Category Archives: genomics

The Butterfly Effect

Posted on 9 Jul, 2015 by Arun Sethuraman

This might just take the prize for the ‘spiciest’ story in molecular co-evolution for 2015, yet. While a lot of the press coverage sounds like caterpillar thanksgiving, the science behind this study stands for the almost incredible power of molecular phylogenetics … Continue reading →

Posted in adaptation, evolution, genomics, natural history, population genetics, selection, speciation, transcriptomics | Tagged , , , , | 1 Comment

Mixed modeling of methylation measures (increase your power by 60%)

Posted on 7 Jul, 2015 by Noah Snyder-Mackler

Do you want to increase your power to detect differentially methylated CpG sites by 60%*? Yes?! Then do I have the pre-print for you.

Posted in bioinformatics, genomics, methods, next generation sequencing, software | Tagged , , | 1 Comment

Societal constructs, and Genetic diversity

Posted on 2 Jul, 2015 by Arun Sethuraman

While we grapple with numerous discoveries of variation in genomic diversity in humans, interest has subsequently risen in understanding their causes/results. Two recent papers describe experiments to determine (a) the effects of marital rules (who gets to marry whom) on … Continue reading →

Posted in evolution, genomics, natural history, population genetics, selection, societal structure | Tagged , , , , , , , | Leave a comment

The Kennewick, and the Oase I

Posted on 25 Jun, 2015 by Arun Sethuraman

Last week was glorious for ancient DNA enthusiasts – here are some quick blurbs on findings from genomic analyses of the Kennewick man, and the Oase I individual. The ancestry and affiliations of Kennewick Man, Rasmussen et al. (2015) Nature DOI: … Continue reading →

Posted in evolution, genomics, Paleogenomics, population genetics | Tagged , , , , | Leave a comment

The evolution of phylogeography in the next gen era: 20 years in review

Posted on 15 Jun, 2015 by Melissa DeBiasse

Phylogeographers have long known about the limitations of single locus studies (ie, the effects of selective sweeps, stochasticity in lineage sorting among loci) and that adding loci improves the accuracy of demographic parameter estimates. As we continue to shift towards collecting multi-locus datasets thanks to high throughput … Continue reading →

Posted in evolution, genomics, Molecular Ecology, the journal, next generation sequencing, phylogeography, Uncategorized | 3 Comments

Genomic history of Eurasia

Posted on 11 Jun, 2015 by Arun Sethuraman

The route of modern humans out of Africa has been contentious, with archaeological and genetic finds pointing towards a route through Egypt, versus one through Ethiopia. Pagani et al. (2015) analyze the genomic admixture of individuals sampled from both Egypt … Continue reading →

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Old dogs, and 'carnivorous' pandas

Posted on 4 Jun, 2015 by Arun Sethuraman

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

The genomics of bee sociality

Posted on 27 May, 2015 by Noah Snyder-Mackler

Bee species cover the spectrum of sociality: there are solitary bees, there are eusocial bees – which are divided into facultative eusocial (the ones that can be either solitary or eusocial depending on external cues) and obligate eusocial bees, and … Continue reading →

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Genomic diversity and secondary contact

Posted on 21 May, 2015 by Arun Sethuraman

Under a divergence, or isolation model, the genomes of individuals in a daughter-population are expected to harbor greater differentiation relative to its sister-population, and lower differentiation within the population (after sufficient time since divergence). Divergence thus is a mechanism of … Continue reading →

Posted in evolution, genomics, next generation sequencing, population genetics, theory | Tagged , , | 1 Comment

Another lesson in genomics experimental design and avoiding batch effects

Posted on 12 May, 2015 by Noah Snyder-Mackler

Twitter has been abuzz with Orna Man and Yoav Gilad’s (re)analysis of the data from a recent PNAS paper: “Comparison of the transcriptional landscapes between human and mouse tissues”. The PNAS paper concluded that the gene expression profiles of different … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing, RNAseq | Tagged , , | 3 Comments