Emergence of novel color vision in mice engineered to express a human cone photopigment

Changes in the genes encoding sensory receptor proteins are an essential step in the evolution of new sensory capacities. In primates, trichromatic color vision evolved after changes in X chromosome-linked photopigment genes. To model this process, we studied knock-in mice that expressed a human long-wavelength-sensitive (L) cone photopigment in the form of an X-linked polymorphism. Behavioral tests demonstrated that heterozygous females, whose retinas contained both native mouse pigments and human L pigment, showed enhanced long-wavelength sensitivity and acquired a new capacity for chromatic discrimination. An inherent plasticity in the mammalian visual system thus permits the emergence of a new dimension of sensory experience based solely on gene-driven changes in receptor organization.     

Comment on "Evolutionary paths underlying flower color variation in Antirrhinum"

Although Whibley et al. (Reports, 18 August 2006, p. 963) argue for the presence of high-fitness ridges in the Antirrhinum floral-color adaptive landscape, their data are equally compatible with adaptive landscapes having a single peak and no ridges. Their demonstration of divergent selection across a hybrid zone argues against the presence of adaptive ridges.     

Molecular genetics of inherited variation in human color vision

The hypothesis that red-green "color blindness" is caused by alterations in the genes encoding red and green visual pigments has been tested and shown to be correct. Genomic DNA's from 25 males with various red-green color vision deficiencies were analyzed by Southern blot hybridization with the cloned red and green pigment genes as probes. The observed genotypes appear to result from unequal recombination or gene conversion (or both). Together with chromosome mapping experiments, these data identify each of the cloned human visual pigment genes.     

Is orientation-specific color adaptation in human vision due to edge detectors, afterimages, or "dipoles"?

After one looks alternately at red vertical and green horizontal stripes, vertical and horizontal white stripes appear greenish and pink, respectively. This color aftereffect might imply that contour-detecting cells participate in human vision, or might simply be due to afterimages. A procedure that precludes afterimages still yields aftereffects, but sensory units less complex than edge detectors could be responsible.     

Comment on "A global map of human impact on marine ecosystems"

Halpern et al. (Reports, 15 February 2008, p. 948) integrated spatial data on 17 drivers of change in the oceans to map the global distribution of human impact. Although fishery catches are a dominant driver, the data reflect activity while impacts occur at different space and time scales. Failure to account for this spatial disconnection could lead to potentially misleading conclusions.     

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"

Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported large numbers of differences between DNA and messenger RNA in human cells, indicating unprecedented levels of RNA editing, and including sequence changes not produced by any of the known RNA editing mechanisms. However, common sources of systematic errors in high-throughput sequencing technology, which were not properly accounted for in this study, explain most of the claimed differences.     

Comment on "The consensus coding sequences of human breast and colorectal cancers"

Sj?blom et al. (Research Article, 13 October 2006, p. 268) reported nearly 200 novel cancer genes said to have a 90% probability of being involved in colon or breast cancer. However, their analysis raises two statistical concerns. When these concerns are addressed, few genes with significantly elevated mutation rates remain. Although the biological methodology in Sj?blom et al. is sound, more samples are needed to achieve sufficient power.     

Comment on "Nonreciprocal light propagation in a silicon photonic circuit"

We show that the structure demonstrated by Feng et al. (Reports, 5 August 2011, p. 729) cannot enable optical isolation because it possesses a symmetric scattering matrix. Moreover, one cannot construct an optical isolator by incorporating this structure into any system as long as the system is linear and time-independent and is described by materials with a scalar dielectric function.     

Comment on "From plant traits to plant communities: a statistical mechanistic approach to biodiversity"

Shipley et al. (Reports, 3 November 2006, p. 812) predicted plant community composition and relative abundances with a high level of accuracy by maximizing Shannon's index of information entropy (species diversity), subject to constraints on plant trait averages. We show that the entropy maximization assumption is relatively unimportant and that the high accuracy is due largely to a statistical effect.     

Comment on "Origin of human bipedalism as an adaptation for locomotion on flexible branches"

Thorpe et al. (Reports, 1 June 2007, p. 1328) concluded that human bipedalism evolved from a type of bipedal posture they observed in extant orangutans with seemingly human-like extended knees. However, humans share knuckle-walking characters with African apes that are absent in orangutans. These are most parsimoniously explained by positing a knuckle-walking precursor to human bipedalism.     

Comment on "Transitions to asexuality result in excess amino acid substitutions"

Paland and Lynch (Reports, 17 February 2006, p. 990) showed that in Daphnia pulex, the ratio of amino acid replacement to silent substitution in mitochondrial genes is higher in asexual lineages than in sexual lineages. If this base-composition bias is maintained by selection, it too should alter following transitions in reproductive mode. Analysis reveals no such change in the genomes of D. pulex.     

Comment on "Preindustrial to modern interdecadal variability in coral reef pH"

Based on the boron isotopic composition of coral from the southwestern Pacific, Pelejero et al. (Reports, 30 September 2005, p. 2204) suggested that natural variations in pH can modulate the impact of ocean acidification on coral reef ecosystems. We show that this claim cannot be reconciled with other marine carbon chemistry constraints and highlight problems with the authors' interpretation of the paleontologic data.     

Comment on "Magnetic resonance spectroscopy identifies neural progenitor cells in the live human brain"

Manganas et al. (Reports, 9 November 2007, p. 980) used nuclear magnetic resonance spectroscopy to identify a biomarker of neural progenitor cells. However, their analysis relies on spectral processing methods that are known to be problematic. Absent detection using alternate methods of spectrum analysis or controls to quantify the false discovery rate, their conclusions may be premature.     

Comment on "Pairing and phase separation in a polarized Fermi gas"

Partridge et al. (Reports, 27 January 2006, p. 503) reported pairing and phase separation in a polarized Fermi gas. We argue that it is not possible to distinguish the superfluid from the normal regimes in the presented data, or to discern which clouds were phase-separated. Some of the reported conclusions are inconsistent with recent experiments.     

Comment on "A keystone mutualism drives pattern in a power function"

Vandermeer and Perfecto (Reports, 17 February 2006, p. 1000) maintain that a mutualist ant disrupts the power law distribution of scale insect abundances. However, reanalysis of the data reveals that ants cause an increase in the range of the power law and modify its exponent. We present a tentative, but more realistic, model that is suitable for quantitative predictions.     

Comment on "Long-lived giant number fluctuations in a swarming granular nematic"

Narayan et al. (Reports, 6 July 2007, p. 105) reported giant number fluctuations attributed to curvature-driven active currents specific for nonequilibrium nematic systems. We present data demonstrating that similar results can be found in systems of spherical particles due either to inelastic clustering or persistent density inhomogeneity, suggesting two alternative explanations for their results.