Genomics of Hybridization – Part II, Top three of 2015

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population of Cyprinodon diabolis (census size:35-548 in Devil’s Hole, Nevada).

Cyprinodon (pupfish) species across the Death Valley. Image courtesy:

Using ddRADSeq to genotype 56 individuals across 13000 loci, Martin et al. determined that five populations of Cyprinodon are structured, and individual populations harbored up to 40-fold lower genetic diversity than coastal populations in the clade.
Dating their emergence to around 10,000 ybp, with the confidence interval centered around the last flooding of the Death Valley, their study also determined that a much more recent separation of the five populations (around 200 ybp), dating to the Great Flood of 1862. Interestingly, their study also reports recent gene flow between C. diabolis, C. amargose and C. pectoralis using analysis of admixture, and D-statistics. Significant gene flow between these populations was also estimated by TreeMix analyses.
With surprising levels of morphological diversification in C. diabolis (>5 times that of other Cyprinodon species in the Death Valley), Martin et al’s study points to how despite multiple extinction events, frequent dispersal over thousands of years from multiple populations
may have contributed to concurrent genomic diversity, phenotypic diversification, adaptation, and survival.

Combined with the 60 000 year age of Devils Hole, this suggests that pupfish extinction and gene flow may have happened many times before in this unique habitat and that diabolis may not be the first pupfish population to have survived there. Protecting the connectivity of this region will be essential for this cycle of rebirth to continue.

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth, Martin et al. (2016). Proceedings of the Royal Society B DOI:10.1098/rspb.2015.2334
Also, following Rob and Melissa‘s leads, here were my top 3 posts from 2015!

1) LaTeX hacks to save your life:
I wrote this post to stress the ease with which LaTeX can now be incorporated into your daily academic writing routine. What with numerous great tools out there (eg. Overleaf, PanDoc), I highly recommend that you consider using LaTeX for your publications! But then again, no Word Processor/Type Setter is without its fair share of pros and cons. From a recent infographic (thanks to Rogier Kievit @rogierK), here seems to be the general consensus on using LaTeX.

So perhaps for your own sanity, and that of your co-authors, it would be best to establish what word processor/typesetter would work best for collaborative work beforehand. As Rogier puts it, “They’re all awful”.
2) Migration Circos plots in R:
I’m still twiddling my thumbs for this post to set a new trend for forthcoming papers on visualizing migration patterns. As our fellow blogger, Rob wrote: “beautiful visuals that I love but will likely be hated by a coauthor”. Do I see a trend here (cue my LaTeX post above…)

3) F-Statistics Manhattan Plots in R:
While this post focused on a very simple example, I think that with the wide popularity of utilizing F-statistics (and other similar differentiation measures) to determine so called “outlier” loci, and the ease with which one can visualize them in R, I hope to write some future posts on bettering these. Feel free to leave your comments on what you’d like to see added to these plots!
Here’s looking forward to a great 2016!

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