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PubMed1999

Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models.

In recent years, likelihood ratio tests (LRTs) based on DNA and protein sequence data have been proposed for testing various evolutionary hypotheses. Because conducting an LRT requires an evolutionary model of nucleotide or amino acid substitution, which is almost always unknown, it becomes important to investigate the robustness of LRTs to violations of assumptions of these evolutionary models. Computer simulation was used to examine performance of LRTs of the molecular clock, transition/transversion bias, and among-site rate variation under different substitution models. The results showed that when correct models are used, LRTs perform quite well even when the DNA sequences are as short as 300 nt. However, LRTs were found to be biased under incorrect models. The extent of bias varies considerably, depending on the hypotheses tested, the substitution models assumed, and the lengths of the sequences used, among other things. A preliminary simulation study also suggests that LRTs based on parametric bootstrapping may be more sensitive to substitution models than are standard LRTs. When an assumed substitution model is grossly wrong and a more realistic model is available, LRTs can often reject the wrong model; thus, the performance of LRTs may be improved by using a more appropriate model. On the other hand, many factors of molecular evolution have not been considered in any substitution models so far built, and the possibility of an influence of this negligence on LRTs is often overlooked. The dependence of LRTs on substitution models calls for caution in interpreting test results and highlights the importance of clarifying the substitution patterns of genes and proteins and building more realistic models.

Animals↗

PubMed2000

Lineage-specific evolutionary rate in mammalian mtDNA.

The existence of a lineage-specific nucleotide substitution rate in mammalian mtDNA has been investigated by analyzing the mtDNA of all available species, that is, 35 complete mitochondrial genomes from 14 mammalian orders. A detailed study of their evolutionary dynamics has been carried out on both ribosomal RNA and first and second codon positions (P12) of H-strand protein-coding genes by using two different types of relative-rate tests. Results are quite congruent between ribosomal and P12 sites. Significant rate variations have been observed among orders and among species of the same order. However, rate variation does not exceed 1.8-fold between the fastest (Proboscidea and Primates) and the slowest (Perissodactyla) evolving orders. Thus, the observed mitochondrial rate variations among taxa do not invalidate the suitability of mtDNA for drawing mammalian phylogeny. Dependence of evolutionary rate differences on variations in mutation and/or fixation rates was examined. Body size, generation time, and metabolic rate were tested, and no significant correlation was observed between them and the taxon-specific evolutionary rates, most likely because the latter might be influenced by multiple overlapping variable constraints.

Animals↗

PubMed1993

Unbiased estimation of evolutionary distance between nucleotide sequences.

A new algorithm for estimating the number of nucleotide substitutions per site (i.e., the evolutionary distance) between two nucleotide sequences is presented. This algorithm can be applied to many estimation methods, such as Jukes and Cantor's method, Kimura's transition/transversion method, and Tajima and Nei's method. Unlike ordinary methods, this algorithm is always applicable. Numerical computations and computer simulations indicate that this algorithm gives an almost unbiased estimate of the evolutionary distance, unless the evolutionary distance is very large. This algorithm should be useful especially when we analyze short nucleotide sequences. It can also be applied to amino acid sequences, for estimating the number of amino acid replacements.

Algorithms↗

PubMed1995

A comparison of two methods for constructing evolutionary distances from a weighted contribution of transition and transversion differences.

Since the initial work of Jukes and Cantor (1969), a number of procedures have been developed to estimate the expected number of nucleotide substitutions corresponding to a given observed level of nucleotide differentiation assuming particular evolutionary models. Unlike the proportion of different sites, the expected number of substitutions that would have occurred grows linearly with time and therefore has had great appeal as an evolutionary distance. Recently, however, a number of authors have tried to develop improved statistical approaches for generating and evaluating evolutionary distances (Schöniger and von Haeseler 1993; Goldstein and Polock 1994; Tajima and Takezaki 1994). These studies clearly show that the estimated number of nucleotide substitutions is generally not the best estimator for use in reconstruction of phylogenetic relationships. The reason for this is that there is often a large error associated with the estimation of this number. Therefore, even though its expectation is correct (i.e., on average the expected number of substitutions is proportional to time--but see Tajima 1993), it is not expected to be as useful as estimators designed to have a lower variance.

Algorithms↗

PubMed1985

Biochemical pathways in prokaryotes can be traced backward through evolutionary time.

For the first time, a credible prokaryotic phylogenetic tree is being assembled by Woese and others using quantitative sequence analysis of oligonucleotides in the highly conservative rRNA. This provides an evolutionary scale against which the evolutionary steps that led to the arrangement and regulation of contemporary biochemical pathways can be measured. This paper presents an emerging evolutionary picture of aromatic amino acid biosynthesis within a large superfamily assemblage of prokaryotes that is sufficiently developed to illustrate a new perspective that will be applicable to many other biochemical pathways.

