Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample (Q30947994)

11 August 2017

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample (English)

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11 August 2017

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3

Matthew L Gimmel

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11 August 2017

7

Alfried P Vogler

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11 August 2017

Alexandra Crampton-Platt

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object named as

Alex Crampton-Platt

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11 August 2017

Martijn J T N Timmermans

2

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11 August 2017

Sujatha Narayanan Kutty

4

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11 August 2017

Timothy D Cockerill

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11 August 2017

Chey Vun Khen

6

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11 August 2017

8 May 2015

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Molecular Biology and Evolution

11 August 2017

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11 August 2017

32

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11 August 2017

9

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11 August 2017

2302-2316

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Phylogenomics resolves the timing and pattern of insect evolution

11 August 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Toward better understanding of artifacts in variant calling from high-coverage samples

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Insect mitochondrial genomics: implications for evolution and phylogeny

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Rare failures of DNA barcodes [corrected] to separate morphologically distinct species in a biodiversity survey of Iberian leaf beetles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

One hundred and one new species of Trigonopterus weevils from New Guinea

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

A comparative analysis of complete mitochondrial genomes among Hexapoda.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Genetic aspects of mitochondrial genome evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Qualimap: evaluating next-generation sequencing alignment data.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Reference databases for taxonomic assignment in metagenomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Anchored hybrid enrichment for massively high-throughput phylogenomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Using Tablet for visual exploration of second-generation sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Bayesian phylogenetics with BEAUti and the BEAST 1.7

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Evolutionary informatics: unifying knowledge about the diversity of life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Ramping up biodiversity discovery via online quantum contributions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Quality control and preprocessing of metagenomic datasets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

phangorn: phylogenetic analysis in R

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Guild-specific patterns of species richness and host specialization in plant-herbivore food webs from a tropical forest

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Accelerated species inventory on Madagascar using coalescent-based models of species delineation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Fast and accurate short read alignment with Burrows-Wheeler transform

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Recalibrated tree of leaf beetles (Chrysomelidae) indicates independent diversification of angiosperms and their insect herbivores

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

MEGAN analysis of metagenomic data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Sequence-based species delimitation for the DNA taxonomy of undescribed insects

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

FeatureExtract--extraction of sequence annotation made easy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

A whole-genome assembly of Drosophila

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

RNA sequence analysis using covariance models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4540967

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Building the Coleoptera tree-of-life for >8000 species: composition of public DNA data and fit with Linnaean classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

The Seven Great Questions of Systematic Biology: An Essential Foundation for Conservation and the Sustainable Use of Biodiversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Insect phylogenomics: results, problems and the impact of matrix composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Capturing protein-coding genes across highly divergent species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

Biodiversity inventories, indicator taxa and effects of habitat modificationin tropical forest

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV111

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSV111

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

25957318

1 reference