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S B Hedges

Publications and source records attributed to S B Hedges.

At least 37 records · Page 2Linked to original sources
PubMed1998

Phylogeny and biogeography of ratite birds inferred from DNA sequences of the mitochondrial ribosomal genes.

The origin of the flightless ratite birds of the southern continents has been debated for over a century. Whether dispersal or vicariance (continental breakup) best explains their origin depends largely on their phylogenetic relationships. No consensus has been reached on this issue despite many morphological and molecular studies. To address this question further we sequenced a 2.8-kb region of mitochondrial DNA containing the ribosomal genes in representative ratites and a tinamou. Phylogenetic analyses indicate that Struthio (Africa) is basal and Rhea (South America) clusters with living Australasian ratites. This phylogeny agrees with transferrin and DNA hybridization studies but not with sequence analyses of some protein-coding genes. These results also require reevaluation of the phylogenetic position of the extinct moas of New Zealand. We propose a new hypothesis for the origin of ratites that combines elements of dispersal and vicariance.

Africa↗
PubMed1996

Continental breakup and the ordinal diversification of birds and mammals.

The classical hypothesis for the diversification of birds and mammals proposes that most of the orders diverged rapidly in adaptive radiations after the Cretaceous/Tertiary (K/T) extinction event 65 million years ago. Evidence is provided by the near-absence of fossils representing modern orders before the K/T boundary. However, fossil-based estimates of divergence time are known to be conservative because of sampling biases, and some molecular/time estimates point to earlier divergences among orders. In an attempt to resolve this controversy, we have estimated times of divergence among avian and mammalian orders with a comprehensive set of genes that exhibit a constant rate of substitution. Here we report molecular estimates of divergence times that average about 50-90% earlier than those predicted by the classical hypothesis, and show that the timing of these divergences coincides with the Mesozoic fragmentation of emergent land areas. This suggests that continental breakup may have been an important mechanism in the ordinal diversification of birds and mammals.

Animals↗
PubMed1995

Phylogenetic relationships of the hoatzin, an enigmatic South American bird.

The hoatzin (Opisthocomus hoazin) lives in the humid lowlands of northern and central South America, often in riparian habitats. It is a slender bird approximately 65 cm in length, brownish with lighter streaks and buffy tips to the long tail feathers. The small head has a ragged, bristly crest of reddish-brown feathers, and the bare skin of the face is bright blue. It resembles a chachalaca (Ortalis, Cracidae) in size and shape, but its plumage and markings are similar to those of the smaller guira cuckoo (Guira guira). The hoatzin (pronounced Watson) has been a taxonomic puzzle since it was described in 1776. It usually has been viewed as related to the gallinaceous birds, but alliances to other groups have been suggested, including the cuckoos. We present DNA sequence evidence from the 12S and 16S rRNA mitochondrial genes, and from the nuclear gene that codes for the eye lens protein, alpha A-crystallin. The results indicate that the hoatzin is most closely related to the typical cuckoos and that the divergence occurred at or near the base of the cuculiform phylogenetic tree.

Animals↗
PubMed1995

Origin of West Indian populations of the geographically widespread boa Corallus enydris inferred from mitochondrial DNA sequences.

Corallus enydris (Serpentes: Boidae: Boinae) is an arboreal snake with an extremely wide mainland distribution from southern Costa Rica to southeastern Brazil and is one of two boine species that has invaded the Lesser Antilles (Grenada Bank and St. Vincent). Mitochondrial DNA sequences of samples from seven geographically disparate localities provided evidence of phylogenetic relationships. The monophyly of C. enydris is corroborated and a major dichotomy between northern samples (Panama and Trinidad) and southern samples (Guyana, Perú, southeastern Brazil) was found and corresponds to the two currently recognized subspecies. Unexpectedly, the two samples from the West Indies (southern Lesser Antilles) cluster with the southern rather than the geographically closer northern samples (e.g., Trinidad). The results imply a fairly recent Guianan-Amazonian origin of West Indian populations.

Animals↗
PubMed1995

Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S rRNA, 16S rRNA, and tRNA-valine.

