Measuring the phylogenetic randomness of biological data sets

Two qualitative taxonomic characters are potentially compatible if the states of each can be ordered into a character state tree in such a way that the two resulting character state trees are compatible. The number of potentially compatible pairs (NPCP) of qualitative characters from a data set may be considered to be a measure of its phylogenetic randomness. The value of NPCP depends on the number of evolutionary units (EUs), the number of characters, the number of states in the characters, the distributions of EUs among these states, and the amount and distribution of missing information and so does not directly indicate degree of phylogenetic randomness. Thus, for an observed data set, we used Monte Carlo methods to estimate the probability that a data set chosen equiprobably from among those identical (with respect to all the other above determining features) to the observed data set would have as high (or low) an NPCP as the observed data set. This probability, the realized significance of the observed NPCP, is attractive as an indication of phylogenetic randomness because it does not require the assumptions made by other such methods: No character state trees are assumed and consequently, only potential compatibility can be determined; no particular method of phylogenetic estimation is assumed; and no phylogenetic trees are constructed. We determined the values and significances of NPCP for analyses of 57 data sets taken from 53 published sources. All data sets from 37 of those sources exhibited realized significances of < 0.01, indicating high levels of phylogenetic nonrandomness. From each of the remaining 16 sources, at least one data set was more phylogenetically random. Inclusion of outgroups changed significance in some cases, but not always in the same direction. Data sets with significantly low NPCP may be consistent with an ancient hybrid origin (or other ancient polyphyletic gene exchange, crossing over, viral transfer, etc.) of the study group.     

Inferring and testing hypotheses of cladistic character dependence by using character compatibility

The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before phylogeny reconstruction, or can be used simply to test for correlated evolution. We first develop an approach for visualizing suites of correlated characters by using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilities between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for significant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities, given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of nonphylogenetic correlation in character suites can be attributed to chance alone. We have applied these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers and also identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix.     

Stability of characters and construction of phylogenetic trees.

Parsimony methods infer phylogenetic trees by minimizing number of character changes required to explain observed character states. From the perspective of applicability of parsimony methods, it is important to assess whether the characters used to infer phylogeny are likely to provide a correct tree. We introduce a graph theoretical characterization that helps to assess whether given set of characters is appropriate to use with parsimony methods. Given a set of characters and a set of taxa, we construct a network called character overlap graph. We show that the character overlap graph for characters that are appropriate to use in parsimony methods is characterized by significant under-representation of subnetworks known as holes, and provide a validation for this observation. This characterization explains success in constructing evolutionary trees using parsimony method for some characters (e.g., protein domains) and lack of such success for other characters (e.g., introns). In the latter case, the understanding of obstacles to applying parsimony methods in a direct way has lead us to a new approach for detecting inconsistent and/or noisy data. Namely, we introduce the concept of stable characters which is similar but less restrictive than the well known concept of pairwise compatible characters. Application of this approach to introns produces the evolutionary tree consistent with the Coelomata hypothesis.     

Phylogenetic inference from homologous sequence data: minimum topological assumption, strict mutational compatibility consensus tree as the ultimate solution

Background  

For the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics. The vast majority of these methods are based on specific topological assumptions relating to the resultant genealogical tree. Each of these has been shown to perform effectively in special conditions and for specific data sets while yielding less reliable results in other instances. Moreover, the majority of the methods include information from homoplastic characters in spite of a universally accepted agreement in their ineffectiveness for phylogenetic inference, which may often lead to inaccuracy and inconsistency. As an alternative to such methods, a strict mutational compatibility consensus tree building method as a universally applicable and reliable method is reported.     

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of "Holostei" (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs.     

Graph theory, tionary trees and classification

Many methods have been used for analysing information about organisms in order to understand tionary relationships and/or to determine classifications. The reationship between some of these methods is illustrated for the character state matrix, incompatibility and similarity matrices, minimal unrooted and rooted trees, and tionary classifications. Existing methods of determining the shortest possible tree are described. In addition a new method of building a minimal tree is introduced which starts with the largest possible subset (clique) of characters that is compatible for all pairs of characters. The remaining characters are ranked in order of their increasing number of incompatibilities. These characters are added singly, a tree constructed and then tested for minimality by previously described methods for partitioning characters into subsets. The procedure is repeated at least until the tree can no longer be proved minimal. The relationship between trees and tionary and phylogenetic classifications has been neglected but three methods are metioned and a new criterion suggested. It is suggested that graph theory, rather than statistics, is better suited for the primary analysis of comparative data.     

