Category Archives: genomics

Sequencing round-up 2018

The deluge of new sequencing approaches continues at a pace. It seems that you turn your back for five minutes and there’s a shiny new sequencing platform promising to deliver more for less. What is the current state of play … Continue reading

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Oh my ploidy … diploids evolve more slowly than haploids?

It’s been an embarrassingly long time since I last sat at my keyboard in a TME capacity (#NewPI chat doesn’t really count)! One year ago today, to be exact (writing this on 28 March, for publication on 29 March). Thus, … Continue reading

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Posted in adaptation, blogging, evolution, genomics, haploid-diploid, selection, yeast | Tagged , , , , , , | Leave a comment

Major new microbial groups expand diversity and alter our understanding of the tree of life

I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading

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Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics | Tagged , , , , , , , | Leave a comment

Are population genomic scans for locally adapted loci too successful?

Last Friday, Molecular Ecology released an interesting new systematic review online ahead of print. Colin Ahrens and coauthors at a number of Australian research institutions compiled results from 66 papers reporting tests for locally adapted loci based on either FST … Continue reading

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Genomic signatures of ancient rendezvous and separation in elephant evolution

Evidence from various levels of the tree of life is showing that we’ve been picturing ancient encounters between related species all wrong and admixture events are probably more common than expected. Even rendezvous among primates, caniforms, and majestic proboscideans often … Continue reading

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Posted in conservation, evolution, genomics, hybridization, natural history, Paleogenomics, phylogeography | Tagged , , , , , , | Leave a comment

Exploring the genomic diversity of tubeworm endosymbionts

Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how … Continue reading

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

Climate change and genomic vulnerability

As the world burns and we barrel heedlessly into an ever-smaller and uglier future, predicting how species will respond to climate change will be critical for conservation planning. Intuition suggests most organisms will shift their ranges up in latitude or … Continue reading

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Posted in conservation, evolution, genomics | Tagged | 1 Comment

Molecular ecology, the flowchart

Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for recent natural selection in genetic data. Nielsen provides figures illustrating the effects of a recent selective sweep and the … Continue reading

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Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | Leave a comment

Visualize your genome assemblies

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates visualisations of sequence assemblies that you can interact with. When assembling a genome with your favorite assembler, you are usually building graphs, from which … Continue reading

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Diving deep: Exploring microbial communities under the seafloor

As we all sat staring at three large monitors in the front of the room, the remotely operated vehicle (ROV) Jason hung on to a borehole observatory with one hydraulic arm as the other arm plugged our sampling equipment into … Continue reading

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