Tree-length Distribution Research Articles

Maximum Parsimony and the Skewness Test: A Simulation Study of the Limits of Applicability.

The maximum parsimony (MP) method for inferring phylogenies is widely used, but little is known about its limitations in non-asymptotic situations. This study employs large-scale computations with simulated phylogenetic data to estimate the probability that MP succeeds in finding the true phylogeny for up to twelve taxa and 256 characters. The set of candidate phylogenies are taken to be unrooted binary trees; for each simulated data set, the tree lengths of all (2n − 5)!! candidates are computed to evaluate quantities related to the performance of MP, such as the probability of finding the true phylogeny, the probability that the tree with the shortest length is unique, the probability that the true phylogeny has the shortest tree length, and the expected inverse of the number of trees sharing the shortest length. The tree length distributions are also used to evaluate and extend the skewness test of Hillis for distinguishing between random and phylogenetic data. The results indicate, for example, that the critical point after which MP achieves a success probability of at least 0.9 is roughly around 128 characters. The skewness test is found to perform well on simulated data and the study extends its scope to up to twelve taxa.

Increasing the number of discrete character states for continuous characters generates well‐resolved trees that do not reflect phylogeny

Since the introduction of the cladistic method in systematics, continuous characters have been integrated into analyses but no methods for their treatment have received unanimous support. Some methods require a large number of character states to discretise continuous characters in order to keep the maximum level of information about taxa differences within the coding scheme. Our objective was to assess the impact of increasing the character state number on the outcomes of phylogenetic analyses. Analysis of a variety of simulated datasets shows that these methods for coding continuous characters can lead to the generation of well-resolved trees that do not reflect a phylogenetic signal. We call this phenomenon the flattening of the tree-length distribution; it is influenced by both the relative quantity of continuous characters in relation to discrete characters, and the number of characters in relation to the number of taxa. Bootstrap tests provide a method to avoid this potential bias.

Predicting the Ancestral Character Changes in a Tree is Typically Easier than Predicting the Root State

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rates become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, that, depending on the tree and branch length distribution, reconstructing these changes (i.e., reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony- and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification.

Phylogenetic signal in bone histology of amniotes revisited

Legendre, L, Le Roy, N, Martinez‐Maza, C, Montes, L, Laurin, M & Cubo, J. (2012). Phylogenetic signal in bone histology of amniotes revisited. —Zoologica Scripta,42, 44–53.There is currently a debate about the presence of a phylogenetic signal in bone histological data, but very few rigorous tests have fuelled the discussions on this topic. Here, we performed new analyses using a larger set of seven histological traits and including 25 taxa (nine extinct and 16 extant taxa), using three methods: the phylogenetic eigenvector regression, the tree length distribution and the regressions on distance matrices. Our results clearly show that the phylogenetic signal in our sample of bone histological characters is strong, even after correcting for multiple testing. Most characters exhibit a significant phylogenetic signal according to at least one of our three tests, with the phylogeny often explaining 20–60% of the variation in the histological characters. Thus, we conclude that the phylogenetic comparative method should be systematically used in interspecific analyses of bone histodiversity to avoid problems of non‐independence among observations.

Mosaics of Convergences and Noise in Morphological Phylogenies: What's in a Viverrid-Like Carnivoran?

