Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets

Consensus on the evolutionary relationships of humans, chimpanzees, andgorillas has not been reached, despite the existence of a number of DNAsequence data sets relating to the phylogeny, partly because not all genetrees from these data sets agree. However, given the well-known phenomenonof gene tree-species tree mismatch, agreement among gene trees is notexpected. A majority of gene trees from available DNA sequence data supportone hypothesis, but is this evidence sufficient for statistical confidencein the majority hypothesis? All available DNA sequence data sets showingphylogenetic resolution among the hominoids are grouped according togenetic linkage of their corresponding genes to form independent data sets.Of the 14 independent data sets defined in this way, 11 support a human-chimpanzee clade, 2 support a chimpanzee-gorilla clade, and one supports ahuman-gorilla clade. The hypothesis of a trichotomous speciation eventleading to Homo; Pan, and Gorilla can be firmly rejected on the basis ofthis data set distribution. The multiple-locus test (Wu 1991), whichevaluates hypotheses using gene tree-species tree mismatch probabilities ina likelihood ratio test, favors the phylogeny with a Homo-Pan clade andrejects the other alternatives with a P value of 0.002. When theprobabilities are modified to reflect effective population size differencesamong different types of genetic loci, the observed data set distributionis even more likely under the Homo-Pan clade hypothesis. Maximum-likelihoodestimates for the time between successive hominoid divergences are in therange of 300,000-2,800,000 years, based on a reasonable range of estimatesfor long-term hominoid effective population size and for generation time.The implication of the multiple-locus test is that existing DNA sequencedata sets provide overwhelming and sufficient support for ahuman-chimpanzee clade: no additional DNA data sets need to be generatedfor the purpose of estimating hominoid phylogeny. Because DNA hybridizationevidence (Caccone and Powell 1989) also supports a Homo-Pan clade, theproblem of hominoid phylogeny can be confidently considered solved.     

Accuracy of estimated phylogenetic trees from molecular data

Summary The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.     

A phylogeny of the extant Phocidae inferred from complete mitochondrial DNA coding regions

Despite extensive interest in the systematics of Pinnipedia, questions remain concerning phylogenetic relationships within the Phocidae or "true" seals. Relationships within the phocids and their placement relative to the remaining pinnipeds and major lineages of arctoid carnivores were examined using a large molecular data set consisting of 12 mitochondrial protein coding genes. Phylogenetic analysis including 15 extant species of the Phocidae, and representatives of the Otariidae, Odobenidae, Ursidae, Mustelidae, Canidae, and Felidae confirmed the monophyletic origins of the Pinnipedia within the Arctoidea. Slightly more support was found for an ursid affinity of the pinnipeds, however, this relationship remains contentious. The Phocidae were placed as the sister group to a common odobenid-otariid clade. Within the family Phocidae, strong support for the traditionally accepted subfamilies Phocinae (northern seals), and Monachinae (southern seals plus monk seals) was found. In contrast to recent suggestions, a monophyletic Monachus was strongly supported and was placed in a deep branching position within the Monachinae. Evidence from sequence divergence under a maximum likelihood model illustrated that the rarely used tribal distinction within the Monachinae are comparable, in terms of evolutionary distance, to accepted tribal distinctions within the Phocinae. In addition, results suggest that Pagophilus should be accepted as a genus within the Phocini. Sequence divergence between Phoca, Pusa, and Halichoerus is minimal, supporting a taxonomic reclassification of the three genera into an emended genus Phoca, without subgeneric distinctions.     

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data, these methods require heavy computation, and their application is limited to the analysis of a moderate number of genes and taxa. Distance matrix methods present suitable alternatives for analyzing huge amounts of sequence data. However, the manner in which distance methods can be applied to multilocus sequence data remains unknown. Here, we suggest new procedures to estimate molecular phylogeny using multilocus sequence data and evaluate its significance in the framework of the distance method. We found that concatenation of the multilocus sequence data may result in incorrect phylogeny estimation with an extremely high bootstrap probability (BP), which is due to incorrect estimation of the distances and intentional ignorance of the intergene variations. Therefore, we suggest that the distance matrices for multilocus sequence data be estimated separately and these matrices be subsequently combined to reconstruct phylogeny instead of phylogeny reconstruction using concatenated sequence data. To calculate the BPs of the reconstructed phylogeny, we suggest that 2-stage bootstrap procedures be adopted; in this, genes are resampled followed by resampling of the sequence columns within the resampled genes. By resampling the genes during calculation of BPs, intergene variations are properly considered. Via simulation studies and empirical data analysis, we demonstrate that our 2-stage bootstrap procedures are more suitable than the conventional bootstrap procedure that is adopted after sequence concatenation.     

