Beneficial associations between plants and microbes play an important role in both natural and agricultural ecosystems. For example, associations between fungi of the genus Epichloë, and cool-season grasses are known for their ability to... more
Beneficial associations between plants and microbes play an important role in both natural and agricultural ecosystems. For example, associations between fungi of the genus Epichloë, and cool-season grasses are known for their ability to increase resistance to insect pests, fungal pathogens and drought. However, little is known about the molecular changes induced by endophyte infection. To study the impact of endophyte infection, we compared the expression profiles, based on RNA sequencing, of perennial ryegrass infected with Epichloë festucae with noninfected plants. We show that infection causes dramatic changes in the expression of over one third of host genes. This is in stark contrast to mycorrhizal associations, where substantially fewer changes in host gene expression are observed, and is more similar to pathogenic interactions. We reveal that endophyte infection triggers reprogramming of host metabolism, favouring secondary metabolism at a cost to primary metabolism. Infecti...
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Background/Question/Methods One of the last land masses to be settled by humans was Aotearoa/ New Zealand, when Polynesian voyaging across the Pacific resulted in Māori settlement in ca. 1250 AD. This relatively recent human history... more
Background/Question/Methods One of the last land masses to be settled by humans was Aotearoa/ New Zealand, when Polynesian voyaging across the Pacific resulted in Māori settlement in ca. 1250 AD. This relatively recent human history allows unprecedented opportunity to investigate how Māori ecological principles and practices have developed in response to environmental and societal challenges such as first settlement, faunal extinction events, and accelerating European colonisation after ca.1850 AD. Māori culture has a strongly developed tradition of oral literature. Ancestral sayings (whakataukī) provide an enduring record of tribal memory and represent an important method for transmitting critical information about aspects of life and society. Nonetheless, their meanings may not be apparent without knowing the historical, cultural and linguistic context out of which they emerged. Such codified knowledge depends on language use and structure as a key mechanism for cultural transmiss...
ABSTRACT Cultural transmission of reproductive success states that successful men have more children and pass this greater fecundity to their offspring. Balaresque and colleagues found high frequency haplotypes in a Central Asian Y... more
ABSTRACT Cultural transmission of reproductive success states that successful men have more children and pass this greater fecundity to their offspring. Balaresque and colleagues found high frequency haplotypes in a Central Asian Y chromosome dataset, which they attribute to cultural transmission of reproductive success by prominent historical men, including Genghis Khan. Using coalescent simulation, we show that these high frequency haplotypes are expected simply by chance. Hence, an explanation invoking cultural transmission of reproductive success is statistically unnecessary.
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Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology,... more
Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of...
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Admixture between long-separated populations is a defining feature of the genomes of many species. The mosaic block structure of admixed genomes can provide information about past contact events, including the time and extent of... more
Admixture between long-separated populations is a defining feature of the genomes of many species. The mosaic block structure of admixed genomes can provide information about past contact events, including the time and extent of admixture. Here, we describe an improved wavelet-based technique that better characterizes ancestry block structure from observed genomic patterns. Principal Components Analysis is first applied to genomic data to identify the primary population structure, followed by wavelet decomposition to develop a new characterization of local ancestry information along the chromosomes. For testing purposes, this method is applied to human genome-wide genotype data from Indonesia, as well as virtual genetic data generated using genome-scale sequential coalescent simulations under a wide range of admixture scenarios. Time of admixture is inferred using an approximate Bayesian computation framework, providing robust estimates of both admixture times and their associated l...
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Research Interests: Genetics, Polymorphism, Population Genetics, Molecular Evolution, Humans, and 14 moreMutation, Female, Male, Reproductive Success, Population Size, Effective Population Size, Population Density, Human Genome, PLoS Genetics, Genetic variation, X chromosome, Demographic History, Mutation Rate, and DNA sequence
Research Interests: Plant Biology, Symbiosis, Abiotic Stress, Plant Science, Signal Transduction, and 18 moreNext generation sequencing, Transcriptome, Virulence, Seasonality, Plant diseases, Mutation, Reactive Oxygen Species, Growth Analysis, Plant Roots, Mitogen Activated Protein Kinase, Secondary Metabolites, NADPH oxidase, Very high throughput, Host Pathogen Interactions, Plant immunity, MAP Kinase, Lolium Perenne L., and Experimental Model
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Research Interests: Ancient History, Evolutionary Biology, Genetics, Geography, Molecular Biology, and 17 moreStratification, Colonization, Phylogeny, Mitochondrial DNA, Humans, Haplotypes, Animals, Male, Molecular biology and evolution, Y chromosome, Biological evolution, Ethnic Groups, Asian Continental Ancestry Group, Genetic variation, Genetic Markers, Biochemistry and cell biology, and Gene pool
Three strains of Geobacillus stearothermophilus (designated A1, P3, and D1) were isolated from a New Zealand milk powder manufacturing plant. Here, we describe their draft genome sequences. This information provided the first genomic... more
Three strains of Geobacillus stearothermophilus (designated A1, P3, and D1) were isolated from a New Zealand milk powder manufacturing plant. Here, we describe their draft genome sequences. This information provided the first genomic insights into the nature of G. stearothermophilus strains present in the milk powder manufacturing environment.
