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Genetics and Ecology March eMagazine

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Contents Click below to explore… 3) Introduction 4) Worldwide frequency distribution of the ‘Gait keeper’ mutation in the DMRT3 gene 4) Multiple marker effects of single nucleotide polymorphisms in three genes, AKIRIN2, EDG1 and RPL27A, for marbling development in Japanese Black cattle

5) Expanding the scope of site-specific recombinases for genetic and metabolic engineering 5) Special Issue: Ecology and evolution on oceanic islands: broadening the botanical perspective 6) How fruit developmental biology makes use of flow cytometry approaches

6) Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition 7) Useful Links! Books, Plant Genomes Database, Animal Genetics Databases and Tools 8) Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection

12) Mitochondrial DNA: more than an evolutionary bystander 13) Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus

13) Modelling the spatial spread of a homing endonuclease gene in a mosquito population 14) How to… Conduct flow Analysis and sort Plant Chromosomes 15) Home site advantage in two long-lived arctic plant species: results from two 30-year reciprocal transplant studies 15) Potential for adaptation in response to thermal stress in an intertidal macroalga

16) PopGenReport: simplifying basic population genetic analyses in R 16) Measuring telomere length and telomere dynamics in evolutionary biology and ecology

17) Bioinformatics in Genome Sequencing Projects 17) Genetic Variation and Molecular Evolution

8) Expression patterns of Wnt genes in the venom claws of centipedes

9) How to… Use QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities 10) Will you stop bugging me? Malaria and the evolutionary challenge that won't go away 10) Special Issue: Climate change, adaptation and phenotypic plasticity

18) ‘VISIONS: the art of science’ Reconstruction of the methylome: Visualizing the ontogeny of DNA methylation in the bovine embryo 18) Ecological and genetic factors linked to contrasting genome dynamics in seed plants 19) Seed dispersal in time can counteract the effect of gene flow between natural populations of Arabidopsis thaliana 19) RNA Regulation

11) Useful Links! Encyclopedia of Molecular Cell Biology and Molecular Medicine, Citeable Reviews

20) Special Issue: The Developmental Biology of Sea Urchins: Forefronts and Recent Advances

12) Conservation genetics and management of yellowtail snapper, Ocyurus chrysurus, in the US Caribbean and South Florida

21) Useful Links! Grapevine Gene Database, Laboratory Protocols, 34th ISAG Conference 2


Introduction Welcome to the March Genetics eMagazine!

In this edition, themed on Genetics and Ecology, we bring you some of the leading research and cutting-edge developments in the fields of animal genetics, plant genetics, genetics techniques, and more. Read on for articles, books, useful links, databases, and how-to guides, for use in your research and work.

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Animal Genetics Worldwide frequency distribution of the ‘Gait keeper’ mutation in the DMRT3 gene M. Promerová et al.

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Summary For centuries, domestic horses have represented an important means of transport and served as working and companion animals. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. Image: Frequency distribution of the DMRT3 gait-altering mutation for breeds with at least five samples tested.

Animal Science Journal Multiple marker effects of single nucleotide polymorphisms in three genes, AKIRIN2, EDG1 and RPL27A, for marbling development in Japanese Black cattle Shin Sukegawa et al.

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Summary Marbling in beef, measured by Beef Marbling Standard (BMS) number, is an economically important trait for beef cattle breeding and markets in Japan. We previously detected three single nucleotide polymorphisms (SNPs) associated with BMS number of Japanese Black in Oita prefecture: c.*188G>A in AKIRIN2, g.1471620G>T in EDG1 and g.3109537C>T in RPL27A. Here, we carried out single and multiple marker association analyses for the three SNPs in a different commercial Japanese Black population of 892 genotyped animals. Right: Frequency distributions (%) of the grade of Beef Marbling Standard (BMS) number for the 892 genotyped animals collected from Kagoshima.

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Biotechnology and Bioengineering Expanding the scope of site-specific recombinases for genetic and metabolic engineering Thomas Gaj, Shannon J. Sirk and Carlos F. Barbas III

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Summary Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. Right: Surface illustration of the Flp monomer bound to FRT DNA target. Mutations that contribute to the interactions between evolved Flp variants and unnatural FRT targets are highlighted red. DNA depicted as a gray cartoon.