Preliminary phylogeny of Valerianaceae (Dipsacales) inferred from nuclear and chloroplast DNA sequence data

Valerianaceae is a relatively small (ca. 350 species), but morphologically diverse angiosperm clade. Sequence data from the entire ndhF gene, the trnL-F intergenic spacer region, the trnL intron, the matK region, the rbcL-atpB intergenic spacer region and internal transcribed spacer (ITS) region of nuclear ribosomal DNA were collected for 21 taxa within Dipsacaceae and Valerianaceae (1 and 20, respectively). These data were included in several phylogenetic analyses with previously published sequences from Dipsacales. Results from these analyses (maximum parsimony, maximum likelihood, and Bayesian analysis) are in strong agreement with many of the conclusions from previous studies, most importantly: (1) Valerianaceae is sister to Dipsacaceae; (2) Triplostegia is more closely related to species of Dipsacaceae than to Valerianaceae; and (3) Valeriana appears not to be monophyletic, with Valeriana celtica falling outside the remainder of the species of Valeriana sampled here (with very strong support). With the exception of V. celtica, these data support two major clades within Valeriana; one that is exclusively New World and another that is distributed in both the Old and New World. Although the species of Valerianaceae and its sister group Dipsacaceae plus Triplostegia, are widely distributed in the Northern Hemisphere, and the data imply that Valerianaceae diversified initially in Asia (the Himalayan Patrinia and Nardostachys falling at the base of the clade), the center of modern species diversity for the group is in the Andes of South America with as many as 175 species restricted to that region. Although the exclusively South American taxa form a clade in the chloroplast and combined ITS and chloroplast analyses, support values tend to be low. Future studies will need to include additional data, in the form of both characters and taxa, before any strong conclusions about the character evolution, diversification, and biogeography of the South American valerians can be made.     

A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny

Maximum likelihood phylogeny reconstruction methods are widely used in uncovering and assessing the evolutionary history and relationships of natural systems. However, several simplifying assumptions commonly made in this analysis limit the explanatory power of the results obtained. We present an algorithm that performs the phylogenetic analysis without making the common assumptions for sequence data from at least three leaf nodes in a star phylogeny. In particular, the underlying nucleotide substitution model does not have to be reversible and may include neighbor-dependent processes like the CpG methylation deamination process (CpG-effect). The base composition of the sequences at the external nodes and the one of the ancestral sequence may be different from each other and they do not have to be stationary state distributions of the corresponding substitution model. The algorithm is able to reconstruct the ancestral base composition and accurately estimate substitution frequencies in the branches of the star phylogeny. Extensive tests on simulated data validate the very favorable performance of the algorithm. As an application we present the analysis of aligned genomic sequences from human, mouse, and dog. Different substitution pattern can be observed in the three lineages.     

A molecular phylogeny of eurytomid wasps inferred from DNA sequence data of 28S, 18S, 16S, and COI genes

Using partial DNA sequence data from nuclear 28S and 18S genes and mitochondrial 16S and COI genes, we reconstructed a phylogeny of the family Eurytomidae. Both maximum parsimony and Bayesian methods were employed. The analysis revealed a significant incongruence between the mitochondrial genes and the nuclear genes, and we chose the results from the nuclear genes as our preferred hypothesis. Our phylogeny suggested that the family Eurytomidae is not a monophyletic group; neither are the genera Eurytoma and Bruchophagus. The monophyly of genera Sycophila and Plutarchia was well supported, as was the close association of the genera Aiolomorphus, Tenuipetiolus, Bephratelloides, and Phylloxeroxenus. Our phylogeny also revealed an anticipated pattern, in which species groups from the genera Eurytoma and Bruchophagus are often more closely related to other small genera than to other species groups of the same genus. Subsequent taxonomic revisions include elevating the subfamily Rileyinae to a family status and the divisions of the genera Eurytoma and Bruchophagus.     

Homoplasy and the early hominid masticatory system: inferences from analyses of extant hominoids and papionins

