Robustness of maximum likelihood tree estimation against different patterns of base substitutions

Using PhyloSuite for molecular phylogeny and tree-based analyses

Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree-based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree-based analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, and etc. The step-by-step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick-start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle-based analyses.

Pitfalls of the site-concordance factor (sCF) as measure of phylogenetic branch support

Confidence measures of branch reliability play an important role in phylogenetics as these measures allow to identify trees or parts of a tree that are well supported by the data and thus adequate to serve as basis for evolutionary inference of biological systems. Unreliable branch relationships in phylogenetic analyses are of concern because of their potential to represent incorrect relationships of interest among more reliable branch relationships. The site-concordance factor implemented in the IQ-TREE package is a recently introduced heuristic solution to the problem of identifying unreliable branch relationships on the basis of quartets. We test the performance of the site-concordance measure with simple examples based on simulated data and designed to study its behaviour in branch support estimates related to different degrees of branch length heterogeneities among a ten sequence tree. Our results show that in particular in cases of relationships with heterogeneous branch lengths site-concordance measures may be misleading. We therefore argue that the maximum parsimony optimality criterion currently used by the site-concordance measure may sometimes be poorly suited to evaluate branch support and that the scores reported by the site-concordance factor should not be considered as reliable.

Felsenstein Phylogenetic Likelihood

In 1981, the Journal of Molecular Evolution (JME) published an article entitled “Evolutionary trees from DNA sequences: A maximum likelihood approach” by Joseph (Joe) Felsenstein (J Mol Evol 17:368–376, 1981). This groundbreaking work laid the foundation for the emerging field of statistical phylogenetics, providing a tractable way of finding maximum likelihood (ML) estimates of evolutionary trees from DNA sequence data. This paper is the second most cited (more than 9000 citations) in JME after Kimura’s (J Mol Evol 16:111–120, 1980) seminal paper on a model of nucleotide substitution (with nearly 20,000 citations). On the occasion of the 50th anniversary of JME, we elaborate on the significance of Felsenstein’s ML approach to estimating phylogenetic trees.

Model selection may not be a mandatory step for phylogeny reconstruction

Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure has not been questioned to date. Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not crucial. Moreover, skipping model selection and using instead the most parameter-rich model, GTR+I+G, leads to similar inferences, thus rendering this time-consuming step nonessential, at least under current strategies of model selection.

Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model

The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that for some topologies and branch lengths the reconstruction success of maximum likelihood under the correct model is still low for alignments with a length of 100,000 base positions. Altogether, the high confidence that is put in maximum likelihood trees is not always justified under certain tree shapes even if alignment lengths reach 100,000 base positions.

ImOSM: intermittent evolution and robustness of phylogenetic methods

Among the criteria to evaluate the performance of a phylogenetic method, robustness to model violation is of particular practical importance as complete a priori knowledge of evolutionary processes is typically unavailable. For studies of robustness in phylogenetic inference, a utility to add well-defined model violations to the simulated data would be helpful. We therefore introduce ImOSM, a tool to imbed intermittent evolution as model violation into an alignment. Intermittent evolution refers to extra substitutions occurring randomly on branches of a tree, thus changing alignment site patterns. This means that the extra substitutions are placed on the tree after the typical process of sequence evolution is completed. We then study the robustness of widely used phylogenetic methods: maximum likelihood (ML), maximum parsimony (MP), and a distance-based method (BIONJ) to various scenarios of model violation. Violation of rates across sites (RaS) heterogeneity and simultaneous violation of RaS and the transition/transversion ratio on two nonadjacent external branches hinder all the methods recovery of the true topology for a four-taxon tree. For an eight-taxon balanced tree, the violations cause each of the three methods to infer a different topology. Both ML and MP fail, whereas BIONJ, which calculates the distances based on the ML estimated parameters, reconstructs the true tree. Finally, we report that a test of model homogeneity and goodness of fit tests have enough power to detect such model violations. The outcome of the tests can help to actually gain confidence in the inferred trees. Therefore, we recommend using these tests in practical phylogenetic analyses.

Using MODELTEST and PAUP* to select a model of nucleotide substitution

Models of nucleotide substitution are commonly used in the analysis of DNA sequences. This unit describes the use of the program MODELTEST (coupled with PAUP*) to find the best-fit model of substitution for the sequence alignment at hand. An example data file is analyzed and the interpretation of the results is discussed. Some background theory on model selection and a discussion of the relevance of models is included at the end of the unit.

