Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Background
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.

Results
We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.

Conclusions
The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.

Federico Abascal†, André Corvelo†, Fernando Cruz†, José L. Villanueva-Cañas, Anna Vlasova, Marina Marcet-Houben, Begoña Martínez-Cruz, Jade Yu Cheng, Pablo Prieto, Víctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frias, Paolo Ribeca, Salvador Capella-Gutiérrez, José M. Rodríguez, Francisco Câmara, Ernesto Lowy, Luca Cozzuto, Ionas Erb, Michael L. Tress, Jose L. Rodriguez-Ales, Jorge Ruiz-Orera, Ferran Reverter, Mireia Casas-Marce, Laura Soriano, Javier R. Arango, Sophia Derdak, Beatriz Galán, Julie Blanc, Marta Gut, Belen Lorente-Galdos, Marta Andrés-Nieto, Carlos López-Otín, Alfonso Valencia, Ivo Gut, José L. García, Roderic Guigó, William J. Murphy, Aurora Ruiz-Herrera, Tomas Marques-Bonet, Guglielmo Roma, Cedric Notredame, Thomas Mailund, M. Mar Albà, Toni Gabaldón, Tyler Alioto and José A. Godoy

Genome Biology201617:251
DOI: 10.1186/s13059-016-1090-1](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1090-1)

Selling my first book

Thursday evening last week I got an email from apress.com about my Functional Programming in R book and whether I would be interested in finding a publisher for it. It is already published on leanpub, Amazon and iBooks, but it has never seen a proper editor, and I would love to see it in print, so I wrote back that I would love to hear more.

I got a little more info Friday and was asked for a PDF of the book. I sent that but also the PDF for my Data Science in R book, mentioning that this book is longer and selling better.

Later Friday evening I got an offer for the data science book that I accepted. They are still interested in the functional programming book, but I had some suggestions for how it could be expanded and such, so they want to think a little more about that. The thinking time also gives me some time to judge the experience with editing the first book.

Because I’m selling Data Science in R, it will no longer be online. Not until Apress has made an ebook, at least. I’ve pulled it down from Amazon already, I’m trying to figure out how to remove it from iBooks now, and I will remove it from Leanpub afterwards. If anyone knows how to pull down a book from iBooks, please let me know.

I wrote that I would pull the book offline on twitter and Facebook yesterday, and since I’ve sold a lot of copies. I guess to people who want the book before it goes offline. Thanks for that, guys.

Rplot.png

It will still be available there a few hours more, but it is going down tonight.

Functional Programming will stay online until I figure out what will happen with it, and of course so will Object-oriented Programming in R, which I’m still working on.

I haven’t written on it the last two weeks. I’ve had some other things to work on and I’m a little stuck trying to think of a good example of where you would use refinement of interfaces, but I hope to have the next chapter finished in a week or so.