Charles G. Sibley

The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization

SummaryThe living hominoid primates are Man, the chimpanzees, the Gorilla, the Orangutan, and the gibbons. The cercopithecoids (Old World monkeys) are the sister group of the hominoids. The composition of the Hominoidea is not in dispute, but a consensus has not yet been reached concerning the phylogenetic branching pattern and the dating of divergence nodes. We have compared the single-copy nuclear DNA sequences of the hominoid genera using DNA-DNA hybridization to produce a complete matrix of delta T50H values. The data show that the branching sequence of the lineages, from oldest to most recent, was: Old World monkeys, gibbons, Orangutan, Gorilla, chimpanzees, and Man. The calibration of the delta T50H scale in absolute time needs further refinement, but the ranges of our estimates of the datings of the divergence nodes are: Cercopithecoidea, 27–33 million years ago (MYA); gibbons, 18–22 MYA; Orangutan, 13–16 MYA; Gorilla, 8–10 MYA; and chimpanzees-Man, 6.3–7.7 MYA.

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

SummaryThe 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.

Phylogeny and Classification of Birds Based on the Data of DNA-DNA Hybridization

The elements of phylogeny are clustering, branching, and time. Ideally, to reconstruct the phylogeny of a group of organisms it is necessary to define the monophyletic clusters of taxa, to determine the branching pattern of their divergences, and to place that pattern on the scale of absolute time. This definition is simple, but to reconstruct a phylogeny in which all three elements are correctly determined is far more difficult. To our knowledge it has never been done with a high degree of accuracy.

DNA hybridization evidence of hominoid phylogeny: A reanalysis of the data

SummarySibley and Ahlquist (1984, 1987) presented the results of a study of 514 DNA-DNA hybrids among the hominoids and Old World monkeys (Cercopithecidae). They concluded that the branching order of the living hominoid lineages, from oldest to most recent, was gibbons, orangutan, gorilla, chimpanzees, and human. Thus, a chimpanzee-human clade was indicated, rather than the chimpanzee-gorilla clade usually suggested from morphological evidence. The positions of the gibbon and orangutan branches in the phylogeny are supported by substantial evidence, but whether the chimpanzee lineage branched most recently from the human lineage or from the gorilla lineage remains controversial. The conclusions of Sibley and Ahlquist (1984, 1987) have been supported by several independent studies cited by Sibley and Ahlquist (1987), plus the DNA sequence data of Hayasaka et al. (1988), Miyamoto et al. (1988), Goodman et al. (1989, 1990), and the DNA-DNA hybridization data of Caccone and Powell (1989). The laboratory and data analysis methods have been criticized by Marks et al. (1988) and Sarich et al. (1989). In response to these critics, and for our own interests, we present a reanalysis of the Sibley and Ahlquist data, including a description of the corrections applied to the “raw counts”. The validity of the laboratory methods is supported by the congruence of tree topology and delta values with those of Caccone and Powell (1989), although their tetraethylammonium chloride technique differs from the hydroxyapatite method in several respects. The utility of the T50H distance measure is indicated by its congruence with percent sequence divergence at least to delta T50H 30, as noted by Goodman et al. (1990). The Sibley and Ahlquist uncorrected data indicate thatPan is genetically closer toHomo than toGorilla, but thatGorilla may be genetically closer toPan than toHomo. Melting curves are presented for the pertiment experiments, plus one that includes representatives of most of the groups of living primates.

