Category Archives: transcriptomics

Racing Against the Climate

Sarah Livett wrote this post as a final project for Stacy Krueger-Hadfield’s Introduction to Evolutionary Processes course at the University of Alabama at Birmingham. Sarah was a 5th year MS student at UAB in Dr. Thane Wibbel‘s lab. She worked … Continue reading

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Transcriptome sequencing catches bats’ immune systems napping

A little brown bat (Myotis lucifugans) infected with the white-nose fungus. (Flickr: US Fish and Wildlife Service) Populations of multiple North American bat species have been more than decimated by white-nose syndrome, a fungal disease that spreads within roosting colonies … Continue reading

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They joy of genome sequencing: when genomics meets natural history

When I have a massive pile of papers that I need to read, I can’t help but look at the ones with interesting natural history first. There’s something exceptionally satisfying about using modern tools to dig deeper into the features … Continue reading

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Found in translation: The evolutionary history of RNA viruses in vertebrates

I have to admit, viruses aren’t normally my thing, but this is pretty darn cool. In a study out by Shi and colleagues this week, researchers identified 214 new viruses that, as the authors so succinctly state, reveal “diverse virus-host … Continue reading

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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

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Posted in bioinformatics, community ecology, fieldwork, genomics, metagenomics, microbiology, transcriptomics | Tagged , , , | Leave a comment

Experimental harvesting reduces gene expression variation

Human activities represent unique selective pressures for natural populations. This is especially true for fish species where we routinely harvest individuals from the wild, i.e., through fishing. It has been recognized for some time that overfishing can result in population … Continue reading

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Posted in adaptation, conservation, evolution, genomics, transcriptomics | Tagged , | 1 Comment

The largest mammalian genome is not polyploid

Some 40 million years ago in South America, following the arrival of the common ancestor of caviomorph rodents from the Old World, big changes were afoot. Specifically, the caviomorph colonists were beginning to give rise to an extant evolutionary progeny … Continue reading

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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

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Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics, RNAseq, selection, transcriptomics | Tagged , , , | Leave a comment

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

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Posted in genomics, Molecular Ecology, the journal, next generation sequencing, plants, transcriptomics | Tagged , | Leave a comment

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

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Posted in genomics, next generation sequencing, RNAseq, technical, transcriptomics | Tagged , , , , | 5 Comments