Botanical Journal of the Linnean Society Special Issue: Ecology and evolution on oceanic islands: broadening the botanical perspective

Summary

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Since its foundation, the Botanical Journal of the Linnean Society has participated in the dissemination of scientific research related to the ecology, evolution and conservation of island plants. Recent papers published in the journal have investigated the population genetics, phylogenetic relationships, anatomy and reproductive biology of island plants. We hope that this special issue will contribute, with other forthcoming events (e.g. the Island Biology conference that will be held in Honolulu in July 2014), to put these small and geographically isolated – but scientifically amazing – ‘living’ laboratories on the map. Right: Map of sampled populations of Acmispon from the California Channel Islands and southern California mainland.

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Cytometry A How fruit developmental biology makes use of flow cytometry approaches Julien Pirrello et al.

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Abstract Fleshy fruit species such as tomato are important because of their nutritional and economic value. Fruit growth like all plant organs depends upon the developmental processes of cell division and cell expansion. The activity of cell divisions sets the number of cells that will compose the fruit; the cell expansion activity then determines its final size. Among the various mechanisms that may influence the determination of cell size, endopolyploidy by the means of endoreduplication, i.e. genome amplification in the absence of mitosis, appears to be of great importance in fleshy fruits.

Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition Read More Online John M. Hancock and Marketa J. Zvelebil A thoroughly updated new edition of this acclaimed and comprehensive guide to the fast moving field of bioinformatics and computational biology Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition is a fully revised and updated version of this acclaimed resource. The book provides definitions and often explanations of over 1000 words, phrases and concepts relating to this fast-moving and exciting field, offering a convenient, one-stop summary of the core knowledge in the area. This second edition is an invaluable resource for students, researchers and academics. Available in multiple formats! Paperback Hardcover E-book Updating library reference work

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Useful links! For Wiley’s range of genetics books…

For PlantGDB’s database of plant genomes…

For the AHPC’s collection of animal genetics databases and tools…

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Evolution Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection Jill T. Anderson, Cheng-Ruei Lee and Thomas Mitchell-Olds

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Abstract Fitness trade-offs across episodes of selection and environments influence life-history evolution and adaptive population divergence. Here, we evaluate fitness trade-offs at the levels of the whole organism and the quantitative trait locus (QTL) in a multiyear field study of Boechera stricta (Brassicaceae), a genetically tractable mustard native to the Rocky Mountains. Our analytical framework can be applied to other systems to investigate fitness trade-offs. Right: Fecundity components of fitness increase as a function of the percentage of the genome with Montana alleles (MT%) for the 2008 Montana cohort.

Evolution & Development Expression patterns of Wnt genes in the venom claws of centipedes Luke Hayden and Wallace Arthur

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Abstract The venom claws of centipedes, also known as forcipules, represent an evolutionary novelty that must have arisen in the centipede stem species, as they are not found in any other myriapods. The developmental-genetic changes that are involved in the origin of novelties are of considerable interest. It has previously been shown that centipede forcipules have a unique Hox code. However, this is a combinatorial code: no single Hox gene has a forcipule-specific expression. Here, we focus on Wnt genes. Right: Ventral view of anterior region of Strigamia maritima adult, with forcipule and leg labeled to display differing morphologies.

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How to‌ Use QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities Justin Kuczynski et al.

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Summary Basic Protocol 1: represents the first analysis steps typically performed on 16S DNA sequence data from microbial communities. Basic Protocol 1 consists of acquiring an example dataset, and assigning the DNA sequences in that study to the nine microbial communities included in the study. In typical usage, a researcher would substitute the data produced by a sequencing platform for the example data used here‌ Basic Protocol 2: consists of picking Operational Taxonomic Units (OTUs) based on sequence similarity within the reads, and picking a representative sequence from each OTU. The protocol also assigns taxonomic identities using reference databases, aligns the OTU sequences, creates a phylogenetic tree, and constructs an OTU table, representing the abundance of each OTU in each microbial sample. Basic Protocol 2 requires demultiplexed sequences such as those generated in the seqs.fna file from Basic Protocol 1.