Relationships of the chromosomal species in the eurasian mole rats of theSpalax ehrenbergi group as determined by DNA-DNA hybridization, and an estimate of the spalacid-murid divergence time

SummaryDNA-DNA hybridization was used to measure the average genomic divergence among the four chromosomal species of the Eurasian mole rats belonging to theSpalax ehrenbergi complex (Rodentia: Spalacidae). The percent nucleotide substitutions in the single-copy nuclear DNA among the species ranged from 0 to 5%, suggesting that speciation has occurred with minor genomic changes in these animals. The youngest chromosomal species appear to differ by 0.2–0.6% base pair mismatch, which is only between one and three base differences in a 500-bp fragment. The interspecific values of percent nucleotide differences permit the recognition of two well-separated speciation events in theS. ehrenbergi complex, the older (of Lower Pleistocene age) having isolated the chromosomal species 2n=54 before the divergence of the three other species.DNA-DNA hybridization was also used to compare the Spalacinae (Eurasian mole rats), Murinae (Old World rats and mice), and Arvicolinae (voles and lemmings). These data enabled us to estimate the time of divergence of the spalacids at ca. 19 million years ago. The dates of divergence among the other rodent lineages, as predicted by DNA hybridization results, agree well with paleontological data. These dates of divergence are obtained by the relation between geological time and single-copy nuclear DNA change, a relation that was calibrated by Catzeflis et al. (1987) through the use of fossil Arvicolinae and Murinae data.

Genetic Polymorphism in New Guinea Starlings of the Genus Aplonis

of Hubby and Lewontin (1966) and Lewontin and Hubby (1966), there has been considerable interest in determining the percentage of the genome that may be either heterozygous in individuals or polymorphic in populations. Comparable data for natural populations of many species, both vertebrates and invertebrates being represented, are now available. However, the extent of protein polymorphism and individual heterozygosity in natural avian populations is known for relatively few species (Bush 1967; Sibley and Corbin 1970; Nottebohm and Selander 1972). Several other studies of protein polymorphism in bird populations have dealt with only a few loci (Stratil and Valenta 1966; Brush 1968, 1970; Bush et al. 1970; Ferguson 1971; Brush and Scott 1972). Most of the work on the specific variation of bird proteins involved domestic species. In this category, proteins found to be polymorphic include the serum esterases of the Japanese Quail (Coturnix coturnix) (Kaminski 1964; Manwell and Baker 1969), several species of pigeons (species of Columba and ALAN H. BRUSH

Hybridization in the Red-Eyed Towhees of Mexico: The Populations of the Southeastern Plateau Region

THE extensive and complex patterns of variation resulting from hybridization between the Rufous-sided Towhee (Pipilo erythrophthalmus) and the Collared Towhee (Pipilo ocai) in Mexico have been described in three previous papers (Sibley, 1950, 1954; Sibley and West, 1958). The evolutionary and taxonomic significance of hybridization, with particular reference to birds, has been considered in three additional papers by the senior author (1957, 1959, 1961). Other papers, forming a related series concerned with avian hybridization, are Sibley (1958), Sibley and Short (1959a, 1959b, 1964), Sibley and West (1959), Short (in press), and West (1962). The present paper is based upon new material collected in 1958 in an attempt to clarify the hybrid towhee situation in eastern and southeastern Mexico.