Early hominid masticatory characters are widely considered to be more prone to homoplasy than characters from other regions of the early hominid skull and therefore less reliable for phylogenetic reconstruction. This hypothesis has important implications for current reconstructions of early hominid phylogeny, but it has never been tested. In this paper we evaluate the likely veracity of the hypothesis using craniometric data from extant primate groups for which reliable consensus molecular phylogenies are available.Datasets representing the extant large-bodied hominoid genera and the extant papionin genera were compiled from standard measurements. The data were adjusted to minimise the confounding effects of body size, and then converted into discrete character states using divergence coding. Each dataset was divided into four regional character groups: (1) palate and upper dentition, (2) mandible and lower dentition, (3) face and (4) cranial vault and base. Thereafter, the regional character groups were analysed using cladistic methods and the resulting phylogenetic hypotheses judged against the consensus molecular phylogenies for the hominoids and papionins.The analyses indicated that the regions dominated by masticatory characters-the palate and upper dentition, and the mandible and lower dentition-are no less reliable for phylogenetic reconstruction than the other regions of the skull. The four regions were equally affected by homoplasy and were, therefore, equally unreliable for phylogenetic reconstruction. This finding challenges the recent suggestion that Paranthropus is polyphyletic, which is based on the assumption that masticatory characters are especially prone to homoplasy. Our finding also suggests that, contrary to current practice, there is no a priori reason to de-emphasise the phylogenetic significance of the masticatory similarities between Homo rudolfensis and the australopiths. The corollary of this is that H. rudolfensis is unlikely to be a member of the Homo clade and should therefore be allocated to another genus.     

Estimation of hominoid phylogeny from a DNA hybridization data set

Summary Analysis of the expanded data set of Sibley and Ahlquist (1987) on primate phylogeny using a maximum likelihood mixed model analysis of variance method shows that there is significant evidence for resolving theHomo-Pan-Gorilla trifurcation in favor of aHomo-Pan clade. The resulting tree is close to that estimated by Sibley and Ahlquist (1984). The mixed model can be used to test a number of hypotheses about the existence of components of variance and the linearity of the relationship between branch length and expected distance. No evidence is found that there is a variance component for extract, or for the individual from which the extract was taken. A variance component for experiment does seem to exist, presumably arising as a result of error of measurement of the common standard from which all values in the same experiment were substracted. There is significant evidence that the relationship between total branch length between species and their expected distances is nonlinear, or else that the measurement error on larger distances is greater than on smaller ones. Allowing for the nonlinearity might cause one to infer the time of distant common ancestors as less remote than the measured hybridization values would imply if used directly.     

Functional morphology of the asterionic region in extant hominoids and fossil hominids

Asterionic sutural patterns in Plio-Pleistocene hominid crania have never been examined in detail. We present an analysis of this anatomical region in Australopithecus and Homo and relate different sutural patterns to functional changes in the masticatory apparatus. The great apes and A. afarensis share the common adult higher primate sutural pattern referred to as the "asterionic notch," which develops in response to the hypertrophy of posterior temporalis muscle fibers and the consequent formation of compound temporal/nuchal crests. This sutural configuration also appears to be present on the early Homo cranium KNM-ER 1805. In contrast, adult male A. boisei crania exhibit a unique pattern where the temporal squama overlaps the parietal which, in turn, overlaps the par mastoidea and the upper scale of the occipital bone. We relate this arrangement to the need to reinforce the rear of a thin-walled braincase against the net tensile forces exerted by the temporalis and nuchal muscles. The common juvenile hominoid edge-to-edge asterionic articulation is maintained in adult A. africanus, A. robustus, female A. boisei, and most Homo crania. We discuss the latter pattern in regard to anterior temporalis hypertrophy in A. africanus, A. robustus, and A. boisei and to craniofacial paedomorphosis in Homo.     

Estimation of the age of extant Ephedra using chloroplast rbcL sequence data

The distinctive gymnosperm genus Ephedra is sometimes considered to have originated over 200 million years (Myr) ago on the basis of "ephedroid" fossil pollen. In this article we estimate the age of extant Ephedra using chloroplast rbcL gene sequences. Relative rate tests fail to reject the null hypothesis of equal rates of nucleotide substitution of the rbcL sequences among three landmark lineages (Gnetales, Pinaceae, and Ginkgo). The most divergent sequences we have found in Ephedra differ by only 7 bp for an 1,110 bp region of rbcL sequence, whereas the differences among genera range from 92 to 107 bp in Gnetales and from 35 to 92 bp in Pinaceae. Using three landmark events, the age of extant Ephedra is estimated to be approximately 8-32 Myr. Our result is consistent with the current distribution of many Ephedra species in geologically recent habitats and points out difficulties in the identification of older ephedroid pollen fossils with the modern genus Ephedra.     

