1
|
Díaz-Toribio MH, de-Nova JA, Piedra-Malagón EM, Angulo DF, Sosa V. Wild and cultivated comestible plant species in the Gulf of Mexico: phylogenetic patterns and convergence of type of use. AOB PLANTS 2023; 15:plad063. [PMID: 37899978 PMCID: PMC10601390 DOI: 10.1093/aobpla/plad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/28/2023] [Indexed: 10/31/2023]
Abstract
Cross-cultural research on edible plants might include ecological and evolutionary perspectives to understand processes behind species selection and management. With a database of approximately 500 comestible plants of the Province of the Gulf of Mexico in Mesoamerica, phylogenetic analyses are conducted to identify convergence and phylogenetic signal of type of use and significant clustering in the resulting phylogenetic trees. Analyses considered type of management (wild/managed vs. cultivated), type of use (edible, condiment, for wrapping food) and organ utilized. Elevated phylogenetic diversity and signal are expected for wild comestible taxa, indicating that people are using lineages across the angiosperm tree for food, resulting in broadness in diet and use of their regional resources. Main results are: (i) condiment species were identified in groups with an elevated phylogenetic signal; (ii) hot nodes for lineages utilized for wrapping food were found in many monocot groups as well as in epiphytes of cloud forests with leathery leaves; (iii) edible taxa were identified with the highest significant clustering restricted to certain branches in the phylogeny; (iv) wild and cultivated edible plants belong to identical lineages with replacement of species, implying that same plant groups known for their comestible benefits are substituted by species distributed in the Province and (v) wild versus cultivated lineages for condiment are different. Most food species in the Province belong to four families, namely Fabaceae, Cactaceae, Solanaceae and Asparagaceae. Analyses discovered underutilized wild species in identical clades to managed/cultivated taxa that can be studied further to identify cultivation practices. Results suggest that people are utilizing different lineages in the angiosperm tree available locally, for particular uses, like condiment or for wrapping food. Evidence can be used to study further undervalued edible species closely related to the most common food taxa as well as for bioprospection of their nutritional content.
Collapse
Affiliation(s)
- Milton H Díaz-Toribio
- Jardín Botánico Francisco Javier Clavijero, Instituto de Ecología AC, Carretera antigua a Coatepec 351, El Haya, 91073 Xalapa, Veracruz, Mexico
| | - J Arturo de-Nova
- Instituto de Investigación de Zonas Desérticas, Universidad Autónoma de San Luis Potosí, Altair 200, Colonia el Llano, 78377 San Luis Potosí, San Luis Potosí, Mexico
| | - Eva María Piedra-Malagón
- Jardín Botánico Francisco Javier Clavijero, Instituto de Ecología AC, Carretera antigua a Coatepec 351, El Haya, 91073 Xalapa, Veracruz, Mexico
| | - Diego F Angulo
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, Calle 43 no. 130, Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Victoria Sosa
- Biología Evolutiva, Instituto de Ecología AC, Mexico, Carretera antigua a Coatepec 351, El Haya, 91073 Xalapa, Veracruz, Mexico
| |
Collapse
|
2
|
Tao Y, Zhou XB, Yin BF, Dimeyeva L, Zhang J, Zang YX, Zhang YM. Combining Multiple Plant Attributes to Reveal Differences in Community Structure in Two Distant Deserts in Central Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:3286. [PMID: 37765450 PMCID: PMC10537988 DOI: 10.3390/plants12183286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
International interest is growing in biodiversity conservation and sustainable use in drylands. Desert ecosystems across arid Central Asia are severely affected by global change. Understanding the changes in a plant community is an essential prerequisite to revealing the community assembly mechanism, vegetation conservation, and management. The knowledge of large-scale spatial variation in plant community structure in different Central Asian deserts is still limited. In this study, we selected the Taukum (TD, Kazakhstan) and the Gurbantunggut (GD, China) deserts as the research area, with similar latitudes despite being nearly 1000 km apart. Thirteen and 15 sampling plots were set up and thoroughly investigated. The differences in community structure depending on multiple plant attributes (individual level: plant height, canopy diameter, and plant volume, and community level: plant density, total cover, and total volume) were systematically studied. TD had a better overall environmental status than GD. A total of 113 species were found, with 68 and 74 in TD and GD, respectively. The number of species and plant attributes was unequally distributed across different families and functional groups between deserts. The values of several plant attributes, such as ephemerals, annuals, dicotyledons, and shrubs with assimilative branches in GD, were significantly lower than those in TD. The Motyka indices of six plant attributes (26.18-38.61%) were higher between the two deserts than the species similarity index (20.4%), indicating a more robust convergence for plant functional attributes. The community structures in the two deserts represented by different plant attribute matrices demonstrated irregular differentiation patterns in ordination diagrams. The most variance in community structure was attributed to soil and climatic factors, while geographic factors had the smallest proportion. Consequently, the community structures of the two distant deserts were both different and similar to an extent. This resulted from the long-term impacts of heterogeneous environments within the same region. Our knowledge is further deepened by understanding the variation in community structure in different deserts on a large spatial scale. This therefore provides valuable insights into conserving regional biodiversity in Central Asia.
