Scanning the genome for local adaptation

2012.10.22 - Medicago truncatula

Medicago truncatula in its not-very-natural habitat, the greenhouse.

One of the most obvious and important applications of evolutionary genetics is in figuring out whether natural biological communities are going to be able to adapt to global climate change. The projected rate of climate change over then next century is unprecedented in the evolutionary history of most living things, and we need methods to rapidly assess the genetic capacity of natural and cultivated populations to evolve in response to warming.

Genome scans for loci that are locally adapted to climate provide one tool for that assessment. Unlike traditional quantitative genetics methods, a genome scan doesn’t require cultivating the species of interest in controlled conditions. Instead, genome-wide marker data from a sample of natural populations can be used to find genome regions that are probably important for adaptation to climate, and these can be assayed for variation in populations threatened by changing conditions.

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What we’re reading: Stick insects, Gulf of Mexico oysters, and how many peer reviewers it takes to change a lightbulb joke?

From the Brockhaus and Efron Encyclopedic Dictionary

In the journals

Comeault, A. a., V. Soria-Carrasco, Z. Gompert, T. E. Farkas, C. A. Buerkle, T. L. Parchman, and P. Nosil. 2014. Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae. The American Naturalist. 183:711–727. doi: 10.1086/675497.

Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects.

Anderson, J. D., W. J. Karel, C. E. Mace, B. L. Bartram, and M. P. Hare. 2014. Spatial genetic features of eastern oysters (Crassostrea virginica Gmelin) in the Gulf of Mexico: northward movement of a secondary contact zone. Ecology and Evolution. doi: 10.1002/ece3.1064.

Recent hydrological changes in the area of secondary contact may be promoting migration in areas that were previously inhospitable to eastern oysters, and observed differences in the timing of spawning may limit hybridization between populations. Comparison of these findings with the results of an earlier study of oysters in Texas suggests that the secondary contact zone has shifted approximately 27 km north, in as little as a 23-year span.

In the news

“Dear Academia, I loved you, but I’m leaving you. This relationship is hurting me.”

“If you do have a paper that is going to get a lot attention I think it’s also fair to say that you now should be highly confident in your result prior to publication.”

“I cannot find any serious fault with this joke. Leeson is fully qualified to make it, and has done so carefully and thoroughly. The joke is funny and of comparable quality to jokes found in peer journals. I score it 3/10 and recommend rejection.”

“In short, no, good science does not REQUIRE replication.”

“Tired of generic mass produced palettes for your plots? Short of adding an owl and dressing up your plot in a bowler hat, here’s the most indie thing you can do to one. First round of palettes derived from the amazing Tumblr blog Wes Anderson Palettes.”

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Identifying and quantifying fitness effects across loci

Rainbow spectrum reminds me of 70s logo design

Taking the site frequency spectrum to the next level.

The following guest post by Ethan Jewett is cross-posted from the is cross-posted from the CEHG blog at Stanford. Enjoy!

The degree to which similarities and differences among species are the result of natural selection, rather than genetic drift, is a major question in population genetics. Related questions include: what fraction of sites in the genome of a species are affected by selection? What is the distribution of the strength of selection across genomic sites, and how have selective pressures changed over time? To address these questions, we must be able to accurately identify sites in a genome that are under selection and quantify the selective pressures that act on them.

Difficulties with existing approaches for quantifying fitness effects

A recent paper in Trends in Genetics by David Lawrie and Dmitri Petrov (Lawrie and Petrov, 2014) provides intuition about the power of existing methods for identifying genomic regions affected by purifying selection and for quantifying the selective pressures at different sites. The paper proposes a new framework for quantifying the distribution of fitness effects across a genome. This new framework is a synthesis of two existing forms of analysis – comparative genomic analyses to identify genomic regions in which the level of divergence among two or more species is smaller than expected, and analyses of the distribution of the frequencies of polymorphisms (the site frequency spectrum, or SFS) within a single species (Figure 1). Using simulations and heuristic arguments, Lawrie and Petrov demonstrate that these two forms of analysis can be combined into a framework for quantifying selective pressures that has greater power to identify selected regions and to quantify selective strengths than either approach has on its own.

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What we’re reading: Polygenic mutation-selection balance, demographics of invading mice, and the U.S. consensus on climate change

Bookshelf spectrum 2.0 - mission accomplished!

In the journals

de Vladar HP, N Barton. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. doi: 10.1534/genetics.113.159111.

