Geoffrey K. Chambers

The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time

We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.

The Genetic Structure of Pacific Islanders

Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small “Austronesian” genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there.

Combined Data, Bayesian Phylogenetics, and the Origin of the New Zealand Cicada Genera

We have applied Bayesian and maximum likelihood methods of phylogenetic estimation to data from four mitochondrial genes (COI, COII, 12S, and 16S) and a single nuclear gene (EF1alpha) from several genera of New Zealand, Australian, and New Caledonian cicada taxa. We specifically focused on the heterogeneity of phylogenetic signal among the different data partitions and the biogeographic origins of the New Zealand cicada fauna. The Bayesian analyses circumvent many of the problems associated with other statistical tests for comparing data partitions. We took an information-theoretic approach to model selection based on the Akaike Information Criterion (AIC). This approach indicated that there was considerable uncertainty in identifying the best-fit model for some of the partitions. Additionally, a large amount of uncertainty was associated with many parameter estimates from the substitution model. However, a sensitivity analysis on the combined dataset indicated that the model selection uncertainty had little effect on estimates of topology because these estimates were largely insensitive to changes in the assumed model. This outcome suggests strong signal in our data. Our analyses support a New Caledonian affiliation of the New Zealand cicada genera Maoricicada, Kikihia, and Rhodopsalta and Australian affinities for the genera Amphipsalta and Notopsalta. This result was surprising, given that previous cicada biologists suspected a close relationship between Amphipsalta, Notopsalta, and Rhodopsalta based on genitalic characters. Relationships among the closely related genera Maoricicada, Kikihia, and Rhodopsalta were poorly resolved, the mitochondrial data and the EF1alpha data favoring different arrangements within this clade.

A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous

The question of when modern birds (Neornithes) first diversified has generated much debate among avian systematists. Fossil evidence generally supports a Tertiary diversification, whereas estimates based on molecular dating favor an earlier diversification in the Cretaceous period. In this study, we used an alternate approach, the inference of historical biogeographic patterns, to test the hypothesis that the initial radiation of the Order Psittaciformes (the parrots and cockatoos) originated on the Gondwana supercontinent during the Cretaceous. We utilized broad taxonomic sampling (representatives of 69 of the 82 extant genera and 8 outgroup taxa) and multilocus molecular character sampling (3,941 bp from mitochondrial DNA (mtDNA) genes cytochrome oxidase I and NADH dehydrogenase 2 and nuclear introns of rhodopsin intron 1, tropomyosin alpha-subunit intron 5, and transforming growth factor ss-2) to generate phylogenetic hypotheses for the Psittaciformes. Analyses of the combined character partitions using maximum parsimony, maximum likelihood, and Bayesian criteria produced well-resolved and topologically similar trees in which the New Zealand taxa Strigops and Nestor (Psittacidae) were sister to all other psittaciforms and the cockatoo clade (Cacatuidae) was sister to a clade containing all remaining parrots (Psittacidae). Within this large clade of Psittacidae, some traditionally recognized tribes and subfamilies were monophyletic (e.g., Arini, Psittacini, and Loriinae), whereas several others were polyphyletic (e.g., Cyclopsittacini, Platycercini, Psittaculini, and Psittacinae). Ancestral area reconstructions using our Bayesian phylogenetic hypothesis and current distributions of genera supported the hypothesis of an Australasian origin for the Psittaciformes. Separate analyses of the timing of parrot diversification constructed with both Bayesian relaxed-clock and penalized likelihood approaches showed better agreement between geologic and diversification events in the chronograms based on a Cretaceous dating of the basal split within parrots than the chronograms based on a Tertiary dating of this split, although these data are more equivocal. Taken together, our results support a Cretaceous origin of Psittaciformes in Gondwana after the separation of Africa and the India/Madagascar block with subsequent diversification through both vicariance and dispersal. These well-resolved molecular phylogenies will be of value for comparative studies of behavior, ecology, and life history in parrots.

PHYLOGEOGRAPHY OF THE NEW ZEALAND CICADA MAORICICADA CAMPBELLI BASED ON MITOCHONDRIAL DNA SEQUENCES: ANCIENT CLADES ASSOCIATED WITH CENOZOIC ENVIRONMENTAL CHANGE

Abstract.— New Zealands isolation, its well‐studied rapidly changing landscape, and its many examples of rampant speciation make it an excellent location for studying the process of genetic differentiation. Using 1520 base pairs of mitochondrial DNA from the cytochrome oxidase subunit I, ATPase subunits 6 and 8 and tRNAAsp genes, we detected two well‐differentiated, parapatrically distributed clades within the widespread New Zealand cicada species Maoricicada campbelli that may prove to represent two species. The situation that we uncovered is unusual in that an ancient lineage with low genetic diversity is surrounded on three sides by two recently diverged lineages. Using a relaxed molecular clock model coupled with Bayesian statistics, we dated the earliest divergence within M. campbelli at 2.3 ± 0.55 million years. Our data suggest that geological and climatological events of the late Pliocene divided a oncewidespread species into northern and southern components and that near the middle of the Pleistocene the northern lineage began moving south eventually reaching the southern clade. The southern clade seems to have moved northward to only a limited extent. We discovered five potential zones of secondary contact through mountain passes that will be examined in future work. We predict that, as in North American periodical cicadas, contact between these highly differentiated lineages will exist but will not involve gene flow.