Collapse
Affiliation(s)
- Ye Tao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Xiao-Bing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Ben-Feng Yin
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Liliya Dimeyeva
- Institute of Botany and Phytointroduction, Ministry of Ecology and Natural Resources of the Republic of Kazakhstan, Almaty 050040, Kazakhstan;
| | - Jing Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Yong-Xin Zang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Yuan-Ming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| |
Collapse
|
3
|
Carins-Murphy MR, Cochard H, Deans RM, Gracie AJ, Brodribb TJ. Combined heat and water stress leads to local xylem failure and tissue damage in pyrethrum flowers. PLANT PHYSIOLOGY 2023; 193:356-370. [PMID: 37325893 PMCID: PMC10469517 DOI: 10.1093/plphys/kiad349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/17/2023]
Abstract
Flowers are critical for angiosperm reproduction and the production of food, fiber, and pharmaceuticals, yet for unknown reasons, they appear particularly sensitive to combined heat and drought stress. A possible explanation for this may be the co-occurrence of leaky cuticles in flower petals and a vascular system that has a low capacity to supply water and is prone to failure under water stress. These characteristics may render reproductive structures more susceptible than leaves to runaway cavitation-an uncontrolled feedback cycle between rising water stress and declining water transport efficiency that can rapidly lead to lethal tissue desiccation. We provide modeling and empirical evidence to demonstrate that flower damage in the perennial crop pyrethrum (Tanacetum cinerariifolium), in the form of irreversible desiccation, corresponds with runaway cavitation in the flowering stem after a combination of heat and water stress. We show that tissue damage is linked to greater evaporative demand during high temperatures rather than direct thermal stress. High floral transpiration dramatically reduced the soil water deficit at which runaway cavitation was triggered in pyrethrum flowering stems. Identifying runaway cavitation as a mechanism leading to heat damage and reproductive losses in pyrethrum provides different avenues for process-based modeling to understand the impact of climate change on cultivated and natural plant systems. This framework allows future investigation of the relative susceptibility of diverse plant species to reproductive failure under hot and dry conditions.
Collapse
Affiliation(s)
- Madeline R Carins-Murphy
- School of Natural Sciences, Discipline of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Hervé Cochard
- INRAE, PIAF, Université Clermont-Auvergne, Clermont-Ferrand 63000, France
| | - Ross M Deans
- Department of Viticulture & Enology, University of California, Davis, California 95616, USA
| | - Alistair J Gracie
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Timothy J Brodribb
- School of Natural Sciences, Discipline of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| |
Collapse
|
4
|
Petrone BL, Aqeel A, Jiang S, Durand HK, Dallow EP, McCann JR, Dressman HK, Hu Z, Tenekjian CB, Yancy WS, Lin PH, Scialla JJ, Seed PC, Rawls JF, Armstrong SC, Stevens J, David LA. Diversity of plant DNA in stool is linked to dietary quality, age, and household income. Proc Natl Acad Sci U S A 2023; 120:e2304441120. [PMID: 37368926 PMCID: PMC10319039 DOI: 10.1073/pnas.2304441120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/10/2023] [Indexed: 06/29/2023] Open
Abstract
Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (ρ = 0.40 to 0.63). In adolescents unable to collect validated dietary survey data, trnL metabarcoding detected 111 plant taxa, with 86 consumed by more than one individual and four (wheat, chocolate, corn, and potato family) consumed by >70% of individuals. Adolescent pMR was associated with age and household income, replicating prior epidemiologic findings. Overall, trnL metabarcoding promises an objective and accurate measure of the number and types of plants consumed that is applicable to diverse human populations.
