Spotlight

A showcase of research and scholarship

in selected articles from 2014

2014
Editorial Board

ASSOCIATE EDITORS

EDITOR-IN-CHIEF

Eduard Akhunov
Kansas State University

Brenda J. Andrews
University of Toronto

EXECUTIVE EDITOR

Tracey DePellegrin
DEPUTY EDITOR,
COMPLEX TRAITS

Dirk Jan de Koning

Swedish University of
Agricultural Sciences

DEPUTY EDITOR,
HUMAN GENETICS

Stephen W. Scherer
The Hospital for Sick
Children & University
of Toronto

SENIOR EDITORS

Katrien M. Devos
University of Georgia
Susan L. Forsburg
University of Southern
California
R. Scott Hawley
Stowers Institute for
Medical Research
Stephen I. Wright
University of Toronto

Danika L. Bannasch
University of California,
Davis
Judith Berman
University of Minnesota
& Tel Aviv University
James A. Birchler
University of Missouri
Charles Boone
University of Toronto
Michael Boutros
DKFZ & University of
Heidelberg
Rachel Brem
Buck Institute for
Research on Aging
Julie Brill
The Hospital for Sick
Children
David T. Burke
University of Michigan
Medical School
Rita M. Cantor
University of California,
Los Angeles
Susan Celniker
Lawrence Berkeley
National Laboratory
Aravinda Chakravarti
Johns Hopkins
University School of
Medicine
J. Michael Cherry
Stanford University

ASSISTANT EDITOR

Cristy Gelling
ASSISTANT
MANAGING EDITOR

Ruth Isaacson

Timothy J. Close
University of California,
Riverside
Barak A. Cohen
Washington University
School of Medicine
Josep M. Comeron
University of Iowa
Gloria M. Coruzzi
New York University
William S. Davidson
Simon Fraser University
Kelly Dawe
University of Georgia

Gustavo A. de los
Campos
University of Alabama
at Birmingham
Job Dekker
University of
Massachusetts
Medical School
Fred S. Dietrich
Duke University
Medical Center
Rebecca W. Doerge
Purdue University
Aime M. Dudley
Diabetes Research
Institute
Jay C. Dunlap
Dartmouth Medical
School
Mark Estelle
University of California,
San Diego

James B. Holland
USDA & North Carolina
State University

Corey Nislow
University of British
Columbia

Emma Huang
CSIRO

Andrew H. Paterson
University of Georgia

Kevin Thornton
University of California,
Irvine

Timothy R. Hughes
University of Toronto

Peter Pfaffelhuber
University of Freiburg

David W. Threadgill
Texas A&M University

Scott A. Jackson
University of Georgia

Patrick C. Phillips
University of Oregon

Sue L. Jaspersen
Stowers Institute for
Medical Research

Eric M. Phizicky
University of Rochester
Medical Center

Sarah A. Tishkoff
University of
Pennsylvania

Stephen L. Johnson
Washington University
School of Medicine

Craig S. Pikaard
Indiana University

Mike Tyers
Universit de Montral

Nicholas Katsanis
Duke University

David D. Pollock
University of Colorado
School of Medicine

Veronica J. Vieland
Nationwide Childrens
Hospital

Cynthia Kenyon
University of California,
San Francisco

Julia E. Richards
University of Michigan
School of Public Health

John K. Kim
University of Michigan

Jasper Rine
University of California,
Berkeley

Marian Walhout
University of
Massachusetts
Medical School

Justin D. Faris
USDA-ARS Cereal
Crops Research Unit

Yuseob Kim
Ewha Womans
University

David S. Fay
University of Wyoming

Rob J. Kulathinal
Temple University

Justin C. Fay
Washington University
in St. Louis

Siu Sylvia Lee

Cornell University

Audrey Gasch
University of
Wisconsin-Madison
David J. Gresham
New York University
Erich Grotewold
The Ohio State
University
David J. Grunwald
The University of Utah
Kris Gunsalus
New York University
Ira M. Hall
Washington University
School of Medicine

