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Mitochondrial ND2 sequences were used to investigate the phylogenetic relationships amongst 31 diprotodontid marsupials (kangaroos, wombats, koala, possums, and allies). ND2 sequences were analyzed separately and in conjunction with available 12S rDNA sequences for 22 diprotodontid taxa. Phylogenetic analyses consistently identified monophyly for the Burramyoidea, Phalangeroidea, Petauroidea, Tarsipedoidea, Macropodoidea, and the Vombatiformes. Like previous molecular and morphological studies, relationships between the super-families were less well resolved. Inconsistency between taxonomic rank and genetic distance was identified amongst the diprotodontids.
Mol Phylogenet Evol 2002 Nov
PMID:Molecular phylogenetics of the Diprotodontia (kangaroos, wombats, koala, possums, and allies). 1241 5

The phylogeny of groups within Gobioidei is examined with molecular sequence data. Gobioidei is a speciose, morphologically diverse group of teleost fishes, most of which are small, benthic, and marine. Efforts to hypothesize relationships among the gobioid groups have been hampered by the prevalence of reductive evolution among goby species; such reduction can make identification of informative morphological characters particularly difficult. Gobies have been variously grouped into two to nine families, several with included subfamilies, but most existing taxonomies are not phylogenetic and few cladistic hypotheses of relationships among goby groups have been advanced. In this study, representatives of eight of the nine gobioid familes (Eleotridae, Odontobutidae, Xenisthmidae, Gobiidae, Kraemeriidae, Schindleriidae, Microdesmidae, and Ptereleotridae), selected to sample broadly from the range of goby diversity, were examined. Complete sequence from the mitochondrial ND1, ND2, and COI genes (3573 bp) was used in a cladistic parsimony analysis to hypothesize relationships among the gobioid groups. A single most parsimonious topology was obtained, with decay indices indicating strong support for most nodes. Major phylogenetic conclusions include that Xenisthmidae is part of Eleotridae, and Eleotridae is paraphyletic with respect to a clade composed of Gobiidae, Microdesmidae, Ptereleotridae, Kraemeriidae, and Schindleriidae. Within this five-family clade, two clades are recovered. One includes Gobionellinae, which is paraphyletic with respect to Kraemeriidae, Sicydiinae, Oxudercinae, and Amblyopinae. The other contains Gobiinae, also paraphyletic, and including Microdesmidae, Ptereleotridae, and Schindleriidae. Previous morphological evidence for goby groupings is discussed; the phylogenetic hypothesis indicates that the morphological reduction observed in many goby species has been derived several times independently.
Mol Phylogenet Evol 2003 Mar
PMID:Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). 1264 97

The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.
Mol Phylogenet Evol 2003 Jul
PMID:Mitochondrial DNA, morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae). 1280 73

The fish fauna of the Antarctic Ocean is dominated by five endemic families of the Perciform suborder Notothenioidei, thought to have arisen in situ within the Antarctic through adaptive radiation of an ancestral stock that evolved antifreeze glycoproteins (AFGPs) enabling survival as the ocean chilled to subzero temperatures. The endemism results from geographic confinement imposed by a massive oceanographic barrier, the Antarctic Circumpolar Current, which also thermally isolated Antarctica over geologic time, leading to its current frigid condition. Despite this voluminous barrier to fish dispersal, a number of species from the Antarctic family Nototheniidae now inhabit the nonfreezing cool temperate coasts of the southern continents. The origin of these temperate-water nototheniids is not completely understood. Since the AFGP gene apparently evolved only once, before the Antarctic notothenioid radiation, the presence of AFGP genes in extant temperate-water nototheniids can be used to infer an Antarctic evolutionary origin. Genomic Southern analysis, PCR amplification of AFGP genes, and sequencing showed that Notothenia angustata and Notothenia microlepidota endemic to southern New Zealand have two to three AFGP genes, structurally the same as those of the Antarctic nototheniids. At least one of these genes is still functional, as AFGP cDNAs were obtained and low levels of mature AFGPs were detected in the blood. A phylogenetic tree based on complete ND2 coding sequences showed monophyly of these two New Zealand nototheniids and their inclusion in the monophyletic Nototheniidae consisted of mostly AFGP-bearing taxa. These analyses support an Antarctic ancestry for the New Zealand nototheniids. A divergence time of approximately 11 Myr was estimated for the two New Zealand nototheniids, approximating the upper Miocene northern advance of the Antarctic Convergence over New Zealand, which might have served as the vicariant event that lead to the northward dispersal of their most recent common ancestor. Similar secondary northward dispersal likely applies to the South American nototheniid Paranotothenia magellanica, which has four AFGP genes in its DNA, but not to the sympatric nototheniid Patagonotothen tessellata, which does not appear to have any AFGP sequences in its genome at all.
Mol Biol Evol 2003 Nov
PMID:Functional antifreeze glycoprotein genes in temperate-water New Zealand nototheniid fish infer an Antarctic evolutionary origin. 1288 56