分支分类学中和谐性概念与和谐性分析方法

和谐性是分支分类学中的一个基本概念。本文给出一个和谐性的数学定义,称为Kexue和谐性。并在Kexue和谐性的基础上开发出一个新的和谐性分析方法。并对该方法在分支分类研究中的应用进行讨论。     

Compatibility analysis and its applications

A two-state character is defined as uniquely derived if it has only evolved once in the history of a group, without subsequent reversal. Two independent characters cannot both be uniquely derived if all four possible combinations (or all three excluding that of the two ancestral forms) occur.
A number of ways of choosing compatible sets of uniquely derived characters are discussed and used to derive possible unrooted and rooted trees. Results of these are related to those chosen on parsimony criteria, using data for orthopteroid groups, and the assumptions of both methods are compared. Application of compatibility analysis to the moth genera Teldenia and Argodrepana is also discussed. Compatibility and parsimony methods are complementary rather than exclusive of each other.     

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates [published erratum appears in Mol Biol Evol 1995 May;12(3):525]

Using simulated data, we compared five methods of phylogenetic tree estimation: parsimony, compatibility, maximum likelihood, Fitch- Margoliash, and neighbor joining. For each combination of substitution rates and sequence length, 100 data sets were generated for each of 50 trees, for a total of 5,000 replications per condition. Accuracy was measured by two measures of the distance between the true tree and the estimate of the tree, one measure sensitive to accuracy of branch lengths and the other not. The distance-matrix methods (Fitch- Margoliash and neighbor joining) performed best when they were constrained from estimating negative branch lengths; all comparisons with other methods used this constraint. Parsimony and compatibility had similar results, with compatibility generally inferior; Fitch- Margoliash and neighbor joining had similar results, with neighbor joining generally slightly inferior. Maximum likelihood was the most successful method overall, although for short sequences Fitch- Margoliash and neighbor joining were sometimes better. Bias of the estimates was inferred by measuring whether the independent estimates of a tree for different data sets were closer to the true tree than to each other. Parsimony and compatibility had particular difficulty with inaccuracy and bias when substitution rates varied among different branches. When rates of evolution varied among different sites, all methods showed signs of inaccuracy and bias.      

Higher-Order Homoplasy Tests

The Le Quesne test of character compatibility uses pairwise comparisons of characters to detect homoplasy in phylogenetic character data. If a pair of characters fails this test we can conclude that a minimum of a single extra step is required by the pair of characters. The rationale of the Le Quesne test is extended to comparisons of triplets of characters. The triplet homoplasy test can reveal that that there is a minimum of four extra steps across a triplet of characters and thus that there are at least two extra steps associated with one of the characters. The triplet homoplasy test can thus detect higher orders of homoplasy than can be detected by the pairwise Le Quesne test. The possibility of quartet and other higher-order homoplasy tests is discussed. The utility of higher-order homoplasy tests is discussed. It is suggested higher-order homoplasy tests have potential uses analogous to the uses of the Le Quesne test, particularly with respect to data exploration.     

Ortholog identification in the presence of domain architecture rearrangement

Ortholog identification is used in gene functional annotation, species phylogeny estimation, phylogenetic profile construction and many other analyses. Bioinformatics methods for ortholog identification are commonly based on pairwise protein sequence comparisons between whole genomes. Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain but differ outside this region of homology. While promiscuous domains represent a challenge to all orthology prediction methods, overall structural similarity is highly correlated with proximity in a phylogenetic tree, conferring a degree of robustness to phylogenetic methods. In this article, we review the issues involved in orthology prediction when data sets include sequences with structurally heterogeneous domain architectures, with particular attention to automated methods designed for high-throughput application, and present a case study to illustrate the challenges in this area.     

