Spotlight

A showcase of research and scholarship
in selected articles from 2015

2015/16
Editorial Board
Mark Johnston,
Editor-in-Chief
University of Colorado
School of Medicine
Tracey DePellegrin
Executive Editor
Cristy Gelling
Assistant Editor
Ruth Isaacson
Managing Editor
SENIOR EDITORS

Karen M. Arndt
University of Pittsburgh
Nick H. Barton
Institute of Science and
Technology Austria
Karl Broman
University of
Wisconsin-Madison
Gary A. Churchill
The Jackson Laboratory
Stanley Fields
University of
Washington
Audrey Gasch
University of
Wisconsin-Madison
Oliver Hobert
Columbia University
Mark Johnston
University of Colorado
School of Medicine
Terry R. Magnuson
University of North
Carolina at Chapel Hill
Michael W. Nachman
University of California,
Berkeley
Krista M. Nichols
NOAA Fisheries
Mark D. Rose
Princeton University
John C. Schimenti
Cornell University
John Wakeley
Harvard University
CELLULAR GENETICS

Bruce Beutler
The University of Texas
Southwestern Medical
Center

Sue Biggins
Fred Hutchinson Cancer
Research Center
Orna Cohen-Fix
NIDDK, National
Institutes of Health
Bob Goldstein
University of North
Carolina at Chapel Hill
David I. Greenstein
University of Minnesota
Joseph Heitman
Duke University
Medical Center
Daniel J. Lew
Duke University
Medical Center
Piali Sengupta
Brandeis University
Yongbiao Xue
Chinese Academy of
Sciences
COMPLEX TRAITS

Joshua M. Akey
University of Washington
Justin O. Borevitz
Australian National
University
Alain Charcosset
Institut National
de la Recherche
Agronomique
Stephen Chenoweth
The University of
Queensland
Dirk Jan de Koning
Swedish University of
Agricultural Sciences
Corbin D. Jones
University of North
Carolina at Chapel Hill
Thomas E. Juenger
University of Texas
Loeske E. B. Kruuk
University of Edinburgh
Krista M. Nichols
NOAA Fisheries
Andrew H. Paterson
University of Georgia
Katie Peichel
Fred Hutchinson
Cancer Research
Center

David W. Threadgill
Texas A&M University
Fred van Eeuwijk
Wageningen University
Jason B. Wolf
University of Bath
Naomi R. Wray
The University of
Queensland
Fei Zou
University of North
Carolina at Chapel Hill
DEVELOPMENTAL
AND BEHAVIORAL
GENETICS

Hugo J. Bellen
Baylor College of
Medicine

GENE EXPRESSION

James A. Birchler
University of Missouri
Michael Freitag
Oregon State University
Audrey Gasch
University of
Wisconsin-Madison
Pamela Geyer
University of Iowa
Michael Hampsey
Rutgers Robert Wood
Johnson Medical School
Alan G. Hinnebusch
NICHD, National
Institutes of Health
Ann Hochschild
Harvard Medical School

Giovanni Bosco
Geisel School of
Medicine at Dartmouth

Aaron P. Mitchell
Carnegie Mellon
University

Kym M. Boycott
CHEO Research
Institute

Craig S. Pikaard
Indiana University

Lynn Cooley
Yale University
Robert J. Duronio
University of North
Carolina at Chapel Hill

Oliver J. Rando
University of
Massachusetts
Medical School
Eric U. Selker
University of Oregon

David I. Greenstein
University of Minnesota

Nathan Springer
University of Minnesota

Marnie E. Halpern
Carnegie Institution for
Science

GENOME INTEGRITY
AND TRANSMISSION

Iswar K. Hariharan
University of California,
Berkeley
Abraham A. Palmer
University of Chicago
David M. Parichy
University of Washington
R. Scott Poethig
University of
Pennsylvania

Anne Britt
University of California,
Davis
Sharon E. Bickel
Dartmouth College
Monica P. Colaiácovo
Harvard Medical School
Nancy M. Hollingsworth
Stony Brook University

Trudi Schüpbach
Princeton University

Andreas Houben
Leibniz Institute of
Plant Genetics and
Crop Plant Research

William T. Sullivan
University of California,
Santa Cruz

Neil Hunter
University of California,
Davis

Meera V. Sundaram
University of
Pennsylvania

James R. Lupski
Baylor College of
Medicine

Mariana F. Wolfner
Cornell University

Jac A. Nickoloff
Colorado State
University
Steven J. Sandler
University of
Massachusetts
Jeff Sekelsky
University of North
Carolina at Chapel Hill
Shyam K. Sharan
NCI, National Institutes
of Health
GENOME AND
SYSTEMS BIOLOGY

