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Coral conservation through assisted evolution
Coral reefs occupy a tiny portion of the world’s oceans (see map below) but their biodiversity is hugely disproportionate to their size. More than 450 million people from 109 countries live in close proximity to coral reefs and depend upon the ecosystem services and goods reefs provide, for example, food, tourism, and storm protection. And if their incalculable ecological and economic value isn’t enough to impress you, coral reefs are one of the most beautiful places on the planet.
Unfortunately, like many other incredible ecosystems, coral reefs, and the oceans in general, are in trouble due to a myriad of factors including overfishing, pollution, habitat destruction, ocean warming, and increased acidification (see a striking photographic time series documenting the effects of overfishing here and watch a short video about ocean decline and the problem with shifting baselines here). Continue reading
Posted in adaptation, conservation, evolution, methods
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Show me the power
Describing the patterns of genetic structure and mating system variation in presents challenges from the outset of sample collection to data analysis (see this post and this post). At the beginning of February, I had the pleasure to collaborate with Sean Hoban at NIMBioS (more about that in a later post). He has developed user-friendly software, such as SPOTG (Hoban et al. 2013c), and advocated the use of simulations and the quantification of the relationship between power and sampling strategy in molecular ecology studies.
While at NIMBioS, I took the opportunity to ask Sean a few questions.
Continue reading
Posted in conservation, evolution, genomics, interview, methods, population genetics, software, Uncategorized
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Interspecific gene flow enhances vectorial capacity
There are charismatic cases of gene flow between species, such as Neanderthals (see also Arun’s posts here and here), but the role of introgression in evolution remains poorly documented.
Recently diverged species have incomplete reproductive isolation and can hybridize. Rapid radiations can also lead to stochastic sorting of ancestral polymorphisms. Alleles shared through secondary contact of incomplete lineage sorting are difficult to distinguish, but new methods can tease apart these two processes if the correct branch order is known.
In a new paper in Science, Fontaine et al. (2015) describe the species branching order in the Anopheles gambiae complex.
The lineages that led to the principal human malarial vectors were the first to split and extensive autosomal introgression was likely adaptive.
Bidirectional introgressions across the genome between species probably contributed to their wide ecological flexibility and their vectorial capacity.
Posted in adaptation, bioinformatics, evolution, genomics, phylogenetics, Uncategorized
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Twice Mixed? Testing hypotheses of Neanderthal Introgression
Human migration in, and out of Africa was wrought with complex patterns of admixture (see my previous post summarizing the story so far). Of note were some recent findings on the disparity in amounts of Neanderthal introgression/ancestry between East Asians and Europeans (eg. see Vernot and Akey 2014). In yet another duel of sorts, two recent studies by Vernot and Akey (2015), and Kim and Lohmueller (2015) use separate approaches to test the hypothesis proposing the efficacy of purifying selection in bottlenecked East Asian populations to retain more Neanderthal ancestry (Sankararaman et al. 2014).

Infographic describing Neanderthal admixture into humans. Image courtesy: http://news.bbc.co.uk/nol/shared/spl/hi/sci_nat/10/neanderthal/img/neanderthals_786.gif
Vernot and Akey (2015) partitioned East Asian and European genomes into windows based on B-values (degrees to which neutral variation has been reduced as a result of linked selected sites), and also computed proportions of observed Neanderthal ancestry in the same windows. If indeed greater Neanderthal ancestry in East Asians is due to purifying selection, then these proportions should vary significantly by B-values. Vernot and Akey report that this isn’t true, and yet East Asians have ~17.5% more introgressed sequence. Subsequent explorations of demographic models using ABC indicate only 2 pulse models as acceptable, strongly rejecting the model of a single pulse.
Kim and Lohmueller (2015) test the same hypothesis using forward Wright-Fisher simulations of a million independent informative genomic sites, under the model of a single pulse of Neanderthal admixture, 1900 generations back. Starting proportions of Neanderthal ancestry were varied (although one wouldn’t expect these to vary between East Asian and European genomes under a single pulse model). Remnant Neanderthal ancestry in each population was then measured. Alternate simulations also explored loci with various selection coefficients, dominance effects, and bottlenecks.
