High Levels Of Homoplasy Research Articles

Phylogenetic relationships of the Papuan Swiftlet Aerodramus papuensis and implications for the evolution of avian echolocation

The swiftlets (genera Aerodramus, Collocalia and Hydrochous) are unusual among birds in that many species can orientate in complete darkness using echolocation. The position of the Papuan Swiftlet Aerodramus papuensis in this group has been uncertain historically, in part due to morphological differences between it and other swiftlets (it has three toes instead of the usual four) and a lack of data on its behaviour (there is uncertainty about whether it echolocates). Here we investigate the phylogenetic affinities of the Papuan Swiftlet using DNA sequence data from two mitochondrial genes, cytochrome b and ND2. We present evidence that it is able to echolocate but, unlike previously studied species that use echolocation primarily while flying in caves, A. papuensis uses this ability while active outside caves at night. We also provide new evidence for placement of the monotypic Waterfall Swiftlet Hydrochous gigas, a species that does not echolocate. Our data provide strong support for a basal relationship between A. papuensis and other Aerodramus taxa and suggest that this species and H. gigas are sister taxa, a relationship that would indicate paraphyly of the genus Aerodramus. Our phylogeny provides new insights into how echolocation has evolved in the swiftlets, in particular by indicating higher levels of homoplasy in this trait than was previously thought.

Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores

We sequenced locus Mel 08, with complex short repetitive motifs, in 24 carnivore species belonging to five different families in order to explore mutational changes in the region in the context of locus and species evolution. This non-coding locus includes up to four different parts or repetitive motifs showing size variability. The variability consists of repeat additions and deletions; substitutions, insertions and/or deletions creating interruptions in the repeat; and substitutions, insertions and deletions in the flanking regions. The locus has different repeat expansions in different carnivore subfamilies. We hypothesize that the complexity of this locus is due to a high mutation rate at an ancestral DNA sequence and, thus, prompts the emergence of repeats at mutational hotspots. High levels of homoplasy were evident, with nine electromorphs representing 28 haplotypes never shared across species. The variability in flanking regions was informative for phylogenetic inference and their evolutionary content. Tree topologies were congruent with relevant hypotheses on current conflicts in carnivore phylogenies, such as: (i) the monophyly of Lutrinae, (ii) the paraphyly of Mustelinae, (iii) the basal position of the Eurasian badger, Meles meles , in the Mustelidae, (iv) the classification of skunks as a separate family, Mephitidae, and (v) the placement of the red panda, Ailurus fulgens , as a monotypic family, Ailuridae, at a basal position in the Musteloidea.

Gene Family Content-Based Phylogeny of Prokaryotes: The Effect of Criteria for Inferring Homology

A number of recent papers have suggested that gene family content can be used to resolve phylogenies, particularly in the case of prokaryotes, in which extensive horizontal gene transfer means that individual gene phylogenies may not mirror the organismal phylogeny. However, no study has yet examined how sensitive such analyses are to the criterion of homology assessment used to assemble multigene families. Using data from 99 completely sequenced prokaryotic genomes, we examined the effect of homology criteria in phylogenetic analyses wherein presence or absence of each family in the genome was used as a cladistic character. Different criteria resulted in evidence for contradictory tree topologies, sometimes with high bootstrap support. A moderately strict criterion seemed best for assembling multigene families in a biologically meaningful way, but it was not necessarily preferable for phylogenetic analysis. Instead, a very strict criterion, which broke up gene families into smaller subfamilies, seemed to have advantages for phylogenetic purposes. The poor performance of gene family content-based phylogenetic analysis in the case of prokaryotes appears to reflect high levels of homoplasy resulting not only from horizontal gene transfer but also, more importantly, from extensive parallel loss of gene families in certain bacteria genomes.

Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed.

