Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome
María Muñoz-Amatriaín , Stefano Lonardi , MingCheng Luo , Kavitha Madishetty , Jan Svensson , Matthew Moscou , Steve Wanamaker , Tao Jiang , Andris Kleinhofs , Gary Muehlbauer , Roger Wise , Nils Stein , Yaqin Ma , Edmundo Rodriguez , Dave Kudrna , Prasanna R Bhat , Shiaoman Chao , Pascal Condamine , Shane Heinen , Josh Resnik , Rod Wing , Heather N Witt , Matthew Alpert , Marco Beccuti , Serdar Bozdag , Francesca Cordero , Hamid Mirebrahim , Rachid Ounit , Yonghui Wu , Frank You , Jie Zheng , Hana Šimková , Jaroslav Doležel , Jane Grimwood , Jeremy Schmutz , Denisa Duma , Lothar Altschmied , Tom Blake , Phil Bregitzer , Laurel Cooper , Muharrem Dilbirligi , Anders Falk , Leila Feiz , Andreas Graner , Perry Gustafson , Patrick Hayes , Peggy Lemaux , Jafar Mammadov , Timothy Close
doi: http://dx.doi.org/10.1101/018978

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, since only 6,278 BACs in the physical map were sequenced, detailed fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15,622 BACs representing the minimal tiling path of 72,052 physical mapped gene-bearing BACs. This generated about 1.7 Gb of genomic sequence containing 17,386 annotated barley genes. Exploration of the sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high rates of recombination, there are also gene-dense regions with suppressed recombination. Knowledge of these deviant regions is relevant to trait introgression, genome-wide association studies, genomic selection model development and map-based cloning strategies. Sequences and their gene and SNP annotations can be accessed and exported via http://harvest-web.org/hweb/utilmenu.wc or through the software HarvEST:Barley (download from harvest.ucr.edu). In the latter, we have implemented a synteny viewer between barley and Aegilops tauschii to aid in comparative genome analysis.

A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
Hang Zhou , Sile Hu , Rostislav Matveev , Qianhui Yu , Jing Li , Philipp Khaitovich , Li Jin , Michael Lachmann , Mark Stoneking , Qiaomei Fu , Kun Tang
doi: http://dx.doi.org/10.1101/018929

The spatiotemporal distribution of recent human adaptation is a long standing question. We developed a new coalescent-based method that collectively assigned human genome regions to modes of neutrality or to positive, negative, or balancing selection. Most importantly, the selection times were estimated for all positive selection signals, which ranged over the last half million years, penetrating the emergence of anatomically modern human (AMH). These selection time estimates were further supported by analyses of the genome sequences from three ancient AMHs and the Neanderthals. A series of brain function-related genes were found to carry signals of ancient selective sweeps, which may have defined the evolution of cognitive abilities either before Neanderthal divergence or during the emergence of AMH. Particularly, signals of brain evolution in AMH are strongly related to Alzheimer’s disease pathways. In conclusion, this study reports a chronological atlas of natural selection in Human.

Theoretical consequences of the Mutagenic Chain Reaction for manipulating natural populations
Robert Unckless , Philipp Messer , Andrew Clark
doi: http://dx.doi.org/10.1101/018986

The use of recombinant genetic technologies for population manipulation has mostly remained an abstract idea due to the lack of a suitable means to drive novel gene constructs to high frequency in populations. Recently Gantz and Bier showed that the use of CRISPR/Cas9 technology could provide an artificial drive mechanism, the so-called Mutagenic Chain Reaction (MCR), which could lead to rapid fixation of even a deleterious introduced allele. We establish the equivalence of this system to models of meiotic drive and review the results of simple models showing that, when there is a fitness cost to the MCR allele, an internal equilibrium exists that is usually unstable. Introductions must be at a frequency above this critical point for the successful invasion of the MCR allele. These modeling results have important implications for application of MCR in natural populations.

Driven to Extinction: On the Probability of Evolutionary Rescue from Sex-Ratio Meiotic Drive
Robert Unckless , Andrew Clark
doi: http://dx.doi.org/10.1101/018820

Many evolutionary processes result in sufficiently low mean fitness that they pose a risk of species extinction. Sex-ratio meiotic drive was recognized by W.D. Hamilton (1967) to pose such a risk, because as the driving sex chromosome becomes common, the opposite sex becomes rare. We expand on Hamilton’s classic model by allowing for the escape from extinction due to evolution of suppressors of X and Y drivers. We explore differences in the two systems in their probability of escape from extinction. Several novel conclusions are evident, including a) that extinction time scales approximately with the log of population size so that even large populations may go extinct quickly, b) extinction risk is driven by the relationship between female fecundity and drive strength, c) anisogamy and the fact that X and Y drive result in sex ratios skewed in opposite directions, mean systems with Y drive are much more likely to go extinct than those with X drive, and d) suppressors are most likely to become established when the strength of drive is intermediate, since weak drive leads to weak selection for suppression and strong drive leads to rapid extinction.