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Bangay G, Brauning FZ, Rosatella A, Díaz-Lanza AM, Domínguez-Martín EM, Goncalves B, Hussein AA, Efferth T, Rijo P. Anticancer diterpenes of African natural products: Mechanistic pathways and preclinical developments. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155634. [PMID: 38718637 DOI: 10.1016/j.phymed.2024.155634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/07/2024] [Accepted: 04/11/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND The African continent is home to five biodiversity hotspots, boasting an immense wealth of medicinal flora, fungi and marine life. Diterpenes extracted from such natural products have compelling cytotoxic activities that warrant further exploration for the drug market, particularly in cancer therapy, where mortality rates remain elevated worldwide. PURPOSE To demonstrate the potential of African natural products on the global stage for cancer therapy development and provide an in-depth analysis of the current literature on the activity of cancer cytotoxic diterpenes from African natural sources (to our knowledge, the first of its kind); not only to reveal the most promising candidates for clinical development, but to demonstrate the importance of preserving the threatened ecosystems of Africa. METHODS A comprehensive search by means of the PRISMA strategy was conducted using electronic databases, namely Web of Science, PubMed, Google Scholar and ScienceDirect. The search terms employed were 'diterpene & mechanism & cancer' and 'diterpene & clinical & cancer'. The selection process involved assessing titles in English, Portuguese and Spanish, adhering to predefined eligibility criteria. The timeframe for inclusion spanned from 2010 to 2023, resulting in 218 relevant papers. Chemical structures were visualized using ChemDraw 21.0, PubChem was utilized to search for CID numbers. RESULTS Despite being one of the richest biodiverse zones in the world, African natural products are proportionally underreported compared to Asian countries or otherwise. The diterpenes andrographolide (Andrographis paniculata), forskolin (Coleus forskohlii), ent-kauranes from Isodon spp., euphosorophane A (Euphorbia sororia), cafestol & kahweol (Coffea spp.), macrocylic jolkinol D derivatives (Euphorbia piscatoria) and cyathane erinacine A (Hericium erinaceus) illustrated the most encouraging data for further cancer therapy exploration and development. CONCLUSIONS Diterpenes from African natural products have the potential to be economically significant active pharmaceutical and medicinal ingredients, specifically focussed on anticancer therapeutics.
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Affiliation(s)
- Gabrielle Bangay
- Center for Research in Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; Universidad de Alcalá de Henares. Facultad de Farmacia, Departamento de Ciencias Biomédicas (Área de Farmacología; Nuevos agentes antitumorales, Acción tóxica sobre células leucémicas). Ctra. Madrid-Barcelona km. 33,600 28805 Alcalá de Henares, Madrid, España
| | - Florencia Z Brauning
- Center for Research in Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Andreia Rosatella
- Center for Research in Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Ana María Díaz-Lanza
- Universidad de Alcalá de Henares. Facultad de Farmacia, Departamento de Ciencias Biomédicas (Área de Farmacología; Nuevos agentes antitumorales, Acción tóxica sobre células leucémicas). Ctra. Madrid-Barcelona km. 33,600 28805 Alcalá de Henares, Madrid, España
| | - Eva María Domínguez-Martín
- Center for Research in Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; Universidad de Alcalá de Henares. Facultad de Farmacia, Departamento de Ciencias Biomédicas (Área de Farmacología; Nuevos agentes antitumorales, Acción tóxica sobre células leucémicas). Ctra. Madrid-Barcelona km. 33,600 28805 Alcalá de Henares, Madrid, España
| | - Bruno Goncalves
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Ahmed A Hussein
- Chemistry Department, Cape Peninsula University of Technology, Symphony Rd., Bellville 7535, South Africa
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Patricia Rijo
- Center for Research in Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
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Granweiler J, Cristóbal-Azkarate J, Morton N, Palme R, Shultz S. The paradox of spring: Thyroid and glucocorticoid responses to cold temperatures and food availability in free living Carneddau ponies. Horm Behav 2024; 161:105526. [PMID: 38503098 DOI: 10.1016/j.yhbeh.2024.105526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
