Tag Archives: methods

FISHing for molecules, a link between form and function in animal–bacteria symbioses

Posted on 15 Mar, 2020 by Laetitia Wilkins

I am posting a blog post that was written by Benedikt Geier, a Ph.D. candidate who just handed in his Ph.D. thesis at the Max Planck Institute for Marine Microbiology in Bremen, Germany. In my eyes, these last couple of … Continue reading →

Posted in Coevolution, community ecology, ecology, evolution, genomics, methods, microbiology, natural history, Symbiosis, transcriptomics | Tagged fluorescent in situ hybridization, metabolite, metabolomics, methods, mussle, naturalist, symbiont, symbiosis | Leave a comment

Metabarcoding for every body, every habitat, every time

Posted on 19 Jul, 2018 by Laetitia Wilkins

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading →

Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged biodiversity, bioinformatics, ecology, metabarcoding, methods, microbiome, phylogenetics | 1 Comment

Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies

Posted on 10 Apr, 2018 by Katharine Coykendall

Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading →

Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics | Tagged barcode tags, barcoding, bioinformatics, eukaryotes, Illumina, metagenomics, methods, microbial communities, microbial community analysis, microbiome, NGS | 1 Comment

Unbalanced population sampling and STRUCTURE

Posted on 5 Jan, 2017 by Arun Sethuraman

The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading →

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

Making ecology “count”: a review of the why and how of molecular ecology

Posted on 25 Oct, 2016 by Kelle Freel

It’s likely that everyone has been asked by either a friend or family member “What do you do?” Which, depending on what level of detail you shoot for, might be relatively straight forward. The follow-up question, however, can be a … Continue reading →

Posted in bioinformatics, community, community ecology, metagenomics | Tagged genomics, methods, omics, review | 1 Comment

When your programming may be inadequate to the task: new options for metagenome analysis

Posted on 9 Sep, 2016 by Kelle Freel

There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading →

Posted in bioinformatics, community ecology, metagenomics, methods | Tagged CLARK-S, DESMAN, fine-scale variation, metagenomics, methods, OMICtools | Leave a 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 genomics, methods, PCR duplicates, RADseq | 6 Comments

Catching evolution in the act with the Singleton Density Score

Posted on 23 May, 2016 by Patrícia Chrzanová Pečnerová

A recent study led by Jonathan K. Pritchard at Stanford University brought a media storm with catchy headlines in both of the flagship scientific outlets Nature and Science News. Aside from highlighting the question of preprints without peer review being … Continue reading →

Posted in methods, mutation, population genetics, selection | Tagged human evolution, methods, SDS, selection | 1 Comment

Geographical Heat Maps in R

Posted on 3 Mar, 2016 by Arun Sethuraman

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading →

Posted in bioinformatics, howto, R, software | Tagged data visualization, methods | 2 Comments

Genomics of Hybridization – Part II, Top three of 2015

Posted on 28 Jan, 2016 by Arun Sethuraman

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading →

Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged hybridization, methods, natural selection, population genetics, population structure | Leave a comment