In all cases of evolved loci that matched empirical expectations, however, the proportion of Neanderthal ancestry in East Asians to Europeans was equivalent, also unchanging with altering the length or severity of population bottleneck. The proportion does however change with varying the amount of starting ancestry – indicative of a 2 or more pulse model of Neanderthal introgression.
Two studies with similar conclusions, and indicative of so much more that’s left to learn about the complex anthropological and genomic history of modern humans.
References:
Vernot and Akey, Complex History of Admixture between Modern Humans and Neandertals, The American Journal of Human Genetics (2015), http://dx.doi.org/10.1016/j.ajhg.2015.01.006
Kim and Lohmueller, Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in…, The American Journal of Human Genetics (2015), http://dx.doi.org/10.1016/j.ajhg.2014.12.029
Posted in adaptation, bioinformatics, evolution, genomics, mutation, Paleogenomics, population genetics
Tagged Homo sapiens, population genetics
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Comparing runs and counting K
If you are someone who has any interaction with population genetics, the letter K may cause you a distinct feeling of uneasiness. Identifying the number of distinct genetic clusters (often represented as K) in a data set is a primary component in population genetics analyses, but it often becomes a point of contention. The hierarchical nature of genetic variation can make K difficult to determine and sometimes lead to questions about what the true K actually means.
A helpful tool for making objective determinations of K might be CLUMPAK, a new piece of software authored by Kopelman et al. and appearing in the most recent issue of Molecular Ecology Resources. CLUMPAK offers a simplified method for comparing among runs of different STRUCTURE-like programs, streamlining many of the calculations that have to be sometimes done by hand and providing some new solutions for summarizing runs.
You can check out their web interface (complete with good example files) or download a standalone Linux version.
So go forth and calculate K, but don’t let the clusters consume you!
Kopelman N.M., Mayzel J., Jakobsson M., Rosenberg N.A. & Mayrose I. (2015). Clumpak : a program for identifying clustering modes and packaging population structure inferences across K , Molecular Ecology Resources, n/a-n/a. DOI: http://dx.doi.org/10.1111/1755-0998.12387
The results are in for the journal selection survey
Two weeks ago I wrote a post about a recent paper by Salinas and Munch that presented a model-based method for determining to which journal an author should submit a manuscript for publication. I was curious to know how the readers of The Molecular Ecologist choose where to send their papers so I included a link for a short, informal survey to gauge how people feel about the submission/publication process. Fifty people completed the survey (thank you!) and I have posted the results below.
Career Stage
The majority of people who responded were postdocs followed by graduate students and faculty members, from assistant to full professors. An industry scientist, a museum research scientist, and an NGO scientist also provided feedback giving the survey some diversity.
At what point in the process do people pick a journal?
The majority of people who responded indicated that they decide where to submit a manuscript after they have collected and analyzed the data and before they have started to write the paper. Based on the comments of a few of the respondents, making the decision abut which journal to go with seems to be a fluid process.
“It varies. I usually have ideas of where it might be submitted before or during the experimental stage, but that often shifts as I get closer to the writing stage. Usually by the time I’m seriously working on the manuscript, I have a journal in mind so I can format it the way that journal wants.”
Factors that influence journal choice
According to the responses, journal reputation, the fit of the manuscript to the journal, and the journal impact factor are the three most important criteria people consider when deciding where to submit a manuscript. Because survey takers could write in any answer (as opposed to choosing from predetermined options), I combined some responses into one category to make displaying the results a little easier. For example, “journal reputation,” “prestige,” and “quality” were lumped into one category. Many people who listed journal reputation as a top-three factor also included journal impact factor. To me this suggests that people view reputation as somewhat separate from impact factor- a journal with a high impact factor may not have a great reputation in the opinion of a researcher (or vice versa). I found it interesting that “likelihood of acceptance” fell in the middle of the pack.
Model-based methods
The majority of people were on the fence about using a model-based method, such as the one proposed by Salinas and Munch (2015), to select a target journal for a manuscript.
Taking a risk
The survey asked “How likely would you be to submit to a prestigious journal and risk rejection instead of submitting to a solid, but lower ranked journal where you know your paper has a good shot at being accepted quickly?” Respondents were able to write in any answer so, as objectively as possible, I categorized the responses into “yes,” “no,” and “maybe.” Most respondents were willing to take a risk on getting a paper into a high impact journal although many people said the decision to aim high depended on career stage. Considerations such as the desire to get the data out quickly or avoid time-wasting reformatting for multiple journals were also important.