In seasonal environments, maintaining a constant body temperature poses challenges for endotherms. Cold winters at high latitudes, with limited food availability, create opposing demands on metabolism: upregulation preserves body temperature but depletes energy reserves. Examining endocrine profiles, such as thyroid hormone triiodothyronine (T3) and glucocorticoids (GCs), proxies for changes in metabolic rate and acute stressors, offer insights into physiological trade-offs. We evaluated how environmental conditions and gestation impact on faecal hormone metabolites (fT3Ms and fGCMs) from late winter to spring in a free-living population of Carneddau ponies. Faecal T3Ms were highest in late February and March, when temperatures were lowest. Then, fT3Ms concentrations decreased throughout April and were at the lowest in May before increasing towards the end of the study. The decline in fT3M levels in April and May was associated with warmer weather but poor food availability, diet diversity and diet composition. On the other hand, fGCM levels did not display a clear temporal pattern but were associated with reproductive status, where pregnant and lactating females had higher fGCM levels as compared to adult males and non-reproductive females. The temporal profile of fT3Ms levels highlights metabolic trade-offs in a changing environment. In contrast, the ephemeral but synchronous increase in fGCM concentrations across the population suggest a shared experience of acute stressors (i.e., weather, disturbance or social). This multi-biomarker approach can evaluate the role of acute stressors versus energy budgets in the context of interventions, reproduction, seasonality and environmental change, or across multiple scales from individuals to populations.
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Affiliation(s)
- Jessica Granweiler
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, UK.
| | - Jurgi Cristóbal-Azkarate
- Department of Basic Psychological Processes and their Development, Faculty of Psychology, University of the Basque Country, Donostia, Spain
| | - Nathan Morton
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Rupert Palme
- Unit of Physiology, Pathophysiology and Experimental Endocrinology, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Susanne Shultz
- School of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
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3
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Harvey Sky N, Britnell J, Antwis R, Kartzinel T, Rubenstein D, Toye P, Karani B, Njeru R, Hinchcliffe D, Gaymer J, Mutisya S, Shultz S. Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. Commun Biol 2024; 7:333. [PMID: 38491117 PMCID: PMC10943211 DOI: 10.1038/s42003-024-05983-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy's zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy's zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation.
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Affiliation(s)
- Nick Harvey Sky
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK.
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, CH2 1LH, UK.
| | - Jake Britnell
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, CH2 1LH, UK
| | - Rachael Antwis
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WX, UK
| | - Tyler Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, 85 Waterman Street, Providence, RI, 02912, USA
- Institute at Brown for Environment and Society, Brown University, 85 Waterman Street, Providence, RI, 02912, USA
| | - Daniel Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544-2016, USA
| | - Phil Toye
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Benedict Karani
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Regina Njeru
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Danielle Hinchcliffe
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | | | | | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK
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Anderson TM, Hepler SA, Holdo RM, Donaldson JE, Erhardt RJ, Hopcraft JGC, Hutchinson MC, Huebner SE, Morrison TA, Muday J, Munuo IN, Palmer MS, Pansu J, Pringle RM, Sketch R, Packer C. Interplay of competition and facilitation in grazing succession by migrant Serengeti herbivores. Science 2024; 383:782-788. [PMID: 38359113 DOI: 10.1126/science.adg0744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Competition, facilitation, and predation offer alternative explanations for successional patterns of migratory herbivores. However, these interactions are difficult to measure, leaving uncertainty about the mechanisms underlying body-size-dependent grazing-and even whether succession occurs at all. We used data from an 8-year camera-trap survey, GPS-collared herbivores, and fecal DNA metabarcoding to analyze the timing, arrival order, and interactions among migratory grazers in Serengeti National Park. Temporal grazing succession is characterized by a "push-pull" dynamic: Competitive grazing nudges zebra ahead of co-migrating wildebeest, whereas grass consumption by these large-bodied migrants attracts trailing, small-bodied gazelle that benefit from facilitation. "Natural experiments" involving intense wildfires and rainfall respectively disrupted and strengthened these effects. Our results highlight a balance between facilitative and competitive forces in co-regulating large-scale ungulate migrations.
