Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Gill, Brian A.; Musili, Paul M.; Kurukura, Samson; Hassan, Abidikadir A.; Goheen, Jacob R.; Kress, W. John; Kuzmina, Maria; Pringle, Robert M.; Kartzinel, Tyler R.

doi:10.1111/1755-0998.13001

Cited by 37 publications

(57 citation statements)

References 80 publications

(102 reference statements)

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“…1). We identified 213 unique food-plant sequences from 54 plant families, out of at least 460 plant species from 66 families that are known to occur at this site (27). These food plants were utilized differently by herbivore species (Dataset S2).…”

Section: Resultsmentioning

confidence: 99%

“…B (7, 7) Lepus sp. A (11,11) Papio anubis (7,9) Oryx gazella (22,20) Alcelaphus buselaphus (27,13) Ovis aries (48, 24) Capra hircus (19,19) Aepyceros melampus (129, 25) Nanger granti (46,17) Litocranius walleri (10, 10) Sylvicapra grimmia (2,2) Kobus ellipsiprymnus (6,6) Madoqua guentheri (120, 21) Oreotragus oreotragus (13,12) Bos taurus (163,27) Syncerus caffer (92,20) Taurotragus oryx (54, 27) Tragelaphus strepsiceros (28,15) Tragelaphus scriptus (12,7) Giraffa camelopardalis (58, 29) Hippopotamus amphibius (23,18) Phacochoerus africanus (30,22) Camelus dromedarius (39,18) Ceratotherium simum (13,12) Diceros bicornis (18,18) Equus asinus (29,20) Equus burchellii (106, 19) Equus grevyi (91, 21) Equus caballus (6,6) Heterohyrax brucei (9,9) Procavia capensis…”

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confidence: 99%

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Covariation of diet and gut microbiome in African megafauna

Kartzinel

Hsing

Musili

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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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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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Covariation of diet and gut microbiome in African megafauna

Kartzinel

Hsing

Musili

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

176

226

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“…The resulting amplicons were sequenced on an Illumina HiSeq 2500. To identify food plants, we compared plant DNA sequences from faecal samples with reference DNA sequences from vouchered specimens (Gill et al, 2019; Kartzinel et al, 2015). In most cases, we either observed animals defecating or could identify species of origin based on dung size, shape, and consistency.…”

Section: Methodsmentioning

confidence: 99%

“…The local plant DNA library comprised 1,781 fertile vouchers (representing ~460 species from 66 families, nearly the entire local flora) collected in the study area from 2012 to 2018 (Gill et al, 2019). Specimen identifications were verified or refined by botanists (Dr. Paul Mutuku Musili and colleagues) at the East African Herbarium of the National Museums of Kenya, and with reference to five DNA markers: three standard plant DNA barcodes ( rbc L, mat K, and psb A‐ trn H), nuclear ITS, and the trn L sequences used as dietary markers (Gill et al, 2019; Kartzinel et al, 2015). Of the full‐length reference data evaluated by Gill et al (2019), trn L provided a higher degree of taxonomic resolution than did any other marker.…”

Section: Methodsmentioning

confidence: 99%

“…Using DNA metabarcoding (Taberlet et al, 2007), we generated diet profiles for 25 large‐herbivore species that co‐occur in a Kenyan savanna for which a plant DNA reference database and community phylogeny have been assembled (Gill et al, 2019). These 25 herbivore species spanned >3 orders of magnitude in body mass (2–4,000 kg), >50 million years of evolutionary history (five taxonomic orders), the entire grazer–browser spectrum, and distinct gut architectures (ruminant and non‐ruminant).…”

Section: Introductionmentioning

confidence: 99%

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Multiple dimensions of dietary diversity in large mammalian herbivores

Kartzinel

Pringle

2020

Journal of Animal Ecology

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1. 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'? 2. 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.3. By using DNA metabarcoding to analyse 1,281 faecal samples collected across multiple seasons, we compiled high-resolution diet profiles for 25 sympatric largeherbivore species. For each of these populations, we calculated TDD and PDD with reference to a DNA reference library for local plants.4. 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). 5.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. K E Y W O R D S community phylogenetics, food web networks, grazer-browser continuum, megafauna, niche partitioning, specialism-generalism trade-off, ungulate foraging ecology Additional supporting information may be found online in the Supporting Information section. How to cite this article: Kartzinel TR, Pringle RM. Multiple dimensions of dietary diversity in large mammalian herbivores.

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Development of an environmental DNA metabarcoding assay for aquatic vascular plant communities

2020

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Environmental DNA (eDNA) metabarcodes allow for the simultaneous detection of multiple taxa if the barcode regions meet several key requirements including conserved primer‐binding sites, interspecific variability that exceeds intraspecific variability, and relatively short amplicons. Currently, there are no established metabarcoding assays for aquatic vascular plants, which could limit biodiversity assessments and the early detection of alien species. We used a combination of novel and pre‐existing primers to generate eDNA metabarcodes from three gene regions that are commonly used for plant barcoding: two regions of chloroplast DNA (rbcL and matK) plus a segment of an internal transcribed spacer (ITS2). We optimized the assay on a mock community of 25 known species and then applied it to wild samples collected from two waterbodies in southern Ontario, Canada (Black River and Seymour Lake). Our novel rbcL primers, which amplify a fragment of ~220 bp, provided the most comprehensive description of the mock community, identifying all but one of the taxa to species or genus. In addition, after pooling data from five sites within each sampled waterbody, metabarcodes generated by this same primer pair identified more taxa than all other primer pairs; more specifically, 20 and 26 taxa were identified from Black River and Seymour Lake, respectively, to species or genus. Across the two sites, nine of the identified taxa are alien invasive aquatic plants. Five of these invasive species have no previous reports from our sites, and in some cases have no known established Ontario populations; our data therefore suggest an urgent need to increase surveillance for these aliens. Overall, our study showed that eDNA metabarcoding with a novel rbcL primer pair provides a cost‐effective method for simultaneously detecting multiple aquatic vascular plant taxa and is a valuable tool for the early detection of invasive species.

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Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Cited by 37 publications

References 80 publications

Covariation of diet and gut microbiome in African megafauna

Covariation of diet and gut microbiome in African megafauna

Multiple dimensions of dietary diversity in large mammalian herbivores

Development of an environmental DNA metabarcoding assay for aquatic vascular plant communities

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