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Littleford-Colquhoun B, Kartzinel TR. A CRISPR-based strategy for targeted sequencing in biodiversity science. Mol Ecol Resour 2024; 24:e13920. [PMID: 38153158 DOI: 10.1111/1755-0998.13920] [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: 07/03/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.
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Affiliation(s)
- Bethan Littleford-Colquhoun
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Tyler R Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
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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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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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Rieseberg L, Warschefsky E, Ortiz-Barrientos D, Kane NC, Thresher K, Sibbett B. Editorial 2023. Mol Ecol 2023; 32:1-25. [PMID: 36573261 DOI: 10.1111/mec.16815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/28/2022]
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