Functional adaptations in the craniofacial morphology of malagasy primates: shape variations associated with gummivory in the family Cheirogaleidae

The infraorder Lemuriformes is characterized by a high level of homoplasy that clouds the evolutionary signal. The analysis of the morphological disparity of the Malagasy primates' crania and mandibles demonstrates the high determinism of functional specializations and developmental constraints, regardless of the phylogeny. In the present work, the weight of functional constraints linked to diet--a putative source of homoplasy--is analyzed first at the level of the infraorder Lemuriformes as a whole, and secondly at the level of a single family, the Cheirogaleidae, chosen because it contains taxa with two different diets (omnivory and gummivory). Malagasy primates are characterized by a great variety of dietary habits: some of them are omnivores, folivores, frugivores, gummivores, insectivores or even specialized hard-object feeders. All cheirogaleids feed on tree exudates, but while gum consumption is occasional or limited for Microcebus, Cheirogaleus and Mirza, gums are the dominant food source for Phaner and Allocebus. Craniofacial shape variations are analyzed using geometric morphometrics: methods based on landmark identification (Procrustes superimpositions) are chosen for cranium shape analysis, and methods based on outline decomposition (elliptical Fourier functions) for study of mandible shape. The morphospaces obtained at the level of the infraorder appear to be highly constrained by dietary habits, especially in the case of the mandibles. At the finer level of the family Cheirogaleidae, the analyses permit (1) separation of craniomandibular shape variation associated with the two dietary categories and (2) among the omnivorous category, to distinguish variation associated with the percentage of gum consumption.

Precision and accuracy of divergence time estimates from STR and SNPSTR variation.

Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically < 500 bp) to one or more single-nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should, therefore, be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3% to 7% bias for SNPSTR versus 11% to 20% bias for STR) and more precise than STR-based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.

The Pedigree Rate of Sequence Divergence in the Human Mitochondrial Genome: There Is a Difference Between Phylogenetic and Pedigree Rates

We have extended our previous analysis of the pedigree rate of control-region divergence in the human mitochondrial genome. One new germline mutation in the mitochondrial DNA (mtDNA) control region was detected among 185 transmission events (generations) from five Leber hereditary optic neuropathy (LHON) pedigrees. Pooling the LHON pedigree analyses yields a control-region divergence rate of 1.0 mutation/bp/10(6) years (Myr). When the results from eight published studies that used a similar approach were pooled with the LHON pedigree studies, totaling >2,600 transmission events, a pedigree divergence rate of 0.95 mutations/bp/Myr for the control region was obtained with a 99.5% confidence interval of 0.53-1.57. Taken together, the cumulative results support the original conclusion that the pedigree divergence rate for the control region is approximately 10-fold higher than that obtained with phylogenetic analyses. There is no evidence that any one factor explains this discrepancy, and the possible roles of mutational hotspots (rate heterogeneity), selection, and random genetic drift and the limitations of phylogenetic approaches to deal with high levels of homoplasy are discussed. In addition, we have extended our pedigree analysis of divergence in the mtDNA coding region. Finally, divergence of complete mtDNA sequences was analyzed in two tissues, white blood cells and skeletal muscle, from each of 17 individuals. In three of these individuals, there were four instances in which an mtDNA mutation was found in one tissue but not in the other. These results are discussed in terms of the occurrence of somatic mtDNA mutations.

Phylogenetic Relationships in Iris Series Californicae Based on ITS Sequences of Nuclear Ribosomal DNA

Abstract Cladistic analyses of Iris included 18 ingroup taxa from series Californicae and two outgroup taxa from series Sibiricae. The internal transcribed spacers and the 5.8S subunit of 18–26S nuclear ribosomal DNA were sequenced to provide phylogenetic information. An analysis of DNA data resulted in five most parsimonious trees that concurred in part with morphological data. Species groups in series Californicae that have been informally proposed by previous workers were not supported in this study. Two species complexes, I. tenax and I. hartwegii, were not monophyletic as currently delineated. Support for several internally resolved clades is low with DNA data, probably due to high levels of homoplasy along some branches. The overall level of variation and sequence divergence is relatively high compared to other infrageneric plant groups. Communicating Editor: James F. Smith