Kirsten Bomblies
Harvard University
Charles Boone
University of Toronto
David A. Largaespada
University of Minnesota
Brian P. Lazzaro
Cornell University
Jeffery F. Miller
University of California,
Los Angeles
Alan Moses
University of Toronto
Andrew W. Murray
Harvard University

STATISTICAL
GENETICS AND
GENOMICS

EMPIRICAL
POPULATION
GENETICS

Eleazar Eskin
University of California,
Los Angeles

Daniel A. Barbash
Cornell University

Ina Hoeschele
Virginia Polytechnic
Institute and State
University
Christina Kendziorski
University of
Wisconsin-Madison

Kathryn M. Roeder
Carnegie Mellon
University

Santiago C. GonzálezMartínez
Forest Research
Centre (CIFOR-INIA)

Chiara Sabatti
Stanford University
Saunak Sen
University of Tennessee
Health Science Center
Eric A. Stone
North Carolina State
University
William Valdar
University of North
Carolina at Chapel Hill

Enrico G. Petretto
Duke-NUS Graduate
Medical School
Singapore

METHODS,
TECHNOLOGY, AND
RESOURCES

Lars M. Steinmetz
European Molecular
Biology Laboratory &
Stanford University

Matthew W. Hahn
Indiana University
Lynn B. Jorde
University of Utah
Charles H. Langley
University of California,
Davis
Jeffrey G. Lawrence
University of Pittsburgh
Brian P. Lazzaro
Cornell University
Leonie C. Moyle
Indiana University
John Novembre
University of Chicago

Charles Boone
University of Toronto

Bret A. Payseur
University of
Wisconsin-Madison

George M. Church
Harvard Medical School

Daven Presgraves
University of Rochester

Stanley Fields
University of
Washington

Outi Savolainen
University of Oulu

Norbert Perrimon
Harvard Medical School

Gary D. Stormo
Washington University
School of Medicine

Jeff Sekelsky
University of North
Carolina at Chapel Hill

David Valle
Johns Hopkins
University School of
Medicine

Jay Shendure
University of
Washington

Daniel F. Voytas
University of Minnesota

Deborah Charlesworth
University of Edinburgh
Anna Di Rienzo
University of Chicago

Norbert Perrimon
Harvard Medical School

Jay Shendure
University of
Washington

James J. Bull
University of Texas at
Austin

Neil Risch
University of California,
San Francisco

Nengjun Yi
University of Alabama
at Birmingham

Valerie Reinke
Yale University

David J. Begun
University of California,
Davis

David W. Threadgill
Texas A&M University

Daniel M. Weinreich
Brown University
Stephen I. Wright
University of Toronto
THEORETICAL
POPULATION
GENETICS

Nick H. Barton
Institute of Science and
Technology Austria
Mark A. Beaumont
University of Bristol

Graham Coop
University of California,
Davis
Joachim Hermisson
University of Vienna
Rasmus Nielsen
University of California,
Berkeley and University
of Copenhagen
Sohini Ramachandran
Brown University
Noah A. Rosenberg
Stanford University
Yun S. Song
University of California,
Berkeley
Wolfgang Stephan
University of Munich
Marcy K. Uyenoyama
Duke University
Lindi M. Wahl
Western University
John Wakeley
Harvard University
Jeff D. Wall
University of California,
San Francisco
PRIMERS

Elizabeth A. De Stasio
Lawrence University
PERSPECTIVES

H. Allen Orr
University of Rochester
Adam S. Wilkins
Humboldt University
of Berlin
REVIEWS

Oliver Hobert
Columbia University
Jasper Rine
University of California,
Berkeley
Michael Turelli
University of California,
Davis
Jeffery H. Miller
University of California,
Los Angeles
SERIES

Lauren M. McIntyre
University of Florida

IN THEIR OWN WORDS

Every contact I had was highly professional, and I
appreciate all efforts from the editors or reviewers to
make this study accessible to colleagues. When I download
information for papers relevant to my work. Thank you for your
efforts with the title suggestions.”
Verena Jantsch
University of Vienna

The whole submission process was very positive. Honestly,
I think the reviewers were quite helpful in improving our paper. I
really appreciated their constructive criticism.”
Ian Ehrenreich
University of Southern California

I tremendously enjoyed working with our editor, David
Greenstein, who was very actively and helpfully engaged in
the whole process of submission and revision. The enjoyable
the list of journals for future submissions.”
Stefan Taubert
University of British Columbia

Thanks very much for the feedback and amazingly fast
turnaround time with our paper! It was a great experience to
work to GENETICS.”
John Calarco
Harvard University

2

ON THE COVER Different color pattern forms of Heliconius erato. For more than a
century, biologists have used Heliconius as a model of mimicry. Kronforst and Papa review
the genetics of wing patterning in this genus, charting new insights from genomics into
some of the oldest questions about adaptation. Genetics 200:1–19 Image: Riccardo Papa.

