Mol Ecol's best reviewers

Posted on 5 Feb, 2013 by Tim Vines

A healthy peer review system is essential for the integrity of science, but the anonymity of the process means that good reviewers seldom get recognition from the broader community. This is particularly a problem for junior researchers trying to get funding and jobs. A ‘Reviewer for…’ list appears in most resumes, but since this carries no indication of how often or how well they review, it is given little weight in the selection process.
Molecular Ecology has therefore decided to publish a list of our very best referees from the last two years. Our hope is that the people listed below will put ‘Top Reviewer for Molecular Ecology 2012’ on their resume, and that this will highlight to search committees and granting agencies that they have made a significant contribution to the community as a reviewer.
Everyone who completed a review for Molecular Ecology between 1st December 2010 and 1st December 2012 was eligible, and people were ranked by an index that included the number of reviews completed, the proportion of accepted review requests that led to a review being returned (excluding unassignments before the two week deadline), and the average time taken per review if this was over two weeks. The top 300 (~ 8%) are listed below the fold – thank you so much for your efforts!
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Posted in community, science publishing | Tagged | 6 Comments

What we're reading

Posted on 1 Feb, 2013 by Jeremy Yoder

Library!

As we head into the weekend, here’s some things we’ve been reading that might be worth your screen time.
In the journals
Irschick, D.J., Albertson, R.C., Brennan, P., Podos, J., Johnson, N. a, Patek, S., et al. 2013. Evo-devo beyond morphology: from genes to resource use. Trends in Ecology & Evolution 1–7. doi: 10.1016/j.tree.2012.12.004

We suggest that the fields of evo-devo, functional mor- phology, and evolutionary ecology should be united under a common framework based on three predictions. The first is that morphological disparity should scale positively with functional complexity among different radiations. The second is that functional complexity should correlate negatively with the predictability of evolutionary divergence within lineages, and the third is that functional complexity should define the genetic architecture of adaptive radiations.

Delplancke, M., Alvarez, N., Benoit, L., Espíndola, A., I Joly, H., Neuenschwander, S., et al. 2013. Evolutionary history of almond tree domestication in the Mediterranean basin. Molecular Ecology 22: 1092–104. doi: 10.1111/mec.12129

Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediter- ranean basin.

In the blogosphere
Fixing NIH science funding: First, a vexed conversation, then a righteous rant, then some specific proposals.
Jerry Coyne explains why he thinks epigenetics isn’t going to revolutionize evolutionary biology.

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What we're reading

Posted on 18 Jan, 2013 by Jeremy Yoder

New York Public Library, Nov 2012 - 01

In the journals
Wang, J., Wurm, Y., Nipitwattanaphon, M., Riba-grognuz, O., Huang, Y., Shoemaker, D., et al. 2013. A Y-like social chromosome causes alternative colony organiziation in fire ants. Nature. doi: 10.1038/nature11832

In the fire ant Solenopsis invicta, the existence of two divergent forms of social organization is under the control of a single Mendelian genomic element marked by two variants of an odorant-binding protein gene4, 5, 6, 7, 8. Here we characterize the genomic region responsible for this important social polymorphism, and show that it is part of a pair of heteromorphic chromosomes that have many of the key properties of sex chromosomes.

Vines, T., Andrew, R. & Bock, D. 2013. Mandated data archiving greatly improves access to research data. The FASEB Journal. doi: 10.1096/fj.12-218164

Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE.

In the blogosphere
You’ve had a flu shot for this year, right? Why haven’t you had a flu shot yet?!
Clinical trial shows that fecal microbial transplants can be more effective than antibiotics for preventing recurrent infections of the lower digestive tract.
This behind-the-scenes tour of The University of Montana’s zoological museum is pretty excellent. Money quote: “The whole museum is basically overflow skull storage.” Also watch out for the orgy. No, really. (h/t Hannah Waters)

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Next-gen sequencing field guide, 2013 edition

Posted on 17 Jan, 2013 by Jeremy Yoder

2007.06.23 - am I in there?

