Bears, perennial toppers of the ThreatDown list on The Colbert Report (copyright Comedy Central)
Are guide trees your Kryptonite? Break free with these new species delimitation methods! Picture from http://www.comicbookmovie.com/
The basic idea behind DISSECT is to sample trees in which each tip represents a single individual (or a cluster of individuals which definitely belong in one species), but replace the usual prior density on node heights with one which includes a spike near zero. The dimensionality of the parameter space is fixed, but nodes whose heights have a high posterior probability of being within the spike can be interpreted as ‘probably collapsed’
The analysis can be run in BEAST (version 1.8.1 and later) and Jones et al. provide a nice section describing the workflow of the analysis and some advice on how to set the parameters and priors.
The second paper, Yang and Ranala (2014) present an updated version of their program BPP which eliminates the user-defined guide tree in species delimitation and incorporates phylogenetic uncertainty of the gene trees in a Bayesian framework.
A novel MCMC proposal based on the nearest-neighbor interchange (NNI) algorithm for rooted trees is developed here to change the species tree topology, eliminating the need for a user-specified guide tree. The gene trees for multiple loci are altered in the proposal to avoid conflicts with the newly proposed species tree.
One potential drawback to the method is that it may not be practical for a large number of populations- computation time increases much more quickly with an increase in the number of populations than with an increase in the number of sequences per locus. Nevertheless, the introductions of DISSECT and new version of BPP are exciting steps forward in species delimitation and I am excited to see them tested on empirical systems by other researchers.
Jones, G., Aydin, Z., & Oxelman, B. (2014). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics, btu770. DOI: 10.1093/bioinformatics/btu770
Yang, Z., & Rannala, B. (2014). Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31 (12):3125-3135. DOI: 10.1093/molbev/msu279
© wikipedia
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.
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
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 bifurcata, and then contractions of the southern trailing range edge of the Boreal species Alaria esculenta and Semibalanus balanoides. © Nova Mieszkowska
Dr. Mike Sovic pondering the number of polymorphic loci in this beautiful vista
“My biological clock is TICKING LIKE THIS!” – My Cousin Vinny
Norvin Green State Forest in New Jersey. Photo from Wikipedia
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.
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
spectrum … from crocodiles to coconuts.