Bridges published his proof that genes are carried on
genetics is again at the brink of a major transformation
During this century of incredible advances, GENETICS
crucial forum for scholarly debate.
Thanks to our committed peer editors, reviewers,
and authors, GENETICS continues to innovate and
publish important advances across a wide breadth
of topics. From microbial genetics to human disease,
from statistical genetics to crop improvement, from
evolution to genome engineering, we publish highGENETICS, along with the communities it serves,
has changed. The editors make decisions quickly—
helpful peer-review for which the journal is known.
GENETICS is committed to supporting resources
that serve scientists. We have partnered with BioRxiv
for seamless preprint deposits, with model organism
databases like SGD, FlyBase, WormBase, FungiDB,
and with the protocols.io methods repository.
This Spotlight showcases the diversity of research
and scholarship we published in 2015, and highlights
Centennial Award winners for their outstanding articles
published in the journal’s 99th year. We hope you will
consider publishing your best work in our journal, and
help us shape the next century of GENETICS.

Mark Johnston
Editor-in-Chief, GENETICS

3

CENTENNIAL AWARD: MOLECUL AR GENE TICS

Allelic Imbalance Is a Prevalent and TissueSpecific Feature of the Mouse Transcriptome
Stefan F. Pinter, David Colognori, Brian J. Beliveau, Ruslan I. Sadreyev,
Bernhard Payer, Eda Yildirim, Chao-ting Wu, and Jeannie T. Lee
Genetics June 2015 200:537–549
EDITORS’ NOTE Aside from genes affected by epigenetic phenomena, the
two alleles of a gene are generally assumed to express at equal levels. Pinter
et al. revealed the unexpected extent of allelic imbalance by measuring gene
expression in hybrid offspring from genetically distinct mice. Genetic variation
likely causes most of this imbalance, but surprisingly, some of the genes were
expressed from only one allele in both hybrid and inbred strains.

ABSTRACT In mammals, several classes of monoallelic genes have been

of allelic imbalance in mouse hybrids derived from reciprocal crosses of
divergent strains. We observe that deviation from balanced biallelic expression
is common, occurring in ~20% of the mouse transcriptome in a given tissue.
Allelic imbalance attributed to genotypic variation is by far the most prevalent
imbalance is maintained across tissues and is associated with greater genetic
variation, especially in 5' and 3' termini of transcripts. We further identify novel
penetrance of parental origin even in the setting of large imprinted regions.
Examination of nascent transcripts in single cells from inbred parental strains
reveals that genes showing genotype-based imbalance in hybrids can also
exhibit monoallelic expression in isogenic backgrounds. This surprising
combined impact of cis- and trans-acting variation on expression of a given
relevant to human genetic variation and disease.

4

CENTENNIAL AWARD: QUANTITATIVE GENE TICS

The Nature of Genetic Variation for Complex
Traits Revealed by GWAS and Regional
Heritability Mapping Analyses
Armando Caballero, Albert Tenesa, and Peter D. Keightley
Genetics December 2015 201:1601–1613
EDITORS’ NOTE The mystery of the “missing heritability” of many complex
traits refers to the mismatch between their heritability and the total variance
Caballero et al. used simulations to show that, contrary to previous results,
common variants of substantial effect may be responsible for most variation
and switching to GWAS of full sequence data or carrying out Regional
Heritability Mapping is unlikely to substantially reduce the missing heritability.

ABSTRACT We use computer simulations to investigate the amount of
genetic variation for complex traits that can be revealed by single-SNP

model a large population subject to mutation, recombination, selection, and
drift, assuming a pleiotropic model of mutations sampled from a bivariate
pleiotropic model investigated, in contrast to previous models, implies that
common mutations of large effect are responsible for most of the genetic
show that GWAS applied to the full sequence increases the number of QTL
detected by as much as 50% compared to the number found with SNP
chips but only modestly increases the amount of additive genetic variance
explained. Even with full sequence data, the total amount of additive variance
explained is generally below 50%. Using RHM on the full sequence data,
a slightly larger number of QTL are detected than by GWAS if the same
probability threshold is assumed, but these QTL explain a slightly smaller
amount of genetic variance. Our results also suggest that most of the missing

genetic variation, so their eventual detection is less relevant for resolving the
missing heritability problem.

5

CENTENNIAL AWARD: POPUL ATION & E VOLUTIONARY GENE TICS

Adaptation, Clonal Interference, and FrequencyDependent Interactions in a Long-Term
Evolution Experiment with Escherichia coli
Rohan Maddamsetti, Richard E. Lenski, and Jeffrey E. Barrick
Genetics June 2015 200:619–631
EDITORS’ NOTE Maddamsetti et al. reconstructed the dynamics of 42
mutations over 20,000 generations of bacterial evolution. They show that
was able to complete a selective sweep. In one striking case, two bacterial
types with different sets of mutations coexisted for thousands of generations.

