ISSUE HIGHLIGHTS
Weak selection and protein evolution, pp. 15-31
Hiroshi Akashi, Naoki Osada, and Tomoko Ohta
The rapid proliferation of genome sequence data has renewed interest in the causes of molecular evolution. The authors review the basis of the "nearly neutral" theory of molecular evolution, which proposes that the interaction of genetic drift and weak natural selection is prevalent in genome evolution. They review abundant evidence from population genetic and comparative genomic analyses that supports weak selection, but they also discuss overlapping predictions from other models.
Mapping quantitative trait loci onto a phylogenetic tree, pp. 267-279
Karl W. Broman, Sungjin Kim, Śaunak Sen, Cécile Ané, and Bret A. Payseur
Mapping of quantitative trait loci (QTL) can be aided by considering multiple crosses among related taxa. That approach also offers the opportunity to identify the origin of a QTL allele on the phylogenetic tree. These authors describe a method for this kind of analysis and discuss experimental design issues for such endeavors. They explore the method's performance in computer simulations, and illustrate its use through application to data on HDL cholesterol from a set of four mouse intercrosses among five inbred strains.
Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae, pp. 147-160
Edith Cheng, Jessica A. Vaisica, Jiongwen Ou, Anastasia Baryshnikova, Yong Lu, Frederick P. Roth, and Grant W. Brown
This article illustrates the role DNA replication defects play in causing DNA breaks and chromosome rearrangements. Given the parallels between common fragile sites in yeast and human chromosomes, these findings should inform studies to identify genetic determinants of chromosome fragility in humans.
Ultraconserved elements in the human genome: Association and transmission analyses of highly constrained single-nucleotide polymorphisms, pp. 253-266
Charleston W. K. Chiang, Ching-Ti Liu, Guillaume Lettre, Leslie A. Lange, Neal W. Jorgensen, Brendan J. Keating, Sailaja Vedantam, Nora L. Nock, Nora Franceschini, Alex P. Reiner, Ellen W. Demerath, Eric Boerwinkle, Jerome I. Rotter, James G. Wilson, Kari E. North, George J. Papanicolaou, L. Adrienne Cupples, Genetic Investigation of Anthropometric Traits (GIANT) Consortium, Joanne M. Murabito, and Joel N. Hirschhorn
Ultraconserved elements in the human genome are thought to harbor important biological functions. However, their removal in mice is of little consequence. These investigators test the human consequences of sequence changes in ultraconserved sequences. They report that rare derived alleles of ultraconserved sequences are transmitted from heterozygous parents to offspring in an unbiased way. That would seem to rule out an immediately and strongly deleterious effect of the rare derived alleles.
Parallel genetic changes and nonparallel gene-environment interactions characterize the evolution of drug resistance in yeast, pp. 241-252
Aleeza C. Gerstein, Dara S. Lo, and Sarah P. Otto
The range of mutations required for adaptation to novel environments was determined by identifying the first mutations acquired by yeast during the evolution of resistance to the drug nystatin. The genomic scope for adaptation was found to be narrow: all lines acquired a mutation in one of four genes in the ergosterol biosynthetic pathway. Mutations in different genes have different tolerance to secondary environments, demonstrating that adaptation to one environment can lead populations down different evolutionary trajectories.
Gene discovery using mutagen-induced polymorphisms and deep sequencing: Application to plant disease resistance, pp. 139-146
Ying Zhu, Hyung-gon Mang, Qi Sun, Jun Qian, Ashley Hipps, and Jian Hua
This article describes a new approach to sequence-based positional cloning. Instead of using DNA sequence polymorphisms among different strains, the authors take advantage of polymorphisms induced during mutagenesis. The mutagen ethyl methanesulfonate (EMS) used in an enhancer screen generated enough new polymorphisms to allow mapping of the mutation conferring disease resistance at high temperature in Arabidopsis. The approach has advantages over conventional mapping strategies, particularly for identifying mutations causing subtle phenotypes or phenotypes modified by the genetic background.