Collapse
Affiliation(s)
- Brianna L. Petrone
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC27710
| | - Ammara Aqeel
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Heather K. Durand
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Eric P. Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Holly K. Dressman
- Duke Microbiome Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC27710
| | - Zhengzheng Hu
- Duke Microbiome Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC27710
| | | | - William S. Yancy
- Duke Lifestyle and Weight Management Center, Durham, NC27710
- Department of Medicine, Duke University School of Medicine, Durham, NC27710
| | - Pao-Hwa Lin
- Department of Medicine, Nephrology Division, Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC27705
| | - Julia J. Scialla
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA22903
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA22903
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL60611
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC27710
| | - Sarah C. Armstrong
- Department of Pediatrics, Duke University School of Medicine, Durham, NC27710
| | - June Stevens
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Lawrence A. David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC27710
| |
Collapse
|
5
|
Schlegelmilch K, Wertz AE. Visual segmentation of complex naturalistic structures in an infant eye-tracking search task. PLoS One 2022; 17:e0266158. [PMID: 35363809 PMCID: PMC8975119 DOI: 10.1371/journal.pone.0266158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2022] [Indexed: 11/24/2022] Open
Abstract
An infant’s everyday visual environment is composed of a complex array of entities, some of which are well integrated into their surroundings. Although infants are already sensitive to some categories in their first year of life, it is not clear which visual information supports their detection of meaningful elements within naturalistic scenes. Here we investigated the impact of image characteristics on 8-month-olds’ search performance using a gaze contingent eye-tracking search task. Infants had to detect a target patch on a background image. The stimuli consisted of images taken from three categories: vegetation, non-living natural elements (e.g., stones), and manmade artifacts, for which we also assessed target background differences in lower- and higher-level visual properties. Our results showed that larger target-background differences in the statistical properties scaling invariance and entropy, and also stimulus backgrounds including low pictorial depth, predicted better detection performance. Furthermore, category membership only affected search performance if supported by luminance contrast. Data from an adult comparison group also indicated that infants’ search performance relied more on lower-order visual properties than adults. Taken together, these results suggest that infants use a combination of property- and category-related information to parse complex visual stimuli.
Collapse
Affiliation(s)
- Karola Schlegelmilch
- Max Planck Research Group Naturalistic Social Cognition, Max Planck Institute for Human Development, Berlin, Germany
- * E-mail:
| | - Annie E. Wertz
- Max Planck Research Group Naturalistic Social Cognition, Max Planck Institute for Human Development, Berlin, Germany
| |
Collapse
|
6
|
Cantwell-Jones A, Ball J, Collar D, Diazgranados M, Douglas R, Forest F, Hawkins J, Howes MJR, Ulian T, Vaitla B, Pironon S. Global plant diversity as a reservoir of micronutrients for humanity. NATURE PLANTS 2022; 8:225-232. [PMID: 35210559 DOI: 10.1038/s41477-022-01100-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
With more than two billion people suffering from malnutrition and diets homogenizing globally, it is vital to identify and conserve nutrient-rich species that may contribute to improving food security and diversifying diets. Of the approximately 390,000 vascular plant species known to science, thousands have been reported to be edible, yet their nutritional content remains poorly characterized. Here we use phylogenetic information to identify plants with the greatest potential to support strategies alleviating B-vitamin deficiencies. We predict the B-vitamin profiles of >6,400 edible plants lacking nutritional data and identify 1,044 species as promising key sources of B vitamins. Several of these source species should become conservation priorities, as 63 (6%) are threatened in the wild and 272 (26%) are absent from seed banks. Moreover, many of these conservation-priority source species overlap with hotspots of malnutrition, highlighting the need for safeguarding strategies to ensure that edible plant diversity remains a reservoir of nutrition for future generations, particularly in countries needing it most. Although by no means a silver bullet to tackling malnutrition, conserving a diverse portfolio of edible plants, unravelling their nutritional potentials, and promoting their sustainable use are essential strategies to enhance global nutritional resilience.