The interplay between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2√μ/S remain polymorphic, whereas those with larger effects are fixed.

Gray MM, D Wegmann, RJ Haasl, MA White, SI Gabriel, JB Searle, RJ Cuthbert, PG Ryan, and BA Payseur. 2014. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Molecular Ecology. 23:1923–1939. doi: 10.1111/mec.12715.

Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion.

In the news

“While trying to bluff your way through a qualifying exam isn’t a good strategy, it’s also not going to harm anyone else. In other situations, though, failing to recognize and/or acknowledge what you do and do not know is really important, with the potential to cause harm.”

“In the fight for attention from researchers, there are winners and there are civets.”

“More than 60 percent of Americans in every state favor government-imposed limits on greenhouse gas emissions from businesses and power plants.”

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Why we sign our peer reviews

A Lovely Signature, 1796

Last week I posted the results from a brief survey of our readers, asking whether they usually sign their peer reviews. In that small sample of evolutionary ecologists, the overwhelming majority said they review anonymously, though many participants seem to take things on a case-by-case basis. Participants who review anonymously were more likely to cite habit, and to say that they were concerned about the consequences that non-anonymous reviews might have for their relationships with colleagues.

I also asked participants to send in some more in-depth thoughts on the question of anonymous review, and lots of folks did. These are the responses from those who said they usually sign their reviews—you can find responses from folks who usually review anonymously here. I’ve done only minimal editing for clarity. Thanks to everyone who shared thoughts!

Bryan Carstens, Assistant Professor at the Ohio State University, in the Department of Evolution, Ecology and Organismal Biology.

As a rule, I prefer signed reviews for two reasons. One, they are generally more thorough and thus more useful to the AE and the authors of the manuscript. In my role as the former, I have seen too many cases where people write a short anonymous review that heavily criticizes an aspect of the submitted paper in a less-than-judicious manner. Second, signed reviews are generally more impactful on the authors. I can think of at least two examples of papers that I have written that changed substantially due to a signed review from someone that I deeply respected, and therefore could not ignore the constructive criticism offered in the review.

In most cases I sign, but when I have not signed it was usually due to extenuating circumstances such as the case where I was reviewing a paper written by someone who was in the process of serving as an AE on one of my graduate student’s papers.

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Why we don’t sign our peer reviews

The Mask

Last week I posted the results from a brief survey of our readers, asking whether they usually sign their peer reviews. In that small sample of evolutionary ecologists, the overwhelming majority said they review anonymously, though many participants seem to take things on a case-by-case basis. Participants who review anonymously were more likely to cite habit, and to say that they were concerned about the consequences that non-anonymous reviews might have for their relationships with colleagues.

I also asked participants to send in some more in-depth thoughts on the question of anonymous review, and a number of folks did. These are the responses from those who said they usually review anonymously—you can find responses from folks who usually sign their reviews here. I’ve done only minimal editing for clarity. Thanks to everyone who shared thoughts!

Will Pearse, postdoc at the University of Minnesota, contributor at Phylo-Eco-Geo-Evo Journal Club:

I wrote an article with James Rosindell suggesting a new open peer review system where every aspect of peer review is completely open, yet paradoxically I rarely sign reviews. My concern is appearing sycophantic when I enjoy a paper, I’m actually not worried about more negative reviews because I’m always polite and constructive. I would only sign my review if I were recommending someone cite one of my papers, something I’m not often comfortable doing anyway. I’ve actually done an entirely open review [for Faculty of 1000] and I found the whole experience rather jarring; I wouldn’t have done it if I didn’t already like the software in question, and I think that could be unethical. Scott’s a nice guy and a good scientist; I’m not certain I would have been viewed very favourably being one of the first people to criticise the work of another in the open, despite the fact I think such a system has a number of benefits.

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What we’re reading: Coevolving diversity, gut microbiota and gas, and killing the phrase “next-generation sequencing”

about reading, books, ...

In the journals

Boots M., A. White, A. Best, and R. Bowers. 2014. How specificity and epidemiology drive the coevolution of static trait diversity in hosts and parasites. Evolution. doi: 10.1111/evo.12393

We examine theoretically how epidemiological feedbacks and the characteristics of the interaction between host types and parasites strains determine the coevolution of host–parasite diversity.

Manichanh C., A. Eck, E. Varela, J. Roca, J.C. Clemente, A. González, et al. 2014. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 63(3):401-8. doi: 10.1136/gutjnl-2012-303013.