3-Deoxy-7-Phosphoheptulonate Synthase↗

PubMed1985

Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes.

A mathematical theory for the evolutionary change of restriction endonuclease cleavage sites is developed, and the probabilities of various types of restriction-site changes are evaluated. A computer simulation is also conducted to study properties of the evolutionary change of restriction sites. These studies indicate that parsimony methods of constructing phylogenetic trees often make erroneous inferences about evolutionary changes of restriction sites unless the number of nucleotide substitutions per site is less than 0.01 for all branches of the tree. This introduces a systematic error in estimating the number of mutational changes for each branch and, consequently, in constructing phylogenetic trees. Therefore, parsimony methods should be used only in cases where nucleotide sequences are closely related. Reexamination of Ferris et al.'s data on restriction-site differences of mitochondrial DNAs does not support Templeton's conclusions regarding the phylogenetic tree for man and apes and the molecular clock hypothesis. Templeton's claim that Nei and Li's method of estimating the number of nucleotide substitutions per site is seriously affected by parallel losses and loss-gains of restriction sites is also unsupported.

Animals↗

PubMed1991

Evolutionary rate of immunoglobulin alpha noncoding region is greater in hominoids than in Old World monkeys.

Recent studies on the molecular evolution of primates show that the evolutionary rate among hominoids is considerably slower than that among nonhominoid primates. However, this observation at the nucleotide-sequence level is restricted to the beta-globin family region. In this study, we sequenced orthologous immunoglobulin alpha (C alpha) genes of chimpanzee, gorilla, orangutan, and crab-eating macaque (an Old World monkey) and compared them with that of the human by using noncoding regions for analysis. Since significant differences in rates among hominoids were not found by using the relative rate test, we evaluated the ratio (R) of the evolutionary distance between Old World monkey and human to the distance between orangutan and human. The R value (1.12) for the C alpha gene was much smaller than the expected value (1.38-2.33), showing that the nucleotide substitution rate (= mutation rate per year under selective neutrality) of the C alpha gene is greater in the human lineage than in the Old World monkey lineage. We also did a similar analysis for the gamma 1-, gamma 2-, psi eta-, and delta-globin genes and found a considerable heterogeneity (1.12-2.37) among the R values, including that for the C alpha gene. This indicates that the hominoid slowdown of the evolutionary rate is not a universal phenomenon in primate evolution.

Animals↗

PubMed2005

Detection and reduction of evolutionary noise in correlated mutation analysis.

Direct or indirect inter-residue interactions in proteins are often reflected by mutations at one site that compensate for mutations at another site. Various bioinformatic methods have been developed for detecting such correlated mutations in order to obtain information about intra- and inter-protein interactions. Here, we show by carrying out a correlated mutation analysis for non-interacting proteins that the signal due to inter-residue interactions is of similar magnitude to the 'noise' that arises from other evolutionary processes related to common ancestry. A new method for detecting correlated mutations is presented that reduces this evolutionary noise by taking into account evolutionary distances in the protein family. It is shown that this method yields better signal-to-noise ratios and, therefore, can much better resolve, for example, correlated mutations that reflect true inter-residue interactions.

Computational Biology↗

PubMed1992

Structural and evolutionary relationships among the immunophilins: two ubiquitous families of peptidyl-prolyl cis-trans isomerases.

The immunophilins, protein receptors for the immunosuppressing drugs cyclosporin A and FK506 and related proteins from plants, fungi, and bacteria, have been analyzed structurally and evolutionarily. The cyclosporin A binding proteins (cyclophilins) represent one ubiquitous family of homologous proteins, and the FK506- and rapamycin-binding proteins (FKBPs) constitute a second, unrelated family. Multiple sequence alignments of members of each of these two protein families define the highly conserved residues that are likely to play important structural and functional roles, and mutations in representative members of these two families that abolish or alter function have been evaluated. FKBPs have undergone greater evolutionary divergence than the cyclophilins. Evolutionary trees were constructed using two distinct programs, and these trees establish the structural relationships that allow division of each of these families into subgroups. The results lead to the suggestion that several genes encoding isozymic forms of the FKBPs and possibly also of the cyclophilins existed in prokaryotes before the emergence of eukaryotes on earth and that representatives of these genes were transmitted to both kingdoms to give rise to current subfamilies of these proteins. By contrast, compartmentalization of both classes of immunophilins appears to have arisen independently in prokaryotes and eukaryotes, late in evolutionary history.

Amino Acid Isomerases↗

PubMed2004

Inflammation underlying cardiovascular mortality is a late consequence of evolutionary programming.

