Author Archives: Ethan Linck

Scriptable evolutionary simulations in SLiM 2

Posted on 25 May, 2018 by Ethan Linck

Both empirical and theoretical population genetics are increasingly dependent on evolutionary simulations. How did historical processes lead to the patterns of genetic variation observed in your data set? How do selection, recombination, and drift interact to shape the genome during … Continue reading →

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Book review: Jonathan Losos' Improbable Destinies

Posted on 21 Feb, 2018 by Ethan Linck

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post. Is evolution predictable? This is one of the Big Questions, as much philosophy as it is biology and no less important for not really having an … Continue reading →

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Climate change and genomic vulnerability

Posted on 8 Jan, 2018 by Ethan Linck

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 →

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

Current geography has little to say about gene flow during divergence

Posted on 13 Sep, 2017 by Ethan Linck

The terms we use to describe the geography of speciation are deceptively simple. Mention allopatry, parapatry, or sympatry, and most biologists will have a clear picture of the underlying conceptual model of range limits (and probably some strong opinions about … Continue reading →

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Live from #Evol2017 – Saturday Highlights

Posted on 25 Jun, 2017 by Ethan Linck

A subset of the Molecular Ecologist team is attending this year’s Evolution meeting in Portland, Oregon. As part of our coverage of the meeting, we will recapping the highlights of each day here on the blog, and occasionally previewing upcoming presentations. … Continue reading →

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On hyRAD-X, another option for museum genomics

Posted on 9 Jun, 2017 by Ethan Linck

Last year, I profiled Suchan et al.’s “hyRAD” method for reduced-representation genome sequencing of degraded sources of DNA using RAD probes. While it’s too early to say whether hyRAD will be widely used by molecular ecologists looking to integrate historic … Continue reading →

Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics, RNAseq, selection, transcriptomics | Tagged , , , | Leave a comment

Right reads, wrong index? Concerns with data from Illumina's HiSeq 4000

Posted on 11 Apr, 2017 by Ethan Linck

Commanding around a 70% share of a 1.3 billion USD market, Illumina is the major player in next-generation sequencing (NGS) technology. More likely than not, if you’re a molecular ecologist working with NGS data, you’ve run your samples on a … Continue reading →

Posted in genomics, next generation sequencing, RNAseq, technical, transcriptomics | Tagged , , , , | 5 Comments

An Update on the Great BAMM Controversy

Posted on 1 Mar, 2017 by Ethan Linck

Update, 01 August 2016, 2:50PM. This post has been updated to include information contained in the supplemental material of Rabosky et al. 2017, and clarify the difference between branch-specific and tree-wide rate variation. Back in August, I summarized the main … Continue reading →

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Handling microbial contamination in NGS data

Posted on 6 Jan, 2017 by Ethan Linck

Until recently, I had given little thought to the potential for unwanted microbial contamination in high throughput sequence data. I suspect that if you’re a molecular ecologist who doesn’t primarily study microbes or work with ancient DNA, you’re in a … Continue reading →

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A Primer on the Great BAMM Controversy

Posted on 26 Aug, 2016 by Ethan Linck

Update, 26 August 2016, 2:30PM. A number of readers brought my attention to a series of blog posts by Moore et al. responding to Rabosky’s rebuttal of their published critique of BAMM. I’ve included links to the posts and summarized their … Continue reading →

Posted in evolution, phylogenetics, software, speciation | Tagged , , , , , , | 5 Comments