“As a grad student I would be less inclined to take risks, as quantity of pubs and speed/short review process was a priority. As a postdoc, I’m more inclined to take risks since the expectations are higher.”
“Depends on the urgency to get the data out, but I will risk rejection at a prestigious journal occasionally.”
“It depends on the turn around time for the higher ranked journal. Something like PNAS where rejection is very fast, yes, but somewhere that is notoriously slow like Systematic Biology, no.”
“Rejection is fine, it just means you have to rewrite; prefer submitting to solid, lower-ranked b/c prefer not to rewrite and reformat.”
Final thoughts?
The last question on the survey asked the respondents if they wanted to say anything else generally about the way in which they choose a target journal. Here are some of the most interesting responses and those that did not fit neatly into a category above…
“The size of my data set and my methods are also important in where I decide to submit a paper.”
“I like to publish in “society-based” journals such as Am Nat, Evolution, etc.”
Word limit is sometimes also a factor.”
“My priorities and those of my coauthors often differ, so journal selection is often a negotiation (unless it’s very clear-cut from the get-go).”
“The main thing is to get the work into the public domain.”
“I feel the process is quite subjective, depending on recent pubs in the field and in each journal. Depends on appeal of the paper, desired audience. Can’t imagine a model that would capture all that I think needs to go into the decision.”
I enjoyed very much seeing the results of my informal survey and reading the responses of those who took the time give their opinions. The overall impression I get is that the process of choosing where to send a manuscript for publication is subjective, complex, and often a compromise among many factors. Thanks again to those who filled out the survey. May your acceptances be swift and your rejections few and far between. Happy publishing!
Posted in career, Impact Factors, methods, peer review, science publishing
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Beauty is in the eyes of the beholder
Many animals use visual signals to scope out potential mates. In a new paper in Molecular Ecology, Sandkam et al. (2015) demonstrate that the variation underlying preference in female guppies could be explained by simple changes in expression and coding of opsins. Beauty really may be in the eyes of the beholder.
Populations can diverge rapidly via sexual selection, but there are very few systems in which the variation in female preference is replicated in a consistent manner across populations. Trinidadian guppies are a classic model system exploring the evolution of female mate choice. In response to environmental factors, such as predation, female mate preference varies both within and between populations.
In guppies, there are nine opsin proteins in which each is coded by a single gene and grouped by the light they detect. Changes in gene sequence and expression could alter the tuning of these sensory systems.
Guppy vision differs across populations in a consistent manner based on the opsin expression and allele frequencies in natural populations.
Guppies in low-predation populations express more long wavelength-sensitive opsins than do guppies from high-predation environments and low-predation populations are almost fixed for an alternative amino avid known to affect retinal tuning.
Their data suggest that much of the variation in female preference can be explained by differences in the visual system.
populations with stronger female preference for red/orange coloration invest a strikingly greater proportion of their color vision in detecting those colors and are strongly differentiated for sequence variants [which are known] to change spectral sensitivity.
Genome-wide effects of artificial selection
Humans have been artificially selecting for favorable traits in crops, pets, and livestock over millennia. Years of theoretical predictions and experimental evolution studies have shown the detrimental effects of increased homozygosity, and the population-wide advantages of artificially maintaining heterozygosity. Two new manuscripts (Hedrick (2015), and Kessner and Novembre (2015)) aim at discussing the genome wide effects of artificial selection, albeit focused on different characteristics.

Expected increase in heterozygosity upon introduction of a new allele at a low frequency, plotted at different levels of artificial selection. Image courtesy: http://jhered.oxfordjournals.org/content/106/2/141/F2.expansion.html
Hedrick (2015) reviews the phenomenon of ‘overdominance’, or heterozygote advantage across 12 different traits. The list includes milk yield in dairy cattle, litter size in pigs, tail length in cats, hairlessness in dogs, among other described cases. Hedrick also discusses some theoretical predictions on the perpetration of heterozygosity in artificially selected populations, importantly the strength of selection on fixation times.