Variability in the Electrophoretic Patterns of Avian Serum Proteins

It has been known for more than 50 years that particular proteins characterize every species of plant and animal and that phylogenetic relationships are reflected in protein structure. The first application of this fact to taxonomic studies was by Nuttall ( 1901; 1904) who used the precipitin reaction of immune sera to test degrees of relationship in over 500 species of animals. With refinements in technique have come many more serological studies and the results have justified the statement by Landsteiner (1945) that “chemical differences parallel the variation in structure” and hence are useful in classification. The literattrre on serology is extensive but it has been summarized in the book by Landsteiner ( 1945) and the reviews by Boyden ( 1942 ; 1953). Some of the more recent papers are cited by Stallcup (1954), and Pauly and Wolfe (1957). The development of other methods for protein characterization has suggested that these too might be applied to systematics. Soon after Tiselius (1937) described his apparatus for the electrophoretic separation of colloidal mixtures Landsteiner, Longsworth, and van der Scheer (1938) used it to compare the egg albumins and hemoglobins of five species of birds. Within the next few years there followed the studies by Moore (1945)) Deutsch and Goodloe (1945)) and Deutsch and McShan (1949). These authors investigated the plasma proteins of several species of reptiles, amphibians, fish, birds, mammals, and some invertebrates. They showed that electrophoresis could detect the species specific qualities of proteins and that similarity in proteins paralleled evolutionary relationships. With the development of filter paper electrophoresis the procedure has been simplified and the study of Dessauer and Fox (1956) on the plasma proteins of more than 100 species and subspecies of reptiles and amphibians has been the most extensive to date. Others who have used paper electrophoresis include Zweig and Crenshaw (1957) who found specific characters in the serum proteins of turtles of the genus Pseudemys, and Starr and Fosberg (1958) who published the serum protein patterns of several species of sharks. Woods et al. (1958) used starch gel electrophoresis in a study of the sera of 19 species of invertebrates. The egg white proteins of birds have also been shown to be species specific and to produce excellent electrophoretic profiles. The papers by Bain and Deutsch (1947) and McCabe and Deutsch (1952) are the principal ones to date. The latter reported on 37 species of birds and concluded that the method was applicable to taxonomic problems. Sibley has used paper electrophoresis in a study of the egg white proteins of more than 300 species and has found the conclusions of McCabe and Deutsch fully justified. In 1956, when the senior author began the study described here, the purpose was to determine the uses and limitations of paper electrophoresis in avian taxonomy. Blood serum, rather than egg white, was chosen because of the relatively greater ease of obtaining material. The egg white studies mentioned above were initiated after the work reported here had been completed.

The relationships of the sharpbill (Oxyruncus cristatus)

-The Sharpbill (Oxvruncus cristatus) is a Neotropical suboscine passerine whose affinities have been unclear. The tyrant flycatchers, cotingas, and manakins of the superfamily Tyrannoidea have been suggested as the closest relatives of the Sharpbill. DNA-DNA hybridization comparisons between the radioiodine-labeled single-copy DNA of the Sharpbill and the DNAs of cotingas, manakins, tyrant flycatchers, and representatives of the other Neotropical superfamily, the Furnarioidea, indicate that Oxyruncus is a cotinga. We place it in the subfamily Cotinginae, family Tyrannidae. The Sharpbill (Oxyruncus cristatus) is a medium-sized (ca. 16 cm) suboscine passerine with a straight, pointed bill and short rictal bristles. In the adult male the crested crown has a crimson center bordered by olive feathers tipped with black. The back is bright olivegreen, wings and tail blackish, underparts white with black spots, and the flanks pale greenishyellow. The plumage colors of the adult female are less intense than those of the male and the coronal stripe is inconspicuous. The Sharpbill apparently has a discontinuous range in the humid montane forests of Costa Rica, Panama, southeastern Venezuela, southern Guyana and Surinam, northeastern and southeastern Brazil, southern Paraguay, and central Peru (Mees 1974, Traylor, 1979). Extensive field observations of the Sharpbill have not been recorded but Sick (197 1) reviewed the sparse literature and reported on his encounters with the species during his many years of field studies in Brazil. He found that Sharpbills tend to occur most often in dense tall forest, although they sometimes feed on fruits at the forest edge or in solitary trees. Fruits are the principal food but insects have been found in the stomachs of specimens and Sick observed Sharpbills hanging upside down from twigs to capture insect larvae. The vocalizations are relatively simple and similar to those of certain cotingas. Sick found the birds most often in pairs and in mixed flocks of tanagers, furnariids, troupials, cotingas, woodpeckers, etc. feeding on fruiting trees. A captive Sharpbill ate fruits and cast hard pellets composed of the skins. Bangs and Barbour (1922) also observed Sharpbills feeding in fruiting trees with cotingas; Mees (1974) found them solitary, in pairs, and in mixed bird swarms in Surinam. Wetmore (1972:605) saw “four or five” together in Panama and recorded spiders, ants, and seeds from stomach contents. Brooke et al. (1983) found the first recorded nest of the Sharpbill near the top of a 30-m tree in the montane forest of the Serra do Tingua, 50 km north of Rio de Janeiro, Brazil. The nest, which was built by the female, was “saddled onto a slender (ca. 3 cm) horizontal branch” and was a “simple . . . shallow cup . . . composed of roughly interlaced leguminous petioles . . . and a very few dry leaves.” The outer surface “was a thin coat of mosses, liverworts, and spider’s web. . . with a texture akin to thin cardboard, possibly resulting from the application and subsequent drying of saliva.” The female fed the young by regurgitation, as do cotingas, rather than as in insectivorous tyrannids. Brooke et al. (1983) observed adult Sharpbills feeding in the ways described by Sick (1971).