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.
J Mol Evol 2003 Jul
PMID:Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences. 1296 3

Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c-myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c-myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c-myc. Nuclear FST estimates were approximately 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models.
Mol Ecol 2003 Oct
PMID:Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. 1296 59

The taxonomic relationships within the dwarf chameleons (Bradypodion) of southern Africa have long been controversial. Although informal phenotypic groups have been suggested, the evolutionary relationships among the 15 recognised species in southern Africa have not been previously investigated. To investigate the relationships among species within this genus, fragments of two mitochondrial genes (16S ribosomal RNA and ND2) were sequenced and analysed using maximum parsimony, maximum likelihood and Bayesian inference. All analyses showed congruent topologies, revealing at least 5 well-supported clades distributed across distinct geographic regions. The mtDNA gene tree indicated that in many instances, geographic location has played a role in shaping the evolution of this group, and that the previously suggested phenotypic groupings do not adequately reflect evolutionary relationships. Furthermore, it appears that some of the currently recognised species (described on morphology) are polyphyletic for mitochondrial sequences, most notably those occurring in the isolated forest patches of north-eastern South Africa, near the Drakensberg Escarpment.
Mol Phylogenet Evol 2004 Feb
PMID:Phylogenetics of the southern African dwarf chameleons, Bradypodion (Squamata: Chamaeleonidae). 1471 27

Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages within the superfamily, as well as genera membership in major lineages was also assessed. Analyses suggest that Bombycillidae is not a part of Muscicapoidea, and there is strongly supported evidence to suggest that Turdinae is not part of the Muscicapidae, but is instead sister to a Sturnidae+Cinclidae clade. This clade is in turn sister to Muscicapidae (Muscicapini+Saxicolini). Of the 49 Turdinae and Muscicapidae genera that we included in our analyses, 10 (20%) are shown to be misclassified to subfamily or tribe. Our results place one current Saxicolini genus in Turdinae, two Saxicolini genera in Muscicapini, and five Turdinae and two Muscicapini genera in Saxicolini; these relationships are supported with 100% Bayesian support. Our analyses suggest that c-mos was only marginally useful in resolving these "deep" phylogenetic relationships.
Mol Phylogenet Evol 2004 Feb
PMID:Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea. 1471 30

Accurate estimation of relative mutation rates of mitochondrial DNA (mtDNA) and single-copy nuclear DNA (scnDNA) within lineages contributes to a general understanding of molecular evolutionary processes and facilitates making demographic inferences from population genetic data. The rate of divergence at synonymous sites ( K(s)) may be used as a surrogate for mutation rate. Such data are available for few organisms and no amphibians. Relative to mammals and birds, amphibian mtDNA is thought to evolve slowly, and the K(s) ratio of mtDNA to scnDNA would be expected to be low as well. Relative K(s) was estimated from a mitochondrial gene, ND2, and a nuclear gene, c-myc, using both "approximate" and likelihood methods. Three lineages of congeneric frogs were studied and this ratio was found to be approximately 16, the highest of previously reported ratios. No evidence of a low K(s) in the nuclear gene was found: c-myc codon usage was not biased, the K(s) was double the intron divergence rate, and the absolute K(s) was similar to estimates obtained here for other genes from other frog species. A high K(s) in mitochondrial vs. nuclear genes was unexpected in light of previous reports of a slow rate of mtDNA evolution in amphibians. These results highlight the need for further investigation of the effects of life history on mutation rates.
J Mol Evol 2003 Dec
PMID:Relative rates of nucleotide substitution in frogs. 1474 32

For more than a century, members of the traditional avian order Galliformes (i.e., pheasants, partridges, junglefowl, and relatives) have been among the most intensively studied birds, but still a comprehensive timeframe for their evolutionary history is lacking. Thanks to a number of recent cladistic interpretations for several galliform fossils, candidates now exist that can potentially be used as accurate internal calibrations for molecular clocks. Here, we describe a molecular timescale for Galliformes based on cytochrome b and ND2 using nine mostly internal fossil-based anchorpoints. Beyond application of calibrations spanning the entire evolutionary history of Galliformes, care was taken to investigate the effects of calibration choice, substitution saturation, and rate heterogeneity among lineages on divergence time estimation. Results show broad consistency in time estimation with five out of the nine total calibrations. Our divergence time estimates, based on these anchorpoints, indicate that the early history of Galliformes took place in the Cretaceous, including the origin of the basal-most megapode and perhaps cracid lineages, but that the remaining morphological diversification likely started in the earliest Tertiary. The multi-calibration/multi-genetic partition approach used here highlights the importance of understanding the genetic saturation, variation, and rate constancy spectra for the accurate calculation of divergence times by use of molecular clocks.
Mol Phylogenet Evol 2004 Jan
PMID:Calibration of galliform molecular clocks using multiple fossils and genetic partitions. 1502 59


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