The icy waters of the Neumeyer Channel on the Antarctica Peninsula, and regions nearby, are home to several species of Antarctic icefish, animals that fit Darwin's phrase, a “wreck of nature.” Unique among vertebrates, icefish lack red blood cells and functional hemoglobin genes, have greatly reduced bone mineralization compared to related fish, and have lost the nearly-ubiquitous inducible heat shock response. Image courtesy of John Postlethwait, 2015 recipient of the Genetics Society of America's George W. Beadle Award.
The July issue of GENETICS is out now! Check out the Highlights below of the full Table of Contents here. And don’t miss the essays by winners of 2015 GSA Honors and Awards!
Most genome-wide association studies (GWAS) reveal only regions of association, while the underlying causal variants remain unclear. Chen et al. show that two existing methods for identifying candidate causal variants can be unified in a general Bayesian framework, allowing application of an approximate Bayesian method that uses only the summary information. Through simulations and real data analysis, the authors show the proposed method identified candidate causal variants with high accuracy.
Septins are a family of GTP-binding proteins that self-assemble into higher-order structures. In these companion papers, Finnigan et al. analyzed the function of Shs1 and Cdc11, the paralogous terminal subunits of the septin hetero-octamer. Comprehensive analyses revealed the importance of a C-terminal extension that optimizes recruitment of the protein Bni5, thereby ensuring efficient localization of the type II myosin of the actomyosin contractile ring.
Like the teeth of a bicycle sprocket-wheel, the “sprocket” arginine residues of histones insert into the minor groove of the DNA “chain.” Hodges et al. identify novel functions for histone sprocket arginine residues in gene expression, cryptic transcription, DNA repair, and histone occupancy. These findings reveal simple rules for how the biological function of each “sprocket” residue is influenced by the location and structural mode of DNA binding.
To test many hypotheses of molecular sequence evolution, the gene sequences of ancestral species must be inferred. However, the use of reconstructed ancestral sequences may produce spurious results because systematic biases emerge from using the single best reconstructions while ignoring the suboptimal ones, and from model violations. Matsumoto et al. developed methods to correct for such biases and used simulation to evaluate their performance when nucleotide substitution patterns are not constant. The authors suggest the new methods may be useful for studying complex patterns of nucleotide substitution in large genomic datasets.
Helicobacter pylori is a bacterium that inhabits the stomachs of half of all humans, but the vast majority of infections are asymptomatic. Montano et al. analyze the genomes of 60 strains from around the world and find H. pylori has been co-habiting with our species much longer than previously thought. The authors demonstrate that this long-term interaction has led to the evolution of differential local adaptation. They also outline the potential for future medical, functional, and evolutionary research on H. pylori, our oldest known commensal.
Thompson et al. report a reference genome sequence for the Hawaiian strain CB4856 of C. elegans, widely studied for its phenotypic differences from the N2 laboratory strain. This revealed 61 regions spanning 2.8 Mb that contain a disproportionate number of SNVs and an abundance of genes from large, rapidly evolving gene families. Because of their high divergence—up to 16% differences—these regions had largely escaped detection in prior studies. Comparison with other wild isolates suggests that these regions are maintained over long evolutionary periods by balancing selection.
In genome-wide association studies (GWAS) of metabolites, non-additive genetic effects might be especially important because metabolite phenotypes are closer to the underlying pathways than many other traits. However, most GWAS on metabolites assume additivity. Tsepilov et al. analyzed a panel of 151 metabolites and their ratios (22,801 in total) for non-additive genetic effects in a population based cohort and found that in fact most SNP effects were additive. This provides empirical support for the additivity of genetic control of metabolism.
The relative contribution of regulatory and coding changes to the evolution of phenotypic traits is an important, and highly debated, question in evolutionary biology. Wang et al. show that a single nucleotide change in the gene teosinte glume architecturel (tgal) confers naked kernels in maize vs. encased kernels in the wild maize progenitor. This polymorphism causes an amino acid substitution in the TGA1 transcriptional regulator, and this affects dimer stability. These results show how morphological evolution can be driven by a simple nucleotide change that alters protein function.
“Genetic program” has become a deeply entrenched metaphor which compares organisms to computers executing programs for processes such as reproduction, development, differentiation, apoptosis, homeostasis, and behavior. Based on unpublished archives, Peluffo investigates the genesis of this influential metaphor of the “genetic program,” shows how it solved the problem of purpose in biology, and suggests that there was a shared origin for its independent introduction by two articles in 1961, one by French Nobel laureates Francois Jacob and Jacques Monod and one by prominent American evolutionary biologist Ernst Mayr.
What Use Is Population Genetics?