Research Interests: Genetics, Archaeology, Anthropology, Pacific Island Studies, Austronesian Languages, and 15 moreSoutheast Asia, Claude Lévi-Strauss, Matrilineality, Structuralism, Social behavior, Austronesian, Social organization, Mitochondrial DNA, Anthropological Archaeology, Austronesian linguistics, Austronesian Prehistory, X chromosome, Social Organization, Social Behavior, and Structural model
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Research Interests: Religion, Archaeology, Law, Anthropology, Complex Systems Science, and 22 moreComplexity Theory, Principal Component Analysis, Complex Systems, Complexity, Indonesia, Ecology, Resilience (Sustainability), Social Ecological Systems, Social Class, Bali (Anthropology), Complex Adaptive Systems, Irrigation water Management, Humans, Female, Male, Regime Shifts, Development of complex societies, Critical Transitions, Asian Continental Ancestry Group, Genetic variation, Agricultural Irrigation, and Current anthropology
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Research Interests: Bioinformatics, Demography, Algorithms, Programming Languages, Genomics, and 15 moreComputational Biology, Biological Sciences, DNA, Software, Humans, Automation, Mathematical Sciences, Analytical Method, Theoretical Models, Very high throughput, Genetic Recombination, Genetic variation, Demographic History, Computational Method, and DNA sequence
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Research Interests: Genetics, Genetic Drift, Monte Carlo Simulation, Population Genetics, Molecular Evolution, and 18 moreVanuatu, Humans, Haplotypes, Case Study, Male, Effective Population Size, Population Density, Y chromosome, Clinical Sciences, Annals of Human Genetics, Information Content, Time Factors, Genetic variation, Demographic History, Base Sequence, Monte Carlo Method, Allele Frequency, and Founder Effect
Tandem repeat-containing DNA mutates orders of magnitude faster than normal DNA by insertion and deletion of repeat units. In microbes, hypermutable DNA repeats, when located in open reading frames (ORFs) or promoters in so-called... more
Tandem repeat-containing DNA mutates orders of magnitude faster than normal DNA by insertion and deletion of repeat units. In microbes, hypermutable DNA repeats, when located in open reading frames (ORFs) or promoters in so-called contingency genes, can serve as an ‘insurance’. Their hypermutation constantly replenishes a pool of variants in the population, from which the fittest are chosen. If circumstances change suddenly, for instance if the host launches an immune response against the predominant allele of a contingency gene of a microbial pathogen, the very survival of the population may depend on the presence of rare variant alleles not targeted by this response. Hypermutability is a cost however when the environment is not changing, by constantly generating inferior alleles. Research by us and others has shown that the pathogenic yeast Candida albicans has 2600 hypermutable tandem repeat-containing ORFs (TR-ORFS), but that most of these may not be contingency genes used in sh...
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Research Interests: Genetics, Archaeology, Geochemistry, Pacific Island Studies, Archaeological Science, and 16 morePopulation Genetics, Ancient DNA (Archaeology), Ancient DNA Research, Pacific Archaeology, Oceania archaeology, Solomon Islands, mtDNA, Mitochondrial DNA, Holocene, Case Study, Ancient DNA, Late Holocene, Melanesia Anthropology, Population Decline, Diversity Indices, and Linguistic Modeling
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Background Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the details of, and... more
Background Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the details of, and in some cases challenging, aspects of this general model. Results Here, we present the first comprehensive study of three such isolated populations from Madagascar: the Mikea hunter-gatherers, the neighbouring Vezo fishermen, and the Merina central highlanders (n = 266). Complete mitochondrial DNA genome sequences reveal several unresolved lineages, and a new, deep branch of the out-of-Africa founder clade M has been identified. This new haplogroup, M23, has a limited global distribution, and is restricted to Madagascar and a limited range of African and Southwest Asian groups. Conclusions The geographic distribution, phylogenetic placement and molecular age of M23 suggest that the colonization of Madagascar was more complex than previously thought.
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Research Interests: Genetics, Gene Flow, Population Genetics, Population Dynamics, Mitochondrial DNA, and 11 moreHumans, Markov chains, Markov Chain Monte Carlo, Population Size, Effective Population Size, Population Density, Y chromosome, X chromosome, Base Sequence, sub-Saharan African Literature, and Divergence Time
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Research Interests: Genetics, Genetic Epidemiology, Human Genetics, Genomics, Population Genetics, and 19 moreIndonesia, Population Dynamics, Mitochondria, Molecular Genetics, Epigenetics, Cytogenetics, Phylogeny, Pacific Islands, Mitochondrial DNA, Humans, Haplotypes, Pharmacogenetics, Female, Clinical Genetics, Male, Ethnic Groups, Clinical Sciences, Human Genome, and Genetic variation
High-coverage whole-genome sequence studies have so far focused on a limited number 1 of geographically restricted populations 2–5 , or been targeted at specific diseases, such as cancer 6. Nevertheless, the availability of... more
High-coverage whole-genome sequence studies have so far focused on a limited number 1 of geographically restricted populations 2–5 , or been targeted at specific diseases, such as cancer 6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history 7–9 and refuelled the debate on the mutation rate in humans 10. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long-and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record 11 , and admixture between AMHs and Neanderthals predating the main Eurasian expansion 12 , our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.