CHARACTERS, CONGRUENCE AND QUALITY: A STUDY OF NEUROANATOMICAL AND TRADITIONAL DATA IN CAECILIAN PHYLOGENY

Previous phylogenetic analyses of caecilian neuroanatomical data yield results that are difficult to reconcile with those based upon more traditional morphological and molecular data. A review of the literature reveals problems in both the analyses and the data upon which the analyses were based. Revision of the neuroanatomical data resolves some, but not all, of these problems and yields a data set that, based on comparative measures of data quality, appears to represent some improvement over previous treatments. An extended data set of more traditional primarily morphological data is developed to facilitate the evaluation of caecilian relationships and the quality and utility of neuroanatomical and more traditional data. Separate and combined analyses of the neuroanatomical and traditional data produce a variety of results dependent upon character weighting, with little congruence among the results of the separate analyses and little support for relationships among the ‘higher’ caecilians with the combined data. Randomization tests indicate that: (i) there is significantly less incompatibility within each data set than that expected by chance alone; (2) the between-data-set incompatibility is significantly greater than that expected for random partitions of characters so the two data sets are significantly heterogeneous; (3) the neuroanatomical data appear generally of lower quality than the traditional data; (4) the neuroanatomical data are more compatible with the traditional data than are phylogenetically uninformative data. The lower quality of the neuroanatomical data may reflect small sample sizes. In addition, a subset of the neuroanatomical characters supports an unconventional grouping of all those caecilians with the most rudimentary eyes, which may reflect concerted homoplasy. Although the neuroanatomical data may be of lower quality than the traditional data, their compatibility with the traditional data suggests that they cannot be dismissed as phylogenetically meaningless. Conclusions on caecilian relationships are constrained by the conflict between the neuroanatomical and traditional data, the sensitivity of the combined analyses to weighting schemes, and by the limited support for the majority of groups in the majority of the analyses. Those hypotheses that are well supported are uncontroversial, although some have not been tested previously by numerical phylogenetic analyses. However, the data do not justify an hypothesis of ‘higher’ caecilian phylogeny that is both well resolved and well supported.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

A statistical approach to the evaluation of characters to estimate evolutionary relationships among the species of the aquatic subterranean genus, Iberobathynella (Crustacea, Syncarida)

The 13 known species of the genus Iberobathynella were studied. Twenty-six characters with usually two or three states were revealed to have low within-species variability but show clear differences among some species. These characters were hypothesized to have states convex on the branching pattern of the phylogenetic lines that gave rise to these 13 species (i.e. be uniquely derived). Each pair of these hypotheses was tested for logical compatibility; then, for each character, a new character was created by choosing equiprobably one of the possible permutations of the 13 species to rename the species in each state. Characters created in this random way would have convex states only by chance, not by evolution. This random character was tested with each of the remaining 25 for logical compatibility as hypotheses of convexity. For each character, one thousand such random characters were created and tested. Sixteen observed characters were compatible with more other observed characters than 90% of their randomly generated counterparts, and so were considered plausibly non-random. They were used to speculate on branching patterns of the phylogenetic lines among the 13 species.     

On the biochemical systematics of selected mammalian taxa: empirical comparison of qualitative and quantitative approaches in the evaluation of protein electrophoretic data

