This Month's Centennial Articles
A new century of GENETICS, pp. 1–2
Editor-in-Chief Mark Johnston launches the second century of GENETICS and our year-long centennial celebrations.
Sewall Wright on evolution in Mendelian populations and the “Shifting Balance,” pp. 3–4
Nicholas H. Barton
Associate Editor Nicholas H. Barton introduces Sewall Wright’s 1931 GENETICS Classic, Evolution in Mendelian populations, a remarkable synthesis of population genetics and its application, presenting, in essentially its modern form, the population genetics of allele frequency evolution.
Theodosius Dobzhansky on hybrid sterility and speciation, pp. 5–7
Jerry A. Coyne
Jerry A. Coyne introduces Theodosius Dobzhansky’s 1936 GENETICS Classic, Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Recognizing that explaining the existence of species was identical to explaining the origin of “isolating mechanisms” that prevent gene flow, Dobzhansky’s 1936 work was the first concerted effort to work out the genetic changes producing a puzzling reproductive barrier: hybrid sterility.
Admixture models and the breeding systems of H. S. Jennings: a GENETICS connection, pp. 9–13
Noah A. Rosenberg
The first population genetics work published in GENETICS was H.S. Jennings on The numerical results of diverse systems of breeding, the second article of the journal’s first issue. Associate Editor Noah A. Rosenberg describes how he and Amy Goldberg uncovered a surprising connection between their work on genetic admixture on the X chromosome and the 1916 article, showing how Jennings uncovered the X-chromosomal behavior of the Hardy-Weinberg model and anticipated questions of interest in modern admixture studies.
The centenary of Genetics: bridges to the future, pp. 15–23
Barry Ganetzky and R. Scott Hawley
In the first article published in the first issue of GENETICS, Calvin Bridges provided the world with evidence that genes lie on chromosomes and laid the groundwork for much of the century of genetic research that has followed. In this Perspectives article, Barry Ganetzky and R. Scott Hawley describe the lasting impact the work has had on modern research and how Bridges’ ideas have been built upon and refined.
The differences between cis- and trans-gene inactivation caused by heterochromatin in Drosophila, pp. 93–106
Yuriy A. Abramov, Aleksei S. Shatskikh, Oksana G. Maksimenko, Silvia Bonaccorsi, Vladimir A. Gvozdev, and Sergey A. Lavrov
The heterochromatin position-effect—in which a gene’s expression is disrupted by insertion into heterochromatin—remains enigmatic. The authors characterized position-effect variegation in a new Drosophila system using a high throughput approach. They found opposing effects on genes expression that varied at different developmental stages. Cis- repression near the new eu-heterochromatin border was independent of trans-inactivation of reporter genes on the homologous, non-rearranged chromosome, with distinct molecular features.
Spindle assembly and chromosome segregation requires central spindle proteins in Drosophila oocytes, pp. 61–75
Arunika Das, Shital J. Shah, Bensen Fan, Daniel Paik, Daniel J. DiSanto, Anna Maria Hinman, Jeffry M. Cesario, Rachel A. Battaglia, Nicole Demos, and Kim S. McKim
Oocytes segregate chromosomes in the absense of centrosomes, and the central spindle plays a conserved and critical role in this acentrosomal process. Das et al. investigate central spindle protein function in acentrosomal spindle assembly and chromosome segregation, identifying genes that interact with the Kinesin 6 Subito and the Chromosome passenger complex component Incenp. They also identify cytokinesis proteins and downstream effectors that are required for homologous chromosome bi-orientation at metaphase I. These results suggest a novel meiotic function for proteins normally involved in mitotic anaphase and cytokinesis.
Deep history of East Asian populations revealed through genetic analysis of the Ainu, pp. 261–272
Choongwon Jeong, Shigeki Nakagome, and Anna Di Rienzo
The Ainu descend from prehistoric Japanese hunter-gatherers. Jeong et al. use genome-wide variation data to show that they represent one of the deepest branches of human diversity in East Asia, basal to all present-day East Asian farmers. Interestingly, they do not detect signatures of a connection between the Ainu and Tibetans, rejecting a long-held hypothesis based on Y chromosome data. Unlike other East Asians, the Ainu are more closely related to northeast than central Siberians, suggesting a potential connection between the Ainu ancestors and Beringian populations, whose descendants became the first people of the Americas.
Genetical genomics of behavior: a novel chicken genomic model for anxiety behavior, pp. 327–340
Martin Johnsson, Michael J. Williams, Per Jensen, and Dominic Wright
The identification of genes responsible for behavioral variation has ramifications ranging from medical research to evolutionary theory on personality syndromes. To identify the genes underlying anxiety behaviors the authors used a combination of conventional and expression QTL analysis, and an advanced intercross between wild and domestic chickens. This approach yielded 10 potentially causal genes for anxiety that were also correlated with mouse anxiety behavior and human pyschiatric disorders, indicating the potentially translatable nature of genes underlying anxiety.
