Rebecca L. Cann

mtDNA History of the Cayapa Amerinds of Ecuador: Detection of Additional Founding Lineages for the Native American Populations

mtDNA variation in the Cayapa, an Ecuadorian Amerindian tribe belonging to the Chibcha-Paezan linguistic branch, was analyzed by use of hypervariable control regions I and II along with two linked regions undergoing insertion/deletion mutations. Three major maternal lineage clusters fit into the A, B, and C founding groups first described by Schurr and colleagues in 1990, whereas a fourth lineage, apparently unique to the Cayapa, has ambiguous affinity to known clusters. The time of divergence from a common maternal ancestor of the four lineage groups is of sufficient age that it indicates an origin in Asia and supports the hypothesis that the degree of variability carried by the Asian ancestral populations into the New World was rather high. Spatial autocorrelation analysis points out (a) statistically significant nonrandom distributions of the founding lineages in the Americas, because of north-south population movements that have occurred since the first Asian migrants spread through Beringia into the Americas, and (b) an unusual pattern associated with the D lineage cluster. The values of haplotype and nucleotide diversity that are displayed by the Cayapa appear to differ from those observed in other Chibchan populations but match those calculated for South American groups belonging to various linguistic stocks. These data, together with the results of phylogenetic analysis performed with the Amerinds of Central and South America, highlight the difficulty in the identification of clear coevolutionary patterns between linguistic and genetic relationships in particular human populations.

Mitochondrial and Nuclear Genetic Relationships among Pacific Island and Asian Populations

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.

mtDNA lineage analyses: origins and migrations of Micronesians and Polynesians.

The islands of Micronesia and Polynesia collectively comprise the last major region of the globe to be settled by humans. Both of these groups of islands were colonized within the last 4,000 years by Austronesian-speaking agriculturists. Based on biogeographic and linguistic patterns, central-eastern Micronesia and Polynesia are included by many in a single category called Remote Oceania. Similarities of biologic, linguistic, and cultural traits within Remote Oceania highlight a question central to Oceanic studies: Are similarities among islands due to a common origin of isolated communities, to ongoing interactions among islands, or both? Analyses of mitochondrial DNA (mtDNA) sequences reveal that most remote Oceanic populations are polyphyletic. These polyphyletic populations violate the assumptions of many genetic distance and population demography models and so are problematic to interpret. The majority of mtDNA sequences from Micronesian and Polynesian populations are derived from Asia, whereas others are inferred to have originated in New Guinea. These data support an Island Southeast Asian origin and a colonization route along the north coast of New Guinea. The Marianas and Yap proper (main island) appear to have been independently settled directly from Island Southeast Asia, and both have received migrants from Central-Eastern Micronesia since then. Palau clearly demonstrates a complex prehistory including a significant influx of lineages from New Guinea. Thus genetic similarities among Micronesian and Polynesian populations result, in some cases, from a common origin, and in others, from extensive gene flow.