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Affiliation(s)
- T Michael Anderson
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Staci A Hepler
- Department of Statistical Sciences, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Ricardo M Holdo
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Jason E Donaldson
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Robert J Erhardt
- Department of Statistical Sciences, Wake Forest University, Winston-Salem, NC 27109, USA
| | - J Grant C Hopcraft
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Matthew C Hutchinson
- Department of Life & Environmental Sciences, University of California Merced, Merced, CA 95343, USA
| | - Sarah E Huebner
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Thomas A Morrison
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Jeffry Muday
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Issack N Munuo
- Serengeti Wildlife Research Centre, 2113 Lemara, Arusha, TZ
| | - Meredith S Palmer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Johan Pansu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert Sketch
- Department of Statistical Sciences, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Craig Packer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
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Britnell JA, Kerley GIH, Antwis R, Shultz S. A grazer's niche edge is associated with increasing diet diversity and poor population performance. Ecol Lett 2024; 27:e14357. [PMID: 38193626 DOI: 10.1111/ele.14357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024]
Abstract
The core-periphery hypothesis predicts niche cores should be associated with greater survivorship, reproductive output and population performance rates than marginal habitats at niche edges. However, there is very little empirical evidence of whether niche centrality influences population trends in animals. Using the Cape mountain zebra (Equus zebra zebra) as a model system, we evaluated whether niche centrality is associated with population trends, resource availability and diet across a core-periphery gradient. Population growth rates and density progressively declined towards niche peripheries. Niche peripheries were resource-poor and Cape mountain zebra consumed more phylogenetically diverse diets dominated by non-grass families. In core habitats they consumed grass-rich diets and female reproductive success was higher. This combination of spatial niche modelling and functional ecology provides a novel evaluation of how bottom-up resource limitation can shape species distributions, population resilience and range change and can guide conservation management.
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Affiliation(s)
- J A Britnell
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
- North of England Zoological Society (Chester Zoo), Upton-by-Chester, UK
| | - G I H Kerley
- Centre for African Conservation Ecology, Nelson Mandela University, Gqeberha, South Africa
| | | | - S Shultz
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
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Jin L, Shi HY, Li T, Zhao N, Xu Y, Xiao TW, Song F, Ma CX, Li QM, Lin LX, Shao XN, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Du H, Ge XJ. A DNA barcode library for woody plants in tropical and subtropical China. Sci Data 2023; 10:819. [PMID: 37993453 PMCID: PMC10665436 DOI: 10.1038/s41597-023-02742-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.
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Affiliation(s)
- Lu Jin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hao-You Shi
- Central South Academy of Inventory and Planning of NFGA, Changsha, 410014, China
| | - Ting Li
- Yiyang Forestry Bureau, Yiyang, 413000, China
| | - Nan Zhao
- Hunan Police Academy, Changsha, 410138, China
| | - Yong Xu
- Conghua Middle School, Guangzhou, 510900, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Feng Song
- College of Forestry, Central South University of Forestry & Technology, Changsha, 410004, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ju-Yu Lian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hu Du
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
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Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Gill BA, Wittemyer G, Cerling TE, Musili PM, Kartzinel TR. Foraging history of individual elephants using DNA metabarcoding. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230337. [PMID: 37416829 PMCID: PMC10320352 DOI: 10.1098/rsos.230337] [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: 03/18/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Individual animals should adjust diets according to food availability. We used DNA metabarcoding to construct individual-level dietary timeseries for elephants from two family groups in Kenya varying in habitat use, social position and reproductive status. We detected at least 367 dietary plant taxa, with up to 137 unique plant sequences in one fecal sample. Results matched well-established trends: elephants tended to eat more grass when it rained and other plants when dry. Nested within these switches from 'grazing' to 'browsing' strategies, dietary DNA revealed seasonal shifts in food richness, composition and overlap between individuals. Elephants of both families converged on relatively cohesive diets in dry seasons but varied in their maintenance of cohesion during wet seasons. Dietary cohesion throughout the timeseries of the subdominant 'Artists' family was stronger and more consistently positive compared to the dominant 'Royals' family. The greater degree of individuality within the dominant family's timeseries could reflect more divergent nutritional requirements associated with calf dependency and/or priority access to preferred habitats. Whereas theory predicts that individuals should specialize on different foods under resource scarcity, our data suggest family bonds may promote cohesion and foster the emergence of diverse feeding cultures reflecting links between social behaviour and nutrition.