Basic Protocol 3: consists of computing the within community diversity (alpha diversity) for each of the 9 microbial communities, and generating rarefaction curves (graphs of diversity versus sequencing depth). Basic Protocol 3 requires an OTU table and phylogenetic tree such as those produced in Basic Protocol 2. An OTU table heatmap showing taxonomy assignment for each OTU.

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Evolutionary Anthropology Will you stop bugging me? Malaria and the evolutionary challenge that won't go away Kenneth M. Weiss and Daniel M. Parker

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Abstract The mosquito's warm affinity for humans provides an itch we have to scratch, but malaria is driven by various other and more subtle factors: the parasite's life cycle, swampy water, human red blood cells, and the like. These interactions have often been seen as a three-way genetic contest, among the genomes of the parasite, insect, and mammalian host. From the fundamental dependency of each upon the other, one would expect that resistance would evolve in the victims, but that predators would then evolve the continued ability to inflict their affections. However, evolution is rarely that simple‌

Evolutionary Applications Special Issue: Climate change, adaptation and phenotypic plasticity Read More Online

Introduction Many studies have recorded phenotypic changes in natural populations and attributed them to climate change. However, controversy and uncertainty has arisen around three levels of inference in such studies. We here review the various ways in which these inferences have been attempted, and evaluate the strength of support that each approach can provide. Summarizing and relying on the results of these reviews, we arrive at the conclusion that evidence for genetic adaptation to climate change has been found in some systems, but is still relatively scarce. Right: Examples of model species utilized in research on genetic underpinnings of climate change responses.

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Encyclopedia of Molecular Cell Biology and Molecular Medicine Editor(s): Dr. Robert A. Meyers Read More Online

Updated quarterly, this Encyclopedia covers both the molecular and cellular basis of life and medicine.

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For Wiley’s range of citeable reviews in the life sciences‌

www.els.net

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Fisheries Management and Ecology Conservation genetics and management of yellowtail snapper, Ocyurus chrysurus, in the US Caribbean and South Florida E. A. Saillant et al.

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Abstract Population-genetic structure and average long-term effective size of yellowtail snapper, Ocyurus chrysurus (Bloch), sampled offshore from the Florida Keys and four localities in the US Caribbean, were investigated using nuclear-encoded microsatellites and a fragment of the mitochondrially encoded ND-4 gene. Levels of genetic variability and estimates of average, long-term effective size (Ne) indicate that yellowtail snapper at all five localities have, at present, sufficient genetic variation to maintain long-term integrity and sustainability. Right: Parsimony network of Ocyurus chrysurus mtDNA haplotypes.

Functional Ecology Mitochondrial DNA: more than an evolutionary bystander J. William O. Ballard and Nicolas Pichaud

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Summary Mitochondria are cellular organelles that provide cells with energy and contain their own DNA (mitochondrial DNA or mtDNA). Mitochondria have their own unique pattern of inheritance, and in the twentieth century many ecologists and evolutionary biologists used mtDNA as a marker to infer demographic and historical patterns, without pondering the underlying functional implications. In this review we delve into the literature and show that a more complete understanding of mitochondrial functions can enable important ecological and evolutionary insights. Right: Picture of an Australian Cattle Dog chasing a ball. In nature the ability to capture prey is likely to be dependent on energy production from mitochondria and this is heritable. Photograph courtesy of Outdoor Action Photography.

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Journal of Applied Ecology Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus Tony Dejean et al.

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Introduction Alien invasive species (AIS) constitute one of major causes of biodiversity loss and global homogenization. The ability to detect an AIS at low densities greatly determines the success of an eradication operation, decreases the costs of control and reduces the impact on ecosystems. In this study, we propose to use the newly developed environmental DNA (eDNA) barcoding approach, using water samples as the DNA source. This method has been successfully implemented in the detection of invasive or secretive species. We compare and consider the potential errors of both methods (surveys and eDNA). Right: Distribution of introduced bullfrog populations in France.