Adaptive convergence in morphological characters has not been thoroughly investigated, and the processes by which phylogenetic relationships may be misled by morphological convergence remains unclear. We undertook a case study on the morphological evolution of viverrid-like feliformians (Nandinia, Cryptoprocta, Fossa, Eupleres, Prionodon) and built the largest morphological matrix concerning the suborder Feliformia to date. A total of 349 characters grouped into four anatomical partitions were used for all species of Viverridae and viverrid-like taxa plus representatives of the Felidae, Hyaenidae, Herpestidae, and one Malagasy mongoose. Recent molecular phylogenetic analyses suggest that viverrid-like morphotypes appeared independently at least three times during feliformian evolution. We thus used a synthetic molecular tree to assess morphological evolutionary patterns characterizing the viverrid-like taxa. We examined phylogenetic signal, convergence and noise in morphological characters using (a) tree-length distribution (g1), (b) partitioned Bremer support, (c) RI values and their distribution, (d) respective contributions of diagnostic synapomorphies at the nodes for each partition, (e) patterns of shared convergences among viverrid-like taxa and other feliformian lineages, (f) tree-length differences among alternative hypotheses, and (g) the successive removal of convergent character states from the original matrix. In addition, the lability of complex morphological structures was assessed by mapping them onto the synthetic molecular tree. The unconstrained morphological analysis yielded phylogenetic groupings that closely reflected traditional classification. The use of a synthetic molecular tree (constraint) combined with our thorough morphological investigations revealed the mosaics of convergences likely to have contributed to part of the historical uncertainty over viverrid classification. It also showed that complex morphological structures could be subjected to reversible evolutionary trends. The morphological matrix proved useful in characterizing several feliformian clades with diagnostic synapomorphies. These results support the removal from the traditionally held Viverridae of several viverrid-like taxa into three distinct families: Nandiniidae (Nandinia), Prionodontidae (Prionodon), and the newly defined Eupleridae (including Cryptoprocta, Fossa, Eupleres plus all "mongoose-like" Malagasy taxa). No clearly "phylogenetically misleading" data subsets could be identified, and the great majority of morphological convergences appeared to be nonadaptive. The multiple approaches used in this study revealed that the most disruptive element with regards to morphological phylogenetic reconstruction was noise, which blured the expression of phylogenetic signal. This study demonstrates the crucial need to consider independent (molecular) phylogenies in order to produce reliable evolutionary hypotheses and should promote a new approach to the definition of morphological characters in mammals. [Constrained analysis; convergence; evolutionary scenario; Feliformia; morphology; noise; phylogenetic signal; phylogeny; Viverridae.].

Phylogenetic Signal in Bone Microstructure of Sauropsids

In spite of the fact that the potential usefulness of bone histology in systematics has been discussed for over one and a half centuries, the presence of a phylogenetic signal in the variation of histological characters has rarely been assessed. A quantitative assessment of phylogenetic signal in bone histological characters could provide a justification for performing optimizations of these traits onto independently generated phylogenetic trees (as has been done in recent years). Here we present an investigation on the quantification of the phylogenetic signal in the following bone histological, microanatomical, and morphological traits in a sample of femora of 35 species of sauropsids: vascular density, vascular orientation, index of Haversian remodeling, cortical thickness, and cross-sectional area (bone size). For this purpose, we use two methods, regressions on distance matrices tested for significance using permutations (a Mantel test) and random tree length distribution. Within sauropsids, these bone microstructural traits have an optimal systematic value in archosaurs. In this taxon, a Mantel test shows that the phylogeny explains 81.8% of the variation of bone size and 86.2% of the variation of cortical thickness. In contrast, a Mantel test suggests that the phylogenetic signal in histological traits is weak: although the phylogeny explains 18.7% of the variation of vascular density in archosaurs, the phylogenetic signal is not significant either for vascular orientation or for the index of Haversian remodeling. However, Mantel tests seem to underestimate the proportion of variance of the dependent character explained by the phylogeny, as suggested by a PVR (phylogenetic eigenvector) analysis. We also deal with some complementary questions. First, we evaluate the functional dependence of bone vascular density on bone size by using phylogenetically independent contrasts. Second, we perform a variation partitioning analysis and show that the phylogenetic signal in bone vascular density is not a by-product of phylogentic signal in bone size. Finally, we analyze the evolution of cortical thickness in diapsids by using an optimization by squared change parsimony and discuss the functional significance of this character in terms of decreased buoyancy in crocodiles and mass saving in birds. These results are placed in the framework of the constructional morphology model, according to which the variation of a character in a clade has a historical (phylogenetic) component, a functional (adaptive) component, and a structural (architectural) component.