…given very strong selection from an environmental or other change, a new mutant that has an advantage as a heterozygote might increase in frequency. However, if it had a lowered fitness as a homozygote, it would be maintained as a polymorphism due to its overall heterozygote advantage…
Kessner and Novembre (2015) describe an analysis pipeline using forqs, and utilize simulations to predict the effects of artificial selection at QTLs, based on population sizes (drift, efficacy of selection), proportion of individuals chosen to propagate, length of the experiment, and replication. Forward simulations indicate (1) predictable trajectories of fixation of new alleles under constant selection (also predicted by the scenarios described by Hedrick (2015) above), (2) qualitative differences in trajectories of allele frequencies of linked QTLs, (3) increase in power to detect selected QTLs (versus neutrally evolving loci) with increased replication, and starting population sizes, and importantly, (4) the effect of recombination (which reduces the interference, and LD between linked QTLs).
We emphasize that the opportunity for recombination is a key factor in the power to detect and localize QTLs, and that this should be taken into account by future designers of artificial selection experiments.
References:
Hedrick, Philip W. “Heterozygote Advantage: The Effect of Artificial Selection in Livestock and Pets” J Hered (2015) 106 (2): 141-154 http://dx.doi.org/10.1093/jhered/esu070
Kessner, Darren, and John Novembre. “Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits.” Early Online February 10, 2015, http://dx.doi.org/10.1534/genetics.115.175075
Kessner, Darren, and John Novembre. “forqs: forward-in-time simulation of recombination, quantitative traits and selection.” Bioinformatics 30.4 (2014): 576-577. http://dx.doi.org/10.1093/bioinformatics/btt712
Posted in bioinformatics, evolution, genomics, methods, mutation, population genetics, theory
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How do you unite the stage and actors of the evolutionary play?
When you are forced to give your one sentence, off-the-cuff response to “what kind of scientist are you?”, who do you become?
A landscape geneticist? Community geneticist? Landscape epidemiologist?
A new opinion in Trends in Ecology and Evolution by Brian Hand, Winsor Lowe, and others calls for less distinction between these identities to answer contemporary and compelling questions in evolution and ecology.
The consideration of both biotic (think community genetics/ecology) and abiotic (think landscape genetics) factors and their effects on patterns of genetic variation are often pursued as part of separate investigations. Hand, Lowe, and their coauthors make the comparisons to G. Evelyn Hutchinson’s “Ecological Theater and the Evolutionary Play”, suggesting that the actors (the species and their interactions) and the stage (the abiotic environment) are not considered together often enough.
Landscape genetics and community genetics have developed as largely-independent disciplines, growing in popularity and importance, but without capitalizing on the complementary nature of the two approaches.
The sort of data required to ask questions in the framework proposed is a serious challenge (adaptive and neutral genetic data, geographic information, demographics, etc.). The authors point towards burgeoning field of metagenomics as leading the way in some of these new ways of thinking, but there are certainly labs who read this blog that bridge these interdisciplinary divides already. What remains to be seen is if these researchers can effectively roll all of these techniques together under the common title of “Landscape Community Genetics”.
Hand B.K., Lowe W.H., Kovach R.P., Muhlfeld C.C. & Luikart G. (2015). Landscape community genomics: understanding eco-evolutionary processes in complex environments, Trends in Ecology and Evolution, DOI: http://dx.doi.org/10.1016/j.tree.2015.01.005
Posted in community ecology, evolution, genomics, population genetics
Tagged landscape genetics, opinion
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Harry Smith, the founder of Molecular Ecology, has died

Harry Smith. (Molecular Ecology: Elinor Smith)
We’ve received word that Harry Smith, the founder of Molecular Ecology, passed away yesterday.
Smith had a prolific and well-regarded career studying the molecular basis of plants’ responses to their environments. In particular, he helped to demonstrate how plants perceive the color, and thereby the quality, of light, and adjust their growth in response. In addition to editing Molecular Ecology from its 1992 launch through 2008, Smith was founding editor of the journals Plant, Cell & Environment and Global Change Biology. On his departure from the editorship, he was awarded the 2008 Molecular Ecology prize, and profiled in the journal by Peter Quail, who wrote:
… Harry Smith is a scholar, mentor, internationally renowned researcher, eloquent speaker and author, pioneering journal editor and highly valued colleague who has contributed greatly in multiple ways to plant science and the community.
Our thoughts are with Smith’s friends and family.
Posted in community, Molecular Ecology, the journal, science publishing
Tagged Harry Smith, in memoriam
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