Journal of Applied Ecology Modelling the spatial spread of a homing endonuclease gene in a mosquito population Ace North, Austin Burt and H. Charles J. Godfray

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Summary Homing endonuclease genes (HEGs) are a type of autonomously spreading genetic element found naturally in some single-celled eukaryotes (Burt & Trivers 2006). There are a number of ways that HEGs might be used to help combat vector-borne diseases . The aim of the work described here was to develop the appropriate modelling framework and explore which aspects of landscape structure have the greatest effect on spatial spread and optimum release strategy. Factors that increase the extent of mosquito dispersal heighten the probability an introduced HEG becomes established and causes population extinction.

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How to… Conduct flow Analysis and sort Plant Chromosomes Jaroslav Doležel, Jiří Macas and Sergio Lucretti

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Summary Basic Protocol 1: a procedure for accumulation of cells in metaphase. Alternate Protocol 1: a modification of the procedure that is suitable for cereals such as barley (Hordeum vulgare) and rye (Secale cereale). Basic Protocol 2: preparation of chromosome suspensions from synchronized root tips. Alternate Protocol 2: the modification of Basic Protocol 1 for the use with immortal root (hairy root) cultures. Basic Protocol 3: univariate flow analysis of isolated chromosomes. Alternate Protocol 3: bivariate analysis of isolated chromosomes. Basic Protocol 4: provides a procedure for physical gene mapping. Alternate Protocol 4: presents a procedure for two-step sorting that is useful for sorting chromosomes whose frequency in the original suspension is too low, or for chromosomes that are difficult to sort with acceptable purity.

Bivariate flow k aryotypes of two field bean chromosome translocation lines.

Support Protocol 2: describes the alignment of the flow cytometer, crucial for achieving the highest purity of sorted chromosome fractions. Support Protocol 3: gives a method for detecting contamination of the sorted fractions and for estimating the degree of purity.

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Journal of Ecology Home site advantage in two long-lived arctic plant species: results from two 30-year reciprocal transplant studies Cynthia C. Bennington et al.

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Summary Reciprocal transplant experiments designed to quantify genetic and environmental effects on phenotype are powerful tools for the study of local adaptation. For long-lived species, especially those in habitats with short growing seasons, however, the cumulative effects of many years in novel environments may be required for fitness differences and phenotypic changes to accrue. Here, we report the results of two 30-year-old reciprocal transplant experiments in Alaskan tundra plants. Right: Map of interior Alaska showing approximate locations of transplant gardens for Dryas octopetala and Eriophorum vaginatum.

Journal of Phycology Potential for adaptation in response to thermal stress in an intertidal macroalga Jennifer S. Clark et al.

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Summary Understanding responses of marine algae to changing ocean temperatures requires knowledge of the impacts of elevated temperatures and the likelihood of adaptation to thermal stress. The potential for rapid evolution of thermal tolerance is dependent on the levels of heritable genetic variation in response to thermal stress within a population. Here, we use a quantitative genetic breeding design to establish whether there is a heritable variation in thermal sensitivity in two populations of a habitat-forming intertidal macroalga, Hormosira banksii (Turner) Descaisne. Right: Representative embryo morphology at 20째C and 28째C after 24 and 120 h.

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Methods in Ecology & Evolution PopGenReport: simplifying basic population genetic analyses in R Aaron T. Adamack and Bernd Gruber

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Introduction Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but using R can be challenging for many researchers due to its steep learning curve. PopGenReport is a new R package that simplifies performing population genetics analyses in R, through the use of a new report-generating function‌

Read more here.

Methods in Ecology & Evolution Measuring telomere length and telomere dynamics in evolutionary biology and ecology Read More Online

Daniel N. Hussey et al.

Summary Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. We discuss the key issues to consider and wherever possible try to provide current consensus view regarding best practice with regard to sample collection and storage, DNA extraction and storage, and the five main methods currently available to measure TL. Right: Schematic showing k ey stages in decision-making process when considering a study of telomere length and the important questions to consider at each stage.

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eLS Bioinformatics in Genome Sequencing Projects

Cornelis Victor Jongeneel

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Abstract Genome sequencing and analysis is a field that has evolved very rapidly over the 10 years since a final draft of the human genome sequence was published in 2003. From obtaining a full genome sequence from a representative individual or strain of a small number of species, the genomics community has moved to documenting genetic diversity within species, with an emphasis on humans, and more generally by sequencing the genomes of a rapidly growing number of species. A new generation of software tools has been designed to handle the very large numbers of short sequences, commonly referred to as reads, produced by the new machines, and has also propelled the field of computational genomics into the realm of Big Data that require large and sophisticated computer systems for their management and analysis.

