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.     

Phylogenetic relationships within Passerida (Aves: Passeriformes): a review and a new molecular phylogeny based on three nuclear intron markers

The avian clade Passerida was first identified based on DNA-DNA hybridization data [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Monophyly of the Passerida, with the exception of a few taxa, has later been corroborated in several studies; however, the basal phylogenetic relationships have remained poorly understood. In this paper, we review the current knowledge of the phylogenetic relationships within Passerida and present a new phylogeny based on three nuclear introns (myoglobin intron 2, ornithine decarboxylase introns 6 and 7, as well as beta-fibrinogen intron 5). Our findings corroborate recent molecular hypotheses, but also identify several hitherto unrecognized relationships.     

Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds

Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyrebirds unambiguously belong to the oscine radiation, and that they are the sister taxon to all other oscines. The results do not support the suggestion based on DNA-DNA hybridization data (Sibley and Ahlquist, 1990) that the treecreepers and bowerbirds are part of the lyrebird clade. Nevertheless, treecreepers and bowerbirds are sister taxa to all other oscines (except the lyrebirds) and may constitute a monophyletic group, although bootstrap support values for this clade are low. A major disagreement between the present analysis and that based on DNA-DNA hybridization data is that the Corvida (sensu Sibley and Ahlquist, 1990) and Passerida are not reciprocally monophyletic, as we find the latter group be nested within the Corvida. Also, the superfamilies Meliphagoidea and Corvoidea sensu, are not recovered as monophyletic in the present study. Within the oscine radiation, all taxa belonging to the earliest splits are confined to the Australo-Papuan region. This suggests strongly that the origins and early radiation of the oscines occurred in the southern supercontinent Gondwana. A new classification of the major groups of passerines is presented following from the results presented in the present study, as well as those published recently on analyses of sequence data from the nuclear c-myc and RAG-1 genes (Ericson et al., 2002; Irestedt et al., 2001).     

Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences

Phylogenetic relationships among the families of passerine birds have been the subject of many debates. These relationships have been investigated by using a number of different character sets, including morphology, proteins, DNA-DNA hybridization, and mitochondrial DNA gene sequences. Our objective was to examine the phylogenetic relationships of a set of passerine songbirds (Oscines) and to test the taxonomic relationships proposed by. We sequenced 1403 aligned bases encompassing the mitochondrial transfer-RNA-Valine and 16S ribosomal RNA genes in 27 species from 14 families (including a Suboscine outgroup). Our results differ in significant ways from the superfamily designations of Sibley and Ahlquist by questioning the monophyly of the Sylvioidea and by placing the Regulidae in the Corvoidea.     

A phylogeny for the Cisticolidae (Aves: Passeriformes) based on nuclear and mitochondrial DNA sequence data, and a re-interpretation of an unique nest-building specialization

Based on some general similarities in feeding adaptations, a large number of Old World passerine birds were in the past lumped in one broad family, the Sylviidae. Recent molecular studies, starting with the DNA-DNA hybridization work by Sibley et al. [Sibley, C.G., Ahlquist, J.E., 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution, Yale University Press, New Haven, CT], have revealed that this group is in fact a paraphyletic assemblage, mainly in the superfamily Sylvioidea, and within this assemblage a distinct group (the Cisticolidae) can be identified around the genus Cisticola. In this study we try to define natural lineages within it, based on DNA sequence data from 35 ingroup taxa representing 12 putative genera. Both nuclear myoglobin intron II (630 bp in our study) and mitochondrial ND2 (1041 bp) genes were sequenced, and 1671 bp were aligned and subjected to parsimony, maximum likelihood and Bayesian analyses. The results strongly support the monophyly of a cisticolid clade, with the Malagasy warblers Neomixis constituting the deepest branch within the clade. Three major clades receive statistical support, but not all relationships between and within these are well resolved. All species of the genus Bathmocercus belong to the Cisticolidae but in two different clades. The tailorbirds appear also polyphyletic with most species of the genus Orthotomus (but O. cucullatus falling in the outgroup) and the African metopias being in two different clades. Also the genus Apalis is polyphyletic, but all other included genera seem to be confirmed as natural units. Based on these findings we resurrect the genera Scepomycter and Artisornis. Calamonastes is confirmed to be in the Cisticolidae and grouped with Camaroptera. Main basic nest types do not follow the phylogenetic branching, and notably the peculiar "tailorbird" technique of stitching leaves together around the nest is found in different parts of the phylogeny. The basic types of nests seem to be found in particular environments, and the sewing may therefore have evolved in some ancestor of the Cisticolidae and was later lost or modified in some genera or species following the spread of drier habitats from the mid-Miocene.     

