Rescue me

Posted on 6 Feb, 2015 by Stacy Krueger-Hadfield

© wikipedia

© wikipedia


Whiteley et al. (2015) review genetic rescue (GR), or the increase in population fitness (growth) owing to immigration of new alleles, in a new paper in TREE.
Genetic rescue is a controversial and hasn’t been applied to any great extent in conservation efforts.  In small populations of conservation concern, a small number of individuals introduced into an isolated population could restore genetic diversity and mask inbreeding depression. But, debate has centered on:

whether translocation of individuals or alleles into small, imperiled populations will have the desired effect of increasing population growth rates and maintaining a diverse array of local populations, or reduce population fitness through outbreeding depression and decrease biodiversity by homogenizing distinct gene pools.

The authors point to recent work in which re-establishing gene flow among populations that were recently connected will increase fitness (e.g., Hwang et al. 2011).
Genomic approaches will aid in the implementation and effectiveness of GR by improving the ID of the best populations or even individuals for GR and monitoring the outcome of GR attempts with adjustments implemented as necessary.
Hwang AS, Northrup SL, Alexander JK, Vo KT, Edmands S (2011) Long-term experimental hybrid swarms between moderately incompatible Tigriopus californicus populations: hybrid inferiority in early generations yields to hybrid superiority in later generations. Conserv Genet, 12, 895-909
Whiteley AR, Fitzpatrick SW, Funk WC, Tallmon DA (2015) Genetic rescue to the rescue. TREE 30, 42-49.

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Phonemes and Genomes

Posted on 5 Feb, 2015 by Arun Sethuraman

Human phonemes and genomes are thought to have evolved hand-in-glove out of Africa. Several recent studies have attempted to capture a picture of this global variation in languages and peoples, often supporting (and rejecting) a serial founder model (eg. see Atkinson 2011, Perreault and Mathew 2012, Hunley et al. 2012). In a recent large-scale study of microsatellite loci from 246 human populations and phonemic variation across >3000 languages, Creanza et al. (2015) use a PCA (and tests of correlation) to report several interesting patterns in the co-evolution of phonemes and genomes.

Phonemic diversity decline with distance from Eurasia. Figure 3 from Creanza et al. (2015) Image courtesy: http://www.pnas.org/content/112/5/1265/F3.large.jpg


Of note are the observations that (1) there is no universal concordance in genetic and phonemic diversities despite most diversity in both were observed in Africa, (2) there exists a strong correlation in differences among populations and geographic distance (and a reduction in number of phonemes with distance from Eurasia), but (3) phonemic diversity is informative of more recent divergence history, rather than of ancient divergence (also indicated by spatial autocorrelation), and (4) a Eurasian origin to all languages analyzed.
Importantly, their analyses indicate that phonemes, unlike genomes, don’t necessarily reflect vertical evolutionary descent, warranting newer models to study the evolution of languages.
Reference:
Creanza, Nicole, et al. “A comparison of worldwide phonemic and genetic variation in human populations.” Proceedings of the National Academy of Sciences (2015): 201424033. http://dx.doi.org/10.1073/pnas.1424033112

Posted in bioinformatics, evolution, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

Night at the museum

Posted on 5 Feb, 2015 by Stacy Krueger-Hadfield

Many population genetic and genomic studies document snapshots of a given population’s genetic diversity. Yet, there are many reasons to document changes over time in population parameters in response to perturbations, such as biological invasions (both in terms of the invader and the invaded).
There is a rich history of long-term ecological monitoring in which the abundance and distribution of species are recorded. For example, the MarClim project has continued efforts by the Marine Biological Association of the United Kingdom of monitoring intertidal zones, in which records date back to the 1950s. However, these monitoring projects tend to be concerned with ecological patterns rather than documenting genetic change through time.

Extension of the leading range edges occurring in the Lusitanian species Perforatus perforatus, Phorcus lineatus, Gibbula umbilicalis, Chthamalus stellatus, Bifurcaria, and then contractions of the southern trailing range edge of the Boreal species Alaria esculenta and Semibalanus balanoides. © Nova Mieszkowska

Extension of the leading range edges occurring in the Lusitanian species Perforatus perforatus, Phorcus lineatus, Gibbula umbilicalis, Chthamalus stellatus, Bifurcaria bifurcata, and then contractions of the southern trailing range edge of the Boreal species Alaria esculenta and Semibalanus balanoides. © Nova Mieszkowska


There are studies in which genetic change through time has been studied, such as Reem et al. (2013) in which limited gene flow associated with high mutation rates was documented in the ascidian Botryllus schlosseri over a 13-year period. But, what about larger scales, both spatial and temporal?
Continue reading →

Posted in DNA barcoding, evolution, genomics, natural history, next generation sequencing, phylogenetics, population genetics, speciation, Uncategorized | Tagged , , , | Leave a comment

