Beneficial associations between plants and microbes play an important role in both natural and ag... 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...
Background/Question/Methods One of the last land masses to be settled by humans was Aotearoa/ New... 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 child... 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.
Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, a... 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...
Admixture between long-separated populations is a defining feature of the genomes of many species... 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...
Beneficial associations between plants and microbes play an important role in both natural and ag... 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...
Background/Question/Methods One of the last land masses to be settled by humans was Aotearoa/ New... 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 child... 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.
Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, a... 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...
Admixture between long-separated populations is a defining feature of the genomes of many species... 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...
High-coverage whole-genome sequence studies have so far focused on a limited number 1 of geograph... 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.
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Papers by Murray Cox