Myrtaceae revisited: a reassessment of infrafamilial groups

Cladistic analyses are presented of matK sequence data as well as a nonmolecular database for an identical set of exemplar species chosen to represent the core genera or groups of genera in Myrtaceae. Eleven robust clades are recognized on the molecular data. Polyphyly of the previously recognized Metrosideros and Leptospermum alliances is confirmed, and several smaller informal taxonomic groupings are recognized from among the members of the former alliance, i.e., the Tristania, Tristaniopsis, Metrosideros, and Lophostemon groups. The nonmolecular analysis provides only limited resolution of relationships. A degree of congruence exists between the two analyses in that two separate fleshy-fruited clades, the Acmena and Myrtoid groups, are identified, as are the Eucalypt and Tristania groups, and Psiloxylon and Heteropyxis are the first lineages to diverge in both analyses. A combined analysis recognized all 11 clades that received strong support from the molecular data. A high level of homoplasy is revealed in many of the nonmolecular characters when they are examined against the combined estimate of phylogeny.

Mining the Mammalian Genome for Artiodactyl Systematics

A total of 7,806 nucleotide positions derived from one mitochondrial and eight nuclear DNA segments were used to provide a robust phylogeny for members of the order Artiodactyla. Twenty-four artiodactyl and two cetacean species were included, and the horse (order Perissodactyla) was used as the outgroup. Limited rate heterogeneity was observed among the nuclear genes. The partition homogeneity tests indicated no conflicting signal among the nuclear genes fragments, so the sequence data were analyzed together and as separate loci. Analyses based on the individual nuclear DNA fragments and on 34 unique indels all produced phylogenies largely congruent with the topology from the combined data set. In sharp contrast to the nuclear DNA data, the mtDNA cytochrome b sequence data showed high levels of homoplasy, failed to produce a robust phylogeny, and were remarkably sensitive to taxon sampling. The nuclear DNA data clearly support the paraphyletic nature of the Artiodactyla. Additionally, the family Suidae is diphyletic, and the nonruminating pigs and peccaries (Suiformes) were the most basal cetartiodactyl group. The morphologically derived Ruminantia was always monophyletic; within this group, all taxa with paired bony structures on their skulls clustered together. The nuclear DNA data suggest that the Antilocaprinae account for a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa, and the Giraffidae are more primitive.

Molecular Phylogenetics of Subfamily Calamoideae (Palmae) Based on nrDNA ITS and cpDNA rps16 Intron Sequence Data

Phylogenetic relationships among the 22 genera of the palm subfamily Calamoideae were investigated using DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast rps16 intron. The rps16 intron displayed low levels of variation, corroborating previous reports that the chloroplast genome of palms is highly conserved. High levels of within-individual polymorphism were identified in the ITS region, indicating that concerted evolution is not effectively homogenizing the ITS repeats. In the majority of cases, multiple clones from individuals resolved as monophyletic. However, the high levels of homoplasy in the ITS dataset, along with generally poor jackknife support for many clades, led to concerns that topologies obtained from these data might be unreliable. Nevertheless, congruence between trees based on ITS data alone and those based on rps16 intron data was high. Simultaneous analyses of both datasets yielded well-resolved topologies with high levels of jackknife support. A number of exciting groups emerged from the analyses: the African rattan clade comprising the endemic African rattan genera Laccosperma, Eremospatha, and Oncocalamus; the Lepidocaryeae–Raphia clade comprising the fan-leaved New World tribe Lepidocaryeae and the African genus Raphia; and the Asian clade comprising all Asian genera except Eugeissona. The position of Eugeissona was variable, although it did not resolve inside any of the three major clades mentioned above.

Discriminating and locating character covariance: an application of permutation tail probability (PTP) analyses.

The ability of permutation tail probability (PTP) analyses to discriminate between character covariance and noise is investigated with both hypothetical and published data sets. PTP is shown to be a powerful tool, not only for detecting character covariance, but also for locating that covariance on trees. PTP is especially useful for evaluating DNA sequence data that may have a high level of homoplasy. A three-step PTP procedure for locating covaried characters is presented.