The Drosophila Alcohol Dehydrogenase Gene–Enzyme System

Publisher Summary The earliest report of genetic variation at the alcohol dehydrogenase (Adh) locus of drosophila melanogaster was presented by Johnson and Denniston. This chapter presents the diversity of interest in Adh and reviews several recent papers on genetic research on Adh. It also provides a clear picture of the basic genetic features of any gene–enzyme system. The utility of Adh + and Adh null as selectable markers are beginning to promote the use of the Adh gene by workers primarily interested in other systems or even radically different problems such as control of insect Pests, aging, or space exploration. The detailed molecular analysis of transcription at the Adh locus is developing rapidly. The Adh gene is enjoying a new lease on life as a subject of the current molecular biological approach to population genetics. It is also growing in significance and utility as a character in Drosophila phylogeny, in studies of enzyme evolution, and as a problem in biochemical evolution in its own right. A fuller appreciation of all three subjects will be gained if the present intensity of biochemical work on ADH is maintained and especially if a three dimensional structure of the enzyme can be obtained.

Using molecular methods to understand the Gondwanan affinities of the New Zealand biota: three case studies

The application of new molecular technologies is central to the search for causal mechanisms capable of explaining the modern-day biogeography of the southern continents. Projects have previously focused on marine mammals and birds, but in recent years they have begun to expand in scope. We now describe the results from three studies carried out recently on parakeets (genus Cyanoramphus), cicadas (genus Maoricicada) and geckos (genera Hoplodactylus and Naultinus) in the context of the Gondwanan affinities of the New Zealand biota. The work described here has been the subject of independent reports (see text for individual references) and their findings have been brought together for the first time here in a more general synthesis.

Genetic variation in island populations of tuatara (Sphenodon spp) inferred from microsatellite markers

Tuatara (Sphenodon spp) populations are restricted to 35 offshore islands in the Hauraki Gulf, Bay of Plenty and Cook Strait of New Zealand. Low levels of genetic variation have previously been revealed by allozyme and mtDNA analyses. In this new study, we show that six polymorphic microsatellite loci display high levels of genetic variation in 14 populations across the geographic range of tuatara. These populations are characterised by disjunct allele frequency spectra with high numbers of private alleles. High FST (0.26) values indicate marked population structure and assignment tests allocate 96% of all individuals to their source populations. These genetic data confirm that islands support genetically distinct populations. Principal component analysis and allelic sequence data supplied information about genetic relationships between populations. Low numbers of rare alleles and low allelic richness identified populations with reduced genetic diversity. Little Barrier Island has very low numbers of old tuatara which have retained some relictual diversity. North Brother Island’s tuatara population is inbred with fixed alleles at 5 of the 6 loci.

Absence of daily cycles in plasma sex steroids in male and female tuatara (Sphenodon punctatus), and the effects of acute capture stress on females

The possible existence of daily cycles in plasma concentrations of sex steroids was examined in wild male and female tuatara (Sphenodon punctatus). Samples were collected from freshly captured animals at dusk, middle of the night, dawn, and middle of the day in January (summer) and July (winter). Males showed daily cycles in mean body temperature (Tb) in both seasons but no daily cycle in mean plasma testosterone concentration in either season. Vitellogenic female tuatara in January and females in mixed reproductive condition in July also showed significant daily variation in Tb. However, there were no daily cycles in mean plasma concentrations of estradiol, testosterone, or progesterone in either group of females. Vitellogenic female tuatara subjected to an acute capture stress (3-hr confinement) in January had mean plasma concentrations of estradiol and testosterone that did not differ from those of free-roaming females. However, progesterone and Tb were significantly higher in captives than in free-roaming females. The elevation in progesterone may result from physical confinement, the difference in Tb, or both. These data suggest that seasonal fluctuations in circulating concentrations of plasma sex steroids in tuatara can be determined using samples collected at different times of the 24-hr cycle. However, the effects of acute capture stress and/or changes in Tb on plasma progesterone concentrations need to be considered in future studies on this and possibly other female reptiles.

Origin and expression of an alcohol dehydrogenase gene duplication in the genus Drosophila

The origin of variation in regulatory mechanisms and the subsequent evolution of different regulatory systems may have fundamental importance in transspecific evolution (e.g., Dobzhansky et al., 1977). The timing and coordinated expression of enzymes ultimately extends to morphological and biochemical developmental patterns. The mechanisms which lead to regulatory changes are the subject of speculation, but changes in the genetic information at any level from nucleotide substitutions to large scale additions of genomic material may be important in the realization of new patterns of development. One mode of achieving new patterns of gene expression during development is gene duplication followed by divergence in the expression of the two copies (Ohno, 1970; Zuckerkandl, 1978). In this paper we document an alcohol dehydrogenase (Adh) gene duplication associated with a major adaptive radiation within the genus Drosophila. The duplicate Adh genes differ in developmental expression within and among species of the mulleri subgroup. Study of this gene duplication is attractive because of extensive knowledge of the phylogenetic history of the family Drosophilidae, the considerable information on the habits and habitats of the mulleri subgroup and the extensive studies of the Adh gene-enzyme system in Drosophila melanogaster that provide