With the increase in life expectancy, death from cardiovascular disease has risen greatly. There is increasing evidence that inflammation plays an important role in cardiovascular disease. We postulate that the development of cardiovascular disease in old age is a late consequence of evolutionary programming for a pro-inflammatory response to resist infections in early age. In 311 women, aged 85 yr old, the production of the pro- and anti-inflammatory cytokines tumor necrosis factor (TNF)-alpha and interleukin (IL)-10 was determined in lipopolysaccharide-stimulated whole blood samples and studied prospectively in association with cardiovascular mortality. High TNF-alpha was a risk factor for death from cardiovascular disease (relative risk [RR] = 1.56; 95% confidence interval [CI]: 1-2.40), whereas high IL-10 was protective (RR = 0.58; 95% CI: 0.40-0.85). A genetic variant of the IL-10 gene promoter, which is associated with lower IL-10 production, was found to predispose to a 2.8-fold higher cardiovascular mortality risk (95% CI: 1.17-6.60). Reproductive success, which was studied as a measure of evolutionary programming because it trades off with early survival by pro-inflammatory resistance genes, was negatively associated with an increasing production of TNF-alpha (RR = 0.77; 95% CI: 0.68-0.88), while a positive association with IL-10 was found (RR = 1.22; 95% CI: 1.05-1.41). We suggest that cardiovascular mortality is a late consequence of evolutionary programming for a pro-inflammatory response.

Adult↗

PubMed2005

Infanticide in female forensic patients: the view from the evolutionary standpoint.

Evolutionary theory predicts that very young mothers would be more likely to kill an infant than older women, given that the younger mother has a much greater ability to "replace" the dead child through subsequent pregnancies and thus to produce offspring for the next generation. Evolutionary theory also predicts that a woman would be more likely to kill a child if the child was obviously defective, the pregnancy was the result of incest or rape, or if the mother's means of supporting the child were severely compromised. The authors hypothesized that mentally ill mothers would behave in a way that differed significantly from evolutionary expectations, i.e., that they would be more likely to kill children who were older than those killed by mothers in the general population and that the mothers themselves would be likely to be older than mothers in the general population when the murders occurred. To test this hypothesis, the authors compared infanticides (both filicides and neonaticides) committed by mentally ill mothers with those committed by mothers in the general population. They examined two samples: 1) all cases of maternal infanticide from the Mid-Hudson Forensic Psychiatric Hospital from 1978 (when the hospital began admitting female patients) through the year 2000 and 2) a general population sample from a 10-year Canadian study reported by Daly and Wilson in 1998. The authors focused on the following variables: ages of the mothers, ages of the child-victims, whether the pregnancy was the result of rape or incest, whether the child had significant behavioral or physical problems, and whether there were problems supporting the child (e.g., having no partner, poverty, mother's lack of education). The results of the analyses supported the authors' hypothesis about ages of mothers and children. The mentally ill mothers in the Mid-Hudson sample were generally older when they killed their children and the children who were killed were generally older than in the Daly and Wilson general population sample (where the majority of the cases involved neonaticide and the mothers were generally younger than 25 years of age). The three factors, poverty, low education level (or low intellectual capacity), and lack of a spouse were common in both samples. Findings concerning cultural factors, motives, and methods used will be presented in separate publications.

Adolescent↗

PubMed1999

Does interspecific hybridization influence evolutionary rates? An experimental study of laboratory adaptation in hybrids between Drosophila serrata and Drosophila birchii.

The low initial fitness of progeny from interspecific crosses in animals and the rarity of interspecific hybridization in natural environments have led to a debate about the evolutionary importance of this phenomenon. Here we directly assess the effects of hybridization between Drosophila serrata and Drosophila birchii on evolutionary rates. We looked at the effects on laboratory adaptation over 30 generations in two laboratory environments, one of which involved nutrition and temperature stress. Laboratory adaptation occurred over time in both environments as reflected by a marked change in viability. However, whilst hybrid lines at no stage performed poorly relative to parental lines, their rate of adaptation never exceeded that of the parentals. Thus, there was no evidence that hybridization increased evolutionary rates. Instead, hybrid lines converged phenotypically with one of the parental species.

Analysis of Variance↗

PubMed2000

Step-parents and infanticide: new data contradict evolutionary predictions.

Evolutionary psychologists have hypothesized, inspired by evolutionary biology, that parents should care less for children with whom they are not genetically related since these young do not contribute to the genetic fitness of the parents. Based on this, evolutionary psychologists have predicted that there will be an overrepresentation of step-parents as offenders in family-related killings of children. Data on child homicide, particularly from Canada, have supported this prediction in that the frequency of children killed was relatively high in families where one of the two parents was a step-parent. Here we present a survey of all child homicide that occurred in Sweden between 1975 and 1995. In contrast to the Canadian data, children in Sweden living in families with a step-parent were not at an increased risk compared with children living together with two parents to whom they were genetically related. In addition, there were no other indications that step-parents are overrepresented as offenders.

