Gene regulatory networks and the evolution of animal body plans

Development of the animal body plan is controlled by large gene regulatory networks (GRNs), and hence evolution of body plans must depend upon change in the architecture of developmental GRNs. However, these networks are composed of diverse components that evolve at different rates and in different ways. Because of the hierarchical organization of developmental GRNs, some kinds of change affect terminal properties of the body plan such as occur in speciation, whereas others affect major aspects of body plan morphology. A notable feature of the paleontological record of animal evolution is the establishment by the Early "Cambrian of virtually all phylum-level body plans. We identify a class of GRN component, the kernels" of the network, which, because of their developmental role and their particular internal structure, are most impervious to change. Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts.     

Comment on "Asymmetric coevolutionary networks facilitate biodiversity maintenance"

Bascompte et al. (Reports, 21 April 2006, p. 431) used network asymmetries to explain mathematical conditions necessary for stability in historic models of mutualism. The Lotka-Volterra equations they used artificially created conditions in which some factor, such as asymmetric interaction strengths, is necessary for community coexistence. We show that a more realistic model incorporating nonlinear functional responses requires no such condition and is consistent with their 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 "Impaired respiratory and body temperature control upon acute serotonergic neuron inhibition"

Ray et al. (Reports, 29 July 2011, p. 637) assume that clozapine-N4-oxide (CNO) represents a "biologically inert synthetic ligand" that selectively activates the M4 muscarinic receptor-based DREADD (designer receptor exclusively activated by a designer drug). In contrast, due to the redox cycling of CNO with clozapine and to their cell membrane permeability, CNO is biologically active and its conversion products are capable of undermining DREADD effects.     

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.     

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 "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.     

Comment on "Reconstructing the origin of Andaman islanders"

On the basis of mitochondrial DNA sequence analyses, Thangaraj et al. (Brevia, 13 May 2005, p. 996) proposed that Andaman islanders descended from the first humans to migrate out of Africa. We identified mitochondrial DNA from two northeast Indian Rajbanshi individuals that shares three specific mutations with the M31a lineage observed in the Great Andamanese, which suggests that the predecessor of haplogroup M31 originated on the Indian subcontinent.     

Comment on "Habitat split and the global decline of amphibians"

Becker et al. (Reports, 14 December 2007, p. 1775) reported that forest amphibians with terrestrial development are less susceptible to the effects of habitat degradation than those with aquatic larvae. However, analysis with more appropriate statistical methods suggests there is no evidence for a difference between aquatic-reproducing and terrestrial-reproducing species.     

Comment on "Detecting awareness in the vegetative state"

Owen et al. (Brevia, 8 September 2006, p. 1402) claimed that a patient's brain activity revealed that she was consciously responding to commands despite being in a vegetative state. However, several alternative explanations were not eliminated. Specifically, the activity could reflect unconscious reactions to the last word in the command, not conscious decisions to respond. A refined experimental design could clarify these issues.     

Comment on "Roadless space of the conterminous United States"

Watts et al. (Reports, 6 May 2007, p. 736) introduced a metric of landscape pattern called roadless volume (RV). However, as with most previous metrics, RV does not explicitly address ecological processes. We demonstrate that RV can produce results inconsistent with the notion of landscape connectivity and contend that more ecologically relevant metrics are available.     

Comment on "Dynamics of dpp signaling and proliferation control"

Wartlick et al. (Research Articles, 4 March 2011, p. 1154) reported that growth rates in the Drosophila wing disc correlate with increasing Dpp signaling levels, suggesting that the rate of Dpp increase determines the cell-cycle length. Contradicting their model, we found that cells in which the increase of Dpp signaling levels was genetically abrogated grew at rates comparable to those of wild-type cells.