Articular morphology of the proximal ulna in extant and fossil hominoids and hominins

Extant hominoids share similar elbow joint morphology, which is believed to be an adaptation for elbow stability through a wide range of pronation-supination and flexion-extension postures. Mild variations in elbow joint morphology reported among extant hominoids are often qualitative, where orangutans are described as having keeled joints, and humans and gorillas as having flatter joints. Although these differences in keeling are often linked to variation in upper limb use or loading, they have not been specifically quantified. Many of the muscles important in arboreal locomotion in hominoids (i.e., wrist and finger flexors and extensors) take their origins from the humeral epicondyles. Contractions of these muscles generate transverse forces across the elbow, which are resisted mainly by the keel of the humeroulnar joint. Therefore, species with well-developed forearm musculature, like arboreal hominoids, should have more elbow joint keeling than nonarboreal species. This paper explores the three- and two-dimensional morphology of the trochlear notch of the elbow of extant hominoids and fossil hominins and hominoids for which the locomotor habitus is still debated. As expected, the elbow articulation of habitually arboreal extant apes is more keeled than that of humans. In addition, extant knuckle-walkers are characterized by joints that are distally expanded in order to provide greater articular surface area perpendicular to the large loads incurred during terrestrial locomotion with an extended forearm. Oreopithecus is characterized by a pronounced keel of the trochlear notch and resembles Pongo and Pan. OH 36 has a morphology that is unlike that of extant species or other fossil hominins. All other hominin fossils included in this study have trochlear notches intermediate in form between Homo and Gorilla or Pan, suggesting a muscularity that is less than in African apes but greater than in humans.     

A complete generic phylogeny of Malpighiaceae inferred from nucleotide sequence data and morphology

? Premise of the study: The Malpighiaceae include ～1300 tropical flowering plant species in which generic definitions and intergeneric relationships have long been problematic. The goals of our study were to resolve relationships among the 11 generic segregates from the New World genus Mascagnia, test the monophyly of the largest remaining Malpighiaceae genera, and clarify the placement of Old World Malpighiaceae. ? Methods: We combined DNA sequence data for four genes (plastid ndhF, matK, and rbcL and nuclear PHYC) from 338 ingroup accessions that represented all 77 currently recognized genera with morphological data from 144 ingroup species to produce a complete generic phylogeny of the family. ? Key results and conclusions: The genera are distributed among 14 mostly well-supported clades. The interrelationships of these major subclades have strong support, except for the clade comprising the wing-fruited genera (i.e., the malpighioid+Amorimia, Ectopopterys, hiraeoid, stigmaphylloid, and tetrapteroid clades). These results resolve numerous systematic problems, while others have emerged and constitute opportunities for future study. Malpighiaceae migrated from the New to Old World nine times, with two of those migrants being very recent arrivals from the New World. The seven other Old World clades dispersed much earlier, likely during the Tertiary. Comparison of floral morphology in Old World Malpighiaceae with their closest New World relatives suggests that morphological stasis in the New World likely results from selection by neotropical oil-bee pollinators and that the morphological diversity found in Old World flowers has evolved following their release from selection by those bees.     

A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence

The family Percidae is among the most speciose families of northern hemisphere fishes with > 178 178 North American species and 14 Eurasian species. Previous phylogenetic studies have been hampered by a lack of informative characters, inadequate taxonomic sampling, and conflicting data. We estimated phylogenetic relationships among 54 percid species (9 of 10 genera and all but one subgenus of darters) and four outgroup taxa using mitochondrial DNA data from the 12S rRNA and cytochrome b genes. Four primary evolutionary lineages were consistently recovered: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Perca, Luciopercinae (Romanichthys, Sander, and Zingel), and Gymnocephalus. Except Etheostoma and Zingel, all polytypic genera were monophyletic. The Etheostoma subgenus Nothonotus failed to resolve with other members of the genus resulting in a paraphyletic Etheostoma. The subfamily Percinae (Gymnocephalus and Perca) was not recovered in phylogenetic analyses with Gymnocephalus sister to Luciopercinae. Etheostomatinae and Romanichthyini were never resolved as sister groups supporting convergent evolution as the cause of small, benthic, stream-inhabiting percids in North American and Eurasian waters.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

Man's place in hominoidea revealed by mitochondrial DNA genealogy

Summary Molecular biology has resurrected C. Darwin and T.H. Huxley's question about the origin of humans, but the precise branching pattern and dating remain controversial. To settle this issue, a large amount of sequence information is required. We determined mitochondrial (mt) DNA sequences for five hominoids; pygmy and common chimpanzees, gorilla, orangutan, and siamang. The common region compared with the known human sequence is 4759 by long, encompassing genes for 11 transfer RNAs and 6 proteins. Because of the high substitution rates in mammalian mtDNA and an unprecedentedly large region compared, the sequence differences clearly indicate that the closest relatives to human are chimpanzees rather than gorilla. For dating the divergences of human, chimpanzee, and gorilla, we used only unsaturated parts of sequence differences in which the mtDNA genealogy is not obscured by multiple substitutions. The result suggests that gorilla branched off 7.7 ± 0.7 million years (Myr) ago and human 4.7 ± 0.5 Myr ago; the time difference between these divergences being as long as 3 Myr.Offprint requests to: S. Horai