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Affiliation(s)
- Brian A. Gill
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA
| | - George Wittemyer
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
- Save the Elephants, Nairobi, Kenya
| | - Thure E. Cerling
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Paul M. Musili
- Botany Department, East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Tyler R. Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA
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Chen S, Yin X, Han J, Sun W, Yao H, Song J, Li X. DNA barcoding in herbal medicine: Retrospective and prospective. J Pharm Anal 2023; 13:431-441. [PMID: 37305789 PMCID: PMC10257146 DOI: 10.1016/j.jpha.2023.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 06/13/2023] Open
Abstract
DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.
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Affiliation(s)
- Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xianmei Yin
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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Christophoryová J, Krajčovičová K, Šťáhlavský F, Španiel S, Opatova V. Integrative Taxonomy Approach Reveals Cryptic Diversity within the Phoretic Pseudoscorpion Genus Lamprochernes (Pseudoscorpiones: Chernetidae). INSECTS 2023; 14:122. [PMID: 36835691 PMCID: PMC9964657 DOI: 10.3390/insects14020122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Pseudoscorpions represent an ancient, but homogeneous group of arachnids. The genus Lamprochernes comprises several morphologically similar species with wide and overlapping distributions. We implemented an integrative approach combining molecular barcoding (cox1), with cytogenetic and morphological analyses in order to assess species boundaries in European Lamprochernes populations. The results suggest ancient origins of Lamprochernes species accompanied by morphological stasis within the genus. Our integrative approach delimited three nominal Lamprochernes species and one cryptic lineage Lamprochernes abditus sp. nov. Despite its Oligocene origin, L. abditus sp. nov. can be distinguished from its closest relative only by molecular and cytogenetic differences, or alternatively, by a complex multivariate morphometric analysis involving other Lamprochernes species. The population structure and common haplotype sharing across geographically distant populations in most Lamprochernes species suggest that a phoretic manner of dispersal is efficient in this group.
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Affiliation(s)
- Jana Christophoryová
- Department of Zoology, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Katarína Krajčovičová
- Department of Zoology, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 23 Bratislava, Slovakia
| | - Vera Opatova
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
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11
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Botha D, du Plessis M, Siebert F, Barnard S. Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions. PLoS One 2023; 18:e0286144. [PMID: 37205700 DOI: 10.1371/journal.pone.0286144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.
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Affiliation(s)
- Danielle Botha
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mornè du Plessis
- Core Sequencing Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Frances Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Sandra Barnard
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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12
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The generality of cryptic dietary niche differences in diverse large-herbivore assemblages. Proc Natl Acad Sci U S A 2022; 119:e2204400119. [PMID: 35994662 PMCID: PMC9436339 DOI: 10.1073/pnas.2204400119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families-grasses and legumes-accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.
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13
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Harvey Sky N, Jackson J, Chege G, Gaymer J, Kimiti D, Mutisya S, Nakito S, Shultz S. Female reproductive skew exacerbates the extinction risk from poaching in the eastern black rhino. Proc Biol Sci 2022; 289:20220075. [PMID: 35414243 PMCID: PMC9006021 DOI: 10.1098/rspb.2022.0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Variation in individual demographic rates can have large consequences for populations. Female reproductive skew is an example of structured demographic heterogeneity where females have intrinsic qualities that make them more or less likely to breed. The consequences of reproductive skew for population dynamics are poorly understood in non-cooperatively breeding mammals, especially when coupled with other drivers such as poaching. We address this knowledge gap with population viability analyses using an age-specific, female-only, individual-based, stochastic population model built with long-term data for three Kenyan populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli). There was substantial reproductive skew, with a high proportion of females not breeding or doing so at very low rates. This had a large impact on the projected population growth rate for the smaller population on Ol Jogi. Moreover, including female reproductive skew exacerbates the effects of poaching, increasing the probability of extinction by approximately 70% under a simulated poaching pressure of 5% offtake per year. Tackling the effects of reproductive skew depends on whether it is mediated by habitat or social factors, with potential strategies including habitat and biological management respectively. Investigating and tackling reproductive skew in other species requires long-term, individual-level data collection.
