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Category Archives: next generation sequencing
The eyes have it!
Eyes are pretty darn complicated, which makes them cool models for studying complex trait evolution. Maybe the first time I realized how interesting eyes are when I saw this by the oatmeal about the amazing-ness of the mantis shrimp (are they your … Continue reading
Posted in bioinformatics, evolution, genomics, next generation sequencing, phylogenetics
Tagged Cnidaria, complex trait evolution, eyes, opsins
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Metabarcoding for every body, every habitat, every time
The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading
What is DAS? A new tool to recover genomes from metagenomes
There are a lot of data out there, and if you haven’t already noticed the ‘omics train has steadily stayed its path through the fruitful (but challenging) world of metagenomics. Metagenomics offers the chance to unravel complex microbial communities without … Continue reading
Chromosomal inversions and the maintenance of species barriers
Chromosomal inversions have long fascinated evolutionary biologists for their role in adaptation and speciation. These structural variants are abundant in natural populations and can have diverse evolutionary consequences. They can cause reproductive isolation through hybrid sterility or protect sets of … Continue reading
Posted in adaptation, genomics, hybridization, next generation sequencing, speciation
Tagged chromosome structure, inversions
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DNA extraction for PacBio sequencing
PacBio is emerging as the favoured sequencing approach for assembling high-quality reference genomes. But the big issue with PacBio sequencing is that to get long sequence reads you need to start with high molecular weight DNA. For my first foray … Continue reading
Posted in genomics, next generation sequencing, Uncategorized
Tagged DNA extraction, museum genomics, PacBio, quality control
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Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies
Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading
Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics
Tagged barcode tags, barcoding, bioinformatics, eukaryotes, Illumina, metagenomics, methods, microbial communities, microbial community analysis, microbiome, NGS
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Sequencing round-up 2018
The deluge of new sequencing approaches continues at a pace. It seems that you turn your back for five minutes and there’s a shiny new sequencing platform promising to deliver more for less. What is the current state of play … Continue reading
Posted in genomics, next generation sequencing
Tagged BGISEQ, Illumina sequencing, MinION, PacBio
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Major new microbial groups expand diversity and alter our understanding of the tree of life
I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading
Retrieving a million sequences and avoiding primer bias, a new method that might have it all
We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA … Continue reading
Posted in bioinformatics, evolution, metagenomics, methods, microbiology, next generation sequencing
Tagged 16S rRNA, classification, taxonomy
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Molecular ecology, the flowchart
Update: You can now buy a poster print of the Flowchart, with proceeds going to support The Molecular Ecologist! Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for … Continue reading