A Comparative Electrophoretic Study of Avian Plasma Proteins

relationships has led to the study of many characters. In addition to comparative morphology some systematists have utilized ecology, behavior, serology, and biochemistry as clues to the degrees of genetic relatedness among organisms. Because protein molecules are primary gene products it is logical to assume that comparisons among homologous proteins from different organisms should provide useful systematic data. The rationale behind this approach to systematics has been discussed by several authors including Sibley (1960, 1962, 1964, 1965, 1967), Zuckerkandl and Pauling (1965), and Dessauer (1969). The plasma proteins are an obvious choice for investigation because they are easy to collect and because a great deal is known about their properties and functions. Plasma is the fluid portion of blood in which the blood cells are suspended. It is a complex mixture of proteins, carbohydrates, lipids, steroids, and free ions whose composition varies with sex, age, starvation, season, etc. (Moore 1948; Clegg et al. 1951; Vanstone et al. 1955; Dessauer and Fox 1956; Saito 1957b). The protein constituents of plasma, while often quantitatively variable, usually show a high degree of qualitative species specificity when examined by any standard biochemical technique (Morris and Courtice 1955; Zweig and Crenshaw 1957; Drilhon et al. 1958; Woods et al. 1958; Sulya et al. 1961). Some of these studies were based upon serum, the fluid portion of the plasma which is extruded from a blood clot. Plasma thus contains the blood proteins involved in clotting while serum lacks them. Most of the research on plasma proteins has dealt with human material although there has been a great deal of work on other mammalian species and the domestic fowl, Gallus gallus. The major protein components of plasma are albumin, the alpha-, beta-, and gamma-globulins, and various subfractions thereof. The nomenclature of the various components is usually determined by their electrophoretic mobilities with reference to normal human plasma. Thus, albumin is the fastest fraction, alpha-globulin the next fastest and gammaglobulin the slowest. The identification of plasma proteins under different conditions can be difficult (Espinosa 1961; Beaton et al. 1961). Up to 70 different proteins have been found in normal human plasma (Dessauer and Fox 1964) while Baker et al. (1966) found 40 electrophoretic bands in pheasant serum, 14 of which were identifiable. The review by Putnam (1960) provides information on the chemical composition of plasma. In paper electrophoresis at pH 8.6 the fastest c mponent in human plasma is albumin. It has a molecular weight of about 69,000 and is is electric at pH 4.7 (Phelps and Putnam 1960). It may be assumed that the values for other mammals and for birds are similar (Phelps and Putnam 1960:169). Plasma albumin has the same chemical properties as alpha livetin of egg yolk (Williams 1962a) but it has no known specific biological functions (Foster 1960). There are several alpha-globulins, which presumably have different functions. The best known are the hemoglobin-binding haptoglobins and the copper-binding ceruloplasmin. Human haptoglobin has a molecular weight of 85,000 and it is isoelectric at pH 4.1, while ceruloplasmin has a molecular weight of 151,000 and is isoelectric at pH 4.4 (Phelps and Putnam 1960). There are several discrete beta-globulins, most of which have unknown functions. The best known of these are the transferrins. Tra sferrin, also called siderophilin, is an ironbinding protein with a molecular weight of approximately 90,000; it is isoelectric at pH 5.9 (Phelps and Putnam 1960). It has been found that the protein moiety of the transferrin molecule is identical to that of the conalbumin of egg white. They differ only in their 1 Present address: Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27412.