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Distance-based methods for phylogeny reconstruction are the fastest and easiest to use, and their popularity is accordingly high. They are also the only known methods that can cope with huge datasets of thousands of sequences. These methods rely on evolutionary distance estimation and are sensitive to errors in such estimations. In this study, a novel Bayesian method for estimation of evolutionary distances is developed. The proposed method enables the use of a sophisticated evolutionary model that better accounts for among-site rate variation (ASRV), thereby improving the accuracy of distance estimation. Rate variations are estimated within a Bayesian framework by extracting information from the entire dataset of sequences, unlike standard methods that can only use one pair of sequences at a time. We compare the accuracy of a cascade of distance estimation methods, starting from commonly used methods and moving towards the more sophisticated novel method. Simulation studies show significant improvements in the accuracy of distance estimation by the novel method over the commonly used ones. We demonstrate the effect of the improved accuracy on tree reconstruction using both real and simulated protein sequence alignments. An implementation of this method is available as part of the SEMPHY package.

Data Partitions and Complex Models in Bayesian Analysis: The Phylogeny of Gymnophthalmid Lizards

Phylogenetic studies incorporating multiple loci, and multiple genomes, are becoming increasingly common. Coincident with this trend in genetic sampling, model-based likelihood techniques including Bayesian phylogenetic methods continue to gain popularity. Few studies, however, have examined model fit and sensitivity to such potentially heterogeneous data partitions within combined data analyses using empirical data. Here we investigate the relative model fit and sensitivity of Bayesian phylogenetic methods when alternative site-specific partitions of among-site rate variation (with and without autocorrelated rates) are considered. Our primary goal in choosing a best-fit model was to employ the simplest model that was a good fit to the data while optimizing topology and/or Bayesian posterior probabilities. Thus, we were not interested in complex models that did not practically affect our interpretation of the topology under study. We applied these alternative models to a four-gene data set including one protein-coding nuclear gene (c-mos), one protein-coding mitochondrial gene (ND4), and two mitochondrial rRNA genes (12S and 16S) for the diverse yet poorly known lizard family Gymnophthalmidae. Our results suggest that the best-fit model partitioned among-site rate variation separately among the c-mos, ND4, and 12S + 16S gene regions. We found this model yielded identical topologies to those from analyses based on the GTR+I+G model, but significantly changed posterior probability estimates of clade support. This partitioned model also produced more precise (less variable) estimates of posterior probabilities across generations of long Bayesian runs, compared to runs employing a GTR+I+G model estimated for the combined data. We use this three-way gamma partitioning in Bayesian analyses to reconstruct a robust phylogenetic hypothesis for the relationships of genera within the lizard family Gymnophthalmidae. We then reevaluate the higher-level taxonomic arrangement of the Gymnophthalmidae. Based on our findings, we discuss the utility of nontraditional parameters for modeling among-site rate variation and the implications and future directions for complex model building and testing.

NJML+: an extension of the NJML method to handle protein sequence data and computer software implementation

While the maximum-likelihood (ML) method of tree reconstruction is statistically rigorous, it is extremely time-consuming for reconstructing large trees. We previously developed a hybrid method (NJML) that combines the neighbor-joining (NJ) and ML methods and thus is much faster than the ML method and improves the performance of NJ. However, we considered only nucleotide sequence data, so NJML is not suitable for handling amino acid sequence data, which requires even more computer time. NJML+ is an implementation of a further improved method for practical data analyses (including protein sequence data). Our extensive simulations using nucleotide and amino acid sequences showed that NJML+ gave good results in tree reconstruction. Indeed, NJML+ showed substantial improvements over existing methods in terms of both computational times and efficiencies, especially for amino acid sequence data. We also developed a "user-friendly" interface for the NJML+ program, including a simple tree viewer.

Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1)

The blind use of models of nucleotide substitution in evolutionary analyses is a common practice in the viral community. Typically, a simple model of evolution like the Kimura two-parameter model is used for estimating genetic distances and phylogenies, either because other authors have used it or because it is the default in various phylogenetic packages. Using two statistical approaches to model fitting, hierarchical likelihood ratio tests and the Akaike information criterion, we show that different viral data sets are better explained by different models of evolution. We demonstrate our results with the analysis of HIV-1 sequences from a hierarchy of samples; sequences within individuals, individuals within subtypes, and subtypes within groups. We also examine results for three different gene regions: gag, pol, and env. The Kimura two-parameter model was not selected as the best-fit model for any of these data sets, despite its widespread use in phylogenetic analyses of HIV-1 sequences. Furthermore, the model complexity increased with increasing sequence divergence. Finally, the molecular-clock hypothesis was rejected in most of the data sets analyzed, throwing into question clock-based estimates of divergence times for HIV-1. The importance of models in evolutionary analyses and their repercussions on the derived conclusions are discussed.

