Phylogenetics of Perissodactyla and Tests of the Molecular Clock

Two mitochondrial genes, the protein-coding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for calibrating molecular clocks and comparing estimates of divergence times using both genes and two fossil calibration points. Secondary objectives included clarification of previously unresolved relationships within Tapiridae and comparison of the results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all three families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species of rhinoceros, and two species of Equus. The application of a relatively recent fossil calibration point and a relatively ancient calibration point produced greatly different estimates of evolutionary rates and divergence times for both genes, even though a relative rates test did not find significant rate differences among taxa. A likelihood-ratio test, however, rejected a molecular clock for both genes. Neither calibration point produced estimates of divergence times consistent with paleontological evidence over a range of perissodactyl radiations. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional views of interfamilial relationships and supports monophyly of neotropical tapirs. Combining the data sets increases support for most nodes but decreases the support for a neotropical tapir clade because the COII and 12S rRNA data sets are in conflict for tapir relationships. Received: 6 January 1999 / Accepted: 2 August 1999     

Use of RNA Secondary Structure for Studying the Evolution of RNase P and RNase MRP

Secondary structure is evaluated for determining evolutionary relationships between catalytic RNA molecules that are so distantly related they are scarcely alignable. The ribonucleoproteins RNase P (P) and RNase MRP (MRP) have been suggested to be evolutionarily related because of similarities in both function and secondary structure. However, their RNA sequences cannot be aligned with any confidence, and this leads to uncertainty in any trees inferred from sequences. We report several approaches to using secondary structures for inferring evolutionary trees and emphasize quantitative tests to demonstrate that evolutionary information can be recovered. For P and MRP, three hypotheses for the relatedness are considered. The first is that MRP is derived from P in early eukaryotes. The next is that MRP is derived from P from an early endosymbiont. The third is that both P and MRP evolved in the RNA-world (and the need for MRP has since been lost in prokaryotes). Quantitative comparisons of the pRNA and mrpRNA secondary structures have found that the possibility of an organellar origin of MRP is unlikely. In addition, comparison of secondary structures support the identity of an RNase P–like sequence in the maize chloroplast genome. Overall, it is concluded that RNA secondary structure is useful for evaluating evolutionary relatedness, even with sequences that cannot be aligned with confidence. Received: 19 July 1999 / Accepted: 3 May 2000     

The Molecular Clock Runs at Different Rates Among Closely Related Members of a Gene Family

The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor. From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise to the vitamin D–binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin (ALB) gene and a common precursor to α-fetoprotein (AFP) and α-albumin (ALF). This precursor itself duplicated about 250 Myr ago, giving rise to the youngest family members, AFP and ALF. It should be possible to correlate these dates with the phylogenetic distribution of members of the gene family among different species. All four genes are found in mammals, but AFP and ALF are not found in amphibia, which diverged from reptiles about 360 Myr ago, before the divergence of the AFP-ALF progenitor from albumin. Although individual family members display an approximate clock-like evolution, there are significant deviations—the rates of divergence for AFP differ by a factor of 7, the rates for ALB differ by a factor of 2.1. Since the progenitor of this gene family itself arose by triplication of a smaller gene, the rates of evolution of individual domains were also calculated and were shown to vary within and between family members. The great variation in the rates of the molecular clock raises questions concerning whether it can be used to infer evolutionary time from contemporary sequence differences. Received: 28 February 1995 / Accepted: 6 October 1997     

Evolved psychology in a novel environment

The human “environment of evolutionary adaptedness” can only be inferred indirectly. In contrast, the behavior of some nonhuman animals can be compared among “natural” and various altered environments. As an example, male immigration tactics in unprovisioned versus provisioned macaque (Macaca) populations are compared using Tooby and Cosmides’s (1992) framework for evolutionary functional analysis. In unprovisioned populations, social groups contain few males, and immigrant male takeovers of alpha rank occur frequently. In provisioned populations, groups contain many males, and males almost invariably enter social groups at very low rank and rise in rank only as more dominant males emigrate or die. Male conformity to the “seniority rule” is hypothesized to represent the behavioral output of an evolved decision-making algorithm (psychological mechanism) that takes into account (1) the net payoff of each rank in the dominance hierarchy and (2) the power of male group size as a predictor of the likelihood of successful immigrant takeover. Joseph H. Manson is Assistant Professor of Anthropology at the University of California, Los Angeles. His research interests are social relationships in nonhuman primates and humans, with particular emphases on mate choice, courtship tactics, intrasexual competition, and (currently) mother-infant relationships and infant handling. He has conducted fieldwork on rhesus macaques at Cayo Santiago and white-faced capuchins in Costa Rica.     

Possible effects of interprotein variation in mean rate of amino acid substitution on the relationship of genetic distance with time since evolutionary divergence

Published data on mean rates of genetic divergence for a substantial number of protein molecules is used to examine the hypothetical effect of variations in these rates upon the expected relationship between evolutionary time and Nei's (1972, American Naturalist, 106: 283) genetic distance, D. Results indicate that at higher values D can be expected to deviate significantly from stochastic linearity with time. However, over the sort of time scale over which D values are normally estimated, deviation is slight and likely to be insignificant when compared to other potential sources of error. It is concluded that for most practical purposes interprotein differences in mean rates of amino acid substitution need not be taken into account when calibrating genetic distance estimates against evolutionary time.     

Female sperm use and storage between fertilization events drive sperm competition and male ejaculate allocation

Sperm competition theory has traditionally focused on how male allocation responds to female promiscuity, when males compete to fertilize a single clutch of eggs. Here, we develop a model to ask how female sperm use and storage across consecutive reproductive events affect male ejaculate allocation and patterns of mating and paternity. In our model, sperm use (a single parameter under female control) is the main determinant of sperm competition, which alters the effect of female promiscuity on male success and, ultimately, male reproductive allocation. Our theory reproduces the general pattern predicted by existing theory that increased sperm competition favors increased allocation to ejaculates. However, our model predicts a negative correlation between male ejaculate allocation and female promiscuity, challenging the generality of a prevailing expectation of sperm competition theory. Early models assumed that the energetic costs of precopulatory competition and the level of sperm competition are both determined by female promiscuity, which leads to an assumed covariation between these two processes. By modeling precopulatory costs and sperm competition independently, our theoretical framework allows us to examine how male allocation should respond independently to variation in sperm competition and energetic trade‐offs in mating systems that have been overlooked in the past.     

Video game play and lucid dreams: Implications for the development of consciousness.

The improvement of various cognitive skills associated with video game play has been well documented; however, the development of consciousness implications have not been considered. In the present study several potential indicators of consciousness development, including and especially lucid dreaming frequency, were examined as a function of video game play. In the first study, high video game players were more likely to report lucid dreams, observer dreams, and dream control when dream recall frequency and motion disorientation during play were controlled. There were no similar differences in other consciousness development indices. In the second study, a slightly different pattern of results occurred because of respondents all being frequent players. (PsycINFO Database Record (c) 2010 APA, all rights reserved)