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Category Archives: next generation sequencing
Mitogenomes from extinct New Zealand wrens shed light on the oldest songbird lineage
The order Passeriformes, commonly known as “perching birds” or “songbirds,” contains over half of all known avian species. Sister to all other Passeriformes are the acanthisittid wrens, a small and enigmatic family of New Zealand endemics. Though their providential phylogenetic … Continue reading →
Posted in genomics, next generation sequencing, Paleogenomics, phylogenetics
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Tagged Acanthisittidae, ancient DNA, Gondwana, mitochondrial genome, mitogenome, New Zealand, Passeriformes, wrens
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The not so singular process of hybridization
What, if anything, are hybrids? Zach Gompert and Alex Buerkle ask this question in a special issue in Evolutionary Applications. Hybrids occur when unrelated individuals mate, but how distant do the taxa need to be to constitute a cross? The varied … Continue reading →
Posted in bioinformatics, conservation, domestication, evolution, genomics, natural history, next generation sequencing, plants
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Tagged gene flow, hybridization, management, plants
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Steelhead in a random forest: identifying the genetic basis of migration
Genome-wide association studies (GWAS) have been quite successful in identifying variants associated with various phenotypes (I suppose there is some debate surrounding this statement. For an interesting, if dated, discussion look here). While most of this work was originally conducted … Continue reading →
Poorly updated databases will affect your results
If you’re anything like me, your research is heavily dependent on the many wonderful database resources available online. NCBI, UniProtKB, Ensembl, Swiss-Prot, EMBL-EBI, and many other sites and organizations offer highly useful (and often curated) molecular information. Can you imagine … Continue reading →
Posted in bioinformatics, genomics, next generation sequencing, software
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Tagged databases, DAVID, gene ontology, GO, pathway enrichment analysis, reactome
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RADseq and missing data: some considerations
Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading →
Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory
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Tagged ddRADseq, missing data, null alleles, RADseq
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6 Comments
Analysis of the human microbiome reveals you are (at least related to) what you eat, in a manner of speaking
Understanding microbial symbioses, and more specifically how the human microbiome affects our health, is currently a hot topic in the land of microbiology and metagenomics. The most recent special edition of Science focuses on reviews and articles centered on understanding … Continue reading →
Results of the Molecular Ecologist's Survey on High-Throughput Sequencing
Some days ago, we asked our readers to fill in a survey (now closed) on your use of high-throughput sequencing techniques. We got a lot of responses, a total of 260 people filled in the form. Thank you! Here are the results of your answers. The … Continue reading →
Posted in bioinformatics, genomics, next generation sequencing
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Tagged molecular ecologist, NGS, NGS Field Guide, Sequencing, survey
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hyRAD and museum genomics
While the RAPTURE may have arrived, the development of novel restriction digest-based library prepartation techniques — and portmanteaus — continues unabated. In a paper published in PLoS ONE last month (and previously available as a preprint on bioRxiv), Tomasz Suchan … Continue reading →
Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics
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Tagged ddRADseq, hybridization RAD, hyRAD, museum genomics, RADseq, sequence capture
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3 Comments
The Molecular Ecologist's Survey on High-Throughput Sequencing
Last week we updated the Field Guide to Next Generation DNA Sequencers to better reflect the sequencing techniques of 2016. The NGS Field Guide is one of the most popular resources on the Molecular Ecologist web site, but we don’t know much about how our readers use … Continue reading →
Posted in bioinformatics, genomics, methods, next generation sequencing
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Tagged molecular ecologist, NGS, NGS Field Guide, Sequencing, survey
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2 Comments
The why's of sex
Sex isn’t quite what it seems – while superficially wasteful in an evolutionary sense (why inherit on only one half of your genes, when you can inherit all of them asexually, or why waste resources in mating when you don’t … Continue reading →
Posted in adaptation, evolution, genomics, mutation, natural history, next generation sequencing, population genetics, selection, theory, yeast
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Tagged Evolution, genomics, natural selection, population genetics, yeast
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