The selfish Segregation Distorter gene complex of Drosophila melanogaster, pp. 33-53
Amanda M. Larracuente and Daven C. Presgraves
One of the most striking examples of meiotic drive is the result of the Segregation Distorter (SD) gene complex of Drosophila melanogaster. These authors review the established facts and lingering mysteries concerning the genetics, molecular biology, and evolution of SD.
Genetic and genomic toolbox of the chordate Ciona intestinalis, pp. 119-130
Alberto Stolfi and Lionel Christiaen
We launch the new Toolbox series (see Editorial in this issue) of review articles with one on the state-of-the-art of genetics of the ascidian Ciona intestinalis (sea squirt). The simplicity of its embryo permits analysis of chordate-specific developmental features, offering high resolution in both space and time. These properties and the wealth of genetic and genomic resources promise to launch ascidians as simple chordate models for research.
This Month's Perspectives
Reginald Crundall Punnett: First Arthur Balfour Professor of Genetics, Cambridge, 1912, pp. 3-13
A. W. F. Edwards
Punnett's square is familiar to beginning genetics students, but its creator is only dimly remembered as a collaborator of William Bateson and a substantial contributor to the establishment of modern genetics. This month's "Perspectives" recounts the story and work of Reginald Punnett, the first Professor of Genetics at the University of Cambridge, on the centenary of his appointment.
This Month in the American Journal of Human Genetics and G3: Genes|Genomes|Genetics
DUF1220 domain copy number implicated in human brain size pathology and evolution, Am. J. Hum. Genet. 91(2)
Laura J. Dumas, Majesta S. O'Bleness, Jonathan M. Davis,C. Michael Dickens, Nathan Anderson, Jonathon G. Keeney, Jay Jackson, Megan Sikela, Armin Raznahan, Jay Giedd, Judith Rapoport, Sandesh S. C. Nagamani, Ayelet Erez, Nicola Brunetti-Pierri, Rachel Sugalski, James R. Lupski, Tasha Fingerlin, Sau Wai Cheung, James M. Sikela
and
Evolutionary history and genome organization of DUF1220 protein domains, G3: Genes, Genomes, Genetics 2(9)
Majesta S. O'Bleness, C. Michael Dickens, Laura J. Dumas, Hildegard Kehrer-Sawatzki, Gerald J. Wyckoff, and James M. Sikela
Protein domains called DUF1220, which show the largest human lineage-specific increase in copy number of any protein coding region, are correlated with brain size in primates. Interestingly, microcephaly and macrocephaly map to regions of the genome that contain large families of DUF1220 domain containing genes. Dumas et al. report in this article in the AJHG that reduced DUF1220 copy number is associated with microcephaly, and that larger brain size is associated with increased DUF1220 copy number. A companion article in G3 reports the analysis of 41 animal genomes that provides the most complete account to date of the evolutionary history and genome organization of these domains that may play a role in determining brain size.
INFORMATION:
ABOUT GENETICS: Since 1916, GENETICS has covered high quality, original research on a range of topics bearing on inheritance, including population and evolutionary genetics, complex traits, developmental and behavioral genetics, cellular genetics, gene expression, genome integrity and transmission, and genome and systems biology. GENETICS, a peer-reviewed, peer-edited journal of the Genetics Society of America is one of the world's most cited journals in genetics and heredity.
ABOUT GSA: Founded in 1931, the Genetics Society of America (GSA) is the professional membership organization for scientific researchers, educators, bioengineers, bioinformaticians and others interested in the field of genetics. Its nearly 5,000 members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. GSA is dedicated to promoting research in genetics and to facilitating communication among geneticists worldwide through its conferences, including the biennial conference on Model Organisms to Human Biology, an interdisciplinary meeting on current and cutting edge topics in genetics research, as well as annual and biennial meetings that focus on the genetics of particular organisms, including C. elegans, Drosophila, fungi, mice, yeast, and zebrafish. GSA publishes GENETICS, a leading journal in the field and an online, open-access journal, G3: Genes|Genomes|Genetics. For more information about GSA, please visit www.genetics-gsa.org. Also follow GSA on Facebook at facebook.com/GeneticsGSA and on Twitter @GeneticsGSA.
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