TREECON: A software package for the construction and drawing of evolutionary trees

A package of programs (run by a management program called TREECON)was developed for the construction and drawing of evolutionarytrees. The program MATRIX calculates dissimilarity values andcan perform bootstrap analysis on nucleic acid sequences. TREEimplements different evolutionary tree constructing methodsbased on distance matrices. Because some of these methods produceunrooted evolutionary trees, a program ROOT places a root onthe tree. Finally, the program DRAW draws the evolutionary tree,changes its size or topology, and produces drawings suitablefor publication. Whereas MATRIX is suited only for nucleic acids,the modules TREE, ROOT and DRAW are applicable to any kind ofdissimilarity matrix. The programs run on IBM-compatible microcomputersusing the DOS operating system.     

A practical method for calculating evolutionary trees from sequence data

In a previous paper (Klotz et a1., 1979) we described a method for determining evolutionary trees from sequence data when rates of evolution of the sequences might differ greatly. It was shown theoretically that the method always gave the correct topology and root when the exact number of mutation differences between sequences and from their common ancestor was known. However, the method is impractical to use in most situations because it requires some knowledge of the ancestor. In this present paper we describe another method, related to the previous one, in which a present-day sequence can serve temporarily as an ancestor for purposes of determining the evolutionary tree regardless of the rates of evolution of the sequences involved. This new method can be carried out with high precision without the aid of a computer, and it does not increase in difficulty rapidly as the number of sequences involved in the study increases, unlike other methods.     

Progress with methods for constructing evolutionary trees

Evolutionists dream of a tree-reconstruction method that is efficient (fast), powerful, consistent, robust and falsifiable. These criteria are at present conflicting in that the fastest methods are weak (in their use of information in the sequences) and inconsistent (even with very long sequences they may lead to an incorrect tree). But there has been exciting progress in new approaches to tree inference, in understanding general properties of methods, and in developing ideas for estimating the reliability of trees. New phylogenetic invariant methods allow selected parameters of the underlying model to be estimated directly from sequences. There is still a need for more theoretical understanding and assistance in applying what is already known.     

A conflict between two evolutionary levels in trees

Due to the lack of germ line segregation in plants, it is possible to consider plant evolution (but not the evolution of most animals) as being composed of two evolutionary levels: 1. Intra-organism, in which the replicating unit is a part of the tree (e.g. a branch), reproduction is asexual, mutations are somatic, and selection operates only upon traits relevant to vegetative growth. 2. Inter-organism, in which the replicating unit is the whole tree, reproduction is sexual, and selection operates upon all the traits. In this work, a case of a conflict between these two levels is studied. The dynamics of a mutation, which is advantageous on the branch level but harmful for the whole tree, are discussed for a one-locus two-allele model. Several cases are considered: dominant, partially dominant, and haploid. Necessary and sufficient conditions for fixation of such a mutation are found. The model predicts that as the longevity of a tree species increases, the trees are expected to be more strongly shifted from their optimal growth-to-reproduction ratio towards growth, and resource allocation between branches and other tree parts is expected to be shifted in favor of the branches. Traditional approach, considering the second level only, is justified as a limit case for short longevity.     

DRAWNA: A program for drawing schematic views of nucleic acids

A program for drawing automatically exact and schematic views of nucleic acids is described. The program is written in C ANSI and uses the Silicon Graphics GL and Xirisw libraries within the X1 1/Motif environment. Through menus, the user can choose, specify, and manipulate in real time the three-dimensional views to be displayed. Drawing options include partitioning of structures into differently colored or shaped fragments, representation of backbones as flat or with conic-section ribbons, display of paired or free bases as rods, and display of surfaces as filled or outlined and stereo or depth-cued views.     

QDist--quartet distance between evolutionary trees

SUMMARY: QDist is a program for computing the quartet distance between two unrooted trees, i.e. the number of quartet topology differences between the trees, where a quartet topology is the topological subtree induced by four species. The program is based on an algorithm with running time O(n log2 n), which makes it practical to compare large trees. Available under GNU license. AVAILABILITY: http://www.birc.dk/Software/QDist     

A program for at-risk high school students informed by evolutionary science

Improving the academic performance of at-risk high school students has proven difficult, often calling for an extended day, extended school year, and other expensive measures. Here we report the results of a program for at-risk 9th and 10th graders in Binghamton, New York, called the Regents Academy that takes place during the normal school day and year. The design of the program is informed by the evolutionary dynamics of cooperation and learning, in general and for our species as a unique product of biocultural evolution. Not only did the Regents Academy students outperform their comparison group in a randomized control design, but they performed on a par with the average high school student in Binghamton on state-mandated exams. All students can benefit from the social environment provided for at-risk students at the Regents Academy, which is within the reach of most public school districts.     

Estimation of evolutionary distance for reconstructing molecular phylogenetic trees

The most commonly used measure of evolutionary distance in molecular phylogenetics is the number of nucleotide substitutions per site. However, this number is not necessarily most efficient for reconstructing a phylogenetic tree. In order to evaluate the accuracy of evolutionary distance, D(t), for obtaining the correct tree topology, an accuracy index, A(t), was proposed. This index is defined as D'(t)/square root of[D(t)], where D'(t) is the first derivative of D(t) with respect to evolutionary time and V[D(t)] is the sampling variance of evolutionary distance. Using A(t), namely, finding the condition under which A(t) gives the maximum value, we can obtain an evolutionary distance which is efficient for obtaining the correct topology. Under the assumption that the transversional changes do not occur as frequently as the transitional changes, we obtained the evolutionary distances which are expected to give the correct topology more often than are the other distances.      