雀形目高级阶元分类与起源研究概况

对雀肜目鸟类高级阶元的分类和系统发育的研究进行了简要概述.经典分类与应用分子生物学方法建立的分类系统在高级阶元(总科)有较大差异,但科级的分类基本一致.在雀形目鸟类起源研究方面,古生物学研究结果认为其起源于劳亚古陆;而分子生物学的证据则认为其起源于冈瓦纳古陆.由于化石的证据与"分子钟"的推测年代相差较大,因此对雀形目鸟类的起源还存在争议,但是目前的研究更倾向于"冈瓦纳起源"假说.     

DNA Hybridization as a Guide to Phylogenies: a Critical Analysis

Abstract— This article evaluates the use of DNA hybridization for estimating the extent of divergence among the single-copy fractions of vertebrate genomes. It focuses, in particular, on the nature and informational content of the melting profiles as a guide to phylogenetic relationships. While concluding that the DNA hybridization approach remains the best and most cost-effective guide to such relationships over its useful range, it demonstrates serious flaws in certain recent attempts to apply the method to specific cases among primates and birds. The major points are:

• 1 The T₅₀H statistic is flawed as a measure of mean sequence divergence, and also, therefore, as a measure of phylogenetic distance.
• 2 The T_mode statistic overcomes many of the problems inherent in interpreting thermal stabilities of DNA heteroduplexes for phylogenetic purposes.
• 3 The phylogenetic significance of ΔT_modes of > 15d? or so cannot be accurately assessed.
• 4 The putative slowdown in the rate of nuclear DNA sequence change among the lemurs is not justified by the data.
• 5 The claims of Sibley and Ahlquist to have resolved the human/chimpanzee/gorilla trichotomy are not supported by their data.
• 6 There are major problems in the published Sibley and Ahlquist avian phylogenies; in particular, with those containing evolutionary “staircases” of nodes separated by less than 1d? from one another.
• 7 There would appear to be a lineage misplacement involving a ΔT of at least 4d? in a recent publication on avian phylogeny.
• 8 Certain of the published ΔT₅₀ H values seem not to be representative of the actual data on which they are based.
• 9 Most important, it is recommended that no phytogenies based on DNA hybridization comparisons should be presented without being accompanied by the data relevant to each claim of a resolved lineage.

     

Rates and Patterns of Scndna and Mtdna Divergence within the Drosophila Melanogaster Subgroup

Levels of DNA divergence among the eight species of the Drosophila melanogaster subgroup and D. takahashii have been determined using the technique of DNA-DNA hybridization. Two types of DNA were used: single-copy nuclear DNA (scnDNA) and mitochondrial DNA (mtDNA). The major findings are: (1) A phylogeny has been derived for the group based on scnDNA which is congruent with chromosomal data, morphology, and behavior. The three homosequential species, simulans, sechellia, and mauritiana, are very closely related; the scnDNA divergence indicate the two island species are a monophyletic group. (2) The rates of change of scnDNA and mtDNA are not greatly different; if anything scnDNA evolves faster than mtDNA. (3) The rates of scnDNA evolution are not closely correlated to chromosomal (inversion) evolution. (4) The Drosophila genome appears to consist of two distinct classes of scnDNA with respect to rate of evolutionary change, a very rapidly evolving fraction and a relatively conservative fraction. (5) The absolute rate of change was estimated to be at least 1.7% nucleotide substitution per one million years. (6) DNA distance estimates based on restriction site variation are correlated with distances based on DNA-DNA hybridization, although the correlation is not very strong.     

Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data

Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.     