Howard D. Lipshitz
University of Toronto
Jianxin Ma
Purdue University
Christian R. Marshall
The Hospital for Sick
Children
Andrew S. McCallion
Johns Hopkins
University School of
Medicine
John H. McCusker
Duke University
Medical Center
Kim S. McKim
Rutgers University

Jay R. Hesselberth
University of Colorado
School of Medicine

Donald G. Moerman
University of British
Columbia

Charles S. Hoffman
Boston College

Chad L. Myers
University of
Minnesota

Antonis Rokas
Vanderbilt University
Jeffrey Ross-Ibarra
University of California,
Davis
Fritz P. Roth
University of Toronto

Hidenori Tachida
Kyushu University

Olga Troyanskaya
Princeton University

Marilyn Warburton
USDA-ARS Corn
Host Plant Resistance
Research Unit
Jonathan F. Wendel
Iowa State University
Brian S. Yandell
University of
Wisconsin-Madison

Matthew S. Sachs
Texas A&M University

Zhenbiao Yang
University of California,
Riverside

Helen K. Salz
Case Western Reserve
University

Nevin D. Young
University of Minnesota

Michael J. Scanlon
Cornell University

Dani Zamir
The Hebrew University
of Jerusalem

David S. Schneider
Stanford University
Robert A. Sclafani
University of Colorado
School of Medicine
Tanja Slotte
University of Stockholm
Marcus B. Smolka
Cornell University
Lars M. Steinmetz
European Molecular
Biology Laboratory &
Stanford University

Monique Zetka
McGill University

SEA ANEMONE & FRIENDS Coral reefs around the world are bleaching,
a threat caused by breakdown of the symbiosis between the coral animals
and the dinoflagellate algae that live within their cells. Unfortunately, this
crucial symbiotic partnership is poorly understood. Lehnert et al. studied
gene expression patterns associated with the symbiotic state using the sea
anemone Aiptasia. This fast-growing cousin of corals maintains a similar
symbiotic relationship with dinoflagellates, but it can also survive without its
symbiotic friends. This image shows Aiptasia hosting different concentrations
of dinoflagellate symbionts. Although the anemone tissue is nearly transparent,
the dinoflagellates are visible via their red chlorophyll fluorescence.
Image courtesy of Jan C. DeNofrio.

Extensive Differences in Gene Expression Between Symbiotic

and Aposymbiotic Cnidarians
Erik M. Lehnert, Morgan E. Mouchka, Matthew S. Burriesci,
Natalya D. Gallo, Jodi A. Schwarz, and John R. Pringle
G3: Genes | Genomes | Genetics February 2014 4:277295

G3: Genes | Genomes | Genetics:

turning four and growing fast!
What makes us different from other journals? G3 was
open access journal with the same high standards for
sister journal GENETICS. G3 has established itself as a

editors in human genetics, bioinformatics, statistical,

any stage? Because G3 is dedicated to genetics and

sea of thousands of articles. We promote G3 papers

Journals blog Genes to Genomes
within a month and papers are published as Early

like copyediting, proofs, and accessible editors.

who make the decisions on all papers, colleagues youll
see at meetings and whose names you recognize. Last
year, we named Stephen Scherer as Deputy Editor for
Human Genetics, and DJ de Koning as Deputy Editor
for Complex Traits, and appointed Stephen Wright as
Senior Editor for Population Genetics and Genomics.
chosen a selection of excellent papers for this Spotlight.
See what people are talking about, and submit to G3.

Brenda J. Andrews
G3: Genes | Genomes | Genetics
ON THE COVER In 1883, Emil Christian Hansen isolated the first pure lager yeast
strain, Saccharomyces carlsbergensis. In 2014, Walther et al. assembled the genome of
S. carlsbergensis (see p. 22). This artwork shows a 1908 photo of Hansen, his signature,
and Circos presentations of the hybrid genome. Image courtesy of Andrea Walther.

IN THEIR OWN WORDS

rejected is a fundamental aim of an editor. I am impressed by the editors

appropriate reasons if the article is rejected.

