Ottawa, July 6th 2012

Posted on November 14, 2011 by Tim Vines

Unlike most of the big journals in the field, Mol Ecol isn’t affiliated with an academic society, and one consequence is that there’s never been a ‘molecular ecology’ get together along the lines of the Evolution meetings or ESEB. Seeing as 2012 is the 20th year of the journal and it coincides with the big SSE/ESEB/CSEE/ASN/SSB conference in Ottawa, we’ve organised a ‘Molecular Ecology’ symposium for the 6th July, the opening day of the main conference (i.e. the one with registration and the evening reception).

The overall goal is to showcase some of the best research in each of the fields covered by the journal (adaptation, speciation, phylogeography etc.) and then map out future research priorities with panel discussions. We may even give out t-shirts. I’ve put the current speaker line-up here.

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Dr. Prepper

Posted on November 5, 2011 by Brant Faircloth

Library preparation for next-gen sequencing has become a fact of life in many labs working with model and non-model organisms. The problems with library preparation are that (1) library prep is slow and (2) library prep is expensive. Generally speaking, you can improve #1 OR you can improve #2, but you can’t do both simultaneously.

Most of us can justify time in the lab as long as we can reduce per-sample costs, so I wanted to quickly present a few options for library preparation along with their per-sample (list price/units) cost. In the following, I’m going to focus on the exact “kits” that you would use to prepare DNA libraries for Illumina sequencing using the TruSeq (Tm) adapter/reagent system:

Continue reading →

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Stretching in new directions – Part II: Interview with Jane Lubchenco

Posted on October 21, 2011 by Dilara Ally

On May 7, NOAA Administrator Jane Lubchenco received an aerial tour of coastal Louisiana with Nancy Sutley, chair of the White House Counsel on Environmental Quality. NOAA Corps CAPT Michele Finn coordinated the flight. Here, Lubchenco and Finn discuss the situation after the survey. Credit: NOAA.

So how does one become a successful academic and then turn around and create an equally successful career as a scientific leader and advisor to the, ahem, President of the United States? One important factor, that arose not with just Jane Lubchenco but with all the women I interviewed, was explicit mentorship.   Each one of these women described a mentor(s), who championed them as scientists and encouraged them to step beyond what they might imagine for themselves.  In Part II of our interview, Dr. Lubchenco summed it up nicely when she said, “Each of my mentors told me in their own way to believe in myself and to stretch in new directions.”  What else contributed to her astounding success?  Read on.

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Science in our society – Part I. An interview with Dr. Jane Lubchenco

Posted on October 13, 2011 by Dilara Ally

In early July, Dr. Lubchenco was kind enough to spend some time with me over the telephone talking a little bit about her life as the under secretary of commerce for oceans and atmosphere and administrator of NOAA.

NOAA Administrator Dr. Jane Lubchenco, NOAA Fisheries Assistant Administrator Dr. Eric Schwaab, and Council on Environmental Quality Chair Nancy Sutley assess how the sample is processed aboard the Research Vessel Caretta and chain of custody protocol used when handling specimens associated with the oil spill. Credit: NOAA.

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When should you make a complaint?

Posted on October 4, 2011 by Tim Vines

I’m writing this post with some trepidation, as dealing with complaints is the most difficult part of being an editor. However, I think there is much to be gained from bringing some clarity to the process and by giving a few broad guidelines on when it’s appropriate to challenge a decision.

First, some general suggestions that will make it more likely that any challenge will be successful: Continue reading →

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Easing the pain of titration

Posted on September 21, 2011 by Brant Faircloth

Quickly following up on Nick’s post re: Illumina Library Prep, Travis Glenn pointed me towards a manuscript in Nature Protocols that proposes an alternative to the oft-grumbled-about process of titrating libraries for 454/Ion Torrent sequencing:

Zongli Zheng et al. Titration-free 454 sequencing using Y adapters. doi: 10.1038/nprot.2011.369

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A Tweak to Illumina Library Prep

Posted on September 19, 2011 by Nicholas Crawford

For those readers who are making Illumina libraries for NGS, which I assume is many of you, I’d like to direct you to this new paper by Sheila Fisher’s group at the Broad Institute. In this paper Fisher describes the Broad’s method for targeted re-sequencing. However, of broader (pun intended) interest is her description of a ‘tweak’ the the general Illumina Library prep protocol.

This tweak is a simplification of the reaction clean-ups. I’m assuming most labs have moved away from Qiagen PCR purifications to magnetic bead cleanups. If you haven’t I highly recommend doing so. I also recommend the Agencourt SPRIPlate Super Magnet Plate. Although it’s a bit more expensive than an entry level 96 well plate magnet, the extra strength of the rare-earth magnets really keeps the beads stuck to the sides of the wells. Anyway, I digress. The tweak Fisher describes involves keeping the beads in the wells during the End-Repair, Plus-A, and Ligation steps. This reduces the number of beads used by two-thirds, but more importantly it helps keep your DNA in the tubes and thus increases yields. Honestly, I can’t wait to try this out.

Anyway, this paper is definitely worth a look-see. There’s a lot more in it that I glossed over.

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Videocast for the Wheat et al paper

Posted on August 31, 2011 by Tim Vines

We published a fascinating paper on the genetics of life history adaptation in a butterfly metapopulations back in May, and the authors very kindly put together a Q&A videocast about their work. This is available on our Wiley Online Library podcasts section (the audio version is there as well).

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Some overdue thoughts on impact factors

Posted on August 26, 2011 by Tim Vines

OK, I know this is late (they were released in July!), but the recent editorial board meeting in Tübingen forced me to put the vague thoughts I had about the 2010 impact factors into actual words and pictures:

Molecular Ecology did very well, moving from 5.96 to 6.45, and kept at fifth in the evolution rankings. Since the journals above Mol Ecol are two systematics journals (Systematic Biology and Cladistics) and two reviews-only journals (TREE and AREES), we’re very pleased with how it’s going. Furthermore, if you multiply the number of papers published per year by the impact factor (Loren’s somewhat tongue in cheek ‘Clout Factor’), you can see that Mol Ecol is putting out a lot of good papers:

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Data archiving guide

Posted on June 24, 2011 by Tim Vines

I put together a short guide that goes through the different data types commonly used in Molecular Ecology and suggests the type of file that ought to be archived to fulfil our Joint Data Archiving Policy. It’s available here. Comments and suggestions for things I’ve missed are very welcome…

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