Encyclopedia of Molecular Cell Biology and Molecular Medicine Genetic Variation and Molecular Evolution

Wemer Arber

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Abstract Evolutionary biology has traditionally devoted its major attention to the comparison of phenotypical traits of higher organisms, both of those actually living and of those that have been extinct (paleontological fossils). The resulting theory of descent is, together with other criteria, at the basis of the systematic classification of living organisms. synoptical insight into the various molecular mechanisms contributing to the generation of genetic variations represents a molecular synthesis between the neo-Darwinian theory and molecular genetics. This synthesis can confirm the Darwinian evolution at the molecular level.

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Molecular Reproduction & Development VISIONS: the art of science Reconstruction of the methylome: Visualizing the ontogeny of DNA methylation in the bovine embryo Read More Online

New Phytologist Ecological and genetic factors linked to contrasting genome dynamics in seed plants A. R. Leitch and I. J. Leitch

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Introduction Seed plants today comprise the Angiospermae (hereafter referred to as the angiosperms or flowering plants) and the Acrogymnospermae (hereafter referred to as the gymnosperms). To appreciate differences between angiosperm and gymnosperm genomes, we first explore the relationships between these two groups, so that available genomic data can be viewed in an appropriate evolutionary context. We then examine the broad nature and extent of genomic differences across vascular plants (lycophytes, monilophytes, gymnosperms and angiosperms) and finally we speculate as to which aspects of seed plant biology may have influenced, or been influenced by, genome dynamics.

Image: Fluorescent in situ hybridization (FISH) to chromosomes of Pinus taeda using probes for 45S ribosomal DNA and interstitial telomere sequences.

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New Phytologist Seed dispersal in time can counteract the effect of gene flow between natural populations of Arabidopsis thaliana Mohsen Falahati-Anbaran, Sverre Lundemo and Hans K. Stenøien

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Abstract Many plant species increase their chances to persist and cope with unfavorable environmental conditions through delayed germination (seed bank formation) or migration to and establishment in more favorable habitats (colonization). The main objectives of this study were to quantify persistence of genotypes in soil seed banks over time and to infer what proportion of present-day individuals descend directly from seeds shed more than one generation ago; and to estimate immigration rates in the populations over a 5 year period. Left: Genetic structure of 222 cohorts across 36 Norwegian populations of Arabidopsis thaliana monitored for five consecutive years.

RNA Regulation Robert A. Meyers

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Everything you need to know about RNA biology in two comprehensive volumes. Based on one of the leading encyclopedic resources in cell and molecular biology worldwide, this two-volume work contains more than 75% new content, not previously published in the Encyclopedia. All the other chapters have been carefully updated. The result is a comprehensive overview of the different functions of the various forms of RNA in living organisms, with each contributor carefully selected and an internationally recognized expert on his or her field. Special focus is on the different forms of expression regulation through RNA, with medical applications in the treatment of diseases -- from cancers and immune responses to infections and aging -- covered in detail. At least 45 of the 55 articles are new content previously not published in the Encyclopedia. Available in: Hardcover

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genesis: The Journal of Genetics and Development Special Issue: The Developmental Biology of Sea Urchins: Forefronts and Recent Advances

Summary

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In this special issue of genesis: The Journal of Genetics and Development, we focus on reviews of recent studies on early embryonic patterning, cell interactions, morphogenesis, and the evolution of developmental processes that highlight the enduring strength of sea urchins as an experimental model. This Special Issue is guest edited by Charles A. Ettensohn (Carnegie Mellon University), Robert D. Burke (University of Victoria) and David R. McClay (Duke University).

Containing reviews on…  The echinoderm larval skeleton as a possible model system for experimental evolutionary biology  Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms  Telling left from right: Left-right asymmetric controls in sea urchins

Image: Effector and regulatory genes in sea urchins

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Useful links! For the University of Adelaide’s database for grapevine genes…

For Wiley’s range of laboratory protocols…

For the 34th ISAG conference…

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Genetics and Ecology March eMagazine