When challenged with flatulogenic diet, patients’ microbiota developed instability in composition, exhibiting variations in the main phyla and reduction of microbial diversity, whereas healthy subjects’ microbiota were stable. Taxa from Bacteroides fragilis or Bilophila wadsworthia correlated with number of gas evacuations or volume of gas evacuated, respectively.

In the news

“I’ve developed a data scraper that gathers information on student dissertations, such as page length, year and month of graduation, major, and primary advisor.”

“I hate the phrase next-generation sequencing (NGS) with a passion. Here’s why …” [Plus addendum.]

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Do we sign our peer reviews? Mostly, no.

Last week, inspired by discussions with my co-bloggers and a post by Terry McGlynn, I asked our readers to tell me whether they do peer review anonymously, and why. A total of 87 folks responded to a brief online survey, and here’s what they said: most of us review anonymously, and a lot of us do it to protect ourselves in interactions with senior colleagues.

First, the headline result: how many Molecular Ecologist readers review anonymously? Of the 87 survey participants, 82% (71) said that generally they do no sign their peer reviews.


But I also asked participants how many reviews they’d done in the last year, and how many of those were anonymous—and this revealed that those general statements aren’t ironclad.

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Posted in community, peer review, science publishing | 7 Comments

Journals must boost data sharing

Here’s the text from Tim’s recent (3rd April) Correspondence piece in Nature

The journal ecosystem is a powerful filter of scientific literature, promoting the best work into the best journals. Why not use a similar mechanism to encourage more comprehensive data sharing? Several journals have introduced policies mandating that data be shared on a public archive at publication (see, for example, here).

However, these have met with limited success, perhaps because of authors’ fear of losing control, being scooped in subsequent papers or having errors exposed. Moreover, compliance with data sharing policies is typically only checked after the paper has been accepted.

To spur excellence in data sharing, journals must recognize that better sharing leads to stronger papers, and judge submissions accordingly. Articles associated with feeble sharing efforts should either improve or be rejected. A focus on publishing verifiable research will boost journal reputation. It also signals to the community of authors that withholding data will restrict them to publication in less prestigious journals.

Timothy H. Vines, University of British Columbia, Vancouver, Canada

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What we’re reading: Genomics for conservation, SNPs versus microsats, and imbalance in the peer-review ecosystem


In the journals

Harrisson K.A., A. Pavlova, M. Telonis-Scott and P. Sunnucks. 2014. Using genomics to characterize evolutionary potential for conservation of wild populations. Evolutionary Applications. doi: 10.1111/eva.12149.

… screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s).

Lozier J.D. 2014. Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing. Molecular Ecology. 23:788–801. doi: 10.1111/mec.12636.

Previous microsatellite-based analyses have shown that gene diversity is lower in the declining [Bombus] pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species.

Petchey O.L., J.W. Fox, L. Haddon. 2014. Imbalance in individual researcher’s peer review activities quantified for four British Ecological Society journals, 2003-2010. PLoS ONE 9: e92896. doi: 10.1371/journal.pone.0092896. (See also discussion by author Jeremy Fox at Dynamic Ecology)

The majority of researchers (64%) did not have balanced contributions and withdrawals. Depending on assumptions, 12% to 44% contributed more than twice as much as required; 20% to 52% contributed less than half as much as required.

In the news

“In the face of climate change, scientists like [Ruth] Shaw have begun to measure how effective evolution might be as a survival strategy.”

“Observers lauded [David] Wright’s appointment in December 2011 … But on 25 February, he fired off a fiery resignation letter to his boss (see below), HHS Assistant Secretary for Health (ASH) Howard Koh.”

“But after a few years … you are given the chance to reflect and summarize, even rewrite your own narrative. You’ve identified collaborators and programs that make your collective program greater than the sum of its parts.”

“But just as the spherical cow is logically rigorous but of limited empirical insight, so the relentless tautologies of adaptationism leave us in the dark as to how human cultural and social diversity came about.”

“The problem is that most people don’t know what ‘the flu’ is, and relying on Google searches by people who may be utterly ignorant about the flu does not produce useful information.”

“So upon their predictable failure (in the free national labor market!) to turn up a qualified candidate, they wound up with a man whose views on issues relevant to the course are not only outside the scientific mainstream, but are demonstrably, factually incorrect and who likely has in the past abused such a position to advance his agenda.”

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