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Category Archives: community ecology
For flexible eDNA analysis, just capture whatever you want
Environmental DNA sampling for multi-taxa species detection (i.e., the inference of species presence from genetic material in the environment) has been a hot topic lately. Some of the most exciting recent work has used high-throughput sequence (HTS) to simultaneously screen … Continue reading
Posted in community ecology, DNA barcoding, metagenomics, methods
Tagged environmental dna, sequence capture
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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
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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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
Exploring the genomic diversity of tubeworm endosymbionts
Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how … Continue reading
Posted in bioinformatics, Coevolution, community ecology, evolution, genomics, metagenomics, microbiology
Tagged endosymbionts, Escarpia, tubeworms
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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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Diving deep: Exploring microbial communities under the seafloor
As we all sat staring at three large monitors in the front of the room, the remotely operated vehicle (ROV) Jason hung on to a borehole observatory with one hydraulic arm as the other arm plugged our sampling equipment into … Continue reading
Genomes are coming: Sequence libraries from the honey bee reflect associated microbial diversity
One of the coolest of reasons that cheap sequencing is nifty, in my opinion, is that it has allowed researchers to study individual eukaryotic organisms, and their associated microbes (their microbiome). Let’s be real, we are in the midst of … Continue reading
Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing
Tagged ecology, Lactobacilli, microbiome
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Like Turtles, Terrapin Research Moves a Little Slow
Marlee Hayes wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Her primary interests focus on challenges in conservation and sustainability. Previously, she evaluated fitness of post-hatchling Diamondback terrapins (Malaclemys terrapin), … Continue reading