Empirical data sets of Artiodactyla (Antilocapridae, Bovidae, Cervidae, Suidae), Carnivora (Mustelidae) and Rodentia (Sciuridae, Cricetidae, Arvicolidae, Muridae), obtained by horizontal starch el electrophoresis of 15–34 isoenzyme sstems, were used to calculate genetic distances and to construct phylogenetic trees by the following methods: Nei's D (corrected for small sample sizes) - UPGMA, FITCH, KITSCH (out of Felsenstein's PHYLIP-package); Rogers -distance - distance-Wanger tree; maximum likelihood approach (cavalli -Sforza -Edwards ); maximum parsimony method (wagner ); Hennigian cladogram. The results were re-examined using the statisticar methods of jackknife and bootstrap. The following problems became apparent and were studied in more detail: inconstancy of molecular evolutionary rate among taxa, non-uniformity of evolutionary rate among isoenzymes, possible convergence of alloenzymes, different evolutionary histories of taxa (radiations/bottlenecks), methodological influences sample sizes / rare alleles, comparability of data sets). The results show, that many branches of the various phylogenetic trees are fairly constant. The ambiguous position of the remaining OTU's is due to insufficient evidence in the primary data rather than to theroperties of cluster algorithms. However, since these problematic cases are also uncertain in phylogenies based on morphological characters and palaeontological results, even an increased data set may not lead to a cyear decision unless additional taxa of crucial importance are examined. Molecular evolutionary rate among taxa seems to be accelerated in some cases, possibly due to random fixation of different alleles during bottlenecks, when a highly polymorpic ancestral form underwent a series of adaptive radiations. Isoenzymes can be divided into groups with different evolutionary rates. Thus, data sets are only comparable with respect to genetic variability and differentiation, when they contain a similar amount of representatives of each of these categories.     

Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions

The character compatibility approach, which removes all homoplasic characters and involves finding the largest clique of compatible characters in a dataset, in principle, provides a powerful means for obtaining correct topology in difficult to resolve cases. However, the usefulness of this approach to generalized molecular sequence data for phylogeny determination has not been studied in the past. We have used this approach to determine the topology of 23 proteobacterial species (6 each of α-, β- and γ-, 3 δ-, and 2 ε-proteobacteria) using sequence data for 10 conserved proteins (Hsp60, Hsp70, EF-Tu, EF-G, alanyl-tRNA synthetase, RecA, GyrA, GyrB, RpoB and RpoC). All sites in the sequence alignments of these proteins where only two amino acids were found, with each amino acid present in at least two species, were selected. Mutual compatibility determination on these binary state sites was carried out by two means. In one case, all of these sites were combined into a large dataset (Set A; 957 characters) prior to compatibility analysis. In the second case, compatibility analysis was carried out on characters from individual proteins and all compatible sites were combined into a large dataset (Set B; 398 characters) for further studies. Upon compatibility analyses, the largest cliques that were obtained from Sets A and B consisted of 337 and 323 compatible characters, respectively. In these cliques, all proteobacterial subgroups were clearly distinguished and branching orders of most of the species were also resolved. The ε-proteobacteria exhibited the earliest branching, whereas the β- and γ-subgroups were found to have emerged last. The relative placement of the α- and δ-subgroups, however, was not resolved. The topology of these species was also determined based on 16S rRNA sequences and a concatenated dataset of sequences for all 10 proteins by means of neighbor-joining, maximum likelihood, and maximum parsimony methods. In the protein trees, all proteobacterial groups were reliably resolved and they branched in the following order: (ε(δ(α(β,γ)))). However, in the rRNA trees, the γ- and β-subgroups exhibited polyphyletic branching and many internal nodes were not resolved. These results indicate that the character compatibility analysis using generalized molecular sequence data provides a powerful means for evolutionary studies. Based on molecular sequences, it should be possible to obtain very large datasets of compatible characters that should prove very helpful in clarifying difficult to resolve phylogenetic relationships. [Reviewing Editor: Dr. Yves Van de Peer]     

Testing character correlation using pairwise comparisons on a phylogeny

In comparative biology, pairwise comparisons of species or genes (terminal taxa) are used to detect character associations. For instance, if pairs of species contrasting in the state of a particular character are examined, the member of a pair with a particular state might be more likely than the other member to show a particular state in a second character. Pairs are chosen so as to be phylogenetically separate, that is, the path between members of a pair, along the branches of the tree, does not touch the path of any other pair. On a given phylogenetic tree, pairs must be chosen carefully to achieve the maximum possible number of pairs while maintaining phylogenetic separation. Many alternative sets of pairs may have this maximum number. Algorithms are developed that find all taxon pairings that maximize the number of pairs without constraint, or with the constraint that members of each pair have contrasting states in a binary character, or that they have contrasting states in two binary characters. The comparisons chosen by these algorithms, although phylogenetically separate on the tree, are not necessarily statistically independent.     

