Showing papers by "Allan J. Baker published in 2002"
TL;DR: The mean estimate for the origin of modern birds at about 123 million years ago (Myr ago) is quite close to recent estimates using both nuclear and mitochondrial genes, and supports theories of continental break–up as a driving force in avian diversification.
Abstract: To test the hypothesis put forward by Feduccia of the origin of modern birds from transitional birds, we sequenced the first two complete mitochondrial genomes of shorebirds (ruddy turnstone and blackish oystercatcher) and compared their sequences with those of already published avian genomes. When corrected for rate heterogeneity across sites and non-homogeneous nucleotide compositions among lineages in maximum likelihood (ML), the optimal tree places palaeognath birds as sister to the neognaths including shorebirds. This optimal topology is a re-rooting of recently published ordinal-level avian trees derived from mitochondrial sequences. Using a penalized likelihood (PL) rate-smoothing process in conjunction with dates estimated from fossils, we show that the basal splits in the bird tree are much older than the Cretaceous-Tertiary (K-T) boundary, reinforcing previous molecular studies that rejected the derivation of modern birds from transitional shorebirds. Our mean estimate for the origin of modern birds at about 123 million years ago (Myr ago) is quite close to recent estimates using both nuclear and mitochondrial genes, and supports theories of continental break-up as a driving force in avian diversification. Not only did many modern orders of birds originate well before the K-T boundary, but the radiation of major clades occurred over an extended period of at least 40 Myr ago, thus also falsifying Feduccia's rapid radiation scenario following a K-T bottleneck.
136 citations
TL;DR: Estimating the locations of refugia where chaffinches survived the last glacial episode was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene, and Divergence time estimates suggest that European populations began diverging about 60,000 years before present.
Abstract: We analyzed sequences from a 275-bp hypervariable region in the 5' end of the mitochondrial DNA control region in 190 common chaffinches (Fringilla coelebs) from 19 populations in Europe and North Africa, including new samples from Greece and Morocco. Coalescent techniques were applied to estimate the time to the most recent common ancestor (TMRCA) and divergence times of these populations. The first objective of this study was to infer the locations of refugia where chaffinches survived the last glacial episode, and this was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene. Although extant populations in Iberia, Corsica, Greece, and North Africa harbor haplotypes that are basal in a phylogenetic tree, this information alone cannot be used to infer that these localities served as refugia, because it is impossible to infer the ages of populations and their divergence times without also considering the population genetic processes of mutation, migration, and drift. Provided we assume the TMRCAs of populations are a reasonable estimate of a population's age, coalescent-based methods place resident populations in Iberia, Corsica, Greece, and North Africa during the time of the last glacial maximum, suggesting these regions served as refugia for the common chaffinch. The second objective was to determine when populations began diverging from each other and to use this as a baseline to estimate current levels of gene flow. Divergence time estimates suggest that European populations began diverging about 60,000 years before present. The relatively recent divergence of populations in North Africa, Italy, and Iberia may explain why classic migration estimates based on equilibrium assumptions are high for these populations. We compare these estimates with nonequilibrium-based estimates and show that the nonequilibrium estimates are consistently lower than the equilibrium estimates.
90 citations
TL;DR: Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses of this large data set produced similar trees, whereas the MP tree indicated that guans are the sister group to (horned guan, (curassows, chachalacas), whereas the ML andBayesian analysis recovered a tree where the horned Guan is a sister clade to curassows and these two clades had the chach alacas as a sister group.
Abstract: The Cracidae is one of the most endangered and distinctive bird families in the Neotropics, yet the higher relationships among taxa remain uncertain. The molecular phylogeny of its 11 genera was inferred using 10,678 analyzable sites (5,412 from seven different mitochondrial segments and 5,266 sites from four nuclear genes). We performed combinability tests to check conflicts in phylogenetic signals of separate genes and genomes. Phylogenetic analysis showed that the unrooted tree of ((curassows, horned guan) (guans, chachalacas)) was favored by most data partitions and that different data partitions provided support for different parts of the tree. In particular, the concatenated mitochondrial DNA (mtDNA) genes resolved shallower nodes, whereas the combined nuclear sequences resolved the basal connections among the major clades of curassows, horned guan, chachalacas, and guans. Therefore, we decided that for the Cracidae all data should be combined for phylogenetic analysis. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses of this large data set produced similar trees. The MP tree indicated that guans are the sister group to (horned guan, (curassows, chachalacas)), whereas the ML and Bayesian analysis recovered a tree where the horned guan is a sister clade to curassows, and these two clades had the chachalacas as a sister group. Parametric bootstrapping showed that alternative trees previously proposed for the cracid genera are significantly less likely than our estimate of their relationships. A likelihood ratio test of the hypothesis of a molecular clock for cracid mtDNA sequences using the optimal ML topology did not reject rate constancy of substitutions through time. We estimated cracids to have originated between 64 and 90 million years ago (MYA), with a mean estimate of 76 MYA. Diversification of the genera occurred approximately 41-3 MYA, corresponding with periods of global climate change and other Earth history events that likely promoted divergences of higher level taxa.
81 citations
TL;DR: Seven dinucleotide microsatellite loci developed from the red-billed gull are described and are likely to be useful for studies of mating systems and population genetics in a wide range of gull species.
Abstract: We describe the isolation and characterization of seven dinucleotide microsatellite loci developed from the red-billed gull (Larus novaehollandiae scopulinus). Locus-specific primers were used to genotype individuals from 13 populations of this subspecies as well as individuals from closely related subspecies from Australia and New Caledonia. The primers were tested successfully on other species of gulls and shorebirds. The number of alleles observed within the red-billed gull ranged from three to 17, and observed heterozygosity varied from 0.359 to 0.787. These microsatellites are likely to be useful for studies of mating systems and population genetics in a wide range of gull species.
47 citations