ABSTRACT Twelve replicate populations of Escherichia coli have been
evolving in the laboratory for >25 years and 60,000 generations. We analyzed
bacteria from whole-population samples frozen every 500 generations through
42 known mutations in these samples, we reconstructed the history of this
population’s genotypic evolution over this period. The evolutionary dynamics of

conveying no information about their order of origination; we present several
possible explanations for the existence of these mutational cohorts. Against
a backdrop of rapid selective sweeps both earlier and later, two genetically
diverged clades coexisted for >6000 generations before one went extinct.
In that time, many additional mutations arose in the clade that eventually
prevailed. We show that the clades evolved a frequency-dependent interaction,
which prevented the immediate competitive exclusion of either clade, but
prevailed. Clonal interference and frequency dependence can occur even
in the simplest microbial populations. Furthermore, frequency dependence
may generate dynamics that extend the period of coexistence that would
otherwise be sustained by clonal interference alone.

6

7

REAL-TIME EVOLUTION Estimated frequencies of 42 mutations in over
20,000 generations of an E. coli population. Sectors represent new mutations
nested within previous ones. Mutation labels preceded by a dot indicate the
mutation became fixed in the population. From Maddamsetti et al.

GENE TIC TOOLBOX RE VIE WS

This series reviews practical and intellectual resources for genetics and
genomics, including the study of less commonly used experimental
organisms. If you know an experimental frontier in need of a guidebook,
the editors welcome suggestions for new Genetic Toolbox Reviews!

Jeremy A. Lynch
Genetics April 2015 199: 897–904

Nasonia vitripennis and Its Relatives

(Oryzias latipes)
Stephan Kirchmaier, Kiyoshi Naruse, Joachim Wittbrodt, and Felix Loosli
Genetics April 2015 199: 905–918
Zea mays
Natalie J. Nannas and R. Kelly Dawe
Genetics March 2015 199: 655–669

Tamily A. Weissman and Y. Albert Pan
Genetics February 2015 199: 293–306

Priti Singh, John C. Schimenti, and Ewelina Bolcun-Filas
Genetics January 2015 199: 1–15

8

CHASING BRAINBOWS Brainbow expression in a living, 2-day old
zebrafish. A somatosensory neuron in the spinal cord (light pink) projects
fine processes ventrally throughout the trunk. The brainbow cell-labeling
technique, reviewed in Weissman and Pan, can be used in many different
living organisms for distinguishing between individual cells or between
clones of dividing cells. Image: Zachary Tobias and Tamily Weissman.

9

DE VELOPMENTAL & BEHAVIOR AL GENE TICS

A Novel Paradigm for Nonassociative LongTerm Memory in Drosophila: Predator-Induced
Changes in Oviposition Behavior
Balint Z. Kacsoh, Julianna Bozler, Sassan Hodge, Mani Ramaswami, and
Genetics April 2015 199:1143–1157
EDITORS’ NOTE Most work on Drosophila memory has relied on
another. Kacsoh et al. explore a natural, nonassociative behavior, in which
in alcohol-rich food. Persistence of this behavior depends on several genes
involved in long-term learning and memory.

ABSTRACT Learning processes in Drosophila have been studied through
the use of Pavlovian associative memory tests, and these paradigms have
been extremely useful in identifying both genetic factors and neuroanatomical
structures that are essential to memory formation. Whether these same
genes and brain compartments also contribute to memory formed from
nonassociative experiences is not well understood. Exposures to environmental
stressors such as predators are known to induce innate behavioral responses
and can lead to new memory formation that allows a predator response to
persist for days after the predator threat has been removed. Here, we utilize a
unique form of nonassociative behavior in Drosophila
the presence of endoparasitoid predatory wasps and alter their oviposition
behavior to lay eggs in food containing high levels of alcohol. The predatorare removed, and this persistence in behavior requires a minimum continuous
exposure time of 14 hr. Maintenance of this behavior is dependent on multiple
long-term memory genes, including orb2, dunce, rutabaga, amnesiac, and
Fmr1. Maintenance of the behavior also requires intact synaptic transmission
of the mushroom body. Surprisingly, synaptic output from the mushroom

with wasps. This suggests that perception of this predator that leads to an
acute change in oviposition behavior is not dependent on the MB or dependent
on learning and memory gene functions. Because wasp-induced oviposition
behavior can last for days and its maintenance requires a functional MB and the
wild-type products of several known learning and memory genes, we suggest
that this constitutes a paradigm for a bona fide form of nonassociative longterm memory that is not dependent on associated experiences.

