Michael M. Miyamoto

Mutation rate variation in multicellular eukaryotes: causes and consequences

A basic knowledge about mutation rates is central to our understanding of a myriad of evolutionary phenomena, including the maintenance of sex and rates of molecular evolution. Although there is substantial evidence that mutation rates vary among taxa, relatively little is known about the factors that underlie this variation at an empirical level, particularly in multicellular eukaryotes. Here we integrate several disparate lines of theoretical and empirical inquiry into a unified framework to guide future studies that are aimed at understanding why and how mutation rates evolve in multicellular species.

Phylogeography and population structure of the Atlantic and Mediterranean green turtle Chelonia mydas: a mitochondrial DNA control region sequence assessment

Mitochondrial (mt) DNA sequences were analysed to resolve the phylogeography and population genetic structure of Atlantic and Mediterranean populations of green turtles (Chelonia mydas). Analysis of sequence variation over 487 base pairs of the control (D‐loop) region identified 18 haplotypes among 147 individuals from nine nesting populations. Pairwise comparisons of haplotype frequencies distinguished most nesting colonies, indicating significant genetic differentiation among rookeries and a strong propensity for natal homing behaviour by nesting females. Comparison of control region sequence data to earlier restriction fragment length polymorphism (RFLP) data for the same individuals demonstrates approximately a sixfold higher substitution rate in the 5′ end of the control region. The sequence data provide higher resolution both in terms of the number of mtDNA genotype variants and the phylogeographic relationships detected within the Atlantic region, and reveal a gene genealogy that distinguishes two groups of haplotypes corresponding to (i) the western Caribbean and Mediterranean, and (ii) eastern Caribbean, South Atlantic and West Africa. The data suggest that phylogeographic patterns in the Atlantic Ocean may be interpreted in terms of female nest site fidelity and episodic dispersal events. The distribution of mtDNA haplotypes within the region is thus explained by the geological and climatic alternations (glacial and interglacial) over the last million years.

A Three-Stage Colonization Model for the Peopling of the Americas

Background We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis. Methodology/Findings Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting ≈15,000 years ago. Conclusions/Significance These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas ≈15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of ≈1,000–5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.

A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins

Changes in protein function can lead to changes in the selection acting on specific residues. This can often be detected as evolutionary rate changes at the sites in question. A maximum-likelihood method for detecting evolutionary rate shifts at specific protein positions is presented. The method determines significance values of the rate differences to give a sound statistical foundation for the conclusions drawn from the analyses. A statistical test for detecting slowly evolving sites is also described. The methods are applied to a set of Myc proteins for the identification of both conserved sites and those with changing evolutionary rates. Those positions with conserved and changing rates are related to the structures and functions of their proteins. The results are compared with an earlier Bayesian method, thereby highlighting the advantages of the new likelihood ratio tests.

Analysis of DNA sequence data: phylogenetic inference.

Publisher Summary The chapter discusses phylogenetic inference for the analysis of DNA sequence data. There are five basic steps in the phylogenetic analysis of DNA sequences. The sequences under study must first be aligned so that positional homologs (the units of comparison) may be analyzed. Alignment may be straightforward if pairwise differences are small and most differences result from substitutions but it becomes increasingly difficult as the sequences become more divergent and insertion/deletion events become more common. Once sequences are aligned, some assessment of the presence of phylogenetic signal is necessary. If phylogenetic signal is present in a matrix of sequences, then the third step is selecting a method of phylogenetic inference. Once a method has been selected and the appropriate software has been obtained, a strategy must be developed for finding the best tree under the selected optimality criterion. Once a tree has been obtained, some statement of confidence in the results is desirable, such as deciding which nodes of the tree are well-supported by the data, and which are not.

Support for Natal Homing in Green Turtles from Mitochondrial DNA Sequences

Mitochondrial DNA (mtDNA) sequences of the control region were obtained for the Costa Rica and Florida colonies of the green turtle (Chelonia mydas) to test the hypothesis that gravid females return to their natal beaches to lay their eggs. Analyses of intra- and intergroup variation of these sequences revealed that the two colonies are structured differentially along maternal lineages and that mtDNA diversity is unusually high in the Florida population. The former result supports the hypothesis of natal homing in green turtles. For the latter, two explanations are provided: (1) that the Florida colony is the product of admixture (immigration from multiple sources); or (2) that it is a remnant of a larger, ancestral population. The presence or absence of Florida haplotypes among other western Atlantic populations will provide a critical test of these alternate hypotheses.

Updated Three-Stage Model for the Peopling of the Americas

Background We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. ∼40,000 years ago) expansion signal we had proposed for the proto-Amerind population. Methodology/Findings Bayesian skyline plot analysis of a new dataset of Native American mitochondrial coding genomes confirms the absence of an early expansion signal for the proto-Amerind population and allows us to reduce the variation around our estimate of the New World founder population size. In addition, genetic variants that define New World founder haplogroups are used to estimate the amount of time required between divergence of proto-Amerinds from the Asian gene pool and expansion into the New World. Conclusions/Significance The period of population isolation required for the generation of New World mitochondrial founder haplogroup-defining genetic variants makes the existence of three stages of colonization a logical conclusion. Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.

Phylogenetic Assessment of Molecular and Morphological Data for Eutherian Mammals

The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequences and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests, which were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., > or = 95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla (Artiodactyla and Cetacea) and Paenungulata (Hyracoidea, Proboscidea, and Sirenia). In turn, some reasonable to strong evidence (> or = 85%) was obtained for Hyracoidea with Sirenia, Dermoptera with Scandentia, Glires (Lagomorpha with Rodentia), and Afrotheria (Amblysomus, Macroscelidea, Paenungulata, and Tubulidentata). Otherwise, no other interordinal clades were supported at these reasonable to strong levels. This overall lack of resolution for eutherian interordinal clusters agrees with other studies that suggest further progress will continue to be slow and difficult. Further resolution will require the integration of more recently published data, the continued sampling of taxa and characters, and the use of more powerful methods of data analysis.

Origin of Hawksbill Turtles in a Caribbean Feeding Area as Indicated by Genetic Markers

Hawksbill turtles move between nesting colonies and feeding grounds, but in most cases it is not known which reproductive populations occupy a particular feeding habitat. In this study, genetic markers derived from mitochondrial DNA sequences are used to estimate the contribution of Caribbean nesting colonies to a feeding ground at Mona Island, Puerto Rico (n = 41). Maximum likelihood analysis indicates that this feeding population is not composed primarily of turtles from the neighboring nesting colony (also on Mona Island), but is drawn from nesting populations throughout the Caribbean region. A sampled nesting colony in the southern hemisphere (Bahia, Brazil) did not contribute, at detectable levels, to the Mona Island feeding ground. From this evidence, we concluded that hawksbill turtles recruitment to feeding grounds over a scale of hundreds of kilometres, but not over the scale of 7000 km that separate Mona Island from Bahia, Brazil. These data indicate that a hawskbill turtle harvest on feeding grounds will reduce nesting populations throughout the Caribbean region.

Comment on "Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals"

Bazin et al. (Reports, 28 April, 2006, p. 570) found no relationship between mitochondrial DNA (mtDNA) diversity and population size when comparing across large groups of animals. We show empirically that species with smaller populations, as represented by eutherian mammals, exhibit a positive correlation between mtDNA and allozyme variation, suggesting that mtDNA diversity may correlate with population size in these animals.