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Category Archives: next generation sequencing
On hyRAD-X, another option for museum genomics
Last year, I profiled Suchan et al.’s “hyRAD” method for reduced-representation genome sequencing of degraded sources of DNA using RAD probes. While it’s too early to say whether hyRAD will be widely used by molecular ecologists looking to integrate historic … Continue reading →
Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics, RNAseq, selection, transcriptomics
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Tagged hyRAD, hyRAD-X, museum genomics, RNAseq
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Molecular adaptation in a deep-sea alien…*ahem* amphipod
Space: the final frontier…or is it? I was inspired Jeremy’s post yesterday to talk about that deep dark abyss that takes up the vast majority of our mostly blue planet. For the record, I’m in agreement with the assessments for the … Continue reading →
Posted in adaptation, evolution, genomics, Molecular Ecology, the journal, next generation sequencing
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Tagged amphipod, Hirondellea gigas, Mariana Trench
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Relatively rare tropical trees all agree: avoiding the 'rain of death' seems like a good call
When you think of a tropical jungle, what’s the first thing that comes to mind? Probably a lush green landscape with trees, vines, flowers, and let’s be real, at least one toucan. Tropical forests are made up of diverse groups … Continue reading →
To RADseq or not to RADseq?
It’s a cliche to say that we live in a moment of unprecedented possibility for molecular ecology, as high-throughput sequencing methods drive the cost of collecting DNA sequence data ever lower. But at the same time, it’s a tricky moment, … Continue reading →
You can call her queen bee: the role of epigenetics in honeybee development
Insects have social lifestyles that are often organized in castes. Within the insect community, different individuals specialize, each having a unique role. This efficient method of doling out the workload, ultimately, is believed to be why social insect lifestyles are … Continue reading →
Posted in genomics, haploid-diploid, Molecular Ecology, the journal, next generation sequencing, RNAseq
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Tagged Apis mellifera, expression, honeybee
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Right reads, wrong index? Concerns with data from Illumina's HiSeq 4000
Commanding around a 70% share of a 1.3 billion USD market, Illumina is the major player in next-generation sequencing (NGS) technology. More likely than not, if you’re a molecular ecologist working with NGS data, you’ve run your samples on a … Continue reading →
Posted in genomics, next generation sequencing, RNAseq, technical, transcriptomics
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Tagged high throughput sequencing, HiSeq 4000, Illumina, next gen sequencing, NGS
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Small Molecules, Big Differences
Mary Latimer wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. She is a third year PhD student at UAB studying miRNAs and methionine restriction. Her hobbies include cats, netflix, … Continue reading →
Posted in bioinformatics, blogging, evolution, genomics, natural history, next generation sequencing, RNAseq
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Tagged genomics, micro-RNAs, scicomm, Science Communication, Stress
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Hybridization and adaptive radiations
As an iconic system in evolutionary biology, I’ve always been interested in African cichlids and the origins of their diversity1. These cichlids represent an adaptive radiation; they’ve evolved rapidly from a single origin to exploit and speciate into open niches … Continue reading →
Posted in adaptation, evolution, genomics, next generation sequencing, population genetics, speciation
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Tagged adaptive radiation, Evolution, genomics, hybridization
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Highlights from the Standalone Society of Systematic Biologists meeting – part 2
The 2017 standalone meeting of the Society of Systematic Biologists included expert-led debates on major issues in molecular systematics. Didn’t make it to Baton Rouge? Don’t worry – Melissa DeBiasse and I report on some of the main points (and our favorite lightening … Continue reading →
Handling microbial contamination in NGS data
Until recently, I had given little thought to the potential for unwanted microbial contamination in high throughput sequence data. I suspect that if you’re a molecular ecologist who doesn’t primarily study microbes or work with ancient DNA, you’re in a … Continue reading →
Posted in bioinformatics, genomics, howto, next generation sequencing, technical
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Tagged bioinformatics, contamination, microbes, microbial contamination
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