Molecular evolution : producing the biochemical data

Isolation of DNA from plants with large amounts of secondary metabolites Nucleic Acid Isolation from Environmental Aqueous Samples Nucleic acid isolation from ecological samplesvertebrate gut flora Nucleic acid isolation from ecological samples fungal associations, lichens Nucleic acid isolation from ecological samplesfungal associations, mycorrhizae Nucleic acid isolation from ecological samplesanimal scat and other associated materials Isolation and analysis of DNA from archaeological, clinical and natural history specimens Isolation and characterization of proteins from archaeological and ancient specimens Animal Phylogenomics: Multiple Interspecific Genome Comparisons ISSR techniques for evolutionary biology Use of Amplified Fragment Length Polymorphism (AFLP) markers in surveys of vertebrate diversity Use of AFLP markers in surveys of arthropod diversity Use of AFLP markers in surveys of plant diversity Isolating microsatellite DNA loci Use of microsatellites for parentage and kinship analyses in animals Use of capillary array electrophoresis single strand conformational polymorphism analysis to estimate genetic diversity of candidate genes in germplasm collections Ribosomal RNA probes and microarrays: Their potential use in assessing microbial biodiversity The role of geographic analyses in locating, understanding and using plant genetic diversity In Situ Hybridization of Phytoplankton Using Fluorescently-Labelled rRNA Probes Sequencing and comparing whole mitochondrial genomes of animals Methods for obtaining and analyzing whole chloroplast genome sequences Construction of Bacterial Artificial Chromosome libraries for use in phylogenetic studies Comparative EST analyses in plant systems Isolation of genes from plant Y chromosomes Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation Experimental methods for assaying natural transformation and inferring horizontal gene transfer Use of confocal microscopy in comparative studies of vertebrate morphology PrimerSelect: A transcriptome-wide oligonucleotide primer pair design program for kinetic RT-PCR-based transcript profiling Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids genome-wide analysis of gene expression changes in polyploids Designing experiments using spotted microarrays to detect gene regulation differences within and among species Methods for studying the evolution of plant reproductive structures: Comparative gene expression techniques Developing antibodies to synthetic peptides based on comparative DNA sequencing of multigene families Application of ancestral protein reconstruction in understanding protein function: GFP-like proteins Advances in phylogeny reconstruction from gene order and content data Analytical methods for detecting paralogy in molecular datasets Analytical methods for studying the evolution of paralogs using duplicate gene data sets Supertree construction in the genomic age Maximum-likelihood methods for phylogeny estimation Context Dependence and Co-Evolution among Amino Acid Resideue in Proteins

INCREASE IN AVIAN MALARIA AT UPPER ELEVATION IN HAWAI'I

Abstract Hawaiian honeycreepers (Aves: Drepanidinae) evolved in the absence of mosquito-borne diseases such as avian malaria (Plasmodium spp.). Malaria has been largely responsible for the recent wave of extinctions and endangerment among Hawaiian forest birds, which began by the 1920s. Most honeycreepers, especially endangered species, now persist only in forests above 1500 m elevation, where cool temperatures prevent effective malaria development in mosquitoes. We report here that prevalence of malaria in Hawaiian forest birds at 1900 m on the island of Hawai‘i has more than doubled over a decade. This increase was associated with breeding of mosquitoes and warmer summertime air temperatures. We also report direct evidence of tolerance to malaria, and a possible cost of tolerance, in wild native birds. Tolerance is adding to a reservoir of malaria at upper elevations even while vectors are rare and air temperatures are too low for complete development of the parasite in the vector. The data provide a glimpse of how malaria is becoming an emergent infectious disease at upper elevations.

DNA QUALITY AND ACCURACY OF AVIAN MALARIA PCR DIAGNOSTICS: A REVIEW

Abstract Birds have become increasingly prominent in studies focusing on natural populations and their coevolved pathogens or examining populations under environmental stress from novel and emerging infectious diseases. For either type of study, new DNA-based diagnostic tests, using the polymerase chain reaction (PCR), present challenges in detecting the DNA of pathogens, which exist in low copy number compared with DNA of the host. One example comes from studies of avian malaria: conflicting claims are made by different laboratories about the accuracy of tests using various sets of primers and reagents, especially in relation to blood smears and immunological methods. There is little standardization of protocol or performance among laboratories conducting tests, in contrast to studies of human malaria. This review compares the problems of detecting avian malaria with those of detecting human malaria, and shows definitively that the buffer used to store blood samples following collection is associated with the accuracy of the test. Lower accuracy is associated with use of a lysis buffer, which apparently degrades the DNA in the blood sample and contributes to inhibition of PCR reactions. DNA extraction and purification techniques, and optimization of the PCR reaction, do not appear to be alternative explanations for the effect of storage buffer. Nevertheless, the purest DNA in standard concentrations for PCR is required so that different primers, DNA polymerases, and diagnostic tests can be objectively compared.