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Affiliation(s)
- Nick Harvey Sky
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK.,North of England Zoological Society, Chester Zoo, Caughall Road, Chester CH2 1LH, UK
| | - John Jackson
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Geoffrey Chege
- Lewa Wildlife Conservancy, PO Box, Private Bag, Isiolo 60300, Kenya
| | | | - David Kimiti
- Grevy's Zebra Trust, PO Box 15351-00509, Nairobi, Kenya
| | | | - Simon Nakito
- Ol Pejeta Conservancy, PO Box 167, Nanyuki, Kenya
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
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14
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Hu JL, Ci XQ, Liu ZF, Dormontt EE, Conran JG, Lowe AJ, Li J. Assessing candidate DNA barcodes for Chinese and internationally traded timber species. Mol Ecol Resour 2021; 22:1478-1492. [PMID: 34752673 DOI: 10.1111/1755-0998.13546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.
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Affiliation(s)
- Jian-Lin Hu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Eleanor E Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and Sprigg Geobiology Centre (SGC), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew J Lowe
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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15
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Large herbivores suppress liana infestation in an African savanna. Proc Natl Acad Sci U S A 2021; 118:2101676118. [PMID: 34580170 DOI: 10.1073/pnas.2101676118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
African savannas are the last stronghold of diverse large-mammal communities, and a major focus of savanna ecology is to understand how these animals affect the relative abundance of trees and grasses. However, savannas support diverse plant life-forms, and human-induced changes in large-herbivore assemblages-declining wildlife populations and their displacement by livestock-may cause unexpected shifts in plant community composition. We investigated how herbivory affects the prevalence of lianas (woody vines) and their impact on trees in an East African savanna. Although scarce (<2% of tree canopy area) and defended by toxic latex, the dominant liana, Cynanchum viminale (Apocynaceae), was eaten by 15 wild large-herbivore species and was consumed in bulk by native browsers during experimental cafeteria trials. In contrast, domesticated ungulates rarely ate lianas. When we experimentally excluded all large herbivores for periods of 8 to 17 y (simulating extirpation), liana abundance increased dramatically, with up to 75% of trees infested. Piecewise exclusion of different-sized herbivores revealed functional complementarity among size classes in suppressing lianas. Liana infestation reduced tree growth and reproduction, but herbivores quickly cleared lianas from trees after the removal of 18-y-old exclosure fences (simulating rewilding). A simple model of liana contagion showed that, without herbivores, the long-term equilibrium could be either endemic (liana-tree coexistence) or an all-liana alternative stable state. We conclude that ongoing declines of wild large-herbivore populations will disrupt the structure and functioning of many African savannas in ways that have received little attention and that may not be mitigated by replacing wildlife with livestock.
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16
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Kolter A, Gemeinholzer B. Internal transcribed spacer primer evaluation for vascular plant metabarcoding. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.