Gonadal mosaicism induced by chemical treatment of sperm in Drosophila melanogaster, pp. 157–174
Dan L. Lindsley, Robert W. Hardy, Pedro Ripoll, and Dart Lindsley
Newly induced mutations occasionally appear as mosaics in which only part of the animal expresses the mutation, complicating interpretation of genetic screens. Until now, it was unclear how the frequency and degree of gonadal mosaicism is determined following chemical mutagenesis in Drosophila. The authors show that DNA strands modified by alkylating agents are stable and mutagenic. Each replication of an alkylated strand can result in misreplication and a mutation-bearing daughter nucleus. Daughter nuclei subsequently replicate faithfully and their descendants comprise the embryonic syncytium, from which the gonadal progenitor nuclei are selected.
Genome-wide structural variation detection by genome mapping on nanochannel arrays, pp. 351–362
Angel C. Y. Mak, Yvonne Y. Y. Lai, Ernest T. Lam, Tsz-Piu Kwok, Alden K. Y. Leung, Annie Poon, Yulia Mostovoy, Alex R. Hastie, William Stedman, Thomas Anantharaman, Warren Andrews, Xiang Zhou, Andy W. C. Pang, Heng Dai, Catherine Chu, Chin Lin, Jacob J. K. Wu, Catherine M. L. Li, Jing-Woei Li, Aldrin K. Y. Yim, Saki Chan, Justin Sibert, Željko Džakula, Han Cao, Siu-Ming Yiu, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao, and Pui-Yan Kwok
Comprehensive whole genome structural variation detection is challenging using current approaches. Mak et al. show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for locally phased whole genome structural variation detection without sequencing. The authors generated genome maps from a trio from the 1000 Genomes Project and identified structural variations >5 kb in size. The individuals have many more structural variants than previously published, including some with the potential to disrupt gene function.
Identifying regulators of morphogenesis common to vertebrate neural tube closure and Caenorhabditis elegans gastrulation, pp. 123–139
Jessica L. Sullivan-Brown, Panna Tandon, Kim E. Bird, Daniel J. Dickinson, Sophia C. Tintori, Jennifer K. Heppert, Joy H. Meserve, Kathryn P. Trogden, Sara K. Orlowski, Frank L. Conlon, and Bob Goldstein
Neural tube defects (NTDs) are common and severe birth defects, yet the functions of most NTD genes are unknown. Sullivan-Brown et al. used Caenorhabditis elegans to study NTD gene homologs, finding sptf-3 and members of the WAVE complex were required for Caenorhabditis elegans gastrulation, a process that shares characteristics with vertebrate neural tube closure. Nckap1, a WAVE complex member, was also required for neural tube closure in Xenopus embryos. This work provides a new platform for studying the in vivo roles of NTD genes.
Rapid short-read sequencing and aneuploidy detection using MinlON Nanopore technology, pp. 37–44
Shan Wei and Zev Williams
MinION is a portable nanopore-based sequencer primarily designed for single-molecule sequencing of long DNA fragments (>6 kb). Wei and Williams describe a library preparation and data analysis method to enable rapid sequencing of short fragments (<1 kb) and demonstrated its clinical applicability by performing aneuploidy detection in prenatal and miscarriage samples, with sequencing in less than 4 hours. This broadens the application of MinION technology, making it a promising tool for applications that involve rapid short-read sequencing.
This Month in the American Journal of Human Genetics
Genomic signatures of selective pressures and introgression from archaic hominins at human innate immunity genes, Am. J. Hum. Genet. 97(5): 10.1016/j.ajhg.2015.11.014
Matthieu Deschamps, Guillaume Laval, Maud Fagny, Yuval Itan, Laurent Abel, Jean-Laurent Casanova, Etienne Patin, and Lluis Quintana-Murci
Adaptive variation in human toll-like receptors is contributed by introgression of Neandertal- and Denisovan-like haplotypes, Am. J. Hum. Genet. 97(5): 10.1016/j.ajhg.2015.11.015
Michael Dannemann, Aida M. Andres, and Janet Kelso
Throughout history, human evolution has been shaped by interactions with pathogens. Alleles conferring fitness most often arise from random mutation, but introgression of genomic material from archaic humans can provide a separate reservoir of protective variation. Now, using complementary approaches, Deschamps et al. and Dannemann et al. uncover signatures of selection and evidence of introgression from the Neanderthal and Denisovan genomes in human innate immunity genes. These findings suggest that admixture with archaic humans played a key role in shaping the modern human immune system. Of course, pathogens evolve quickly, and so it will be interesting to determine the modern-day function of these introgressed alleles.
In CBE — Life Sciences Education (LSE)
Preparing biology graduate teaching assistants for their roles as instructors: an assessment of institutional approaches, CBE-Life Sci. Educ. vol. 14(3) ar31
Elisabeth E. Schussler, Quentin Read, Gili Marbach-Ad, Kristen Miller, and Miriam Ferzli
Graduate students can get mixed messages about the importance of teaching; they are often told to limit the time devoted to teaching versus research, and at the same time encouraged to develop teaching skills for the future job market. To learn more about the types of teaching professional development offered, Schussler et al. 2015 surveyed graduate students from 71 different institutions. They found that graduates students were often dissatisfied with professional development that happened before the semester and focused simply on logistics, such as course policies. The authors recommend that institutions include training on pedagogy spaced throughout the academic year, and that faculty and senior graduate students observe new teaching assistants using established classroom observation protocols designed to improve and unify feedback.
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