Collapse
Affiliation(s)
- Aoife Cantwell-Jones
- Science and Solutions for a Changing Planet DTP, and the Department of Life Sciences, Imperial College London, Ascot, UK.
| | - Jenny Ball
- Royal Botanic Gardens, Richmond, Surrey, UK
| | - David Collar
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, USA
| | | | | | | | - Julie Hawkins
- School of Biological Sciences, University of Reading, Reading, Berkshire, UK
| | - Melanie-Jayne R Howes
- Royal Botanic Gardens, Richmond, Surrey, UK
- Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | | | - Bapu Vaitla
- Department of Nutrition, Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | | |
Collapse
|
7
|
Letelier L, Gaete-Eastman C, Peñailillo P, Moya-León MA, Herrera R. Southern Species From the Biodiversity Hotspot of Central Chile: A Source of Color, Aroma, and Metabolites for Global Agriculture and Food Industry in a Scenario of Climate Change. FRONTIERS IN PLANT SCIENCE 2020; 11:1002. [PMID: 32719706 PMCID: PMC7348657 DOI: 10.3389/fpls.2020.01002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/19/2020] [Indexed: 05/09/2023]
Abstract
Two interesting plants within the Chilean flora (wild and crop species) can be found with a history related to modern fruticulture: Fragaria chiloensis subsp. chiloensis (Rosaceae) and Vasconcellea pubescens (Caricaceae). Both species have a wide natural distribution, which goes from the Andes mountains to the sea (East-West), and from the Atacama desert to the South of Chile (North-South). The growing locations are included within the Chilean Winter Rainfall-Valdivian Forest hotspot. Global warming is of great concern as it increases the risk of losing wild plant species, but at the same time, gives a chance for usually longer term genetic improvement using naturally adapted material and the source for generating healthy foods. Modern agriculture intensifies the attractiveness of native undomesticated species as a way to provide compounds like antioxidants or tolerant plants for climate change scenario. F. chiloensis subsp. chiloensis as the mother of commercial strawberry (Fragaria × ananassa) is an interesting genetic source for the improvement of fruit flavor and stress tolerance. On the other hand, V. pubescens produces fruit with high level of antioxidants and proteolytic enzymes of interest to the food industry. The current review compiles the botanical, physiological and phytochemical description of F. chiloensis subsp. chiloensis and V. pubescens, highlighting their potential as functional foods and as source of compounds with several applications in the pharmaceutical, biotechnological, and food science. The impact of global warming scenario on the distribution of the species is also discussed.
Collapse
Affiliation(s)
- Luis Letelier
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Núcleo Científico Multidisciplinario, Dirección de Investigación, Universidad de Talca, Talca, Chile
| | - Carlos Gaete-Eastman
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Patricio Peñailillo
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - María A. Moya-León
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- *Correspondence: Raúl Herrera,
| |
Collapse
|
8
|
Abstract
Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool. Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to characterize diets, but such approaches have not previously been widely applied to humans. Here, we present data derived from sequencing of a chloroplast DNA marker (the P6 loop of the trnL [UAA] intron) in stool samples collected from 11 individuals consuming both controlled and freely selected diets. The DNA metabarcoding strategy resulted in successful PCR amplification in about 50% of samples, which increased to a 70% success rate in samples from individuals eating a controlled plant-rich diet. Detection of plant taxa among sequenced samples yielded a recall of 0.86 and a precision of 0.55 compared to a written diet record during controlled feeding of plant-based foods. The majority of sequenced plant DNA matched common human food plants, including grains, vegetables, fruits, and herbs prepared both cooked and uncooked. Moreover, DNA metabarcoding data were sufficient to distinguish between baseline and treatment diet arms of the study. Still, the relatively high PCR failure rate and an inability to distinguish some dietary plants at the sequence level using the trnL-P6 marker suggest that future methodological refinements are necessary. Overall, our results suggest that DNA metabarcoding provides a promising new method for tracking human plant intake and that similar approaches could be used to characterize the animal and fungal components of our omnivorous diets. IMPORTANCE Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.