Mike Sovic on what comes AftrRAD

Posted on 4 Feb, 2015 by Rob Denton

Pic3-2

Dr. Mike Sovic pondering the number of polymorphic loci in this beautiful vista


We’ve recently been highlighting some discussions comparing different protocols for restriction site-associated DNA sequencing (RADseq). We’ve seen the pros and cons of multiple techniques, but what happens when you finally have thousands of shiny SNPs sitting on your hard drive? Multiple programs have been developed to handle RADseq data, the newest of which called AftrRAD, was just released this week and described in Molecular Ecology Resources.
The lead author on the AftrRAD paper is Dr. Mike Sovic, who just so happens to be down the hall from me in the department of Evolution, Ecology, and Organismal Biology here at Ohio State. In addition to being incredibly knowledgeable about all things RADseq, Mike is genuinely accessible and always willing to apply his experience to others’ scientific challenges. He was kind enough to sit down and answer some questions about AftrRAD and the current state of RADseq: Continue reading →

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Life, death, and DNA methylation

Posted on 3 Feb, 2015 by Noah Snyder-Mackler

“My biological clock is TICKING LIKE THIS!” – My Cousin Vinny


You have a molecular clock ticking inside of you and, if you read it properly, it can predict how much longer you will live. Want to know how to read it? Well, grab your DNA methylation profiler of choice, measure the percent of your genome that is methylated at these 353 CpG sites, and then just go use this online calculator*. Go ahead. Calculate it. I’ll wait…
Continue reading →

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If a tree falls in a forest and no one is around to hear it, does it make a sound?*

Posted on 2 Feb, 2015 by Melissa DeBiasse

Norvin Green State Forest in New Jersey. Photo from Wikipedia

Norvin Green State Forest in New Jersey. Photo from Wikipedia


[We want to know what you think! Please click on the link at the bottom of the post to complete a short survey and/or share your thoughts about the publishing process in the comments section below]
For better or worse, as scientists, our success depends not only on the merit of our work at face value, but also on where we publish and how our work is received after it is published- if a scientist discovers something new and exciting but no one cites the paper, does it matter?
Although journal impact factors** have been shown to be a poor predictor of the success of any given paper (Wang et al. 2013), in the hopes that his or her paper will reach a wide audience and be highly cited, scientists often strive to publish their work in the most prestigious journal possible. Furthermore, because universities and agencies consider journal impact factors when making hiring, promotion, and funding decisions (Adam 2002, Smith 2006), the quality of the journals in which you publish matters in addition to the quantity of papers you publish.
Another element scientists must consider when choosing where to send a paper is the length of time between manuscript submission and publication. Publications are our currency and as an early career scientist working to build my CV, I appreciate the challenge of deciding between submitting to a solid journal you’re confident will accept your manuscript quickly versus submitting to a more prestigious journal, risking a rejection and potentially increasing the length of time before your work gets published (and cited!). Needless to say, deciding where to submit a manuscript is an important decision. Continue reading →

Posted in career, funding, Impact Factors, peer review, science publishing | 1 Comment

Why is science publishing so damn expensive?

Posted on 2 Feb, 2015 by Tim Vines

from http://pixabay.com/static/uploads/photo/2014/08/30/11/10/coins-431537_640.jpg
I read this article today. It kicks off with a familiar complaint about the cost of journal subscriptions:

Taxpayers fund a lot of the science that gets done, academics (many of whom are also funded by public money) peer review it for free, and then journals charge users (again, many of whom paid for the science in the first place!) ludicrous sums of money to view the finished product.

The article then goes on to suggest that Open Access is the answer, on the grounds that at least the science is then available to everyone. This is a common line of argument, but it glosses over the fact that OA journals charge a similar amount per manuscript to make their papers public – except it’s authors that are paying and not libraries.
So why is science publishing so expensive? Non-profit OA journals like PLoS ONE are devoted to reducing the cost of science publishing, so why hasn’t the OA fee at these journals been beaten down to zero?
The simple answer is that quality peer review costs money. As has been regularly pointed out, the reviewers and editors are largely free. However, the managing editors, editorial office staff, and the building they sit in are not. Editorial offices would barely be needed if authors always followed the author guidelines, if editors were able to spread the reviewer workload fairly and always to the right people, if reviewers quickly agreed and then returned high quality reviews, and everyone was fair, honest and objective all the time. In this peer review Utopia, the system would more or less run itself.
In the real world, running an efficient review process takes a lot of time and money*. The editorial office has to make sure that submissions are ready for review, check reviewers for conflicts of interest, resolve identity issues, and answer a few hundred emails per day. The managing editors monitor all papers in review and keep the process moving along. They also check over all decisions, confer with editors on issues arising, and ensure that accepted manuscripts comply with journal policies. Constant vigilance for misconduct is required. Doing all this quickly (as is now expected) takes even more effort.
So, next time you’re watching someone get upset about the high cost of science publishing, check whether they’re being chased for an overdue review or for better quality figures. If they are, they’re adding to the bill.
*journals also have to take care of typesetting, web-hosting, search tools and so on. See this list.