DNA DIVERGENCE AMONG HOMINOIDS

We have determined the degree of single-copy DNA divergence among the extant members of the Hominoidea employing the technique of DNA-DNA hybridization. The species studied include humans, two species of chimpanzees, gorillas, two subspecies of orangutans, and two species of gibbons; as an outgroup we have used a member of the Old World monkeys (Cercopithecidae), the baboon. Our methods are different from those previously used and allow us to control for two factors other than base-pair mismatch that can affect the thermal stability of DNA duplexes: the base composition and duplex length. In addition, we have studied more than one individual for most species and thus are able to assess the effect of intraspecific variation on phylogenetic conclusions. The results indicate that the closest extant relatives of humans are the chimpanzees. Gorillas are the next closest, followed by orangutans and gibbons. This result is strongly supported statistically, as there is virtually no overlap in measurements between different taxa. Our conclusions are in agreement with a growing amount of molecular evidence supporting this pattern of relatedness. The data behave as a reasonably good molecular clock, and we do not see an indication of slowdown in molecular evolution in the clade containing humans and African apes, contrary to what has been documented for protein-coding regions. Because of the clocklike nature of the results, we have estimated that the divergence of humans and chimpanzees occurred about 6–8 million years ago. Results from orangutans indicate that the Borneo and Sumatra populations are genetically distinct, about as different as the named species of chimpanzees.     

The TEACL method of DNA-DNA hybridization: Technical considerations

Summary This paper emanated from a conference concerning the value, accuracy, and technical considerations of DNA-DNA hybridization for evolutionary studies. Our laboratory has been performing the so-called TEACL (tetraethylammonium chloride) method, and we have amassed sufficient data to indicate that this method is very powerful if performed properly with correct analyses. Here we address five technical considerations: (1) We present empirical data that size correction for tracer length is legitimate and accurate. (2) We show that the error of Tm measurement does not significantly increase with increasing distance up to at least 10°C. (3) The error distribution for Tm does not deviate from the expected normal distribution indicating parametric statistics are probably legitimate for analyses. (4) Using a known phylogeny we examined the resolving power of the technique by showing that at least five taxa can be correctly placed in phylogenies with a maximum Tm of 2.5°C. (5) To data, all our data sets based on DNA-DNA hybridization are very robust with respect to analytical procedures in that every algorithm used on the data sets has yielded identical trees with nearly identical branch lengths. Nevertheless, we point out that theoretical analyses of distance data (as generated by DNA-DNA hybridization) are lacking, especially with regard to tests of the molecular clock hypothesis.     

鸟类核型研究：Ⅴ.攀禽类20种（Climbers,Aves）

本文报道了攀禽类8科20种的核型,并对已报道过的16科96种攀禽类鸟类的核型进行了比较研究。攀禽类通常依据表型差异被划分为对趾型,并趾型和异趾型三个类群。Sibley(1988)等则依据DNA差异(通过DNA-DNA分子杂交测定)分为三个小纲:啄木鸟小纲,佛法僧小纲和雀小纲。这两种划分是截然不同的。核型比较的结果支持了Sibley对攀禽类的划分。     

DNA hybridization evidence of hominoid phylogeny: Results from an expanded data set

Summary The living hominoids are human, the two species of chimpanzees, gorilla, orangutan, and nine species of gibbons. The cercopithecoids (Old World monkeys) are the sister group of the hominoids. A consensus about the phylogeny of the hominoids has been reached for the branching order of the gibbons (earliest) and the orangutan (next earliest), but the branching order among gorilla, chimpanzees, and human remains in contention. In 1984 we presented DNA-DNA hybridization data, based on 183 DNA hybrids, that we interpreted as evidence that the branching order, from oldest to most recent, was gibbons, orangutan, gorilla, chimpanzees, and human. In the present paper we report on an expanded data set totaling 514 DNA hybrids, which supports the branching order given above. The ranges for the datings of divergence nodes are Old World monkeys, 25–34 million years (Myr) ago; gibbons, 16.4–23 Myr ago; orangutan, 12.2–17 Myr ago; gorilla, 7.7–11 Myr ago; chimpanzees-human, 5.5–7.7 Myr ago. The possible effects of differences in age at first breeding are discussed, and some speculations about average genomic rates of evolution are presented.     

DNA-DNA hybridization evidence of the rapid rate of muroid rodent DNA evolution

Single-copy nuclear DNAs (scnDNAs) of eight species of arvicoline and six species of murine rodents were compared using DNA-DNA hybridization. The branching pattern derived from the DNA comparisons is congruent with the fossil evidence and supported by comparative biochemical, chromosomal, and morphological studies. The recently improved fossil record for these lineages provides seven approximate divergence dates, which were used to calibrate the DNA-hybridization data. The average rate of scnDNA divergence was estimated as 2.5%/Myr. This is approximately 10 times the rate in the hominoid primates. These results agree with previous reports of accelerated DNA evolution in muroid rodents and extend the DNA-DNA hybridization data set of Brownell.      