Jos Crossa

with

as GENETICS, but without regard for impact of the research. Far from
just names on the masthead,

tune our decisions.

GENESTOGENOMES.ORG

Genes to Genomes

the GSA journals blog

In 2014 the GSA journals launched Genes to Genomes, a blog about genetics
and genomics research and scholarly publishing. The blog features the stories
behind the latest research in GENETICS and G3, guest posts from young
from our editors. Visit
to read the latest posts
and subscribe! Below are a few popular posts from 2014:

white belly, white socks, or other patches

of white fur.

association studies. Melissa Wilson Sayres

and Alon Keinan discuss their 2014 ASHG
meeting session.

Authors can now opt to automatically post

INVESTIG ATIONS

Species-Level Deconvolution of Metagenome

Assemblies with Hi-CBased Contact
Probability Maps
G3: Genes | Genomes | Genetics July 2014 4:13391346
EDITORS NOTE
species and domains. Burton and Liachko et al. introduced a powerful

ABSTRACT Microbial communities consist of mixed populations of organisms,

including unknown species in unknown abundances. These communities

de novo assembly of a metagenome typically yield

a collection of contigs that cannot readily be grouped by species. Methods
e.g., as generated by
and contains both intrachromosomal and interchromosomal information. Here,
genomes of microbial species present within a mixed sample. We apply this
approach to two synthetic metagenome samples, successfully clustering the
genome content of fungal, bacterial, and archaeal species with more than 99%
signal can secondarily be used to create scaffolded genome assemblies of

UNTANGLING THE MIX This soccer-ball-like network diagram from

Burton and Liachko et al. illustrates the genomes of 12 yeast species assembled
from a metagenomic sequencing sample. Image courtesy of Joshua N. Burton.

INVESTIG ATIONS

The Yeast Ess1 Prolyl Isomerase Controls Swi6

and Whi5 Nuclear Localization
G3: Genes | Genomes | Genetics March 2014 4:523537
EDITORS NOTE
isomerase was RNA polymerase II. In this work, Atencio et al. showed that
proposed that Ess1 induces a conformational switch within the transcription

ABSTRACT The Ess1 prolyl isomerase from Saccharomyces cerevisiae

and its human ortholog, Pin1, play critical roles in transcription by regulating

gain insight into Ess1/Pin1 function, we carried out a synthetic genetic array

regulated nucleocytoplasmic shuttling during the cell cycle. Surprisingly,

Ess1 did not control their transcription but instead was necessary for their
nuclear localization. Ess1 associated with Swi6 and Whi5 in vivo and bound
in vitro
kinases. On the basis of these results, we propose a model in which Ess1
induces a conformational switch (cis-trans
would promote nuclear entry and/or retention during late M and G1 phases
and might work by stimulating dephosphorylation at these sites by the Cdc14
than RNA polymerase II.

INVESTIG ATIONS

Pattern and Distribution of Deleterious

Mutations in Maize
G3: Genes | Genomes | Genetics January 2014 4:163171
EDITORS NOTE
One model for the extreme success of hybrid maize is that complementation
masks the effects of many deleterious mutations. This work reported the results
for complementation in heterosis.

ABSTRACT Most nonsynonymous mutations are thought to be deleterious

Together, these data are consistent with the dominance model of heterosis,

INVESTIG ATIONS

Genomic and Phenotypic Characterization

of a Wild Medaka Population: Towards the
Establishment of an Isogenic Population
Genetic Resource in Fish
G3: Genes | Genomes | Genetics March 2014 4:433445
EDITORS NOTE

et al. laid the groundwork for a

ABSTRACT Oryzias latipes

genomes of wild medaka catches obtained from a single Southern Japanese

for the establishment of the proposed panel. Analysis of morphometric traits

data suggest that the Southern Japanese medaka existed as a larger older

in the Southern population. These data indicate that the genetic structure of

population has commenced. Progress of this project can be tracked at

.

