Automatic differentiation in R

I’ve been working on a small R package that does automatic differentiation. It takes a function that computes an arithmetic expression as input and outputs a function that computes the derivative of the expression. You can check it out on GitHub.

I got inspired to write it a few weeks ago when one of our PhD students gave a talk on automatic differentiation. I didn’t attend the talk, but remembered playing around with it as a meta-program in C++ templates ages ago. Now that I am writing a book on meta-programming in R, I thought it would be a cool example to include there—and I have included it in the chapter I just finished. I gave it to a student as a project, but I am not patient enough to let someone else program it, so I have also done it myself.

It is actually a nice exercise to do. Differentiation is pretty simple to program. You just follow the rules you learned in calculus for the arithmetic operations and apply the chain rule for function calls. Nothing complicated there. To make it a meta-program in R, though, you need to know how to work with expressions and how to inspect functions to correctly apply the chain rule. While this is not particularly hard, this example is great at getting around the various corners of working with expressions.

Unless I think up something else to add, I think the meta-programming book will be done after one more chapter. After that, I will take a short break from the R books. I will get back to them in a few weeks, I imagine, but I have a few other projects to focus on before then. Including proof-reading my data science book—that should arrive next week and then I have to get through it in a week before it goes to the printer.

I haven’t decided yet what the next R book should be. I’m thinking either functional data structures and algorithms or embedded domain-specific languages. Let me know what you think.

admixturegraph: An R Package for Admixture Graph Manipulation and Fitting

K Leppälä, SV Nielsen, and T Mailund

Preprint at Bioinformatics

Admixture graphs generalise phylogenetic trees by allowing genetic lineages to merge as well as split. In this paper we present the R package admixturegraph containing tools for building and visualising admixture graphs, for fitting graph parameters to genetic data, for visualising goodness of fit, and for evaluating the relative goodness of fit between different graphs.

Evidence that the rate of strong selective sweeps increases with population size in the great apes

K Nam, K Munch, T Mailund, A Nater, MP Greminger, M Krützenc, T Marquès-Bonet, and MH Schierup

New paper out in PNAS

The rate of genomic adaptation is determined by the rate of environmental change, the availability of beneficial mutations, and the efficiency of positive selection. The relative importance of these factors has been actively discussed. We address the questions using whole genome sequences of great apes, which have very different population sizes whereas their genomic architectures are highly similar. We infer that the impact of selection on the genomic diversity of a species increases with the effective population size, most likely due to the differential influx rate of beneficial mutations. This explanation is, among other possibilities, expected if adaptive evolution is limited by the waiting time for new favorable mutations in great apes.

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)

A genomic history of Aboriginal Australia

Out in Nature now

Anna-Sapfo Malaspinas, Michael C. Westaway, Craig Muller, Vitor C. Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Y. Cheng, Jacob E. Crawford, Tim H. Heupink, Enrico Macholdt, Stephan Peischl, Simon Rasmussen, Stephan Schiffels, Sankar Subramanian, Joanne L. Wright, Anders Albrechtsen, Chiara Barbieri, Isabelle Dupanloup, Anders Eriksson, Ashot Margaryan, Ida Moltke, Irina Pugach, Thorfinn S. Korneliussen, Ivan P. Levkivskyi, J. Víctor Moreno-Mayar, Shengyu Ni, Fernando Racimo, Martin Sikora, Yali Xue, Farhang A. Aghakhanian, Nicolas Brucato, Søren Brunak, Paula F. Campos, Warren Clark, Sturla Ellingvåg, Gudjugudju Fourmile, Pascale Gerbault, Darren Injie, George Koki, Matthew Leavesley, Betty Logan, Aubrey Lynch, Elizabeth A. Matisoo-Smith, Peter J. McAllister, Alexander J. Mentzer, Mait Metspalu, Andrea B. Migliano, Les Murgha, Maude E. Phipps, William Pomat, Doc Reynolds, Francois-Xavier Ricaut, Peter Siba, Mark G. Thomas, Thomas Wales, Colleen Ma’run Wall, Stephen J. Oppenheimer, Chris Tyler-Smith, Richard Durbin, Joe Dortch, Andrea Manica, Mikkel H. Schierup, Robert A. Foley, Marta Mirazón Lahr, Claire Bowern, Jeffrey D. Wall, Thomas Mailund, Mark Stoneking, Rasmus Nielsen, Manjinder S. Sandhu, Laurent Excoffier, David M. Lambert & Eske Willerslev

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated 10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.