Evolutionary implications of hemipenial morphology in the terrestrial Australian elapid snakes

Venomous proteroglyphous or ‘elapid’ snakes are distributed across much of the tropical and subtropical world but are most diverse in Australia. Due to diVering opinions of character weight and problems associated with high levels of homoplasy in traditionally used snake character systems, there is no well accepted hypothesis of phylogenetic relationships for the Australian elapids. Moreover, few or no synapomorphies have been identified to define many of the 20 currently recognized genera. As part of a re-evaluation of previous work, I have undertaken a survey of hemipenial morphology in this diverse radiation in a search for supraspecific synapomorphies. Up to 14 aspects of hemipenial morphology were scored on 756 museum specimens and provide the basis for hemipenial descriptions of 64 species of Australian elapid. Morphology is highly conservative at generic levels and supportive of a number of previously suggested phyletic groups, but divergent between putative monophyletic lineages. Hemipenial morphology provides synapomorphies that define seven, and possibly eight, monophyletic groups at subgeneric, generic, and suprageneric levels: (1) Demansia, Oxyuranus, Pseudonaja, and Pseudechis each display unique hemipenial morphologies but share a number of character states. The following groups each share unique hemipenial types: (2) Simoselaps calonotus and the Simoselaps semifasciatus species group, (3) Vermicella and the Simoselaps bertholdi species group, (4) Cacophis and Furina, (5) Austrelaps, Echiopsis, Hoplocephalus, Notechis, and Tropidechis, (6) Drysdalia and Hemiaspis, (7) Rhinoplocephalus and Suta, and (8) Acanthophis and Denisonia. Higher level associations also are identified. The organs of Cacophis‐Furina and Vermicella‐Simoselaps bertholdi clades are very similar in shape and diVer in only a single character. The Drysdalia‐Hemiaspis and Rhinoplocephalus‐Suta clades share a hemipenial shape and also diVer in only a single character. Where sample sizes were suYcient for comparison, hemipenes displayed little or no intraspecific variation.

Evolutionary implications of hemipenial morphology in the terrestrial Australian elapid snakes

Venomous proteroglyphous or «elapid» snakes are distributed across much of the tropical and subtropical world but are most diverse in Australia. Due to differing opinions of character weight and problems associated with high levels of homoplasy in traditionally used snake character systems, there is no well accepted hypothesis of phylogenetic relationships for the Australian elapids. Moreover, few or no synapomorphies have been identified to define many of the 20 currently recognized genera. As part of a re-evaluation of previous work, I have undertaken a survey of hemipenial morphology in this diverse radiation in a search for supraspecific synapomorphies. Up to 14 aspects of hemipenial morphology were scored on 756 museum specimens and provide the basis for hemipenial descriptions of 64 species of Australian elapid. Morphology is highly conservative at generic levels and supportive of a number of previously suggested phyletic groups, but divergent between putative monophyletic lineages. Hemipenial morphology provides synapomorphies that define seven, and possibly eight, monophyletic groups at subgeneric, generic, and suprageneric levels: (1)Demansia,Oxyuranus,Pseudonaja, andPseudechiseach display unique hemipenial morphologies but share a number of character states. The following groups each share unique hemipenial types: (2)Simoselaps calonotusand theSimoselaps semifasciatusspecies group, (3)Vermicellaand theSimoselaps bertholdispecies group, (4)CacophisandFurina, (5)Austrelaps,Echiopsis,Hoplocephalus,Notechis, andTropidechis, (6)DrysdaliaandHemiaspis, (7)RhinoplocephalusandSuta, and (8)AcanthophisandDenisonia. Higher level associations also are identified. The organs ofCacophis–FurinaandVermicella–Simoselaps bertholdiclades are very similar in shape and differ in only a single character. TheDrysdalia–HemiaspisandRhinoplocephalus–Sutaclades share a hemipenial shape and also differ in only a single character. Where sample sizes were sufficient for comparison, hemipenes displayed little or no intraspecific variation.