A recent analysis of amino acid sequence data (Graur et al.) suggested that the mammalian order Rodentia is polyphyletic, in contrast to most morphological data, which support rodent monophyly. At issue is whether the hystricognath rodents, such as the guinea pig, represent an independent evolutionary lineage within mammals, separate from the sciurognath rodents. To resolve this problem, we sequenced a region (2,645 bp) of the mitochondrial genome of the guinea pig containing the complete 12S ribosomal RNA, 16S ribosomal RNA, and transfer RNA(VAL) genes for comparison with the available sciurognath and other mammalian sequences. Several methods of analysis and statistical tests of the data all show strong support for rodent monophyly (91%-98% bootstrap probability, or BP). Calibration with the mammalian fossil record suggests a Cretaceous date (107 mya) for the divergence of sciurognaths and hystricognaths. An older date (38 mya) for the controversial Mus-Rattus divergence also is supported by these data. Our neighbor-joining analyses of all available sequence data (25 genes) confirm that some individual genes support rodent polyphyly but that tandem analysis of all data does not. We propose that the conflicting results are due to several compounding factors. The unique biochemical properties of some hystricognath metabolic proteins, largely responsible for generating this controversy, may have a single explanation: a cascade effect resulting from inactivation of the zinc-binding abilities of insulin. After excluding six genes possibly affected by insulin inactivation, analyses of all available sequence data (7,117 nucleotide sites, 3,099 amino acid sites) resulted in strong support for rodent monophyly (94% BP for DNA sequences, 90% for protein sequences), which lends support to the insulin-cascade hypothesis.

Animals↗
PubMed1995

Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes.

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).

Animals↗
PubMed1995

Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes.

Nucleotide sequence comparisons were used to investigate ordinal and familial relationships within the class Amphibia. Approximately 850 base pairs of the mitochondrial 16S ribosomal RNA (rRNA) gene from representatives of 28 of the 40 families of extant amphibians were sequenced. Phylogenetic analyses of these data together with published data of the 12S rRNA gene for the same families and both genes for three more taxa (approximately 1,300 base pairs total for 35 taxa) support the monophyly of each of the three amphibian orders: Anura (confidence value with the interior-branch test: P(c) = 99%), Caudata (P(c) = 100%), and Gymnophiona (P(c) = 99%). An analysis using the four-cluster method cannot discriminate significantly between all three possible unrooted trees involving the three orders of amphibians and an outgroup. Within the Anura, there is support for the monophyly of the two suborders: Neobatrachia (P(c) = 100%) and Archaeobatrachia (P(c) = 97%); the latter was believed to be paraphyletic on the basis of morphology. Within the Archaeobatrachia, the following pairs of taxa cluster: Pelobatidae + Pelodytidae (P(c) = 99%), Pipidae + Rhinophrynidae (P(c) = 99%), Ascaphus + Leiopelmatidae (P(c) = 89%), and Bombina + Discoglossidae (P(c) = 99%). The latter six taxa cluster (P(c) = 94%) such that Pelobatidae + Pelodytidae forms a basal lineage within the Archaeobatrachia. Three major lineages are distinguished within the Neobatrachia: the superfamily Bufonoidea sensu Duellman (P(c) = 86%), the superfamily Ranoidea sensu Lynch (P(c) = 99%), and the Sooglossidae. Basal within the Bufonoidea, Myobatrachidae + Heleophrynidae cluster at P(c) = 96%. The enigmatic Dendrobatidae clusters with the bufonoid families (P(c) = 92%) and is excluded from the ranoid families (P(c) = 99%). (ABSTRACT TRUNCATED AT 250 WORDS)

Amphibians↗
PubMed1994

Molecules vs. morphology in avian evolution: the case of the "pelecaniform" birds.

The traditional avian Order Pelecaniformes is composed of birds with all four toes connected by a web. This "totipalmate" condition is found in ca. 66 living species: 8 pelicans (Pelecanus), 9 boobies and gannets (Sula, Papasula, Morus), ca. 37 cormorants (Phalacrocorax), 4 anhingas or darters (Anhinga), 5 frigatebirds (Fregata), and 3 tropicbirds (Phaethon). Several additional characters are shared by these genera, and their monophyly has been assumed since the beginning of modern zoological nomenclature. Most ornithologists classify these genera as an order, although tropicbirds have been viewed as related to terns, and frigatebirds as relatives of the petrels and albatrosses. DNA.DNA hybridization data indicated that the pelicans are most closely related to the Shoebill (Balaeniceps rex), a stork-like bird that lives in the swamps of central Africa; the boobies, gannets, cormorants, and anhingas form a closely related cluster; the tropicbirds are not closely related to the other taxa; and the frigatebirds are closest to the penguins, loons, petrels, shearwaters, and albatrosses (Procellarioidea). Most of these results are corroborated by DNA sequences of the 12S and 16S rRNA mitochondrial genes, and they provide another example of incongruence between classifications derived from morphological versus genetic traits.