Haplotype fine mapping by evolutionary trees

To refine the location of a disease gene within the bounds provided by linkage analysis, many scientists use the pattern of linkage disequilibrium between the disease allele and alleles at nearby markers. We describe a method that seeks to refine location by analysis of "disease" and "normal" haplotypes, thereby using multivariate information about linkage disequilibrium. Under the assumption that the disease mutation occurs in a specific gap between adjacent markers, the method first combines parsimony and likelihood to build an evolutionary tree of disease haplotypes, with each node (haplotype) separated, by a single mutational or recombinational step, from its parent. If required, latent nodes (unobserved haplotypes) are incorporated to complete the tree. Once the tree is built, its likelihood is computed from probabilities of mutation and recombination. When each gap between adjacent markers is evaluated in this fashion and these results are combined with prior information, they yield a posterior probability distribution to guide the search for the disease mutation. We show, by evolutionary simulations, that an implementation of these methods, called "FineMap," yields substantial refinement and excellent coverage for the true location of the disease mutation. Moreover, by analysis of hereditary hemochromatosis haplotypes, we show that FineMap can be robust to genetic heterogeneity.     

Variant evolutionary trees under phenotypic variance

Evolutionary branching, which is a coevolutionary phenomenon of the development of two or more distinctive traits from a single trait in a population, is the issue of recent studies on adaptive dynamics. In previous studies, it was revealed that trait variance is a minimum requirement for evolutionary branching, and that it does not play an important role in the formation of an evolutionary pattern of branching. Here we demonstrate that the trait evolution exhibits various evolutionary branching paths starting from an identical initial trait to different evolutional terminus traits as determined by only changing the assumption of trait variance. The key feature of this phenomenon is the topological configuration of equilibria and the initial point in the manifold of dimorphism from which dimorphic branches develop. This suggests that the existing monomorphic or polymorphic set in a population is not an unique inevitable consequence of an identical initial phenotype.     

Estimating the reliability of evolutionary trees

Six protein sequences from the same 11 mammalian taxa were used to estimate the accuracy and reliability of phylogenetic trees using real, rather than simulated, data. A tree comparison metric was used to measure the increase in similarity of minimal trees as larger, randomly selected subsets of nucleotide positions were taken. The ratio of the observed to the expected number of incompatibilities for each nucleotide position (character) is a good predictor of the number of changes required at that position on the minimal (most-parsimonious) tree. This allows a higher weighting of nucleotide positions that have changed more slowly and should result in the minimal length tree converging to the correct tree as more sequences are obtained. An estimate was made of the smallest subset of trees that need to be considered to include the actual historical tree for a given set of data. It was concluded that it is possible to give a reasonable estimate of the reliability of the final tree, at least when several sequences are combined. With the present data, resolving the rodent- primate-lagomorph (rabbit) trichotomy is the least certain aspect of the final tree, followed then by establishing the position of dog. In our opinion, it is unreasonable to publish an evolutionary tree derived from sequence data without giving an idea of the reliability of the tree.      

A simple computer program for calculating, modifying and drawing circular restriction maps.

An HPL program is described which constructs and draws circular restriction maps given a set of cleavage sites, together with deletion of insertion data if required. This program is of great use in the routine interpretation of restriction patterns for the analysis of recombinant DNA molecules.     

Estimation of evolutionary parameters with phylogenetic trees

An important issue in the phylogenetic analysis of nucleotide sequence data using the maximum likelihood (ML) method is the underlying evolutionary model employed. We consider the problem of simultaneously estimating the tree topology and the parameters in the underlying substitution model and of obtaining estimates of the standard errors of these parameter estimates. Given a fixed tree topology and corresponding set of branch lengths, the ML estimates of standard evolutionary model parameters are asymptotically efficient, in the sense that their joint distribution is asymptotically normal with the variance–covariance matrix given by the inverse of the Fisher information matrix. We propose a new estimate of this conditional variance based on estimation of the expected information using a Monte Carlo sampling (MCS) method. Simulations are used to compare this conditional variance estimate to the standard technique of using the observed information under a variety of experimental conditions. In the case in which one wishes to estimate simultaneously the tree and parameters, we provide a bootstrapping approach that can be used in conjunction with the MCS method to estimate the unconditional standard error. The methods developed are applied to a real data set consisting of 30 papillomavirus sequences. This overall method is easily incorporated into standard bootstrapping procedures to allow for proper variance estimation.     

The evolutionary ecology of mast seeding in trees

The hypothesis that masting by trees is a defensive strategy which satiates seed predators in mast years and starves them in the intervening periods is tested in 59 sets of data on the seed production and pre-dispersal seed-predation of 25 tree species. Twenty-lour of the 59 data-sets support the hypothesis and show a statistically significant positive relationship between the proportion of seeds surviving the pre-dispersal stage and the log₁₀ of the crop size for the same year. Evidence that pre-dispersal seed survival increases with the length of the mast interval is poor.
A positive relationship between the strength of the masting habit and the maxintum observed pre-dispersal seed mortality in a sample of 15 tree species suggests that the masting habit is best developed in predator-prone species. A survey of seed crop frequencies in the woody plant flora of Nortli America shows masting species to be under-represented amongst shrubs and amongst trees which disperse their seeds in fleshy dispersal units. The selection pressures and evolutionary constraints which operate on the evolution of masting plants and their seed predators are discussed.