10

OLD & NEW Medaka have been kept as aquarium fish since the 17th
century, with domesticated varieties in a range of colors. Body color
mutants were key to early medaka research, including Tatuo Aidas
1921 GENETICS paper that was the first to demonstrate Y-linked
inheritance in any organism. This 1835 illustration by Baien Mouri
shows white and orange-red medaka varieties. From the National Diet
Library Digital Collections, Japan, http://www.ndl.go.jp.

11

INVESTIG ATIONS

Multigenic Natural Variation Underlies

Caenorhabditis elegans Olfactory Preference
for the Bacterial Pathogen Serratia marcescens
G3: Genes | Genomes | Genetics February 2014 4:265276
EDITORS NOTE C. elegans smells its way through the world, using
dissected the complex genetic architecture of preference for the odor of
certain bacteria. The authors also compared two common methods for
identifying QTLs, and suggested that the odor preference QTLs were more

ABSTRACT The nematode Caenorhabditis elegans can use olfaction to

discriminate among different kinds of bacteria, its major food source. We

C. elegans strains. The laboratory strain N2 strongly prefers the odor of

Serratia marcescens, a soil bacterium that is pathogenic to C. elegans, to
the odor of Escherichia coli, a commonly used laboratory food source. The
Serratia than the

large effect sizes lead to reduced Serratia preference when introgressed into
with at least two antagonistic QTLs from HW that increase Serratia preference.
The complex genetic architecture of this C. elegans trait is reminiscent of the

12

INVESTIG ATIONS

Sequencing, Assembling, and Correcting Draft

Genomes Using Recombinant Populations
G3: Genes | Genomes | Genetics April 2014 4:669679
EDITORS NOTE
de novo is
challenging. Current methods produce thousands of assembled pieces, none

ABSTRACT Current de novo

Problems with these methods are manifest as: large numbers of scaffolds that

propose a new approach for producing de novo

of the problems encountered in standard genome assembly and that can be

de novo
assembly splitting/collapsing and to order and orient scaffolds within linkage
groups. Recombinant population genome construction can rapidly accelerate

immediate applications. In populations segregating for important functional

We demonstrate our method using simulated Illumina data from a recombinant
population of Caenorhabditis elegans and show that the method can produce a

13

INVESTIG ATIONS

Distinct and Predictive Histone Lysine

Acetylation Patterns at Promoters, Enhancers,
and Gene Bodies
G3: Genes | Genomes | Genetics
EDITORS NOTE Because different types of histone lysine acetylations

ABSTRACT

bodies. Unexpectedly, we found that histone acetylation alone performs well in

of characteristic acetylation patterns with genic regions and association of

testable hypotheses to dissect these roles.

14

INVESTIG ATIONS

The Reference Genome Sequence of

Saccharomyces cerevisiae: Then and Now

G3: Genes | Genomes | Genetics March 2014 4:389398

EDITORS NOTE

efforts during the 1990s.

ABSTRACT The genome of the budding yeast Saccharomyces cerevisiae was

work of a worldwide effort of hundreds of researchers. In the time since, the

Saccharomyces
Genome Database, one of the original model organism databases. To deepen
our understanding of the eukaryotic genome, the S. cerevisiae strain S288C

15

INVESTIG ATIONS

An X-Linked Sex Ratio Distorter in Drosophila

simulans That Kills or Incapacitates Both
Noncarrier Sperm and Sons
G3: Genes | Genomes | Genetics October 2014 4:18371848
EDITORS NOTE

an XY father kill the sex of offspring that does not carry the killer chromosome.
Drosophila simulans.

ABSTRACT

fertilize eggs, then the segregation distortion phenotype could be expanded by

sisters compete for shared limiting resources and/or when brothers reduce

skew) in Drosophila
simulans kills or incapacitates noncarrier sperm and also kills a substantial
proportion of sons, i.e.
to occur in D. simulans
dominant suppressors of Winters (Nmy) and Durham (Tmy) failed to suppress
skew
skew, and a
recombination test failed to detect recombinants between these two sex ratio
distorters, indicating that they are tightly linked and plausibly identical or allelic.
segregation distorters.