Inference of phylogenetic relationships among key angiosperm lineages using a compatibility method on a molecular data set

Phylogenetic relationships among the five key angiosperm lineages,Ceratophyllum,Chloranthaceae,eudicots,magnoliids,and monocots,have resisted resolution despite several large-scale analyses sampling taxa and characters extensively and using various analytical methods.Meanwhile,compatibility methods,which were explored together with parsimony and likelihood methods during the early development stage of phylogenetics.have been greatly under-appreciated and not been used to analyze the massive amount of sequence data to reconstruct thye basal angiosperm phylogeny.In this study,we used a compatibility method on a data set of eight genes (mitochondrial atp1,matR,and nad5,plastid atpB,marK,rbcL,and rpoC2,and nuclear 18S rDNA)gathered in an earlier study.We selected two sets of characters that are compatible with more of the other characters than a random character would be with at probabilities of pM＜0.1 and p＜0.5 respectively.The resulting data matrices were subjected to parsimony and likelihood bootstrap analyses.Our unrooted parsimony analyses showed that Ceratophyllum was immediately related to eudicots,this larger lineage was immediately related to magnoliids,and monocots were closely related to Chloranthaceae.All these relationships received 76%-96% bootstrap support.A likelihood analysis of the 8 gene pM＜0.5 compatible site matrix recovered the same topology but with low support.Likelihood analyses of other compatible site matrices produced different topologies that were all weakly supported.The topology reconstructed in the parsimony analyses agrees with the one recovered in the previous study using both parsimony and likelihood methods when no character was eliminated.Parts of this topology have also been recovered in several earlier studies.Hence,this topology plausibly reflects the true relationships among the five key angiosperm lineages.     

Morphometric variation in the hominoid orbital aperture: a case study with implications for the use of variable characters in Miocene catarrhine systematics

Variable characters are ubiquitous in hominoid systematics and present a number of unique problems for phylogenetic analyses that include extinct taxa. As yet, however, few studies have quantified ranges of variation in complex morphometric characters within extant taxa and then used those data to assess the consistency with which discrete character states can be applied to poorly represented fossil species. In this study, ranges of intrageneric morphometric variation in the shape of the hominoid orbital aperture are estimated using exact randomization of average pairwise taxonomic distances (ATDs) derived from size-adjusted centroid, height-width, and elliptic Fourier (EF) variables. Using both centroid and height-width variables, 19 of the 21 possible ATDs between individuals representing seven extinct catarrhine taxa (Aegyptopithecus, Afropithecus, Ankarapithecus, Ouranopithecus, Paranthropus, Sivapithecus and Turkanapithecus) can be observed within a single extant hominoid subspecies, although generally with low probabilities. A resampling study is employed as a means for gauging the effect that this intrataxonomic variation may have on the consistency with which discrete orbital shape character states can be delimited given the small sample sizes available for most Miocene catarrhine taxa preserving this feature (i.e., n=1). For each type of morphometric variable, 100 cluster (UPGMA) analyses of pairwise ATDs are performed in which a single individual is randomly selected from each hominoid genus and analyzed alongside known extinct taxa; consensus trees are computed in order to obtain the frequencies with which different shape clusters appeared in each of the three analyses. The two major clusters appearing most frequently in all three consensus trees are found in only 57% (centroid variables), 49% (height-width variables), and 36% (EF variables) of these trees. If ranges of variation within represented extinct taxa could also be estimated, these frequencies would certainly be far lower. Hominoids clearly exhibit considerable intrageneric, intraspecific, and even intrasubspecific variation in orbit shape, and substantial morphometric overlap exists between taxa; consequently, discrete character states delimiting these patterns of continuous variation are likely to be highly unreliable in phylogenetic analyses of living and extinct species, particularly as the number of terminal taxa increases. Morphological phylogenetic studies of extant catarrhines that assess the effect of different methods (e.g., use of objective a priori weighting or frequency coding of variable characters, inclusion vs. exclusion of variable characters, use of specific vs. supraspecific terminal taxa) on phylogenetic accuracy may help to improve the techniques that systematists employ to make phylogenetic inferences about extinct taxa.     

Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets.