Sugar Pine, Oil on Canvas, 2002, by Dean Davis. Davis is a retired US Forest Service employee who spent 34 years with the Region 5 Genetics team. This painting was based on a tree on Thompson Ridge in an area heavily blighted by White Pine Blister Rust near the location of many of the initial WPBR resistance selections in the 1950s and 60s. In this issue of GENETICS, Stevens et al. report the sequencing, assembly, and annotation of the sugar pine genome as well as the linkage of the major resistance locus Cr1 to genomic scaffolds. See Stevens et al.

Check out the December issue of GENETICS by looking at the highlights or the full table of contents!

ISSUE HIGHLIGHTS

This Month’s Centennial Articles

Edward East on the Mendelian basis of quantitative trait variation, pp. 1321-1323

Michael Turelli

Reviews editor Michael Turelli introduces Edward East’s 1916 Classic on the Mendelian basis of a continuously varying phenotype. This work exquisitely unified environment effects and polygenic inheritance by examining crosses between inbred lines of Nicotiana longiflora with markedly different corolla lengths

Paul Nurse and Pierre Thuriaux on wee mutants and cell cycle control, pp. 1325-1326

Andrew Murray

Associate Editor Andrew Murray introduces the 1980 Classic by Nurse and Thuriaux that identified a central and conserved component of cell cycle control. The results of their fission yeast screen for small (wee) mutants suggested Cdc2 was a critical regulator of cell division and Wee1 was a dosage-dependent inhibitor of Cdc2 activity

The full breadth of Mendel’s genetics, pp. 1327-1336

Peter J. van Dijk and T. H. Noel Ellis

Gregor Mendel’s fame is based on his experiments in pea plants (Pisum), published 150 years ago. Curiously, Mendel’s later studies on Hieracium (hawkweed) are usually seen as a frustrating failure, because it is assumed that they were intended to confirm the segregation ratios he found in Pisum, while it is now known Hieracium species mostly reproduce by means of clonal seeds. Peter J. van Dijk and T. H. Noel Ellis show that this assumption arises from a misunderstanding that could be explained by a missing page in Mendel’s first letter to Carl Nageli.

A bibliometric history of the journal GENETICS, pp. 1337-1342

Natalie Telis, Benjamin V Lehmann, Marcus W. Feldman, and Jonathan K. Pritchard

In the centennial year of GENETICS, Telis et al. quantify the remarkable shifts in genetic research through textual analysis of publications. The authors characterize changes in the focus of genetic research by studying abstracts and titles of articles published since 1916 in GENETICS. They document a massive expansion in publications in the journal, beginning in the 1950s, and accelerating in the 1980s, as genetic research expanded globally from a few initial locations. They also describe changes in word-usage over time, reflecting evolving research interests, methods and organisms.

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Maternal MEMI promotes female melosls II In response to fertilization In Caenorhabditis elegans, pp. 1461-1477

Maryam Ataeian, Justus Tegha-Dunghu, Donna G. Curtis, Ellen M. E. Sykes, Ashkan Nozohourmehrabad, Megha Bajaj, Karen Cheung, and Martin Srayko

In most animals, female meiosis completes only after fertilization. In Caenorhabditis elegans, fertilization is required to initiate female meiosis II, but it is unclear how the oocyte “senses” sperm entry. Ataeian et al. identify an oocyte-specific factor that is required for the female meiosis II program. Using a sensitive genetic screen, they also identify a sperm-specific phosphatase that could be part of the elusive signal that triggers meiosis II.

Integrated post-GWAS analysis sheds new light on the disease mechanisms of schizophrenia, pp. 1587-1600

Jhih-Rong Lin, Ying Cai, Quanwei Zhang, Wen Zhang, Ruben Nogales-Cadenas, and Zhengdong D. Zhang

Although genome-wide association studies (GWAS) have successfully identified many schizophrenia-associated common variants, it is difficult to use GWAS signals alone to pinpoint the underlying true risk genes. Lin et al. developed a general computational framework for post-GWAS analysis and identified 132 putative schizophrenia risk genes associated with GWAS loci. Involved in distinct biological processes, these genes show distinctive temporal expression patterns and play specific biological roles during brain development.