Maximum likelihood estimation of recombination rates from population data

We describe a method for co-estimating r = C/mu (where C is the per-site recombination rate and mu is the per-site neutral mutation rate) and Theta = 4N(e)mu (where N(e) is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large number of possible reconstructions of the recombinant genealogy, weighting according to their posterior probability with regard to the data and working values of the parameters. Different relative rates of recombination at different locations can be accommodated if they are known from external evidence, but the algorithm cannot itself estimate rate differences. The estimates of Theta are accurate and apparently unbiased for a wide range of parameter values. However, when both Theta and r are relatively low, very long sequences are needed to estimate r accurately, and the estimates tend to be biased upward. We apply this method to data from the human lipoprotein lipase locus.

NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods

In the reconstruction of a large phylogenetic tree, the most difficult part is usually the problem of how to explore the topology space to find the optimal topology. We have developed a "divide-and-conquer" heuristic algorithm in which an initial neighbor-joining (NJ) tree is divided into subtrees at internal branches having bootstrap values higher than a threshold. The topology search is then conducted by using the maximum-likelihood method to reevaluate all branches with a bootstrap value lower than the threshold while keeping the other branches intact. Extensive simulation showed that our simple method, the neighbor-joining maximum-likelihood (NJML) method, is highly efficient in improving NJ trees. Furthermore, the performance of the NJML method is nearly equal to or better than existing time-consuming heuristic maximum-likelihood methods. Our method is suitable for reconstructing relatively large molecular phylogenetic trees (number of taxa >/= 16).

Re: Congruence and phylogenetic reanalysis of perching bird cytochrome b sequences

In a study of the phylogenetic relationships among perching bird mtDNA sequences, Edwards et al. (1991; Proc. R. Soc. London Ser B. 243: 99-107) sequenced part of the mitochondrial cytochrome b gene from 13 perching birds (Passeriformes) and a woodpecker outgroup. However, recently the validity of part of the sequence of the hermit thrush (Catharus guttatus) in that study has been questioned. To determine the effect of inclusion of this apparently chimeric sequence on the conclusions of the original analysis, we reanalyzed these sequences using a different published hermit thrush sequence. In addition, we applied tests of congruence to examine the possibility that the aberrant phylogenetic behavior of chimeric mtDNA sequences might be detected. The reanalysis confirms the ability of slow evolving first and second codon positions of cytochrome b sequences to resolve deep branches in the avian tree. The fact that the new data set does not reject the DNA hybridization tree of these species probably indicates poor ability of the cytochrome b sequences to discriminate among alternative trees, rather than consistency among data sets. Statistical testing of trees based on individual amplified segments of mtDNA indicates that congruence tests may be one useful way of identifying chimeric mtDNA sequences when they have not been detected in the laboratory or during standard phylogenetic analysis.

Evolutionary age of the Galápagos iguanas predates the age of the present Galápagos islands

New geological findings suggest that volcanoes existed over the Galápagos hotspot long before today's islands emerged less than 5 million years ago. The evolution of some of Galápagos' biota might have taken place on these former islands. This study investigates the evolutionary history of two of the archipelagos' older vertebrate taxa, the endemic Galápagos marine and land iguana (genera Amblyrhynchus and Conolophus). Mitochondrial rDNA sequences (in total about one kilobase of the 12S and 16S genes) were obtained from all extant genera of the family Iguanidae and the outgroup Oplurus. The phylogenetic analyses suggest that the Galápagos iguanas are sister taxa. Rate comparisons between the iguanid sequences and a corresponding set of sequences from ungulates with known fossil ages date their separation time at 10 million years, or more. The results strengthen the hypothesis that extended speciation times in the Galápagos are possible and provide an estimate of the minimum time inhabited islands of the archipelago may have existed.

Phylogenetic analysis of tnpR genes in mercury resistant soil bacteria: the relationship between DNA sequencing and RFLP typing approaches

The diversity of resolvase (tnpR) genes carried by a number of mercury resistant soil bacteria has been investigated by DNA sequencing. The resulting DNA sequence information was compared to previously published tnpR DNA sequences and to previously published restriction fragment length polymorphism (RFLP) data, permitting the relationships between DNA sequencing and RFLP approaches to be studied by the use of phylogenetic trees. DNA maximum likelihood and DNA parsimony were used to construct a variety of phylogenetic trees. DNA sequencing confirmed the validity of RFLP analysis and highlighted the importance of restriction endonuclease choice upon the resulting RFLP patterns and dendrogram topology. The tnpR genes of two previously uncharacterised mercury resistant bacteria, T2-7 and T2-12 were also studied. DNA sequence data placed T2-7 in a previously described gene class, tnpR-D and T2-12 in a new gene class, tnpR-F. The significance of this data with respect to the recombination and evolution events occurring within bacterial populations are discussed.

Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

A new method is presented for inferring evolutionary trees using nucleotide sequence data. The birth-death process is used as a model of speciation and extinction to specify the prior distribution of phylogenies and branching times. Nucleotide substitution is modeled by a continuous-time Markov process. Parameters of the branching model and the substitution model are estimated by maximum likelihood. The posterior probabilities of different phylogenies are calculated and the phylogeny with the highest posterior probability is chosen as the best estimate of the evolutionary relationship among species. We refer to this as the maximum posterior probability (MAP) tree. The posterior probability provides a natural measure of the reliability of the estimated phylogeny. Two example data sets are analyzed to infer the phylogenetic relationship of human, chimpanzee, gorilla, and orangutan. The best trees estimated by the new method are the same as those from the maximum likelihood analysis of separate topologies, but the posterior probabilities are quite different from the bootstrap proportions. The results of the method are found to be insensitive to changes in the rate parameter of the branching process.

Phylogenetic analysis using parsimony and likelihood methods

The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were allowed to differ between nucleotides or across sites, the probability that MP recovers the true topology, and especially its performance relative to that of the likelihood method, generally deteriorates. As the complexity of the process of nucleotide substitution in real sequences is well recognized, the likelihood method appears preferable to parsimony. However, the development of a statistical methodology for the efficient estimation of the tree topology remains a difficult open problem.

Sequence analysis of HIV-1 vif gene in Spanish isolates

We have determined the nucleotide sequence of the HIV-1 vif gene in viruses obtained from symptomatic patients of distinct risk groups in Madrid. The genetic diversity among the isolates was estimated in 4.6% (+/- 1.4 standard deviation), a similar value to that obtained for the gag gene 3.9% (+/- 0.8 standard deviation) and env 4.1% (+/- 1 standard deviation) (Rojas et al., Virus Res 31, 331-342, 1994). Amino acid sequence analysis revealed the presence of hypermutable residues at positions 101 and 167, close to antigenically relevant sequential epitopes (comprising amino acids 87-94 and 172-178). Phylogenetic analysis supports the existence of two virus lineages circulating preferentially within different risk groups.

The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis

The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene

The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.

Disparate rates of molecular evolution in cospeciating hosts and parasites

DNA sequences for the gene encoding mitochondrial cytochrome oxidase I in a group of rodents (pocket gophers) and their ectoparasites (chewing lice) provide evidence for cospeciation and reveal different rates of molecular evolution in the hosts and their parasites. The overall rate of nucleotide substitution (both silent and replacement changes) is approximately three times higher in lice, and the rate of synonymous substitution (based on analysis of fourfold degenerate sites) is approximately an order of magnitude greater in lice. The difference in synonymous substitution rate between lice and gophers correlates with a difference of similar magnitude in generation times.

Molecular epidemiology of HIV-1 in Madrid

Thirteen HIV-1 isolates from patients of different risk groups in Madrid (Spain) have been analyzed at the genetic level. Two distinct lineages of subtype B have been detected among the HIV-1 circulating in this area: one was related to SF-2/RF strains, whereas the other consists of a more heterogeneous group related to reference strain III-B. Variants of each lineage appeared to circulate preferentially within a risk group: III-B among intravenous drug users, and RF/SF-2 among male homosexuals.

Toward a more accurate time scale for the human mitochondrial DNA tree

Several estimates of the time of occurrence of the most recent common mitochondrial DNA (mtDNA) ancestor of modern humans have been made. Estimates derived from noncoding regions based on a model that classifies sites into two categories (variable and invariable) have been consistently older than those derived from the third positions of codons. This discrepancy can be attributed to a violation of the assumption of rate homogeneity among variable sites when analyzing the noncoding regions. Additional data from the partial control region sequences allow us to take into account some of this further heterogeneity. By assigning the sites to three classes (highly variable, moderately variable, and invariable) and by assuming that the last common mtDNA ancestor of humans and chimpanzees lived 4 million years ago, the most recent common mtDNA ancestor of humans is estimated to have occurred 211,000 +/- 111,000 years ago (+/- 1 SE), consistent with the estimate, 101,000 +/- 52,000 years, made from third positions of codons and also with those proposed previously. We used the same technique to estimate when a putative expansion of modern humans out of Africa took place and estimated a time of 89,000 +/- 69,000 years ago. Even though the standard errors of these estimates are large, they allow us to reject the multiregional hypothesis of modern human origin.

The inference of evolutionary trees from molecular data

1. Procedures for multiple alignment of sequence data, subsequent phylogenetic inference, and testing of the trees derived are presented. 2. The assumptions underlying different approaches and the extent to which they are valid are discussed.

On the maximum likelihood method in molecular phylogenetics

The efficiency of obtaining the correct tree by the maximum likelihood method (Felsenstein 1981) for inferring trees from DNA sequence data was compared with trees obtained by distance methods. It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolutionary rate differs among lineages.