Category Archives: phylogenetics

Geophylogeny plots in R for Dummies

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading

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Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | 1 Comment

Consuming raw or undercooked frogs may increase your risk of getting a rare tapeworm in your brain

A 50-year-old UK resident had been living with an unwelcome visitor for the past 4 years and it was such a headache. Surgeons from Addenbrooke’s Hospital in Cambridge removed the tapeworm during a biopsy after noticing a small circular lesion … Continue reading

Posted in genomics, medicine, phylogenetics | Tagged , , | 1 Comment

#EntSoc14, a quick review

I have had a wonderful time at my first big bug conference – the annual meeting of the Entomological Society of America, at the Oregon Convention Center in Portland. Amid secretive (or not so secretive) break-out sessions to Voodoo Doughnuts, … Continue reading

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Growing the evolutionary relationship between green algae and salamanders

The presence of  green algae within the developing egg masses of amphibians has been recognized since the early 1900s, but only recently have researchers discovered that the these algae (termed “Oophila”) persist in animal tissues far after leaving the egg. The … Continue reading

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From cats to rats: two studies on domestication and tameness

Anyone who has ever read Charles Darwin is acutely aware of his fascination with domestication – particularly how he fancied fancy pigeons. Darwin drew on his domestication obsession while writing his book, The Variation of Animals and Plants under Domestication, … Continue reading

Posted in adaptation, association genetics, domestication, genomics, methods, next generation sequencing, phylogenetics, quantitative genetics | Tagged , , , , , | Leave a comment

Bugs fighting bugs: the evolution of the arthropod immune system.

Since the beginning of time, animals have needed to protect themselves from invaders. They primarily do so via their innate immune system, in which trained killer cells attack foreign pathogens – ranging from microscopic bacteria to macroscopic worms. While we … Continue reading

Posted in genomics, phylogenetics | 1 Comment

The Tortoise Time Warp

Recent advances in genetic data analysis continue to provide the ability to reveal some amazingly detailed (and previously unattainable) information about species’ evolutionary history. In this recent study from Molecular Ecology, Dr. Ryan Garrick and colleagues use a variety of … Continue reading

Posted in Molecular Ecology, the journal, phylogenetics, speciation | Tagged , , | Leave a comment

Getting started with Ultra Conserved Elements

Cross posted on ngcrawford.com If you attended Evolution 2013, you probably heard quite a lot of chatter about ultra conserved elements. Essentially, ultra conserved elements (UCEs) are parts of the genome that are highly conserved between different species. Although UCEs … Continue reading

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Want to share your code?

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

Will climate change be more relentless than evolution?

Ask any biologist what she considers the most urgently important example of adaptive evolution, and—even if she isn’t currently writing a grant proposal—she’ll probably mention global climate change. More than a century of pumping greenhouse gasses into Earth’s atmosphere has … Continue reading

Posted in phylogenetics, quantitative genetics | Tagged | 6 Comments