Category Archives: microbiology

A race to the bottom with a new card from the coevolutionary deck

I’m a sucker for a clever, amusing title, though I’ve recently read that amusing titles are cited less (see here). Alas, maybe a well placed metaphor can enliven a manuscript and also not get lost in a citation-less abyss? In basic … Continue reading

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Posted in Coevolution, evolution, horizontal gene transfer, microbiology, selection | Tagged , , | Leave a comment

Where’s your wine from?

Human-mediated selection of yeast cultures has played a huge role in the development of numerous unique strains of Sacchromyces cerevisiae, often attributed to production of a wide variety of wines the world over. Previous studies have indicated a single domesticated … Continue reading

Posted in domestication, evolution, genomics, horizontal gene transfer, microbiology, Molecular Ecology, the journal, next generation sequencing, phylogenetics, phylogeography, population genetics, STRUCTURE, yeast | Tagged , , , | 1 Comment

Old dogs, and ‘carnivorous’ pandas

It was a good fortnight for large mammals! Two recent studies attempt to date the emergence of modern canids, and offer insights into the gut microbiomes of giant pandas. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and … Continue reading

Posted in adaptation, evolution, genomics, metagenomics, microbiology, natural history, Paleogenomics, population genetics, speciation | Tagged , , , | Leave a comment

Et tu, Brute? Black-legged ticks use genes co-opted from bacteria to fight bacterial infection

Horizontal gene transfer occurs when genes are passed between individuals by mechanisms other than reproduction. It is common in bacteria and occasionally happens between highly divergent groups (for example, monocot genes transferred to eudicots, fungal genes transferred to aphids, bacterial genes transferred … Continue reading

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Genetics reveal the diversity of pollinators’ other cargo: fungi

The following is a cross-posting from the Stanford CEHG Blog by Jeremy Hsu, a graduate student in Elizabeth Hadley’s lab at Stanford University. Many animals that visit flowers are known to carry microfungal communities; these fungi are important ecologically because … Continue reading

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The broom of the system: Tracking soft selective sweeps in bacteria colonizing the gut

A growing body of population genetic evidence suggests that adaptive evolutionary change often proceeds via soft selective sweeps, in which beneficial mutations on multiple genetic backgrounds—and potentially at multiple loci—all increase in frequency, but none achieve fixation. This process has … Continue reading

Posted in adaptation, microbiology, population genetics | Tagged , , | 1 Comment

Making heatmaps with R for microbiome analysis

Arianne Albert is the Biostatistician for the Women’s Health Research Institute at the British Columbia Women’s Hospital and Health Centre. She earned a PhD from the University of British Columbia under the tutelage of Dolph Schluter before branching off into … Continue reading

Posted in howto, microbiology, R, software | Tagged , , | 56 Comments

Hitchhiking microbes

It is quite clear that humans play a major role in altering ecosystems today. Historic migration of human populations has been shown to have many interesting associated evolutionary consequences1,2. Worldwide travel makes it difficult to stop anything from going anywhere, … Continue reading

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What we’re reading

As we head into the first weekend of the new year, here’s a few things we’ve seen that might be worth your screen-time: In the journals Nicholson, W.L., Krivushin, K., Gilichinsky, D. & Schuerger, A.C. 2012. Growth of Carnobacterium spp. … Continue reading

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