The evolution of modern eukaryotic phytoplankton

The community structure and ecological function of contemporary marine ecosystems are critically dependent on eukaryotic phytoplankton. Although numerically inferior to cyanobacteria, these organisms are responsible for the majority of the flux of organic matter to higher trophic levels and the ocean interior. Photosynthetic eukaryotes evolved more than 1.5 billion years ago in the Proterozoic oceans. However, it was not until the Mesozoic Era (251 to 65 million years ago) that the three principal phytoplankton clades that would come to dominate the modern seas rose to ecological prominence. In contrast to their pioneering predecessors, the dinoflagellates, coccolithophores, and diatoms all contain plastids derived from an ancestral red alga by secondary symbiosis. Here we examine the geological, geochemical, and biological processes that contributed to the rise of these three, distantly related, phytoplankton groups.     

Comment on "Climate, critters, and cetaceans: Cenozoic drivers of the evolution of modern whales"

Marx and Uhen (Reports, 19 February 2010, p. 993) suggested that correlated diversity changes in the fossil record of whales and diatoms reflects secular evolutionary signals of underlying ecological drivers. We question the meaning of this association and outline avenues for more complete testing of correlations between productivity and marine consumers through geologic time.     

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 "Positive selection of tyrosine loss in metazoan evolution"

Tan et al. (Reports, 25 September 2009, p. 1686) argued that loss of tyrosine residues from proteins in metazoans was driven by positive selection to remove potentially deleterious phosphorylation sites. We challenge this hypothesis, providing evidence that the high guanine-cytosine (GC) content of metazoan genomes was the primary driver in the loss of tyrosine residues.     

Comment on "Gene regulatory networks and the evolution of animal body plans"

Davidson and Erwin (Reviews, 10 February 2006, p. 796) argued that known microevolutionary processes cannot explain the evolution of large differences in development that characterize phyla. Instead, they proposed that phyla arise from novel evolutionary processes involving large mutations acting on conserved core pathways of development. I question some of their assumptions and show that natural selection adequately explains the origin of new phyla.     

Comment on "Universality in the evolution of orientation columns in the visual cortex"

Kaschube et al. (Reports, 19 November 2010, p. 1113) argue that pinwheel density in three mammalian species follows a universal constant of π as predicted by their orientation-selective suppressive long-range connectivity model. We dispute their conclusions and suggest that a simple brain size-pinwheel density scaling law suffices in predicting the self-organized and disorganized orientation maps from primates to rodents.     

Comment on "The geometry of musical chords"

Tymoczko (Reports, 7 July 2006, p. 72) proposed that the familiar sonorities of Western tonal music cluster around the center of a multidimensional orbifold. However, this is not true for all tonal progressions. When prototypical three-voice cadential progressions by Bach converge on the tonic, the chords migrate from the center to the edge of the orbifold.     

Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens"

Mekel-Bobrov et al. (Reports, 9 September 2005, p. 1720) suggested that ASPM, a gene associated with microcephaly, underwent natural selection within the last 500 to 14,100 years. Their analyses based on comparison with computer simulations indicated that ASPM had an unusual pattern of variation. However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection.     

Structural dynamics of eukaryotic chromosome evolution

Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.     

Comment on "A test of the snowball theory for the rate of evolution of hybrid incompatibilities"

Matute et al. (Reports, 17 September 2010, p. 1518) tested the theory that the number of genes involved in hybrid incompatibility increases faster than linearly. However, the method they used is inappropriate because it detects genes that are haploinsufficient in a hybrid background but that would not contribute to lethality in wild-type hybrids, thus overestimating the frequency of hybrid inviability.     

Comment on "Age and evolution of the Grand Canyon revealed by U-Pb dating of water table-type speleothems"

Polyak et al. (Reports, 7 March 2008, p. 1377) reported speleothem data leading to their inference that the western Grand Canyon incised much earlier than previously thought. This contradicts several lines of published geological knowledge in the region, hinges upon unjustified hydrogeological assumptions, and is based on two anomalous data points for which we offer alternative explanations.