10

GENE TICS OF COMPLE X TR AITS

Dominance Genetic Variance for Traits Under
Directional Selection in Drosophila serrata
Jacqueline L. Sztepanacz and Mark W. Blows
Genetics May 2015 200:371–384
EDITORS’ NOTE Genetic variance in quantitative traits can be partitioned
into additive, dominance, and interaction effects. Theory predicts that
directional selection will erode additive variance, increasing the proportion
of dominance variance. Sztepanacz and Blows used breeding experiments
in Drosophila serrata to show that morphological traits do not match this

ABSTRACT In contrast to our growing understanding of patterns of additive
genetic variance in single- and multi-trait combinations, the relative contribution
of nonadditive genetic variance, particularly dominance variance, to multivariate
phenotypes is largely unknown. While mechanisms for the evolution of
dominance genetic variance have been, and to some degree remain, subject to
debate, the pervasiveness of dominance is widely recognized and may play a
key role in several evolutionary processes. Theoretical and empirical evidence
suggests that the contribution of dominance variance to phenotypic variance
tests of this hypothesis are few. Using a multigenerational breeding design
in an unmanipulated population of Drosophila serrata, we estimated additive
and dominance genetic covariance matrices for multivariate wing-shape
whether there is an association between directional selection and dominance
variance. Fitness, a trait unequivocally under directional selection, had no
contributing 32% of the phenotypic variance. For single and multivariate
morphological traits, however, no relationship was observed between trait–
and dominance variance was found to contribute to phenotypic variance
for single traits, and double the amount of additive compared to dominance
variance was found for the multivariate trait combination under directional
association between directional selection and dominance genetic variance may
not be expected.

11

GENE E XPRESSION

Paramutation in Drosophila Requires Both
Nuclear and Cytoplasmic Actors of the piRNA
Pathway and Induces Cis-spreading of piRNA
Production
Catherine Hermant, Antoine Boivin, Laure Teysset, Valérie Delmarre, Amna Asif-Laidin,
Marius van den Beek, Christophe Antoniewski, and Stéphane Ronsseray
Genetics December 2015 201:1381–1396
EDITORS’ NOTE
Drosophila, clusters of transgenes can be activated for piRNA production in
ovaries by maternally inherited homologous piRNAs, resulting in an epigenetic
conversion process termed paramutation. Hermant et al. identify genes
needed for this event and show it can occur between partially homologous
loci, indicating that paramutation may play an important role in shaping the
Drosophila germline epigenome.

ABSTRACT Transposable element activity is repressed in the germline in
by genomic loci mostly composed of TE sequences. The mechanism of
induction of piRNA production by these loci is still enigmatic. We have shown
that, in Drosophila melanogaster, a cluster of tandemly repeated P-lacZ-white
transgenes can be activated for piRNA production by maternal inheritance
of a cytoplasm containing homologous piRNAs. This activated state is stably
transmitted over generations and allows trans-silencing of a homologous
transgenic target in the female germline. Such an epigenetic conversion displays
the functional characteristics of a paramutation, i.e., a heritable epigenetic
and trans-silencing capacities of the paramutated cluster depend on the
function of the rhino, cutoff, and zucchini genes involved in primary piRNA
biogenesis in the germline, as well as on that of the aubergine gene implicated
by the paramutated cluster, in addition to 23- to 28-nt piRNAs are not necessary
for paramutation to occur. Production of these 21-nt RNAs requires Dicer-2
but also all the piRNA genes tested. Moreover, cytoplasmic transmission of
piRNAs homologous to only a subregion of the transgenic locus can generate
a strong paramutated locus that produces piRNAs along the whole length
of the transgenes. Finally, we observed that maternally inherited transgenic
small RNAs can also impact transgene expression in the soma. In conclusion,

non fully homologous loci located on different chromosomes, paramutation may
play a crucial role in epigenome shaping in Drosophila natural populations.
12

GENE E XPRESSION

The Chromatin and Transcriptional Landscape
of Native Saccharomyces cerevisiae Telomeres
and Subtelomeric Domains
Aisha Ellahi, Deborah M. Thurtle, and Jasper Rine
Genetics June 2015 200:505–521
EDITORS’ NOTE How and why are genes near telomeres silenced?
Early studies showed that yeast genes near telomeres are silenced in a
Sir-protein-dependent manner. However, these studies inserted reporter
genes next to truncated, rather than natural, telomeres. Ellahi et al.
characterize the chromatin and transcriptional landscape of all native
Saccharomyces cerevisiae telomeres. Surprisingly, few subtelomeric genes
were silenced in a SIR-dependent manner and most were expressed.