A phylogenetic analysis of higher‐level gall wasp relationships (Hymenoptera: Cynipidae)

We present the most comprehensive analysis of higher‐level relationships in gall wasps conducted thus far. The analysis was based on detailed study of the skeletal morphology of adults, resulting in 164 phylogenetically informative characters, complemented with a few biological characters. Thirty‐seven cynipid species from thirty‐one genera, including four genera of the apparently monophyletic Cynipini and almost all of the genera in the other tribes, were examined. The outgroup included exemplar species from three successively more distant cynipoid families: Figitidae (the sister group of the Cynipidae), Liopteridae and Ibaliidae. There was considerable homoplasy in the data, but many groupings in the shortest tree were nonetheless well supported, as indicated by bootstrap proportions and decay indices. Partitioning of the data suggested that the high level of homoplasy is characteristic of the Cynipidae and not the result of the amount of available phylogenetically conservative characters being exhausted. The analysis supported the monophyly of the Cynipini (oak gall wasps) which, together with the Rhoditini (the rose gall wasps), Eschatocerini and Pediaspidini formed a larger monophyletic group of gall inducers restricted to woody representatives of the eudicot subclass Rosidae. The inquilines (Synergini) were indicated to be monophyletic, whereas the Aylacini, primarily herb gall inducers, appeared as a paraphyletic assemblage of basal cynipid groups. The shortest tree suggests that the Cynipidae can be divided into three major lineages: one including the inquilines, the Aylacini genera associated with Rosaceae, and Liposthenes; one consisting entirely of Aylacini genera, among them Aulacidea, Isocolus and Neaylax; and one comprising the woody rosid gallers (the oak and rose gall wasps and allies), the Phanacis‐Timaspis complex and the Aylacini genera associated with Papaveraceae.

A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa

Estimates of phylogenetic relationships among fossil taxa implicitly provide hypotheses about the quality of the fossil record. Phylogenetic inferences also provide hypotheses about character evolution. The likelihood of any hypothesis that makes predictions about two data sets is simply the likelihood of the hypothesis given the first data set times the likelihood of the same hypothesis given the second data set. In this case, data set 1 represents stratigraphy and data set 2 represents morphology. Statistical methods exist for determining the likelihood of hypothesized levels of sampling. The likelihood of a hypothesized amount of character change yielding a particular most-parsimonious solution (i.e, L[hypothesized length | parsimony length] can be evaluated with simulations. A reanalysis of hyaenid phylogeny based on published character and stratigraphic data is presented here, using the maximum likelihood method. Two trees are found, depending on assumptions about ambiguous species, which are 11 and 10 steps longer than the most parsimonious tree (61 or 60 vs. 50 steps). However, the trees invoke far less stratigraphic debt (9 or 12 units vs. 47 units as measured in Mammal Zones). An important feature of the results is that the most likely tree length given hyaenid character data is estimated to be 56 to 62 steps (depending on the model of character evolution) rather than 50 steps. The likelihood tree suggests stronger trends toward bone-crushing specializations than does the parsimony tree and further suggests that high levels of homoplasy caused parsimony to underestimate the true extent of those trends. Simulations based on the character data and fossil record of hyaenids suggest that the maximum likelihood method is better able to estimate correct trees than is parsimony and somewhat better able to do so than previously proposed phylogenetic methods incorporating stratigraphy.

A Test and Review of the Empirical Performance of the Ontogenetic Criterion

The empirical performance of the ontogenetic criterion for determining character po- larities was tested based on three published and one new data set originating from a study of larval Sepsidae (Diptera). The ontogenetic criterion polarizes about as many characters as does outgroup comparison. However, for the four data sets conflicting polarities were inferred for 4- 45% of all characters for which both polarization methods were applicable. Four different versions of the ontogenetic criterion were identified from the literature and were empirically tested. The version used by de Queiroz (1985, Syst. Zool. 34:280-299) and Wheeler (1990, Cladistics 6:225- 268) fared best, as determined by low levels of homoplasy and a small number of inferred equally parsimonious tree roots. For three of four empirical data sets, hypothetical ancestors based on outgroup comparison and the ontogenetic criterion resulted in identical tree roots. Hypothetical ancestors based on outgroup comparison implied less homoplasy than did those based on the ontogenetic criterion, so the ougroup method appears to be superior for character polarization. To test whether polarity decisions from both polarization methods should be combined into one hypothetical ancestor, two different composite ancestors were reconstructed. One comprised only the plesiomorphic states of the characters for which both criteria predicted the same polarity (consensus). It inferred multiple parsimonious roots without distinctly lowering the level of ho- moplasy. The second ancestor comprised the plesiomorphic states as predicted by one or both methods (composite). It tended to infer single roots, even for data sets for which very different rooting positions were identified by the two polarization criteria, thereby obscuring conflict be- tween the two methods. High levels of homoplasy in hypothetical ancestors based on the onto- genetic criterion are not due to the inclusion of presence /absence characters in the data set, for which the application of the ontogenetic criterion would require hypotheses of homology for absent character states across ontogenetic stages of different species. Instead, the ratio of ter- minal deletions to terminal additions is a better predictor for the success of the ontogenetic cri- terion for any particular data set. (Biogenetic law; heterochrony; Nelson's rule; ontogenetic crite- rion; outgroup comparison; recapitulation.)

