Category Archives: transcriptomics

Diving deep: Exploring microbial communities under the seafloor

Posted on 7 Dec, 2017 by Kelle Freel

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 →

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

Experimental harvesting reduces gene expression variation

Posted on 10 Aug, 2017 by Reid Brennan

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 →

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

The largest mammalian genome is not polyploid

Posted on 24 Jul, 2017 by Bryan McLean

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

Posted on 9 Jun, 2017 by Ethan Linck

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 | Tagged , , , | Leave a comment

Relatively rare tropical trees all agree: avoiding the 'rain of death' seems like a good call

Posted on 5 May, 2017 by Kelle Freel

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 →

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

Posted on 11 Apr, 2017 by Ethan Linck

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 | Tagged , , , , | 5 Comments

When the going gets hot the dinoflagellates (sometimes) get going, how viruses might affect coral symbionts

Posted on 7 Dec, 2016 by Kelle Freel

Corals represent more than meets the eye, they host intricate and interesting communities composed of dinoflagellates (also referred to as zooxanthellae), and a suite of microbes that include bacteria, archaea, fungi, protists, and viruses. One such dinoflagellate that often shares … Continue reading →

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Molecular Inversion Probes: phylogenomics without the excess?

Posted on 18 Jul, 2016 by Ethan Linck

The onset of the phylogenomic era has revolutionized molecular ecology and systematics, helping resolve relationships throughout the tree of life that have long eluded researchers working with only a handful of loci and morphological data. Phylogenetic studies of nonmodel organisms … Continue reading →

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The 2016 Next-Generation Sequencing Field Guide Preview: Zombie Systems and New Hope

Posted on 24 Mar, 2016 by Travis Glenn

After a year of minimal activity, we finally have some significant changes in Next Gen Land. In the 2016 update of the NGS Field Guide, I will continue to give my overall interpretation about the various instruments, but with less … Continue reading →

Posted in genomics, howto, methods, RNAseq, transcriptomics | Tagged , , , | 8 Comments

Genomics of Hybridization – Part 1

Posted on 21 Jan, 2016 by Arun Sethuraman

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at … Continue reading →

Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | Leave a comment