Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome

For years evolutionary biologists have been interested in searching for the genetic bases underlying humanness. Recent efforts at a large or a complete genomic scale have been conducted to search for positively selected genes in human and in chimp. However, recently developed methods allowing for a more sensitive and controlled approach in the detection of positive selection can be employed. Here, using 13,198 genes, we have deduced the sets of genes involved in rate acceleration, positive selection, and relaxation of selective constraints in human, in chimp, and in their ancestral lineage since the divergence from murids. Significant deviations from the strict molecular clock were observed in 469 human and in 651 chimp genes. The more stringent branch-site test of positive selection detected 108 human and 577 chimp positively selected genes. An important proportion of the positively selected genes did not show a significant acceleration in rates, and similarly, many of the accelerated genes did not show significant signals of positive selection. Functional differentiation of genes under rate acceleration, positive selection, and relaxation was not statistically significant between human and chimp with the exception of terms related to G-protein coupled receptors and sensory perception. Both of these were over-represented under relaxation in human in relation to chimp. Comparing differences between derived and ancestral lineages, a more conspicuous change in trends seems to have favored positive selection in the human lineage. Since most of the positively selected genes are different under the same functional categories between these species, we suggest that the individual roles of the alternative positively selected genes may be an important factor underlying biological differences between these species

Role of APOBEC3 in Genetic Diversity among Endogenous Murine Leukemia Viruses

The ability of human and murine APOBECs (specifically, APOBEC3) to inhibit infecting retroviruses and retrotransposition of some mobile elements is becoming established. Less clear is the effect that they have had on the establishment of the endogenous proviruses resident in the human and mouse genomes. We used the mouse genome sequence to study diversity and genetic traits of nonecotropic murine leukemia viruses (polytropic [Pmv], modified polytropic [Mpmv], and xenotropic [Xmv] subgroups), the best-characterized large set of recently integrated proviruses. We identified 49 proviruses. In phylogenetic analyses, Pmvs and Mpmvs were monophyletic, whereas Xmvs were divided into several clades, implying a greater number of replication cycles between the integration events. Four distinct primer binding site types (Pro, Gln1, Gln2 and Thr) were dispersed within the phylogeny, indicating frequent mispriming. We analyzed the frequency and context of G-to-A mutations for the role of mA3 in formation of these proviruses. In the Pmv and Mpmv (but not Xmv) groups, mutations attributable to mA3 constituted a large fraction of the total. A significant number of nonsense mutations suggests the absence of purifying selection following mutation. A strong bias of G-to-A relative to C-to-T changes was seen, implying a strand specificity that can only have occurred prior to integration. The optimal sequence context of G-to-A mutations, TTC, was consistent with mA3. At least in the Pmv group, a significant 5′ to 3′ gradient of G-to-A mutations was consistent with mA3 editing. Altogether, our results for the first time suggest mA3 editing immediately preceding the integration event that led to retroviral endogenization, contributing to inactivation of infectivity

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitution rates, the proportionate number of nonsynonymous differences (dN) is divided by the proportionate number of synonymous differences (dS). The resulting ratio (dN/dS) is a widely used indicator for functional divergence to identify particular genes that underwent positive selection. With the ever-growing amount of genome data, summary statistics like mean dN/dS allow gathering information on the mode of evolution for entire species. Both applications hinge on the assumption that dS and mean dS (∼branch length) are neutral and adequately control for variation in substitution rates across genes and across organisms, respectively. We here explore the validity of this assumption using empirical data based on whole-genome protein sequence alignments between human and 15 other vertebrate species and several simulation approaches. We find that dN/dS does not appropriately reflect the action of selection as it is strongly influenced by its denominator (dS). Particularly for closely related taxa, such as human and chimpanzee, dN/dS can be misleading and is not an unadulterated indicator of selection. Instead, we suggest that inconsistencies in the behavior of dN/dS are to be expected and highlight the idea that this behavior may be inherent to taking the ratio of two randomly distributed variables that are nonlinearly correlated. New null hypotheses will be needed to adequately handle these nonlinear dynamics

Propagating spectropolarimetric disturbances in a large sunspot

We present results derived from the analysis of spectropolarimetric measurements of active region AR12546, which represents one of the largest sunspots to have emerged onto the solar surface over the last 20 years. The region was observed with full-Stokes scans of the Fe I 617.3 nm and Ca II 854.2 nm lines with the Interferometric BIdimensional Spectrometer (IBIS) instrument at the Dunn Solar Telescope over an uncommon, extremely long time interval exceeding three hours. Clear circular polarization (CP) oscillations localized at the umbra-penumbra boundary of the observed region were detected. Furthermore, the multi-height data allowed us to detect the downward propagation of both CP and intensity disturbances at 2.5−3~mHz, which was identified by a phase delay between these two quantities. These results are interpreted as a propagating magneto-hydrodynamic surface mode in the observed sunspot

THE HUMAN HEARTH AND THE DAWN OF MORALITY

Stunned by the implications of Colage's analysis of the cultural activation of the brain's Visual Word Form Area and the potential role of cultural neural reuse in the evolution of biology and culture, the authors build on his work in proposing a context for the first rudimentary hominin moral systems. They cross-reference six domains: neuroscience on sleep, creativity, plasticity, and the Left Hemisphere Interpreter; palaeobiology; cognitive science; philosophy; traditional archaeology; and cognitive archaeology's theories on sleep changes in Homo erectus and consequences for later humans. The authors hypothesize that the human genome, when analyzed with findings from neuroscience and cognitive science, will confirm the evolutionary timing of an internal running monologue and other neural components that constitute moral decision making. The authors rely on practical modern philosophers to identify continuities with earlier primates, and one major discontinuitysome bright white moral line that may have been crossed more than once during the long and successful tenure of Homo erectus on Earth.First published: 27 November 2016; 24 month embargoThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]