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Rachel S. Meyer

Bio: Rachel S. Meyer is an academic researcher from University of California, Santa Cruz. The author has contributed to research in topics: Environmental DNA & Biodiversity. The author has an hindex of 22, co-authored 49 publications receiving 2430 citations. Previous affiliations of Rachel S. Meyer include New York Botanical Garden & University of York.


Papers
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Journal ArticleDOI
TL;DR: Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations That occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations.
Abstract: Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

804 citations

Journal ArticleDOI
TL;DR: The overall time required to domesticate a species has decreased since the earliest domestication events, and the frequencies of some domestication syndrome traits have decreased over time, while others have increased.
Abstract: Contents Summary 29 I. Introduction 30 II. Key concepts and definitions 30 III. Methods of review and analysis 35 IV. Trends identified from the review of 203 crops 37 V. Life cycle 38 VI. Ploidy level 40 VII. Reproductive strategies 42 VIII. The domestication syndrome 42 IX. Spatial and temporal trends 42 X. Utilization of plant parts 44 XI. Conclusions 44 Acknowledgements 45 References 45 Summary Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well-studied ‘model’ crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process.

608 citations

Journal ArticleDOI
TL;DR: The inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastids genome, or if present is found in cryptic form at very low levels.
Abstract: Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ~350 sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp,ndh,pet,psa,psb,rbcL), ribosomal RNA genes (rrn16,rrn23), ribosomal protein genes (rps7,rps11,rps16), transfer RNA genes, as well as matK,accD,ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ~33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches—despite success in identifying and developing a draft assembly of the much larger mitochondrial genome—suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if presen ti s found in cryptic form at very low levels.

164 citations

Journal ArticleDOI
TL;DR: A map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces shows a population bottleneck in this species, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation.
Abstract: African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa ∼3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began ∼13,000-15,000 years ago with effective population size reaching its minimum value ∼3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within ∼300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.

154 citations

Journal ArticleDOI
TL;DR: A comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars is presented, which documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.
Abstract: Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

141 citations


Cited by
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19 Apr 2011
TL;DR: Administration of spermidine markedly extended the lifespan of yeast, flies and worms, and human immune cells and inhibited oxidative stress in ageing mice, and found that enhanced autophagy is crucial for polyamine-induced suppression of necrosis and enhanced longevity.
Abstract: Ageing results from complex genetically and epigenetically programmed processes that are elicited in part by noxious or stressful events that cause programmed cell death Here, we report that administration of spermidine, a natural polyamine whose intracellular concentration declines during human ageing, markedly extended the lifespan of yeast, flies and worms, and human immune cells In addition, spermidine administration potently inhibited oxidative stress in ageing mice In ageing yeast, spermidine treatment triggered epigenetic deacetylation of histone H3 through inhibition of histone acetyltransferases (HAT), suppressing oxidative stress and necrosis Conversely, depletion of endogenous polyamines led to hyperacetylation, generation of reactive oxygen species, early necrotic death and decreased lifespan The altered acetylation status of the chromatin led to significant upregulation of various autophagy-related transcripts, triggering autophagy in yeast, flies, worms and human cells Finally, we found that enhanced autophagy is crucial for polyamine-induced suppression of necrosis and enhanced longevity

974 citations

Journal ArticleDOI
TL;DR: It is indicated that the combined action of microbe- microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.

885 citations

Journal ArticleDOI
TL;DR: Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations That occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations.
Abstract: Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

804 citations

Journal ArticleDOI
01 May 1949-Nature
TL;DR: The Wealth of India: A Dictionary of Indian Raw Materials and Industrial Products as mentioned in this paper is a dictionary of the economic products of India that was published during the years 1889-99 by the Government of India.
Abstract: IT may occasion some surprise to those men of science who are ill-acquainted with India, and who so frequently express the view that Governments are unappreciative of the importance of science to learn that as far back as 1886 the Government of India arranged for Dr. George (later Sir George) Watt, professor of botany in the Presidency College, Calcutta, to prepare a "Dictionary of the Economic Products of India". The six volumes of this standard work were published during the years 1889-99. In 1908 Sir George Watt published a condensed version, "The Commercial Products of India". Whatever the defects of these 'dictionaries', they have been of inestimable value to all interested in Indian natural products. The Wealth of India A Dictionary of Indian Raw Materials and Industrial Products. Raw Materials, Vol. 1. Pp. xxvii+254+39 plates. 15 rupees ; 24s. Industrial Products, Part 1. Pp. xii+182+8 plates. 8 rupees ; 12s. (New Delhi : Council of Scientific and Industrial Research, 1948.)

694 citations

Journal ArticleDOI
05 Oct 2017-Cell
TL;DR: It is demonstrated that CRISPR/Cas9 genome editing of promoters generates diverse cis-regulatory alleles that provide beneficial quantitative variation for breeding that provide a foundation for dissecting complex relationships between gene-reg regulatory changes and control of quantitative traits.

673 citations