Category Archives: genomics

Is equilibrium out of reach or are there some sneaky bouts of sex?

Posted on 30 Aug, 2016 by Stacy Krueger-Hadfield

Reproductive systems impact the evolution of genetic diversity at the population level. Yet, we don’t know a lot about organisms that are partially clonal, despite the large component of biodiversity that dabbles in asexual reproduction to varying degrees. Clonal dynamics are … Continue reading →

Posted in bioinformatics, evolution, genomics, natural history, next generation sequencing, theory | Tagged , , , | 1 Comment

The trouble with PCR duplicates

Posted on 25 Aug, 2016 by Reid Brennan

The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading →

Posted in bioinformatics, genomics, methods, next generation sequencing | Tagged , , , | 6 Comments

Of microbes and men: Testing the neutral theory with the human microbiome

Posted on 22 Aug, 2016 by Kelle Freel

There is no doubt that one of the hottest current topics in microbiology revolves around the human microbiome. There have been a suite of recent studies we’ve highlighted, on organisms ranging from bees and mice, to humans. A quick google scholar search identifies … Continue reading →

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

Understanding the pieces of all those meeces: characterizing mice gut microbiota

Posted on 12 Aug, 2016 by Kelle Freel

In an age where a tremendous amount of data is generated, this week has seen some moves towards providing open access to extensive data sets. These attempts have been in the realm of chemistry as well as microbiology, where in a … Continue reading →

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On (mis)interpreting STRUCTURE/ADMIXTURE results

Posted on 5 Aug, 2016 by Arun Sethuraman

STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading →

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , , , | 1 Comment

The Genomics of Rapid Adaptation

Posted on 1 Aug, 2016 by Bryan McLean

Phenology (the timing of life cycle events such as growth, breeding, or migration) is among the most sensitive organismal traits to climate and environmental change. In recent years, phenological shifts have been documented in numerous taxa, in traits such as … Continue reading →

Posted in adaptation, genomics, Molecular Ecology, the journal, plants, population genetics, selection | Leave a comment

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 →

Posted in genomics, next generation sequencing, phylogenetics, phylogeography, population genetics, transcriptomics | Tagged , | Leave a comment

STITCH, in time, could save a lot of array design

Posted on 12 Jul, 2016 by Jeremy Yoder

A new algorithm for processing DNA sequence data, STITCH, could lower costs for studies of genetic variation within species by reconstructing, or “imputing”, the sequences of individual samples within a larger dataset. The ongoing proliferation of high-throughput (or, ugh, “next … Continue reading →

Posted in association genetics, bioinformatics, genomics, methods, next generation sequencing, software | Tagged | Leave a comment

Who’s really riding the subway with you? Characterization of the microbial communities on Boston transport

Posted on 29 Jun, 2016 by Kelle Freel

(Figure modified from Hsu et al., 2016, Boston transport map and wikicommons image of Boston) Understanding the microbes around us is an important challenge to take on. There have been articles covering changes in microbial communities among rural and more … Continue reading →

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

New insight into the genetic basis of industrial melanism

Posted on 9 Jun, 2016 by Reid Brennan

The evolution of coloration in peppered moths during the industrial revolution is one of the most well known examples of natural selection in action. Part of the appeal of the system is the apparent simplicity. The once-abundant light colored morph … Continue reading →

Posted in adaptation, association genetics, genomics, mutation, selection | Leave a comment