16

MUTANT SCREEN REPORT

A Genetic Screen Based on in Vivo RNA

Imaging Reveals Centrosome-Independent
Mechanisms for Localizing gurken Transcripts
in Drosophila
G3: Genes | Genomes | Genetics April 2014 4:749760
EDITORS NOTE Transport of gurken mRNA along microtubules establishes
Drosophila oocyte. This Mutant Screen
Report describes a screen for maternal mutations that disrupt localization of
gurken
independent of the centrosome.

to rapidly assess, and for readers to easily understand the screen and its

ABSTRACT
gurken (grk)
messenger (m)RNA, whose transport along microtubules establishes both major
Drosophila

affecting grk mRNA localization and other aspects of oogenesis, including alleles
of elg1, scaf6, quemao, nudE, Tsc2/gigas, rasp, and Chd5/Wrb
alleles of the armitage
kinesin
light chain
grk
mRNA localization and oocyte centrosome integrity. We also show that initiation
of the dorsoanterior localization of grk mRNA precedes centrosome localization,

17

INVESTIG ATIONS

Revised Annotations, Sex-Biased Expression,

and Lineage-Specific Genes in the Drosophila
melanogaster Group
G3: Genes | Genomes | Genetics December 2014 4:23452351
EDITORS NOTE Drosophila
D. melanogaster, genome annotations
et al. used
Drosophila reference genomes.

ABSTRACT
D. ananassae,
D. yakuba, and D. simulans, which include untranslated regions and empirically

the carcass. We identify thousands of genes that are differentially expressed

across tissues in D. yakuba and D. simulans, with roughly 60% agreement in
expression patterns of orthologs in D. yakuba and D. simulans. We identify

Drosophila species, which are candidates for neofunctionalized proteins and a

18

INVESTIG ATIONS

Performance of High-Throughput Sequencing

in Complete Size-Spectrum Genetic
Variation Discovery
G3: Genes | Genomes | Genetics January 2014 4:6365
EDITORS NOTE
used to identify mutations in disease studies. But can the short reads generated
by these methods and existing annotation tools detect the full spectrum of
et al.

ABSTRACT

number gains harder to delineate than losses. We discuss strategies for

association studies.

19

INVESTIG ATIONS

The Genetic Architecture of Seed Composition

in Soybean Is Refined by Genome-Wide
Association Scans Across Multiple Populations
G3: Genes | Genomes | Genetics
EDITORS NOTE Soybean is recognized as a major contributor to worldwide

ABSTRACT

traits (QTL) in numerous crop species. Yet, it is still unclear how soybeans
in this study, we simulated phenotypes resulting from a range of genetic
architectures. We found that with a heritability of 0.5, ~100% and ~33% of the
rate of less than ~610 per marker tested. Additionally, we demonstrated that

(chromosome 20) protein QTL and identifying additional oil QTL that may allow
some decoupling of highly correlated oil and protein phenotypes. Because
we attempted to identify QTL underlying methionine, threonine, cysteine,

multiple populations. Chromosomes 1 and 8 contain strong candidate alleles

data that will be useful in determining breeding strategies for the continued

20

COVER ART CONTEST WINNER

IMMUNE REPERTOIRE In 2014, the GSA journals launched a

contest inviting image submissions related to genetics and genomics. The
winning entry was created by Jian Han, of the HudsonAlpha Institute
for Biotechnology. It depicts an imprint tree map, with each rectangle
representing a unique gene combination of B or T cell receptors, and the
ability to defend against a particular antigen. The larger the rectangle,
the more expressed the gene combination. Imprints provide not only a
quick graphical representation of the overall diversity of an individuals
immune repertoire, but are also personalized artwork.