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17
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Large herbivores transform plant-pollinator networks in an African savanna. Curr Biol 2021; 31:2964-2971.e5. [PMID: 34004144 DOI: 10.1016/j.cub.2021.04.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022]
Abstract
Pollination by animals is a key ecosystem service1,2 and interactions between plants and their pollinators are a model system for studying ecological networks,3,4 yet plant-pollinator networks are typically studied in isolation from the broader ecosystems in which they are embedded. The plants visited by pollinators also interact with other consumer guilds that eat stems, leaves, fruits, or seeds. One such guild, large mammalian herbivores, are well-known ecosystem engineers5-7 and may have substantial impacts on plant-pollinator networks. Although moderate herbivory can sometimes promote plant diversity,8 potentially benefiting pollinators, large herbivores might alternatively reduce resource availability for pollinators by consuming flowers,9 reducing plant density,10 and promoting somatic regrowth over reproduction.11 The direction and magnitude of such effects may hinge on abiotic context-in particular, rainfall, which modulates the effects of ungulates on vegetation.12 Using a long-term, large-scale experiment replicated across a rainfall gradient in central Kenya, we show that a diverse assemblage of native large herbivores, ranging from 5-kg antelopes to 4,000-kg African elephants, limited resource availability for pollinators by reducing flower abundance and diversity; this in turn resulted in fewer pollinator visits and lower pollinator diversity. Exclusion of large herbivores increased floral-resource abundance and pollinator-assemblage diversity, rendering plant-pollinator networks larger, more functionally redundant, and less vulnerable to pollinator extinction. Our results show that species extrinsic to plant-pollinator interactions can indirectly and strongly alter network structure. Forecasting the effects of environmental change on pollination services and interaction webs more broadly will require accounting for the effects of extrinsic keystone species.
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18
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Jones L, Twyford AD, Ford CR, Rich TCG, Davies H, Forrest LL, Hart ML, McHaffie H, Brown MR, Hollingsworth PM, de Vere N. Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom. Mol Ecol Resour 2021; 21:2050-2062. [PMID: 33749162 DOI: 10.1111/1755-0998.13388] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/09/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding and metabarcoding provide new avenues for investigating biological systems. These techniques require well-curated reference libraries with extensive coverage. Generating an exhaustive national DNA barcode reference library can open up new avenues of research in ecology, evolution and conservation, yet few studies to date have created such a resource. In plant DNA barcoding, herbarium collections provide taxonomically robust material but also pose challenges in lab processing. Here, we present a national DNA barcoding resource covering all of the native flowering plants and conifers of the United Kingdom. This represents 1,482 plant species, with the majority of specimens (81%) sourced from herbaria. Using Sanger sequencing of the plant DNA barcode markers, rbcL, matK, and ITS2, at least one DNA barcode was retrieved from 98% of the UK flora. We sampled from multiple individuals, resulting in a species coverage for rbcL of 96% (4,477 sequences), 90% for matK (3,259 sequences) and 75% for ITS2 (2,585 sequences). Sequence recovery was lower for herbarium material compared to fresh collections, with the age of the specimen having a significant effect on the success of sequence recovery. Species level discrimination was highest with ITS2, however, the ability to successfully retrieve a sequence was lowest for this region. Analyses of the genetic distinctiveness of species across a complete flora showed DNA barcoding to be informative for all but the most taxonomically complex groups. The UK flora DNA barcode reference library provides an important resource for many applications that require plant identification from DNA.
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Affiliation(s)
- Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Alex D Twyford
- Royal Botanic Garden Edinburgh, Edinburgh, UK.,School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | - Col R Ford
- National Botanic Garden of Wales, Llanarthne, UK
| | | | | | | | | | | | - Max R Brown
- School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | | | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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19
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Teske D, Peters A, Möllers A, Fischer M. Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14323-14333. [PMID: 32917087 DOI: 10.1021/acs.jafc.0c03001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.
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Affiliation(s)
- Doreen Teske
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alina Peters
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alexander Möllers
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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20
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Pringle RM, Hutchinson MC. Resolving Food-Web Structure. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024908] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Food webs are a major focus and organizing theme of ecology, but the data used to assemble them are deficient. Early debates over food-web data focused on taxonomic resolution and completeness, lack of which had produced spurious inferences. Recent data are widely believed to be much better and are used extensively in theoretical and meta-analytic research on network ecology. Confidence in these data rests on the assumptions ( a) that empiricists correctly identified consumers and their foods and ( b) that sampling methods were adequate to detect a near-comprehensive fraction of the trophic interactions between species. Abundant evidence indicates that these assumptions are often invalid, suggesting that most topological food-web data may remain unreliable for inferences about network structure and underlying ecological and evolutionary processes. Morphologically cryptic species are ubiquitous across taxa and regions, and many trophic interactions routinely evade detection by conventional methods. Molecular methods have diagnosed the severity of these problems and are a necessary part of the cure.
