July 2017

Sarah M Hird

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Bryan C Carstens

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Bryan C Carstens

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author name string

John E McCormack

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PubMed ID

22197804

31 July 2017

Amanda J Zellmer

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31 July 2017

14 December 2011

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Molecular Phylogenetics and Evolution

31 July 2017

13

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inferred from page(s)

published in

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31 July 2017

66

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31 July 2017

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31 July 2017

526-538

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Direct selection of human genomic loci by microarray hybridization

31 July 2017

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Personalized copy number and segmental duplication maps using next-generation sequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

An SNP map of the human genome generated by reduced representation shotgun sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Rapid SNP discovery and genetic mapping using sequenced RAD markers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNP discovery by transcriptome pyrosequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Ultraconserved Elements in the Human Genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Genome-wide SNP detection in the great tit Parus major using high throughput sequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Targeted retrieval and analysis of five Neandertal mtDNA genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Multilocus phylogeography and phylogenetics using sequence-based markers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Stacks: building and genotyping Loci de novo from short-read sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Identification of genetic variants using bar-coded multiplexed sequencing

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

7 January 2021

To pool, or not to pool?

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Testing for ancient admixture between closely related populations

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

A smörgåsbord of markers for avian ecology and evolution.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Is a new and general theory of molecular systematics emerging?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

High-resolution species trees without concatenation

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Applications of next generation sequencing in molecular ecology of non-model organisms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Resolving postglacial phylogeography using high-throughput sequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Local de novo assembly of RAD paired-end contigs using short sequencing reads

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Field guide to next-generation DNA sequencers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

A hierarchical Bayesian model for next-generation population genomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

High-throughput sequencing of complete human mtDNA genomes from the Philippines

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Bayesian inference of species trees from multilocus data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a 'provisional-reference genome'.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Genome-wide in situ exon capture for selective resequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

CAP3: A DNA sequence assembly program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

High-throughput SNP discovery and assay development in common bean

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Inference of population genetic parameters in metagenomics: a clean look at messy data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Accounting for bias from sequencing error in population genetic estimates

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Effects of an MHC-DRB genotype and allele number on the load of gut parasites in the bank vole Myodes glareolus

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Coalescent genealogy samplers: windows into population history

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Fast and accurate short read alignment with Burrows-Wheeler transform

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SOAP: short oligonucleotide alignment program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

The Sequence Alignment/Map format and SAMtools

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

High density synthetic oligonucleotide arrays

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Coalescent methods for estimating phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Estimating species phylogenies using coalescence times among sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Estimation of allele frequencies from high-coverage genome-sequencing projects

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Target-enrichment strategies for next-generation sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

The impact of next-generation sequencing technology on genetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Multiplexed DNA sequence capture of mitochondrial genomes using PCR products

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Parallel tagged sequencing on the 454 platform

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Tablet--next generation sequence assembly visualization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Dynamic evolution of base composition: causes and consequences in avian phylogenomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Jaatha: a fast composite-likelihood approach to estimate demographic parameters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Decoding a substantial set of samples in parallel by massive sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Targeted capture and massively parallel sequencing of 12 human exomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNPs by AFLP (SBA): a rapid SNP isolation strategy for non-model organisms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Genotype and SNP calling from next-generation sequencing data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Genes mirror geography within Europe

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Microarray-based genomic selection for high-throughput resequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Resolving difficult phylogenetic questions: why more sequences are not enough

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

A guide to the genomics of ecological speciation in natural animal populations.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Next-generation DNA sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

ABySS: a parallel assembler for short read sequence data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Reconstructing population histories from single nucleotide polymorphism data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Automated generation of heuristics for biological sequence comparison

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Adaptation genomics: the next generation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Enrichment of sequencing targets from the human genome by solution hybridization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Microdroplet-based PCR enrichment for large-scale targeted sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Genome-enabled development of DNA markers for ecology, evolution and conservation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms [corrected].

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

AFLP: a new technique for DNA fingerprinting

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

RNA-Seq: a revolutionary tool for transcriptomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Lack of evidence for association of primary sclerosing cholangitis and primary biliary cirrhosis with risk alleles for Crohn's disease in Polish patients.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

SNP identification, verification, and utility for population genetics in a non-model genus

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.12.007

10.1016/J.YMPEV.2011.12.007

7 January 2021

Identifiers

DOI

1 reference

31 July 2017

1 reference

PubMed ID

22197804