ABSTRACT Saccharomyces cerevisiae telomeres have been a paradigm
for studying telomere position effects on gene expression. Telomere position
genes inserted adjacent to truncated telomeres. The reporter genes showed
variable silencing that depended on the Sir2/3/4 complex. Later studies
examining subtelomeric reporter genes inserted at natural telomeres hinted
that telomere position effects were less pervasive than previously thought.
Additionally, more recent data using the sensitive technology of chromatin
discrete and noncontinuous pattern of coenrichment for all three Sir proteins
at a few telomeres, calling the generality of these conclusions into question.
Here we combined the ChIP-Seq of the Sir proteins with RNA sequencing
SIR2, SIR3,
and SIR4 deletion mutants to characterize the chromatin and transcriptional
landscape of all native S. cerevisiae telomeres at the highest achievable
resolution. Most S. cerevisiae chromosomes had subtelomeric genes that
were expressed, with only ~6% of subtelomeric genes silenced in a SIRdependent manner. In addition, we uncovered 29 genes with previously
provided a comprehensive assessment of the chromatin and transcriptional
landscape of the subtelomeric domains of a eukaryotic genome.

13

GENOME & SYSTEMS BIOLOGY

Complementation of Yeast Genes with Human
Genes as an Experimental Platform for
Functional Testing of Human Genetic Variants
Akil Hamza, Erik Tammpere, Megan Kofoed, Christelle Keong, Jennifer Chiang,
Genetics November 2015 201:1263–1274
EDITORS’ NOTE “Humanized” yeast strains can be used to direct functional
studies of human genetic variants. Hamza et al. used complementation
screens to identify 65 human genes that are functionally homologous to yeast
genes, including genes implicated in chromosome instability. The results
potential role in tumorigenesis.

ABSTRACT While the pace of discovery of human genetic variants in tumors,
patients, and diverse populations has rapidly accelerated, deciphering their
functional consequence has become rate-limiting. Using cross-species
complementation, model organisms like the budding yeast, Saccharomyces
cerevisiae,
human genetic variants. To this end, we performed two parallel screens, a
one-to-one complementation screen for essential yeast genes implicated in
chromosome instability and a pool-to-pool screen that queried all possible
essential yeast genes for rescue of lethality by all possible human homologs.
essential yeast genes, including the nonorthologous pair yRFT1/hSEC61A1.
LIG1, hSSRP1, hPPP1CA, and hPPP1CC
for which their yeast gene counterparts function in chromosome stability and
and sensitivity to DNA-damaging agents. This resulted in a set of human–
yeast gene complementation pairs that allow human genetic variants to be
readily characterized in yeast, and a prioritized list of somatic mutations that
could contribute to chromosome instability in human tumors. These data
establish the utility of this cross-species experimental approach.

14

GENOME INTEGRIT Y & TR ANSMISSION

Alternative Transposition Generates New
Chimeric Genes and Segmental Duplications at
the Maize p1 Locus
Dafang Wang, Chuanhe Yu, Tao Zuo, Jianbo Zhang, David F. Weber, and
Thomas Peterson
Genetics November 2015 201:925–935
EDITORS’ NOTE Transposable elements make up approximately 85% of
the maize genome. Wang et al. demonstrate that transposable elements
can generate functional chimeric genes as a direct product of an aberrant
transposition reaction, revealing how these elements can shape the maize
genome and spontaneously create new genes.

ABSTRACT The maize Ac/Ds
Ac/Ds
transposons belong to the hAT family of class II DNA transposons. We
and others have shown that Ac/Ds elements can undergo a process of
alternative transposition in which the Ac/Ds transposase acts on the termini
of two separate, nearby transposons. Because these termini are present in
different elements, alternative transposition can generate a variety of genome
alterations such as inversions, duplications, deletions, and translocations.
Moreover, Ac/Ds elements transpose preferentially into genic regions,
suggesting that structural changes arising from alternative transposition may
potentially generate chimeric genes at the rearrangement breakpoints. Here
by Ac alternative transposition. In each case, a functional chimeric gene was
created by fusion of two linked, paralogous genes; moreover, each event was
associated with duplication of the ~70-kb segment located between the two
paralogs. An extant gene in the maize B73 genome that contains an internal
duplication apparently generated by an alternative transposition event was
duplications may be a source for spontaneous creation of diverse genome
structures and novel genes in maize.