Collapse
|
9
|
Amato KR, Mallott EK, McDonald D, Dominy NJ, Goldberg T, Lambert JE, Swedell L, Metcalf JL, Gomez A, Britton GAO, Stumpf RM, Leigh SR, Knight R. Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome Biol 2019; 20:201. [PMID: 31590679 PMCID: PMC6781418 DOI: 10.1186/s13059-019-1807-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/29/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates. RESULTS Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates. CONCLUSIONS Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.
Collapse
Affiliation(s)
- Katherine R. Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208 USA
| | - Elizabeth K. Mallott
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208 USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, 92093 USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, 92093 USA
| | | | - Tony Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706 USA
| | - Joanna E. Lambert
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, 80302 USA
| | - Larissa Swedell
- Department of Anthropology, City University of New York - Queens College, New York, 11367 USA
| | - Jessica L. Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, 80521 USA
| | - Andres Gomez
- Department of Animal Sciences, University of Minnesota, Minneapolis, 55108 USA
| | | | - Rebecca M. Stumpf
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, 61801 USA
| | - Steven R. Leigh
- Department of Anthropology, University of Colorado Boulder, Boulder, 80302 USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, 92093 USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, 92093 USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, 92093 USA
- Department of Bioengineering, University of California San Diego, San Diego, 92093 USA
| |
Collapse
|
10
|
Wild Plants Potentially Used in Human Food in the Protected Area "Sierra Grande de Hornachos" of Extremadura (Spain). SUSTAINABILITY 2019. [DOI: 10.3390/su11020456] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Natura 2000 is a network of protected spaces where the use of natural resources is regulated through the Habitat Directive of the European Union. It is essential for the conservation of biodiversity in Europe, but its social perception must be improved. We present this work as a demonstration case of the potentialities of one of these protected areas in the southwest (SW) Iberian Peninsula. We show an overview of the catalog of native wild plants of the place, which have nutritional and edible properties, having been used in human food by the peasant local population over the last century, and whose consumption trend is being implemented in Europe mainly through the haute cuisine and ecotourism sectors. What is offered here is a study of the case of what kind of positive contribution systematized botanical or ethnobotanical scientific knowledge can make toward encouraging innovative and sustainable rural development initiatives. A total of 145 wild plants that are potentially useful for leading tourism and consumers toward haute cuisine, new gastronomy, enviromentally-friendly recipes, and Natura 2000 Conservation are retrieved. The methodology used for our proposal is based on recent proposals of food product development and Basque Culinary Center initiatives.
Collapse
|
11
|
Zhang H, Li Y, Zhu JK. Developing naturally stress-resistant crops for a sustainable agriculture. NATURE PLANTS 2018; 4:989-996. [PMID: 30478360 DOI: 10.1038/s41477-018-0309-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 10/17/2018] [Indexed: 05/19/2023]
Abstract
A major problem facing humanity is that our numbers are growing but the availability of land and fresh water for agriculture is not. This problem is being exacerbated by climate change-induced increases in drought, and other abiotic stresses. Stress-resistant crops are needed to ensure yield stability under stress conditions and to minimize the environmental impacts of crop production. Evolution has created thousands of species of naturally stress-resistant plants (NSRPs), some of which have already been subjected to human domestication and are considered minor crops. Broader cultivation of these minor crops will diversify plant agriculture and the human diet, and will therefore help improve global food security and human health. More research should be directed toward understanding and utilizing NSRPs. Technologies are now available that will enable researchers to rapidly improve the genetics of NSRPs, with the goal of increasing NSRP productivity while retaining NSRP stress resistance and nutritional value.