Animals↗
PubMed1994

Molecular evidence for the origin of birds.

The major groups of amniote vertebrates appeared during a relatively short time span at the end of the Paleozoic Era, a fact that has caused difficulty in estimating their relationships. The fossil record suggests that crocodilians are the closest living relatives of birds. However, morphological characters and molecular sequence data from living amniotes have repeatedly challenged this hypothesis by indicating a bird-mammal relationship. DNA sequences from four slow-evolving genes (mitochondrial 12S and 16S rRNA, tRNAVal, and nuclear alpha-enolase) now provide strong statistical support for a bird-crocodilian relationship.

Animals↗
PubMed1993

Phylogeny of xantusiid lizards: concern for data and analysis.

Phylogenetic analyses of new DNA sequence data from the mitochondrial 16S rRNA gene in xantusiid lizards support the intergeneric relationships obtained previously (S.B. Hedges, R.L. Bezy, and L.B. Maxson, 1991, Mol. Biol. Evol. 8:767-780) with data from the 12S rRNA and cytochrome b (cyt b) genes. The total data set now includes 1028 alignable sites, 471 of which are variable and informative for the distance analyses and 281 of which are informative for the parsimony analyses. Crother and Presch (1993), Mol. Phylogenet. Evol. 1:289-294) claim that their reanalyses of our 12S rRNA and cyt b sequence data do not support a robust phylogeny for xantusiid lizards. However, that conclusion is not supported by their own analyses of the combined data from those two genes, which result in the same phylogenetic tree of xantusiid genera that we obtained in the original study with the same method (maximum parsimony). This result was unchanged when Crother and Presch eliminated sites containing insertions/deletions and ambiguities, and when transversions were weighted. The less robust result for the separate cyt b analyses, probably due to the smaller size of the data set, was already noted (Hedges et al., 1991). We believe that the best estimate of relationships, in this case, is obtained by combining the sequence data from these tightly linked mitochondrial genes. We also refute the criticisms by Crother and Presch of the neighbor-joining method. To correct for a higher rate of transitions in mitochondrial sequence data, they weight transversions more heavily (5x) than transitions. We present theoretical criticisms of this weighting method and advocate the use of scaled corrections available with distance methods. Crother and Presch also claim that a robust phylogeny of xantusiid lizards is not obtained when some morphological data (13 informative characters) are combined with the molecular data in a single analysis. However, there are serious problems with their morphological data and methods of analysis. We reevaluate the three pivotal morphological characters in their alternative phylogeny for xantusiid genera and demonstrate that none of the three provides unambiguous support for their alternative arrangement. Crother and Presch implement a new approach whereby the entire morphological data set is weighted equally to the molecular data set in a combined analysis, thus resulting in a very inflated weight assigned to each character in the small morphological data set. Using this rationale, each of the 13 informative morphological characters would receive a greater than million-fold weight if combined with the sequence data for the entire genome of these lizards.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Ancestry of unisexual salamanders.

In eastern North America there are populations of all-female salamanders that incorporate the nuclear genomes of two or three of four sympatric bisexual species. The hybrids can be diploid, triploid, tetraploid or pentaploid, and 18 different combinations have been reported. All hybrids require sperm from a sympatric male of one of the bisexual species to reproduce, but the sperm may or may not be incorporated in the egg. Some of the hybrids are believed to represent separate, clonal species, but little is known of the origin of this hybrid complex. Vertebrate mitochondrial DNA is inherited maternally, allowing identification of the female parent that gave rise to hybrid lineages. A portion of the cytochrome b gene was sequenced from diploid and triploid hybrids that represent combinations of all four species. Nearly all hybrids had a similar mitochondrial genome sequence, independent of nuclear genome composition and ploidy, and the sequence was distinct from that of any of the four bisexual species. The hybrids maintain a mitochondrial lineage that has evolved independently of their nuclear genome and represent the most ancient known unisexual vertebrate lineage.

Ambystoma↗
PubMed1992

Caribbean biogeography: molecular evidence for dispersal in West Indian terrestrial vertebrates.

The geological association of the Greater Antilles with North and South America in the late Cretaceous led to the hypothesis that the present Antillean biota reflects those ancient land connections. Molecular data from diverse West Indian amphibians and reptiles and their mainland relatives support a more recent derivation of the Antillean vertebrate fauna by overwater dispersal. The catastrophic bolide impact in the Caribbean region at the close of the Cretaceous provides a proximate cause for the absence of an ancient West Indian biota.

Journal Article↗