15

HUMAN GENE TICS

In 2014, GENETICS and G3 signaled their intent to publish more articles
that provide insight into human gene function and disease, including
methodological studies and work that uses model organisms to investigate
disease-associated alleles. For more information see GENETICS Editor-inChief Mark Johnston’s editorial, “Humans as a Model Organism: the Time is
Now”: http://www.genetics.org/content/198/2/441.full
A selection of human genetics articles from 2015:

by Humans
Ziyue Gao, Darrel Waggoner, Matthew Stephens, Carole Ober, and Molly Przeworski
Genetics April 2015 199:1243–1254
EDITORS’ NOTE Gao et al. estimated the human recessive lethal mutation
load by using data from a founder population that lives communally and has a
known pedigree.
Automated Assay of Telomere Length Measurement and Informatics for 100,000

Kyle Lapham and Mark N. Kvale et al.
Genetics August 2015 200:1061–1072
EDITORS’ NOTE Lapham and Kvale et al. assayed telomere length in more
than 100,000 individuals enrolled in a cohort study of health and aging.
Dependence of Human Colorectal Cells Lacking the FBW7 Tumor Suppressor on
the Spindle Assembly Checkpoint
Melanie L. Bailey, Tejomayee Singh, Patricia Mero, Jason Moffat, and Philip Hieter
Genetics November 2015 201:885–895
EDITORS’ NOTE Bailey et al. show that cells carrying a mutation of FBW7,
a tumor suppressor gene associated with a range of cancer types, are
dependent on the mitotic checkpoint. This suggests a therapeutic strategy for
targeting FBW7-mutated cancer cells.

16

ME THODS, TECHNOLOGY, & RESOURCES

In 2015, GENETICS published several major improvements and
elaborations on CRISPR genome engineering in C. elegans. At the
2015 C. elegans meeting, a CRISPR/Cas9 workshop highlighted
some of these advances, and proposed a set of common guidelines
and best practices. Read more at the Genes to Genomes blog:
http://genestogenomes.org/worm-crispr-workshop-at-the-internationalc-elegans-meeting/
Rapid and Precise Engineering of the Caenorhabditis elegans
Jordan D. Ward
Genetics February 2015 199:363–377

Behnom Farboud and Barbara J. Meyer
Genetics April 2015 199:959–971
Caenorhabditis elegans
Alexandre Paix, Andrew Folkmann, Dominique Rasoloson, and Geraldine Seydoux
Genetics September 2015 201:47–54

Daniel J. Dickinson, Ariel M. Pani, Jennifer K. Heppert, Christopher D. Higgins, and
Bob Goldstein
Genetics August 2015 200:1035–1049
Caenorhabditis elegans with a Toolkit of Dual-Marker
Selection Cassettes
Adam D. Norris, Hyun-Min Kim, Mónica P. Colaiácovo, and John A. Calarco
Genetics October 2015 201:449–458

Caenorhabditis elegans
Genetics December 2015 201:1295–1306

17

PERSPECTIVES

What Do You Mean, “Epigenetic”?
Carrie Deans and Keith A. Maggert
Genetics April 2015 199:887–896
EDITORS’ NOTE Despite the exploding popularity of epigenetics research,

to move forward.

ABSTRACT

physiology, and even mainstream culture. It has become increasingly clear,
Some employ epigenetics to explain changes in gene expression, others
use it to refer to transgenerational effects and/or inherited expression states.

many ways biased methodologies and interpretations. This article discusses

18

POPUL ATION & E VOLUTIONARY GENE TICS

The Evolutionarily Stable Distribution of
Fitness Effects
Genetics May 2015 200:321–329
EDITORS’ NOTE The fate of an evolving population is determined in part

environment, the genetic architecture of complex traits, and the expected
patterns of genetic diversity. This article shows that the expected DFE in
a constant environment approaches a simple form that holds surprisingly
constant over a wide range of population genetic parameters.

ABSTRACT
key parameter in determining the course of evolution. This fact has motivated
However, just as the DFE determines the course of evolution, the evolutionary
process itself constrains the DFE. Here, we analyze a simple model of genome
evolution in a constant environment in which natural selection drives the

is stable under further evolution and provides a natural null expectation for
the DFE in a population that has evolved in a constant environment for a long
time. We calculate how the shape of the evolutionarily stable DFE depends on
the underlying population genetic parameters. We show that, in the absence of
obeys a simple relationship independent of population genetic details. Finally,
we analyze how the stable DFE changes in the presence of a simple form of
diminishing-returns epistasis.

19

POPUL ATION & E VOLUTIONARY GENE TICS

Allele Sharing and Evidence for Sexuality in a
Mitochondrial Clade of Bdelloid Rotifers
Genetics June 2015 200:581–590
EDITORS’ NOTE Eukaryote lineages don’t usually survive for long without
sex. But bdelloid rotifers—minute freshwater invertebrates—have long been
held as completely asexual oddities of the animal kingdom. Signorovitch et al.
patterns consistent with sexual reproduction and an unusual type of meiosis.