PHYLOGENETIC RELATIONSHIPS OF GOMPHOCYTHERE (OSTRACODA) IN LAKE TANGANYIKA, EAST AFRICA

We examined the distribution of 44 morphological characters for 16 extant species of an ostracode genus, Gomphocythere, in Africa, to test hypotheses concerning character development and speciation patterns. Using heuristic searches conducted with the phylogenetic reconstruction program PAUP (beta version, 4.0), we found 2 trees of 98 steps (CI = 0.56). The skewness of tree length distribution reveals significant phylogenetic structure in the data. Nodes are supported by 1 to 11 character-state changes, and these character changes are sometimes reversed or paralleled elsewhere, accounting for much of the homoplasy in the reconstructions. By systematically removing both hard- and soft-part characters in separate analyses, hard-part characters were found to be far more homoplasious in their distribution across the phylogenetic tree, while soft parts are minimally homoplasious, suggesting that they are far more conservative while the hard parts are more prone to ecophenotypic variation. This phylogeny provides the basis for evaluating speciation mechanisms and the role of ecological factors in the diversification of ostracodes in this lake system.

Phylogenetic Relationships of Gomphocythere (Ostracoda) in Lake Tanganyika, East Africa

We examined the distribution of 44 morphological characters for 16 extant species of an ostracode genus, Gomphocythere, in Africa, to test hypotheses concerning character development and speciation patterns. Using heuristic searches conducted with the phylogenetic reconstruction program PAUP (beta version, 4.0), we found 2 trees of 98 steps |$({\rm CI} = 0.56)$|⁠. The skewness of tree length distribution reveals significant phylogenetic structure in the data. Nodes are supported by 1 to 11 character-state changes, and these character changes are sometimes reversed or paralleled elsewhere, accounting for much of the homoplasy in the reconstructions. By systematically removing both hard- and soft-part characters in separate analyses, hard-part characters were found to be far more homoplasious in their distribution across the phylogenetic tree, while soft parts are minimally homoplasious, suggesting that they are far more conservative while the hard parts are more prone to ecophenotypic variation. This phylogeny provides the basis for evaluating speciation mechanisms and the role of ecological factors in the diversification of ostracodes in this lake system.

Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets.

Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, make up the Amphiesmenoptera. Despite extensive previous morphological work, little phylogenetic agreement has been reached about the relationship among the three suborders--Annulipalpia, Spicipalpia, and Integripalpia--or about the monophyly of Spicipalpia. In an effort to resolve this conflict, we sequenced fragments of the large and small subunit nuclear ribosomal RNAs (1078 nt; D1, D3, V4-5), the nuclear elongation factor 1 alpha gene (EF-1 alpha; 1098 nt), and a fragment of mitochondrial cytochrome oxidase I (COI; 411 nt). Seventy adult and larval morphological characters were reanalyzed and added to molecular data in a combined analysis. We evaluated signal and homoplasy in each of the molecular datasets and attempted to rank the particular datasets according to how appropriate they were for inferring relationships among suborders. This evaluation included testing for conflict among datasets, comparing tree lengths among alternative hypotheses, measuring the left-skew of tree-length distributions from maximally divergent sets of taxa, evaluating the recovery of expected clades, visualizing whether or not substitutions were accumulating with time, and estimating nucleotide compositional bias. Although all these measures cast doubt on the reliability of the deep-level signal coming from the nucleotides of the COI and EF-1 alpha genes, these data could still be included in combined analyses without overturning the results from the most conservative marker, the rRNA. The different datasets were found to be evolving under extremely different rates. A site-specific likelihood method for dealing with combined data with nonoverlapping parameters was proposed, and a similar weighting scheme under parsimony was evaluated. Among our phylogenetic conclusions, we found Annulipalpia to be the most basal of the three suborders, with Spicipalpia and Integripalpia forming a clade. Monophyly of Annulipalpia and Integripalpia was confirmed, but the relationships among spicipalpians remain equivocal.