Negative Effects of an Introduced Bird Species on Growth and Survival in a Native Bird Community

Exploitative competition is a major determinant of community structure in natural assemblages [1, 2], but, introduced species are rarely competitors that lead to extinction of native species [3, 4]. Here we document strong community-wide competition from the Japanese white-eye (Zosterops japonicus) on native Hawaiian passerine birds. Introduced in 1929 [5], white-eye successfully invaded old-growth forest and coexisted with eight native species [6], overlapping multiple foraging substrates with each but evidencing no agonistic interactions [7]. The endangered Hawaii akepa (Loxops coccineus coccineus) was viable during 1987-1999 but became nonviable during 2000-2006 in association with an abrupt increase in white-eyes [7]. We show that after 2000, juveniles of every native bird species measured had lower mass and shorter bills and tarsi. For most species, lower mass led to decreased juvenile survival, and shorter bills to decreased survival of second-year and older adults. Lower survival of smaller birds represents normalizing selection that is restoring previous size means to future generations [8]. Birds at a nearby site with fewer white-eyes had normal size. White-eye had less stunting of bills and did not suffer the survival consequences of native species. Exploitative competition for food between native birds and an introduced species requires intensive management to prevent further declines.

Mhc Allelic Diversity and Modern Human Origins

Abstract. Thirty complete coding sequences of human major histocompatibility complex (Mhc) class II DRB alleles, spanning 237 codons, were analyzed for phylogenetic information using distance, parsimony, and likelihood approaches. Allelic genealogies derived from different parts of the coding sequence (exon 2, the 5′ and 3′ ends of exon 2, respectively, and exons 3–6) were compared. Contrary to prior assertions, a rigorous analysis of allelic genealogies in this gene family cannot be used to justify the claim that the lineage leading to modern humans contained on average at least 100,000 individuals. Phylogenetic inferences based upon the exon 2 region of the DRB loci are complicated by selection and recombination, so this part of the gene does not provide a complete and accurate view of allelic relationships. Attempts to reconstruct human history from genetic data must use realistic models which consider the complicating factors of nonequilibrium populations, recombination, and different patterns of selection.

Changes in Timing, Duration, and Symmetry of Molt of Hawaiian Forest Birds

Food limitation greatly affects bird breeding performance, but the effect of nutritive stress on molt has barely been investigated outside of laboratory settings. Here we show changes in molting patterns for an entire native Hawaiian bird community at 1650–1900 m elevation on the Island of Hawaii between 1989–1999 and 2000–2006, associated with severe food limitation throughout the year beginning in 2000. Young birds and adults of all species took longer to complete their molt, including months never or rarely used during the 1989–1999 decade. These included the cold winter months and even the early months of the following breeding season. In addition, more adults of most species initiated their molt one to two months earlier, during the breeding season. Suspended molt, indicated by birds temporarily not molting primary flight feathers during the months of peak primary molt, increased in prevalence. Food limitation reached the point where individuals of all species had asymmetric molt, with different primary flight feathers molted on each wing. These multiple changes in molt, unprecedented in birds, had survival consequences. Adult birds captured during January to March, 2000–2004, had lower survival in four of five species with little effect of extended molt. Extended molt may be adaptive for a nutrient stressed bird to survive warm temperatures but not cool winter temperatures that may obliterate the energy savings. The changing molt of Hawaiian birds has many implications for conservation and for understanding life history aspects of molt of tropical birds.

On Polymerase Chain Reaction Tests for Estimating Prevalence of Malaria in Birds

Molecular diagnostics have the potential to detect parasites at lower intensities than direct inspection such as microscopy. However, techniques using the polymerase chain reaction (PCR) are sufficiently complex that different laboratories may implement them with varying attention to purity of DNA, recognition of artifacts, and resolution of multiple bands. The result is that some laboratories may be unable to get a published protocol to work or abandon it prematurely. Comparisons of prevalance of maleria in the blood of birds involving the same primers with different implementations show that the original published implementation was most accurate. In particular, false negatives by PCR in samples where parasites can be detected by microscopy reflect problems with laboratory procedure.