Collapse
Affiliation(s)
- Heng Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Yuanyuan Li
- Key Laboratory of Plant Stress Research, Shandong Normal University, Jinan, Shandong, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
12
|
Larkin DJ, Jacobi SK, Hipp AL, Kramer AT. Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species. PLoS One 2016; 11:e0156973. [PMID: 27257671 PMCID: PMC4892560 DOI: 10.1371/journal.pone.0156973] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P < 0.001), i.e., collections comprised less phylogenetic diversity than would be expected had species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the ‘PIECES’ index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet-based decision support tool for North American angiosperms is provided; this tool can be customized to align with different conservation objectives.
Collapse
Affiliation(s)
- Daniel J. Larkin
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, Illinois, United States of America
- * E-mail:
| | - Sarah K. Jacobi
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, Illinois, United States of America
| | - Andrew L. Hipp
- Herbarium, The Morton Arboretum, Lisle, Illinois, United States of America
- Department of Botany, The Field Museum, Chicago, Illinois, United States of America
| | - Andrea T. Kramer
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, Illinois, United States of America
| |
Collapse
|
13
|
Desneux N, Blahnik R, Delebecque CJ, Heimpel GE. Host phylogeny and specialisation in parasitoids. Ecol Lett 2012; 15:453-60. [PMID: 22404869 DOI: 10.1111/j.1461-0248.2012.01754.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The host range of insect parasitoids and herbivores is influenced by both preference-related traits which mediate host choice behaviour, and performance-related traits which mediate the physiological suitability of the consumer-resource interaction. In a previous study, we characterised the influence of preference- and performance-related traits on the host range of the aphid parasitoid Binodoxys communis (Hymenoptera: Braconidae) and herein we build upon those data sets by mapping a series of these traits onto the phylogeny of the (aphid) host species. We found a strong effect of host phylogeny on overall parasitoid reproduction on the 20 host species tested, but no effect of the phylogeny of host plants of the aphids. We found an effect of aphid phylogeny on host acceptance and sting rates (related to preference) from behavioural observations and for pupal survivorship (related to performance), showing that both classes of traits show phylogenetic conservatism with respect to host species.
Collapse
Affiliation(s)
- Nicolas Desneux
- Department of Entomology, University of Minnesota, 1980 Folwell Ave, St. Paul, MN 55108, USA
| | | | | | | |
Collapse
|
14
|
Saslis-Lagoudakis CH, Klitgaard BB, Forest F, Francis L, Savolainen V, Williamson EM, Hawkins JA. The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae). PLoS One 2011; 6:e22275. [PMID: 21789247 PMCID: PMC3138776 DOI: 10.1371/journal.pone.0022275] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 06/17/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce. METHODOLOGY/PRINCIPAL FINDINGS In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships. CONCLUSIONS/SIGNIFICANCE This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds.
Collapse
|
15
|
Stohlgren TJ, Pyšek P, Kartesz J, Nishino M, Pauchard A, Winter M, Pino J, Richardson DM, Wilson JRU, Murray BR, Phillips ML, Ming-yang L, Celesti-Grapow L, Font X. Widespread plant species: natives versus aliens in our changing world. Biol Invasions 2011. [DOI: 10.1007/s10530-011-0024-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
16
|
Abstract
European Paleolithic subsistence is assumed to have been largely based on animal protein and fat, whereas evidence for plant consumption is rare. We present evidence of starch grains from various wild plants on the surfaces of grinding tools at the sites of Bilancino II (Italy), Kostenki 16-Uglyanka (Russia), and Pavlov VI (Czech Republic). The samples originate from a variety of geographical and environmental contexts, ranging from northeastern Europe to the central Mediterranean, and dated to the Mid-Upper Paleolithic (Gravettian and Gorodtsovian). The three sites suggest that vegetal food processing, and possibly the production of flour, was a common practice, widespread across Europe from at least ~30,000 y ago. It is likely that high energy content plant foods were available and were used as components of the food economy of these mobile hunter-gatherers.
Collapse
|