Analysis of the Genetic Relationships Among the Wheat Bunt Fungi Using RAPD and Ribosomal DNA Markers

Ninety-five isolates of Tilletia controversa, T. tritici, T. laevis, and T. fusca var. bromi-tectorum were assayed for random amplified polymorphic DNA (RAPD). Based on 23 RAPD markers, two distinct RAPD groups (RG I and RG II) with 12% similarity were obtained using the distance matrix method. RG included all 66 isolates of the wheat bunt fungi and RG II contained all 29 isolates of T. fusca var. bromi-tectorum, which was considered as an outgroup. RGI was further divided into two subgroups RG IA and RG IB with 75% similarity : RG IA containing 19 isolates of T. controversa and RG IB containing 38 isolates of T. tritici, T. laevis, and six isolates of T. controversa. Bootstrap analysis supported the separation between isolates from wheat and isolates from cheatgrass, but not the clustering of isolates within the wheat bunt group. However, the gl statistic, a measure of the skewness of the tree-length distribution, indicated a significant difference between the dwarf bunt and common bunt clusters (P < 0.05). Restriction digestion analysis of the 5.8s and internal transcribed spacer region of ribosomal DNA in a subset of wheat bunt fungi (28 isolates of T. controversa, 19 isolates of T. tritici, and 12 isolates of T. laevis) showed two distinct patterns. Haplotype A was associated with 24 of 28 isolates of T. controversa and haplotype B was associated with all isolates of common bunt fungi and four isolates of T. controversa. The data suggested that the wheat bunt fungi descended from a common ancestral population that subsequently differentiated into two sublineages. The fact that a considerable number of isolates have reciprocal characteristics of both dwarf and common bunt fungi raises the question of whether natural hybridization is responsible for the apparent recombination of characters.

Phylogeny of the Nemertean Subclass Palaeonemertea (Anopla, Nemertea)

Abstract — A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty-five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum. An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo- and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy-two equally most parsimonious cladograms were found; the consistency index was low but tree-length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.

Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees

The Neognathostomata (comprising the orders Clypeasteroida, Oligopygoida, Neolampadoida, and the paraphyletic Cassiduloida) form one of the three major clades of irregular echinoids. Despite the group's apparent success since the Jurassic and impressive peak diversity in the mid-Cretaceous, most included clades are now severely reduced. A phylogeny is essential for reconstructing the taxonomic, environmental and biogeographic patterns of this decline, and understanding the causal processes responsible for them. I examined the distribution of qualitative morphological characters (including those defining genera) for 97 species from 77 non-clypeasteroid genera and the three clypeasteroid suborders. Following preliminary analyses, I reduced the data to 40 characters (having 60 apomorphic states) and 71 representative genera. Goloboff's data decisiveness, the skewness of tree length distributions, and permutation tests all reveal significant phylogenetic structure in the data. Heuristic searches conducted with PAUP found more than 72 500 trees of 217 steps (CI = 0.276), but only the first 30 000 were evaluated. These exhibit considerable instability in the relationships among taxa. Successive approximations weightings did not reduce the numbers of favoured trees. Analyses using only less homoplasious characters failed to improve the resolution. Fisher's stratigraphic debt provides an objective means of selecting a very few of the morphologically most-parsimonious trees. Most nodes are supported by only one to three character changes, and these are generally reversed or paralleled elsewhere. The results suggest some cassiduloid families can not be separated, and support the reassignment of several genera. Despite the high levels of homoplasy, the most-parsimonious trees require fewer changes than had been previously suggested for evolutionary trends in several characters. Whether the rampant homoplasy present in the data reflects incorrect character analysis, limited structural or developmental options, or the effects of parallel selection, its presence raises severe obstacles to phylogenetic analyses.

Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees

The Neognathostomata (comprising the orders Clypeasteroida, Oligopygoida, Neolampadoida, and the paraphyletic Cassiduloida) form one of the three major clades of irregular echinoids. Despite the group's apparent success since the Jurassic and impressive peak diversity in the mid-Cretaceous, most included clades are now severely reduced. A phylogeny is essential for reconstructing the taxonomic, environmental and biogeographic patterns of this decline, and understanding the causal processes responsible for them. I examined the distribution of qualitative morphological characters (including those defining genera) for 97 species from 77 non-clypeasteroid genera and the three clypeasteroid suborders. Following preliminary analyses, I reduced the data to 40 characters (having 60 apomorphic states) and 71 representative genera. Goloboff's data decisiveness, the skewness of tree length distributions, and permutation tests all reveal significant phylogenetic structure in the data. Heuristic searches conducted with PAUP found more than 72 500 trees of 217 steps (CI = 0.276), but only the first 30,000 were evaluated. These exhibit considerable instability in the relationships among taxa. Successive approximations weightings did not reduce the numbers of favoured trees. Analyses using only less homoplasious characters failed to improve the resolution. Fisher's stratigraphic debt provides an objective means of selecting a very few of the morphologically most-parsimonious trees. Most nodes are supported by only one to three character changes, and these are generally reversed or paralleled elsewhere. The results suggest some cassiduloid families can not be separated, and support the reassignment of several genera. Despite the high levels of homoplasy, the most-parsimonious trees require fewer changes than had been previously suggested for evolutionary trends in several characters. Whether the rampant homoplasy present in the data reflects incorrect character analysis, limited structural or developmental options, or the effects of parallel selection, its presence raises severe obstacles to phylogenetic analyses.

Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation

Part of the mitochondrial 12S ribosomal RNA gene was amplified and sequenced for 26 marsupials. Multiple alignments for these sequences as well as seven additional sequences taken from GenBank were obtained using CLUSTAL. PAUP was used for phylogenetic analysis and to obtain random tree-length distributions. Analyses were performed with and without phylogenetic constraints. Our results clearly show that 12S rDNA contains phylogenetic signal at and above the ordinal level and is thus appropriate for addressing phylogenetic questions deep in the mammalian tree. Standard parsimony analyses provide some support for a clade containing diprotodontians, dasyurids,Dromiciops, andNotoryctes; transversion parsimony analysis suggests the possible inclusion of peramelids as well. Within the Diprotodontia, vombatids and phascolarctids cluster together on transversion parsimony and phalangerids may be associated with this clade. The enigmatic tarsipedids are apparently part of a clade that also contains pseudocheirids, petaurids, and acrobatids. The 12S sequences suggest that the origination of extant marsupial orders peaked 15 million years later than the equivalent taxonomic diversification of extant placental orders and may be entirely post-Cretaceous. Families of diprotodontian marsupials originated during the Eocene and early Oligocene, which is consistent with previous single-copy DNA hybridization results.

ON CORROBORATION: A REPLY TO CARPENTER.

CladisticsVolume 8, Issue 3 p. 265-273 Free Access ON CORROBORATION: A REPLY TO CARPENTER Daniel P. Faith, Daniel P. Faith Division of Wildlife and Ecology, CSIRO, P.O. Box 84, Lyneham, ACT 2602, AustraliaSearch for more papers by this author Daniel P. Faith, Daniel P. Faith Division of Wildlife and Ecology, CSIRO, P.O. Box 84, Lyneham, ACT 2602, AustraliaSearch for more papers by this author First published: September 1992 https://doi.org/10.1111/j.1096-0031.1992.tb00070.xCitations: 19AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL REFERENCES Arghie J.W.. 1989a. A randomization test for phylogenetic information in systematic data. Syst. Zool. 38: 219– 252. Arghie J.W.. 1989b. Phylogenies of plant families: a demonstration of phylogenetic randomness in DNA sequence data derived from proteins. Evolution 43: 1796– 1800. Bryant H.N.. 1989. An evaluation of cladistic and character analyses as hypotheticodeductive procedures, and the consequences for character weighting. Syst. Zool. 38: 214– 227. Bryant H.N.. 1992. The role of permutational probability tests in phylogenetic systematics. Syst. Biol. 41: 258– 263. Carpenter J.M.. 1992. Random cladistics. Cladistics 8: 147– 153. Faith D.P.. 1990. Chance marsupial relationships. Nature 345: 393– 394. Faith D.P.. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40: 366– 375. Faith D.P. and P.S. Cranston. 1991. Could a cladogram this short have arisen by chance alone?: on permutation tests for cladistic structure. Cladistics 7: 1– 28. Faith D.P. and P.S. Cranston. 1992. Probability, parsimony and Popper. Syst. Biol. 41: 252– 257. Farris J.S.. 1983. The logical basis of phylogenetic analysis. In : N.I. Platnick and V.A. Funk, (eds.). Advances in Cladistics, Vol. 2. Columbia , New York . 7– 36. Gilinsky N.L.. 1991. Cross sections through evolutionary trees: theory and applications. Syst. Zool. 40: 1932. Harper C.W.. 1979. A Bayesian probability view of phylogenetic systematics. Syst. Zool. 28: 547– 553. Huelsenbeck J.P.. 1991. Tree-length distribution skewness: an indicator of phylogenetic information. Syst. Zool. 40: 257– 270. Oakes M., 1986. Statistical Inference: a Commentary for the Social and Behavioural Sciences. Wiley, New York . Popper K., 1959. The Logic of Scientific Discovery. Hutchinson, London . Popper K., 1963. Conjectures and Refutations: the Growth of Scientific Knowledge. Harper & Row, New York . Sanderson M.J.. 1989. Confidence limits on phylogenies: the bootstrap revisited. Cladistics 5: 113– 129. West J.G. and D.P. Faith. 1990. Data, methods and assumptions in phylogenetic inference. Aust. Syst. Bot. 3: 9– 20. Citing Literature Volume8, Issue3September 1992Pages 265-273 ReferencesRelatedInformation