A Molecular Phylogeny of the Aphidiinae (Hymenoptera: Braconidae)

Phylogenetic relationships within the Aphidiinae, and between this and other subfamilies of Braconidae (Hymenoptera), were investigated using sequence data from three genes: elongation factor-1α, cytochrome b, and the second expansion segment of the 28S ribosomal subunit. Variation in both protein-coding genes was characterized by a high level of homoplasy, but analysis of the expansion segment—robust over a range of alignment methods and parameters—resolved some of the older divergences. Parsimony analysis of the combined data suggests the following tribal relationships: (Ephedrini + (Praini + (Aphidiini + Trioxini))). In addition, the cyclostome subfamilies were found to form a clade separate from the Aphidiinae, but relationships between the Aphidiinae and the noncyclostome braconids could not be resolved. The inferred phylogeny also supported a secondary loss of internal pupation within the Praini and a polyphyletic origin of endoparasitism within the Braconidae.

TOPIARY PRUNING AND WEIGHTING REINFORCE AN AFRICAN ORIGIN FOR THE HUMAN MITOCHONDRIAL DNA TREE.

A method is presented for removing recent homoplastic events from a phylogenetic tree. This "topiary pruning" method produces a series of progressively modified duplicates of the original set of data, from which more and more of the most recent substitutions have been removed. The edited sets of data have increased amounts of information per remaining taxon, while similar but randomized data sets subjected to topiary pruning do not. The ability of topiary pruning to "unscramble" artificial data sets that have high levels of homoplasy is demonstrated, and is shown to be similar in its effects to the weighting method of Kluge and Farris (1969), although with the additional advantage of reducing the number of taxa to the point where bootstrapping is feasible. Pruning and weighting used together produce closer approximations to the "true" tree than either method used separately. It is further shown that in these artificial data sets midpoint rooting is more likely to be accurate than outgroup rooting. When pruning and weighting are applied to the extensive sets of mitochondrial DNA data of Cann et al. (1987) and Vigilant et al. (1991), trees result that have deep branch points, some of which lead to entirely African branches. In the case of the Vigilant et al. data, the three African branches have bootstrap values between 0.94 and 1.0, and the consensus and bootstrap midpoint roots also have high bootstrap values and occur on these African branches near their junction. An African origin of the human mitochondrial tree is not proved by this approach, particularly since sequences from non-African groups are underrepresented in current data sets, but it is rendered more likely.

Phylogenetic analysis of Eucalyptus informal subgenus Symphyomyrtus section Maidenaria

Eucalyptus informal subgenus Symphyomyrtus section Maidenaria includes 86 currently recognised taxa endemic to south-eastern Australia. Cladistic methodology and a morphological data set have been used to examine the phylogenetic relationships of these taxa and an additional two unnamed forms that may be worthy of taxonomic recognition. Maidenaria may be defined as a monophyletic group by the presence of oil glands in the phloem, although this feature is not unique to the group. Informal series Ovatae is paraphyletic, having been defined by plesiomorphic features such as petiolate juvenile leaves. Informal series Vitninales is monophyletic, defined by juvenile leaves that are opposite, sessile and cordate for many nodes. The analysis was a difficult one because of a high level of homoplasy (82%), problems with intergrading complexes of taxa, and coding of characters that are continuously varying. The cladogram produced for Maidenaria can be viewed as a statement of the pattern of variation of morphological characters in the group. It is likely to be only an approximate representation of the phylogeny due to problems of character coding.