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Affiliation(s)
- Robert M. Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Matthew C. Hutchinson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
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21
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Kartzinel TR, Pringle RM. Multiple dimensions of dietary diversity in large mammalian herbivores. J Anim Ecol 2020; 89:1482-1496. [PMID: 32163591 DOI: 10.1111/1365-2656.13206] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/31/2020] [Indexed: 12/01/2022]
Abstract
Theory predicts that trophic specialization (i.e. low dietary diversity) should make consumer populations sensitive to environmental disturbances. Yet diagnosing specialization is complicated both by the difficulty of precisely quantifying diet composition and by definitional ambiguity: what makes a diet 'diverse'? We sought to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD) in a species-rich community of large mammalian herbivores in a semi-arid East African savanna. We hypothesized that TDD and PDD would be positively correlated within and among species, because taxonomically diverse diets are likely to include plants from many lineages. By using DNA metabarcoding to analyse 1,281 faecal samples collected across multiple seasons, we compiled high-resolution diet profiles for 25 sympatric large-herbivore species. For each of these populations, we calculated TDD and PDD with reference to a DNA reference library for local plants. Contrary to our hypothesis, measures of TDD and PDD were either uncorrelated or negatively correlated with each other. Thus, these metrics reflect distinct dimensions of dietary specialization both within and among species. In general, grazers and ruminants exhibited greater TDD, but lower PDD, than did browsers and non-ruminants. We found significant seasonal variation in TDD and/or PDD for all but four species (Grevy's zebra, buffalo, elephant, Grant's gazelle); however, the relationship between TDD and PDD was consistent across seasons for all but one of the 12 best-sampled species (plains zebra). Our results show that taxonomic generalists can be phylogenetic specialists, and vice versa. These two dimensions of dietary diversity suggest contrasting implications for efforts to predict how consumers will respond to climate change and other environmental perturbations. For example, populations with low TDD may be sensitive to phylogenetically 'random' losses of food species, whereas populations with low PDD may be comparatively more sensitive to environmental changes that disadvantage entire plant lineages-and populations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulnerable of all.
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Affiliation(s)
- Tyler R Kartzinel
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
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22
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Abstract
Diet and gut microbiome composition are important for health and nutrition in mammals, but how they covary in response to environmental change remains poorly understood—both because diet composition is rarely quantified precisely, and because studies of diet−microbiome linkages in captive animals may not accurately reflect the dynamics of natural communities. By analyzing diet−microbiome linkages in an assemblage of large mammalian herbivores in Kenya, we found that seasonal changes in diet and microbiome composition were strongly correlated within some populations, whereas other populations exhibited little temporal turnover in either diet or microbiome. Identifying mechanisms that generate species-specific variation in the sensitivity of the diet−microbiome nexus to environmental changes could help to explain differential population performance and food-web structure within ecological communities. A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of nonhuman microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples from an assemblage of 33 sympatric large-herbivore species (27 native, 6 domesticated) in a semiarid East African savanna, which enabled high-resolution assessment of seasonal variation in both diet and microbiome composition. Phylogenetic relatedness strongly predicted microbiome composition (r = 0.91) and was weakly but significantly correlated with diet composition (r = 0.20). Dietary diversity did not significantly predict microbiome diversity across species or within any species except kudu; however, diet composition was significantly correlated with microbiome composition both across and within most species. We found a spectrum of seasonal sensitivity at the diet−microbiome nexus: Seasonal changes in diet composition explained 25% of seasonal variation in microbiome composition across species. Species’ positions on (and deviations from) this spectrum were not obviously driven by phylogeny, body size, digestive strategy, or diet composition; however, domesticated species tended to exhibit greater diet−microbiome turnover than wildlife. Our results reveal marked differences in the influence of environment on the degree of diet−microbiome covariation in free-ranging African megafauna, and this variation is not well explained by canonical predictors of nutritional ecology.
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