Adolescent↗

PubMed2001

Evolutionary history and speciation modes in the cyprinid genus Barbus.

Phylogenetic relationships and evolutionary patterns in the genus Barbus were examined through the analysis of the complete sequences of three mitochondrial genes: ATPases 8 and 6, which overlap slightly, and cytochrome b. This complex genus includes diploid as well as tetraploid and hexaploid species that are distributed throughout the Palaearctic, Ethiopian and Asiatic biogeographical regions. Given that genome duplication is an important evolutionary mechanism in eukaryotes, in the present report we attempt to describe its role in the evolution of the genus Barbus, as well as drawing systematic and phylogenetic conclusions. The phylogenetic results indicated the splitting of the current Barbus genus into five main mitochondrial lineages corresponding to (i) the genus Barbus sensu stricto (tetraploid, which is subdivided into the subgenera Barbus and Luciobarbus), (ii) the hexaploid species, (iii) the Ethiopian tetraploid species, (iv) the African diploid species, and (v) the Asian diploid species. The branching of 'foreign' genera as sister groups of some of these monophyletic assemblages (such as Aulopyge is to Barbus sensu stricto or Varicorhinus is to the hexaploid barbels) demonstrates the polyphyly of the group. Moreover, the relationships between the proposed lineages also show that genome duplication may be considered as a homoplasic character since it must have occurred over at least three independent periods and/or in three independent areas. In relation to the possible saltational evolutionary model for the polyploid species examined here, it was found that, although feasible at the nuclear level, the mitochondrial markers looked at do not appear to have undergone this type of evolution. Rather, they seem to have experienced more or less constant change through time.

Adenosine Triphosphatases↗

PubMed2003

Evolutionary coherence of the mammalian amygdala.

Despite great interest in the role of the amygdala in animal and human behaviour, its very existence as a structurally and functionally unified brain component has been questioned, on the grounds that cell groups within it display divergent pharmacological and connectional characteristics. We argue that the question of whether particular brain nuclei constitute a valid structural and functional unit is inherently an evolutionary question, and we present a method for answering it. The method involves phylogenetic analysis of comparative data to determine whether or not separate regions of the putative brain structure show statistically correlated evolution. We find that, in three separate groups of mammals (primates and two groups of insectivores), evolutionary changes in the volumes of amygdala components are strongly correlated, even after controlling for volumetric change in a wide range of limbic and other brain structures. This allows us to reject the strong claim that the amygdala is neither a structural nor a functional unit, and demonstrates the importance of evolutionary analysis in resolving such issues in systems neuroscience.

Amygdala↗

PubMed2003

Evolutionary models of phylogenetic trees.

The most widely used evolutionary model for phylogenetic trees is the equal-rates Markov (ERM) model. A problem is that the ERM model predicts less imbalance than observed for trees inferred from real data; in fact, the observed imbalance tends to fall between the values predicted by the ERM model and those predicted by the proportional-to-distinguishable-arrangements (PDA) model. Here, a continuous multi-rate (MR) family of evolutionary models is presented which contains entire subfamilies corresponding to both the PDA and ERM models. Furthermore, this MR family covers an entire range from 'completely balanced' to 'completely unbalanced' models. In particular, the MR family contains other known evolutionary models. The MR family is very versatile and virtually free of assumptions on the character of evolution; yet it is highly susceptible to rigorous analyses. In particular, such analyses help to uncover adaptability, quasi-stabilization and prolonged stasis as major possible causes of the imbalance. However, the MR model is functionally simple and requires only three parameters to reproduce the observed imbalance.

Animals↗

PubMed2004

Environmental energy and evolutionary rates in flowering plants.

The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.

Biodiversity↗

PubMed2005

Evolutionary dynamics of altruism and cheating among social amoebas.

Dictyostelium discoideum is a eukaryotic amoeba, which, when starvation is imminent, aggregates to form fruiting bodies consisting of a stalk of reproductively dead cells that supports spores. Because different clones may be involved in such aggregations, cheater strategies may emerge that allocate a smaller fraction of cells to stalk formation, thus gaining a reproductive advantage. In this paper, we model the evolutionary dynamics of allocation strategies in Dictyostelium under the realistic assumption that the number of clones involved in aggregations follows a random distribution. By determining the full course of evolutionary dynamics, we show that evolutionary branching in allocation strategies may occur, resulting in dimorphic populations that produce stalkless and stalked fruiting bodies. We also demonstrate that such dimorphisms are more likely to emerge when the variation in the number of clones involved in aggregations is large.

Altruism↗