Calibration of avian molecular clocks

Molecular clocks can be calibrated using fossils within the group under study (internal calibration) or outside of the group (external calibration). Both types of calibration have their advantages and disadvantages. An internal calibration may reduce extrapolation error but may not be from the best fossil record, raising the issue of nonindependence. An external calibration may be more independent but also may have a greater extrapolation error. Here, we used the advantages of both methods by applying a sequential calibration to avian molecular clocks. We estimated a basal divergence within birds, the split between fowl (Galliformes) and ducks (Anseriformes), to be 89.8 +/- 6.97 MYA using an external calibration and 12 rate-constant nuclear genes. In turn, this time estimate was used as an internal calibration for three species-rich avian molecular data sets: mtDNA, DNA-DNA hybridization, and transferrin immunological distances. The resulting time estimates indicate that many major clades of modern birds had their origins within the Cretaceous. This supports earlier studies that identified large gaps in the avian fossil record and suggests that modern birds may have coexisted with other avian lineages for an extended period during the Cretaceous. The new time estimates are concordant with a continental breakup model for the origin of ratites.     

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

Consensus on the evolutionary relationships of humans, chimpanzees, and gorillas has not been reached, despite the existence of a number of DNA sequence data sets relating to the phylogeny, partly because not all gene trees from these data sets agree. However, given the well-known phenomenon of gene tree-species tree mismatch, agreement among gene trees is not expected. A majority of gene trees from available DNA sequence data support one hypothesis, but is this evidence sufficient for statistical confidence in the majority hypothesis? All available DNA sequence data sets showing phylogenetic resolution among the hominoids are grouped according to genetic 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 a human-gorilla clade. The hypothesis of a trichotomous speciation event leading to Homo; Pan, and Gorilla can be firmly rejected on the basis of this data set distribution. The multiple-locus test (Wu 1991), which evaluates hypotheses using gene tree-species tree mismatch probabilities in a likelihood ratio test, favors the phylogeny with a Homo-Pan clade and rejects the other alternatives with a P value of 0.002. When the probabilities are modified to reflect effective population size differences among different types of genetic loci, the observed data set distribution is even more likely under the Homo-Pan clade hypothesis. Maximum-likelihood estimates for the time between successive hominoid divergences are in the range of 300,000-2,800,000 years, based on a reasonable range of estimates for long-term hominoid effective population size and for generation time. The implication of the multiple-locus test is that existing DNA sequence data sets provide overwhelming and sufficient support for a human-chimpanzee clade: no additional DNA data sets need to be generated for the purpose of estimating hominoid phylogeny. Because DNA hybridization evidence (Caccone and Powell 1989) also supports a Homo-Pan clade, the problem of hominoid phylogeny can be confidently considered solved.      

Assessing the passerine "Tapestry": phylogenetic relationships of the Muscicapoidea inferred from nuclear DNA sequences

This study presents new comparative sequence data from the nuclear RAG-1 gene for an increased taxon sample in order to investigate phylogenetic relationships among a diverse songbird superfamily, the Muscicapoidea, which has variously included the waxwings, silky flycatchers, Palm Chat, dippers, starlings, mockingbirds, thrushes, chats, and Old World flycatchers. At the same time, our results provide a test of the often-cited relationships inferred from the phenetic studies of Sibley and Ahlquist [Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press, New Haven, 1990] using DNA hybridization distances. Nuclear DNA sequences confirm the monophyly of the "core muscicapoid" group, as defined by Barker et al. [Proc. R. Soc. Lond. B 269 (2002) 295] and also support the sister-group relationship of the Sturnidae and Mimidae, on the one hand, and the large-bodied thrushes (Turdini)+the Old World flycatchers and robins, on the other. The results of the phylogenetic analysis allow preliminary inferences about muscicapoid biogeographic history.     

Reconstruction of molecular phylogeny of extant hominoids from DNA sequence data

Evolutionary distance matrices of the extant hominoids are computed from DNA sequence data, and hominoid DNA phylogenies are reconstructed by applying the neighbor-joining method to these distance matrices. The chimpanzee is clustered with the human in most of the phylogenetic trees thus obtained. The proportion of the distance between human and chimpanzee to that between human/chimpanzee and orangutan is estimated. Both mitochondrial DNA and nuclear DNA show a similar value (0.44), which is close to values derived from DNA-DNA hybridization data.