Stochasticity in the genotype-phenotype map: implications for the robustness and persistence of bet-hedging, pp. 1523-1539

Daniel Nichol, Mark Robertson-Tessi, Peter Jeavons, and Alexander R.A Anderson

Stochastic variation in phenotypes, or bet-hedging, can serve as a survival mechanism in unpredictable environments. In isogenic bacterial populations, dormant ‘persisted cells emerge stochastically, buffering the population from extinction during antibiotic therapy. Nichol et al. introduce a mathematical model to demonstrate that the evolutionary fate of this phenomenon is dependent on the structure of the molecular networks that drive it. Critically, they find the genotype-phenotype map is key in predicting how bet-hedging is lost through natural selection, and in designing therapeutic strategies to overcome bet-hedging-driven drug resistance.

Genetics of skeletal evolution in unusually large mice from Gough Island, pp. 1559-1572

Michelle D. Parmenter, Melissa M. Gray, Caley A. Hogan Irene N. Ford, Karl W. Broman Christopher J. Vinyard, and Bret A. Payseur

Organisms on islands often undergo rapid morphological evolution, but the genetic basis of this conspicuous pattern of evolutionary change remains poorly understood. Gough Island provides a striking example, harboring the largest wild house mice on record. The authors used this unique population to dissect the genetics of skeletal evolution associated with island colonization. They identified loci responsible for global expansion of the skeleton and shape changes in the skull and limbs, positioning Gough Island mice as a model system for understanding rapid evolution in the wild.

Evolution of the genotype-to-phenotype map and the cost of pleiotropy in mammals, pp. 1601-1612

Arthur Porto, Ryan Schmelter, John L. VandeBerg, Gabriel Marroig, and James M. Cheverud

The genetic architecture of traits holds important microevolutionary consequences. Yet, studies comparing genetic architecture across species are rare, and discussions of the evolution of genetic systems hinge on theoretical arguments rather than empirical evidence. Using laboratory populations of opossums and mice, Porto et al. look at the evolution of the genetic architecture of craniofacial traits. These species diverge in the genetic architecture of cranial traits, suggesting that genotype-to-phenotype maps can change even when species share most of their genes. This highlights the context dependency of gene effects and is relevant to current discussions concerning the cost of pleiotropy.

Detecting sources of transcriptional heterogeneity in large-scale RNA-Seq data sets, pp. 1391-1396

Brian C. Searle, Rachel M. Gittelman, Ohad Manor, and Joshua M. Akey

Gene expression levels are dynamic molecular phenotypes that respond to biological, environmental, and technical perturbations. Searle et al. develop a novel method for discovering transcriptional signatures and apply it to the Genotype-Tissue Expression (GTEx) dataset. The method identified many factors contributing to expression heterogeneity, including collection center and ischemia time, and can statistically stratify these factors by effect strength. Strikingly, transcriptional expression in blood alone could help predict heart disease and stroke in some patients.

Sequence of the sugar pine Megagenome, pp. 1613-1626

Kristian A. Stevens, Jill L. Wegrzyn, Aleksey Zimin, Daniela Puiu, Marc Crepeau, Charis Cardeno, Robin Paul, Daniel Gonzalez-Ibeas, Maxim Koriabine, Ann E. Holtz-Morris, Pedro J. Martinez-Garcia, Uzay U. Sezen, Guillaume Marfais, Kathy Jermstad, Patrick E. McGuire, Carol A. Loopstra, John M. Davis, Andrew Eckert, Pieter de Jong, James A. Yorke, Steven L. Salzberg, David B. Neale, and Charles H. Langley

The sugar pine has the largest genome assembled to date, with nearly 50% more DNA than the current record holder. It is also the first representative of the Pinus subgenus Strobus (white pines) to be sequenced. Stevens et al. describe the first draft of the reference genome. The data reveal the genomic origins of the major dominant gene for resistance to the devastating pathogen white pine blister rust, including a promising candidate gene.

Reconstructing demography and social behavior during the neolithic expansion from genomic diversity across Island Southeast Asia, pp. 1495-1506

Franfois Vallee, Aurelien Luciani, and Murray P Cox

The farming revolution drove human groups from mainland Asia into the islands of Southeast Asia. Key features of this migration remain poorly understood. An ‘agent based’ model was built to simulate human interactions across this region from the Neolithic period to the present. The genomes of 2,299 Island Southeast Asians showed that greater migration was more influential than higher birth rates, that offspring preferentially resulted from Asian women and Papuan men, and that individuals with Asian ancestry were likely distributed across parts of western Island Southeast Asia before the farming expansion.

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