Posted in peer review, science publishing | 10 Comments

From crocodiles to coconuts

Posted on 30 Jan, 2015 by Stacy Krueger-Hadfield

The first plant trypanosomatids were discovered in plant tissues over 100 years ago, but we know very little about their biology, life cycle or how they have adapted to life inside plants.
Jaskowska et al. (2015) provide a review of Phytomonas parasites and our current state of knowledge in light of the release of the first genomes in this genus.

Phytomonas © www.cas.cz

Phytomonas © www.cas.cz


They highlight some recent genome-wide analyses identified several aspartyl proteases, which are known to be secreted by plant pathogenic fungi.  But, these proteases were absent from the trypanosomatids that infect animals.  Future comparisons between plant and animal trypanosomatids may help elucidate the evolution of cell surfaces for plant-adapted and mammalian-adpated parasites.
With genomic resources it will be possible to explore the huge morphological diversity exhibited in Phytomonas species. Do morphological differences represent different life cycle stages (i.e., different selection pressures in discrete host environments as found in other trypanosomatids) or something adaptive and important to virulence within plants?
Comparative genomics will shed light on the evolution of these organisms that inhabit such a diverse

spectrum … from crocodiles to coconuts.

Jaskowska E, Butler C, Preston G, Kelly S (2015) Phytomonas: Trypanosomatids Adapted to Plant Environments. PLoS Pathog 11(1): e1004484. doi:10.1371/journal.ppat.1004484

Posted in adaptation, Coevolution, evolution, genomics, natural history | Leave a comment

Discordance in ancestry inference using human mtDNA and autosomes

Posted on 29 Jan, 2015 by Arun Sethuraman

Mitochondrial haplotypes have been used extensively over the last few decades for inference of a population structure in humans. Key findings from these studies include what has come to be known as the “Mitochondrial Eve” hypothesis (see the controversial Cann, Stoneking, and Willson (1987), subsequent reviews by Templeton (2002), Stoneking (1997)), numerous studies on the identification of mitochondrial haplogroups (for a complete list see, van Oven and Kayser (2009) – http://www.phylotree.org/), and the basis for several commercially available ancestry inference kits.

mtDNA-haplogroup membership might not be associated with autosomal ancestry proportions. Figure 5 from Emery et al. (2015)


In a recent study, Emery et al. (2015) compared estimates of global ancestry using autosomes and mtDNA haplogroups, and report discordance between ancestry inferred using mtDNA haplogroups and their `true’ continental-ancestry proportion. The authors mined the HGDP-CEPH, and the 1000 Genome Project data to analyze 28 diagnostic SNP’s for mtDNA haplotyping, and >650k SNP’s for autosomal continental-ancestry determination using ADMIXTURE (Alexander et al. 2009). They further determined the correlation between the two using a multinomial logistic regression model.
Key findings from the study include (1) more than one unique mtDNA haplogroup in most populations, (2) less information for inferring individual ancestry from mtDNA haplogroups, (3) high misclassification rates of continental-ancestry using mtDNA, and (4) low association between ancestry determined by mtDNA haplogroups and autosomes. As the authors rightly state,

Overall, our results question the validity of making anything but fairly crude inferences of continental ancestry on the basis of most mtDNA lineage tests. The limitations of lineage-based ancestry inference should be acknowledged by researchers and made explicit to consumers of commercial ancestry-testing products.

References:
Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup, Emery, Leslie S. et al. (2015) The American Journal of Human Genetics http://dx.doi.org/10.1016/j.ajhg.2014.12.015

Posted in genomics, population genetics | Tagged , | Leave a comment

Estimating the ticks and tocks of molecular clocks

Posted on 28 Jan, 2015 by Rob Denton

clock
Like many undergraduate students, I learned about the linear, universal molecular clock: the homogeneous rate of nucleotide change over time. When I sat down to actually do analyses of molecular data, I was confounded by the array of options to treat DNA sequences with a molecular clock. Relaxed clock? Strict clock? Local clock? I had no idea what was going on.

With the growing amount of sequence data, the performance of molecular-clock analyses will increasingly rely on rigorous model selection and the identification of accurate, informative calibrations.

Ho and Duchêne have recently provided a nice, practical review for choosing methods to apply molecular clocks to sequence data. Even though some molecular clock parameters are reduced to a single check box in some buried software menu, the consequences of not considering your options can lead to significant error in the estimation of evolutionary timescales. Using this review, you should be able to make an informed choice based on your taxa, question, data set, and evolutionary time frame.
Ho S.Y.W. & Duchêne S. (2014). Molecular-clock methods for estimating evolutionary rates and timescales, Molecular Ecology, 23 (24) 5947-5965. DOI: http://dx.doi.org/10.1111/mec.12953

Posted in evolution, Molecular Ecology, the journal, mutation, software | Tagged | Leave a comment