21

INVESTIG ATIONS

Genome Sequence of Saccharomyces

carlsbergensis, the Worlds First Pure Culture
Lager Yeast
G3: Genes | Genomes | Genetics May 2014 4:783793
EDITORS NOTE Crisp lagers taste different from robust ales because they
Saccharomyces carlsbergensis, the strain that

ABSTRACT
known as the bottom fermenting Saccharomyces carlsbergensis, which was
originally termed Unterhefe No. 1 by Emil Chr. Hansen and has been used
in production in since 1883. S. carlsbergensis
lager yeast strains and is better adapted to cold growth conditions than
e.g., the Weihenstephan strain WS34/70.
S. carlsbergensis
technologies. Lager yeasts are descendants from hybrids formed between
a S. cerevisiae parent and a parent similar to S. eubayanus. Accordingly,
the S. carlsbergensis
Mb S. cerevisiae
the S. cerevisiae genome, and by using directed polymerase chain reaction
for gap closure, we generated a chromosomal map of S. carlsbergensis
S. carlsbergensis
S. cerevisiae
sorting analysis, we determined the ploidy of S. carlsbergensis. This inferred
that this strain is basically triploid with a diploid S. eubayanus and haploid
S. cerevisiae genome content. In contrast the Weihenstephan strain,
S. cerevisiae and S. eubayanus
between the parental genomes in S. carlsbergensis and the Weihenstephan

22

WORMS IN THE FIELD The nematode Caenorhabditis remanei is an

obligate outcrosser with separate males (fanned tail) and females (pointed
tail). In contrast to its primarily self-reproducing relative, C. elegans, natural
populations of C. remanei display large amounts of genetic variation, providing
an ideal model system for capitalizing on functional knowledge gained from
C. elegans for use in studies of molecular population genetics.
Image courtesy of Kristin Sikkink.

Caenorhabditis remanei
G3: Genes | Genomes | Genetics June 2014 4:11231133
Caenorhabditis remanei
Kristin L. Sikkink, Rose M. Reynolds, Catherine M. Ituarte,
William A. Cresko, and Patrick C. Phillips
G3: Genes | Genomes | Genetics June 2014 4:11031112

23

MULTIPARENTAL POPUL ATIONS

In September 2014, the GSA journals launched an ongoing special collection

featuring articles on QTL mapping in multiparental populations (MPPs). We
continue to welcome submissions of both experimental and methodological
your article greater exposure, both to prominent researchers working with
MPPs and to the wider readership of GENETICS and G3.

Scutari et al.
Genetics September 2014 198:129137
Arunas P. Verbyla et al.
G3: Genes | Genomes | Genetics September 2014 4:15691584
Gatti et al.
G3: Genes | Genomes | Genetics September 2014 4:16231633
Zea mays
Lehermeier et al.
Genetics September 2014 198:316

Munger et al.
Genetics September 2014 198:5973
Ram et al.
Genetics September 2014 198:7586

et al.
Genetics September 2014 198:87101
F2
Parker et al.
Genetics September 2014 198:103116
Ahfock et al.
Genetics September 2014 198:117128
et al.
Genetics September 2014 198:139156
24

Giraud et al.
Genetics December 2014 198:17171734
Arabidopsis thaliana
Gnan et al.
Genetics December 2014 198:17511758

Mackay et al.
G3: Genes | Genomes | Genetics September 2014 4:16031610

Wrschum et al.
G3: Genes | Genomes | Genetics September 2014 4:15851591

Higgins et al.
G3: Genes | Genomes | Genetics September 2014 4:15931602
Zea mays
et al.
G3: Genes | Genomes | Genetics September 2014 4:16111621

Apobec1
Smallwood et al.
G3: Genes | Genomes | Genetics December 2014 4:23532363
Zfp30
Rutledge et al.
Genetics October 2014 198:735745
Tsaih et al.
Genetics September 2014 198:1729
Drosophila melanogaster
King et al.
Genetics September 2014 198:3143
Drosophila
Marriage et al.
Genetics September 2014 198:4557
25

Why publish in GENETICS & G3?

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Initial call on whether to send for review takes just days.

Within days of initial manuscript submission, we will let you know whether the
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At least

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Your manuscripts will be handled by practicing scientists like you, who understand
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If you submit a manuscript to GENETICS that reports high-quality and

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Within days, manuscripts are published Early Online, indexed in

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Our journals are run by and for scientists under the aegis of the Genetics Society
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GENETICS and G3 have long been committed to integrating with community resources.
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Our data policy, instituted in 2009, requires that all primary data
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