ABSTRACT Rotifers of Class Bdelloidea are common freshwater invertebrates
of ancient origin whose apparent asexuality has posed a challenge to the
view that sexual reproduction is essential for long-term evolutionary success
in eukaryotes and to hypotheses for the advantage of sex. The possibility
nevertheless exists that bdelloids reproduce sexually under unknown or
inadequately investigated conditions. Although certain methods of population
have not previously been applied to bdelloid rotifers. We conducted such
a test with bdelloids belonging to a mitochondrial clade of Macrotrachela
quadricornifera. This revealed a striking pattern of allele sharing consistent with
sexual reproduction and with meiosis of an atypical sort, in which segregation
occurs without requiring homologous chromosome pairs.

20

STATISTICAL GENE TICS & GENOMICS

Efficient Multiple-Trait Association and
Estimation of Genetic Correlation Using the
Matrix-Variate Linear Mixed Model
Genetics May 2015 200:59–68
EDITORS’ NOTE Existing approaches to multiple-trait association mapping
are computationally intractable for large sample sizes. Furlotte and Eskin
introduce a mathematical and computational construct that overcomes
associations between genetic variants and multiple correlated traits.

ABSTRACT Multiple-trait association mapping, in which multiple traits are
traits, has recently attracted interest. One class of approaches for this
problem builds on classical variance component methodology, utilizing a
multitrait version of a linear mixed model. These approaches both increase
power and provide insights into the genetic architecture of multiple traits.
In particular, it is possible to estimate the genetic correlation, which is a
measure of the portion of the total correlation between traits that is due to
additive genetic effects. Unfortunately, the practical utility of these methods
is limited since they are computationally intractable for large sample sizes.
In this article, we introduce a reformulation of the multiple-trait association
approach reduces the computational time necessary to perform maximumlikelihood inference in a multiple-trait model by utilizing a data transformation.
By utilizing a well-studied human cohort, we show that our approach
provides more than a 10-fold speedup, making multiple-trait association
feasible in a large population cohort on the genome-wide scale. We take
data. By decomposing gene coexpression into a genetic and environmental
component, we show that our method provides fundamental insights into the
nature of coexpressed genes. An implementation of this method is available at
http://genetics.cs.ucla.edu/mvLMM.

21

RE VIE WS

Genetic Diversity and Societally Important
Disparities
Genetics September 2015 201:1–12
EDITORS’ NOTE Rosenberg and Kang discuss the real-world
consequences of differences in genetic diversity between human
populations, including disparities in forensic genetics, transplantation
matching, and representation in disease GWAS. They also reanalyzed data
from a study relating a population’s genetic diversity to its rate of economic

ABSTRACT The magnitude of genetic diversity within human populations
spread throughout the world. Beyond its use in human evolutionary genetics,
worldwide variation in genetic diversity sometimes can interact with social
processes to produce differences among populations in their relationship to
modern societal problems. We review the consequences of genetic diversity
match probabilities in bone marrow transplantation, and representation in
genome-wide association studies of disease. In each of these three cases, the
contribution of genetic diversity to social differences follows from populationgenetic principles. For a fourth setting that is not similarly grounded, we
reanalyze with expanded genetic data a report that genetic diversity differences
for the claim. The four examples describe a limit to the importance of genetic
diversity for explaining societal differences while illustrating a distinction that
certain biologically based scenarios do require consideration of genetic diversity
for solving problems to which populations have been differentially predisposed
by the unique history of human migrations.

22

FACING DISPARITIES 16 x 16 Colourful Faces from the British Library
Collection, by Mario Klingemann. The result of data mining the British
Library Commons Collection, identifying colorful plates using image analysis
and subsequently using face detection to extract the faces contained therein.
CC BY-NC 2.0

23

GENESTOGENOMES.ORG

Genes to Genomes

a blog from the Genetics Society of America

Don’t miss the latest at Genes to Genomes! Sign-up for email alerts at
.

How to write titles that tempt
A paper’s title should not be a miniabstract that gives away the ending, writes
GENETICS Editor-in-Chief Mark Johnston.

Calvin Bridges:
Bringing genes down to earth
In 1916, a sharp-eyed grad student called
Calvin Bridges published his compelling proof
that genes lie on chromosomes. It was the

offspring stronger
When a C. elegans starves early in its life
cycle, its offspring are more resistant to
starvation; however, this life-saving inheritance

On November 11, 1954, Syuiti Mori turned out
than sixty years later, their descendents—a
a life of constant darkness.

24

RE VIE W COLLECTIONS

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YeastBook

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WormBook

Editor-in-Chief
Alan G. Hinnebusch
National Institutes of Health

Editor-in-Chief
Lynn Cooley
Yale University

Editor-in-Chief
Iva Greenwald
Columbia University

Co-Editor-in-Chief
John R. Carlson
Yale University
Co-Editor-in-Chief
R. Scott Hawley
Stowers Institute for
Medical Research
Co-Editor-in-Chief
Therese Ann Markow
University of California,
San Diego

25

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