Category Archives: genomics

Microbes are going to infinity and beyond! Monitoring community changes on a simulated space station

Posted on 8 Jun, 2016 by Kelle Freel

As we’ve discussed previously here, understanding microbes in the natural and built environment around us, has implications related to human health and disease. It has turned out to be pretty tricky to clarify what is going on with our most … Continue reading →

Posted in community ecology, genomics, microbiology | Tagged , | Leave a comment

Mitogenomes from extinct New Zealand wrens shed light on the oldest songbird lineage

Posted on 7 Jun, 2016 by Ethan Linck

The order Passeriformes, commonly known as “perching birds” or “songbirds,” contains over half of all known avian species. Sister to all other Passeriformes are the acanthisittid wrens, a small and enigmatic family of New Zealand endemics. Though their providential phylogenetic … Continue reading →

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The Great Migration and African-American Genomic History

Posted on 1 Jun, 2016 by Arun Sethuraman

Over 45 million African-Americans share a recent common history largely shaped by “The Great Migration” (1910-1970) from out of the Southern United States. And yet, the admixture history of the African-American community, and its consequences for public health are little … Continue reading →

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The not so singular process of hybridization

Posted on 27 May, 2016 by Stacy Krueger-Hadfield

What, if anything, are hybrids? Zach Gompert and Alex Buerkle ask this question in a special issue in Evolutionary Applications. Hybrids occur when unrelated individuals mate, but how distant do the taxa need to be to constitute a cross? The varied … Continue reading →

Posted in bioinformatics, conservation, domestication, evolution, genomics, natural history, next generation sequencing, plants | Tagged , , , | 1 Comment

Data, data everywhere and another tool to use: Taxonomer, a web-tool for metagenomics data analysis

Posted on 26 May, 2016 by Kelle Freel

Because sequencing. With all the affordable genome and metagenome sequencing available, we’ve reached an unprecedented point at which we can profile microbial communities more accurately than ever before. For this reason, it’s essential to develop efficient methods for data analysis. … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, software | Tagged , , , | 1 Comment

Steelhead in a random forest: identifying the genetic basis of migration

Posted on 25 May, 2016 by Reid Brennan

Genome-wide association studies (GWAS) have been quite successful in identifying variants associated with various phenotypes (I suppose there is some debate surrounding this statement. For an interesting, if dated, discussion look here). While most of this work was originally conducted … Continue reading →

Posted in association genetics, bioinformatics, conservation, genomics, next generation sequencing | Leave a comment

Poorly updated databases will affect your results

Posted on 24 May, 2016 by Elin Videvall

If you’re anything like me, your research is heavily dependent on the many wonderful database resources available online. NCBI, UniProtKB, Ensembl, Swiss-Prot, EMBL-EBI, and many other sites and organizations offer highly useful (and often curated) molecular information. Can you imagine … Continue reading →

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Ice-Age Euro-trips

Posted on 19 May, 2016 by Arun Sethuraman

Recent works that attempt to get at human migrations inside Europe paint a complex portrait of migratory events, admixture with archaic hominids, and adaptive evolution to new geographies, and a changing global climate. Analyzing whole genomes of 51 ancient humans … Continue reading →

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

What's all the buzz about? Bees got microbiomes too!

Posted on 11 May, 2016 by Kelle Freel

So I know we are all blabbing about the human microbiome, who isn’t fascinated by the impressive roles tiny microbes have in our lives!? Trying to unravel what exactly our microbial communities do for us, and how they relate to … Continue reading →

Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology | Tagged , , | 2 Comments

RADseq and missing data: some considerations

Posted on 10 May, 2016 by Ethan Linck

Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading →

Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory | Tagged , , , | 6 Comments