Signal, noise, and reliability in molecular phylogenetic analyses.

DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.

Rates of evolution and fossils in phylogenetic analysis: a computer simulation approach

Whereas many studies have examined the performance of various character-data sets in phylogenetic analysis, little work has been done on the effect that various classes of taxa have on phylogenetic reconstruction. In particular, the “fossil versus living taxa” debate has concentrated mainly on the effects of fossils in reconstructing vertebrate and plant relationships. While this work has contributed to the understanding of the role that fossils play in systematics, a computer model clarifies the relationship among the main determinants of the fossil-taxa problem. In addition, simulations of phylogenies over a wide spectrum of evolutionary rates clarify the relative efficiencies of various tree-estimation procedures.In this study, computer generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis.The importance of fossil taxa varied depending on their completeness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased.

When are Fossils Better than Extant Taxa in Phylogenetic Analysis?

Computer-generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis. The importance of fossil taxa varied depending on their com- pleteness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased. A simple analytical model is proposed to explain these results. (Fossils; phylogeny reconstruction; simulation.)

Tree-Length Distribution Skewness: An Indicator of Phylogenetic Information

Computer simulations in which phylogenies were generated under various conditions were used to examine the relationship between the phylogenetic signal of a character data set, the skewness of the tree-length distribution, and the position of the real tree relative to the most parsimonious tree for a four-character-state system. Character data that are consistent with one phylogenetic hypothesis produce tree-length distributions that are highly skewed to the left, whereas character data consistent with many phylogenetic hypotheses produce more symmetrical tree-length distributions that cannot be distinguished from tree-length distributions produced by random character data. The relationship between the skewness of the tree-length distribution, as measured by the g1 statistic, and the amount of phylogenetic signal varies depending on tree topology, the proportion of the sequence that is informative (e.g., informative change at only the first codon position as opposed to informative change at the first and second codon positions), and the number of sequence data. However, in all simulations that produced tree-length distributions that were significant at the 1% level under Hillis's (1991, in Phylogenetic analysis of DNA sequences [M. M. Miyamoto and J. Cracraft, eds.], Oxford Univ. Press, Oxford, England [in press]) statistical test, the real tree was very close to or was the most parsimonious tree. Conversely, in trees with nonsignificantly skewed tree-length distributions, the real tree could be almost anywhere in the distribution. However, the real tree tended to be closer to the most parsimonious tree than would be expected at random. This study suggests that tree-length distribution skewness provides a useful criterion for judging the phylogenetic information content of character data. [Tree-length distribution; skewness; phylogenetic information.]