Travis Glenn has updated his Field Guide to Next-Generation Sequencing, originally published in 2011, to account for changes to this almost axiomatically dynamic field. The 2013 update to the Field Guide tables is online here. Previous editions of the tables remain online, as archives. The Molecular Ecologist is proud to continue hosting this valuable community resource, and grateful to Travis for keeping it up-to-date.

Posted in bioinformatics, data archiving, next generation sequencing | Tagged | Leave a comment

STACKS: A program for identifying and genotyping loci with next-generation sequencing data

Posted on 15 Jan, 2013 by Mark Christie


If you have recently collected or are in the process of collecting next-generation sequencing data, then you may be wondering what the next step to working with your data will entail.  Hopefully, you have been working a little bit with a Linux and/or Mac command line:  enough so that you can move files, create directories, install software etc.  You are now ready to analyze your sequencing data and, in particular, you want to use your next-gen data to identify and genotype loci.  Regardless of whether you are interested in linkage mapping, phylogenetics, or population genomics, the program STACKS may be just what you are looking for.  STACKS is a program that specializes in identifying and genotyping loci from next-generation sequencing data, in particular RAD-seq data: that is large numbers of short reads collected throughout the genome using restriction enzyme cut sites.  STACKS was created by Julian Catchen et al. at the University of Oregon (click here for the associated paper; here for the program website).  The program was initially developed to handle data types associated with linkage mapping, but the program can be more generally applied to identify and call loci from barcoded individuals collected from natural populations.  The program runs on both Linux and Mac machines.  I’d imagine that the program could also be run with a Linux virtual machine on Windows, but it would probably be much less memory-intensive to set up your PC to dual boot Linux and Windows.  STACKS can be run with the command line as well as with a web interface.  The web interface is designed to interact with a mySQL database, and is required for some of the analyses.  To address some questions associated with first using STACKS, some of the program developers (well, at least one) have agreed to a Q&A here on the Molecular Ecologist in the next few weeks – so stay tuned!  Below, I explore the general idea and functionality of the program. Continue reading →

Posted in methods, next generation sequencing, population genetics, software | Tagged , , | 3 Comments

What we're reading

Posted on 11 Jan, 2013 by Jeremy Yoder

Library

As we head into the weekend, here’s a few things we’ve seen that might be worth your screen-time.
In the journals
Cameron, E.Z., Gray, M.E. & White, A.M. 2012. Is publication rate an equal opportunity metric? Trends in Ecology & Evolution 28: 7–8. doi: 10.1016/j.tree.2012.10.014

Publication quantity is frequently used as a ranking metric for employment, promotion, and grant success, and is considered an unbiased metric for comparing applicants. However, research suggests that women publish fewer papers, such that the measure may not be equitable.

Calvignac-Spencer, S., Merkel, K., Kutzner, N., Kühl, H., Boesch, C., Kappeler, P.M., et al. 2013. Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology doi: 10.1111/mec.12183

Carrion feeding flies are ubiquitous and can be expected to feed on many vertebrate carcasses. Hence, we tested whether fly-derived DNA analysis may also serve as a novel tool for mammalian diversity surveys. We screened DNA extracted from 201 carrion flies collected in tropical habitats of Côte d’Ivoire and Madagascar for mammal DNA using multiple PCR systems and retrieved DNA sequences from a diverse set of species (22 in Côte d’Ivoire, four in Madagascar) exploiting distinct forest strata and displaying a broad range of body sizes. Deep sequencing of amplicons generated from pools of flies performed equally well as individual sequencing approaches.

In the blogosphere
Is the problem for women in science really their self-confidence?
Ed Yong on using carrion flies to survey mammal diversity.
Overly honest methods.

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What we're reading

Posted on 4 Jan, 2013 by Jeremy Yoder

reading

As we head into the first weekend of the new year, here’s a few things we’ve seen that might be worth your screen-time:
In the journals
Nicholson, W.L., Krivushin, K., Gilichinsky, D. & Schuerger, A.C. 2012. Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars. Proceedings of the National Academy of Sciences online early. doi: 10.1073/pnas.1209793110

Six bacterial isolates were obtained from a permafrost borehole in northeastern Siberia capable of growth under conditions of low temperature (0 °C), low pressure (7 mbar), and a CO(2)-enriched anoxic atmosphere.

Holt, B.G., Lessard, J.-P., Borregaard, M.K., Fritz, S. a., Araujo, M.B., Dimitrov, D., et al. 2012. An update of Wallace’s zoogeographic regions of the world. Science 339: 74–78.

Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere.

In the blogosphere
An article in National Geographic examines the population genetic changes accompanying human range expansion.

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In the holiday spirit

Posted on 24 Dec, 2012 by kimgilbert

Christmas Time

It’s that time of year again, where conifers across the globe are chopped down and taken into people’s homes or workplaces in celebration of Christmas. According to the IUFRO (International Organizations of Forest Organizations), over 80 million trees are consumed annually across the globe for Christmas. Though this number pales in comparison to industrial logging for timber, it nonetheless garners significance in the scientific community.
To start at the beginning, why do we even have what is today often called the Christmas tree, or also a holiday tree? The tradition appears to have begun in an entirely secular manner. The quality of retaining needles year-round, which gives evergreens their names, was often used as a symbol of eternal life by the ancient Egyptian, Chinese, and Hebrew.  Evergreen boughs celebrated winter and the fact that spring would once again return. [1, 2, 3]
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What we're reading (under the tree)

Posted on 21 Dec, 2012 by Jeremy Yoder

Pine tree

Buschiazzo, E., Ritland, C., Bohlmann, J. & Ritland, K. 2012. Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evolutionary Biology 12: 8. doi: 10.1186/1471-2148-12-8

Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10-9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution.

In the blogosphere
What not to say to the graduate student who’s home for the holidays.
What it’s like to snuggle a baby walrus.
How Santa keeps tabs on bioinformaticians.

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Q&A: Stacey Dunn chases pronghorn fawns up Bateman's slope

Posted on 18 Dec, 2012 by Jeremy Yoder

A pronghorn buck watches over his harem. Photo courtesy Stacey Dunn.


Stacey Dunn is, objectively, pretty amazing. She started grad school at the Univeristy of Idaho a year before I did, studying sexual selection in pronghorn antelope on the National Bison Range in Montana. In between catching baby pronghorn (so as to track their parentage), she backpacked through most of Glacier National Park, ran ultramarathons, and started a family — she defended her dissertation about a month before her son was born. When I saw some of her pronghorn research in the pages of Science, I knew I wanted to cover it here at The Molecular Ecologist. Stacey agreed to take some questions via e-mail, and I’m reproducing her answers below with only a couple minor edits. — Jeremy
Byers, J. & Dunn, S. 2012. Bateman in nature: Predation on offspring reduces the potential for sexual selection. Science 338: 802–804. doi: 10.1126/science.1224660.
Q: What’s a “Bateman slope,” and why would we want to measure it?
Sexual selection occurs due to competition over mates, with the final outcome being offspring production. The Bateman slope is the regression slope of male mate number on male offspring number. It is a measure of the potential for sexual selection. Knowledge of the intensity of sexual selection is critical to the understanding of mating system evolution and sexual dimorphism.
Q: There are, apparently, some serious questions about the methods Bateman used in his original study on sexual selection in fruit flies. How does yours improve on that work?
Bateman’s calculations relied on a pedigree developed from phenotypic data on fruit flies, which led to biased results. We used a multi-generational pedigree developed from genetic parentage data to estimate sexual selection in pronghorn. This allowed us to make unbiased calculations of mate number and offspring number.
Q: Tell me about your data set, and what it took to put it together.
The National Bison Range pronghorn have been studied extensively by John [Byers] and his lab since 1981. Each spring, we captured nearly all fawns born in the population. During captures, we weighed, measured, sexed and tagged the fawns and took a tissue sample for genetic analysis. We genotyped each individual alive since 1999 at 19 microsatellite loci. We determined paternity for all fawns based on genotype. Maternity was known from fawn captures, but was also confirmed genetically. We then used that information to reconstruct a multi-generational pedigree of the pronghorn population.
Continue reading →

Posted in interview, pedigree | Tagged , , , , , | 1 Comment