Covariation of diet and gut microbiome in African megafauna.

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.

Foraging history of individual elephants using DNA metabarcoding.

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.

Ecological Niche Modeling of Water Lily (Nymphaea L.) Species in Australia under Climate Change to Ascertain Habitat Suitability for Conservation Measures.

The International Panel on Climate Change (IPCC) projects a global temperature rise of 4.3 ± 0.7 °C by 2100 and an extinction of 8.5% in one out of every six species. Australia's aquatic ecosystem is no exception; habitat loss, fragmentation, and loss of biodiversity are being experienced. As the center for Nymphaea species distribution, it presents the culturally, ecologically, and scientifically important genus as the best candidate for habitat suitability assessment in climate change, whose habitat suitability is presumed to decline. The models were run according to the maximum entropy (MaxEnt) method, using one general circulation model (GCM). Projections were made for the current, past, and future in medium (4.5) and high (8.5) representative concentration pathways. Significantly, bio2 and bio15 were highly preferred among the species. Less distribution was noted in West Australia compared to the north, east, and south of the continent, while north of the continent in Western Australia, Northern Territory, and Queensland indicate more habitat contractions compared to the east and southeast of Queensland and New South Wales, although it receives high precipitation. Generally, the species respond variably to both temperature and precipitation variables which is a key species response factor for planners and decision makers in species habitat and biodiversity conservation.

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment.

Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes within diverse LMH guilds are difficult to pinpoint, and the magnitude and even direction of these effects often depends on environmental context. Since 2008, we have maintained the Ungulate Herbivory Under Rainfall Uncertainty (UHURU) experiment, a series of size-selective LMH exclosures replicated across a rainfall/productivity gradient in a semiarid Kenyan savanna. The goals of the UHURU experiment are to measure the effects of removing successively smaller size classes of LMH (mimicking the process of size-biased extirpation) and to establish how these effects are shaped by spatial and temporal variation in rainfall. The UHURU experiment comprises three LMH-exclusion treatments and an unfenced control, applied to nine randomized blocks of contiguous 1-ha plots (n = 36). The fenced treatments are MEGA (exclusion of megaherbivores, elephant and giraffe), MESO (exclusion of herbivores ≥40 kg), and TOTAL (exclusion of herbivores ≥5 kg). Each block is replicated three times at three sites across the 20-km rainfall gradient, which has fluctuated over the course of the experiment. The first 5 years of data were published previously (Ecological Archives E095-064) and have been used in numerous studies. Since that publication, we have (1) continued to collect data following the original protocols, (2) improved the taxonomic resolution and accuracy of plant and small-mammal identifications, and (3) begun collecting several new data sets. Here, we present updated and extended raw data from the first 12 years of the UHURU experiment (2008-2019). Data include daily rainfall data throughout the experiment; annual surveys of understory plant communities; annual censuses of woody-plant communities; annual measurements of individually tagged woody plants; monthly monitoring of flowering and fruiting phenology; every-other-month small-mammal mark-recapture data; and quarterly large-mammal dung surveys. There are no copyright restrictions; notification of when and how data are used is appreciated and users of UHURU data should cite this data paper when using the data.

Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region.

With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis.

The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.

Medicinal Plants and Their Traditional Uses in Local Communities around Cherangani Hills, Western Kenya.

* Correspondence: zhouyd@wbgcas [...].

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

Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL-F, trnH-psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra- and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack "barcode gaps", defined as disparities between the maximum intra- and minimum interspecific genetic distances. We found barcode gaps for 72%-89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode-gap presence or absence for all of the markers in combination and for matK, trnL-F, and trnH-psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.

Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia) drepanolobium.

The Acacia drepanolobium (also known as Vachellia drepanolobium) ant-plant symbiosis is considered a classic case of species coexistence, in which four species of tree-defending ants compete for nesting space in a single host tree species. Coexistence in this system has been explained by trade-offs in the ability of the ant associates to compete with each other for occupied trees versus the ability to colonize unoccupied trees. We seek to understand the proximal reasons for how and why the ant species vary in competitive or colonizing abilities, which are largely unknown. In this study, we use RADseq-derived SNPs to identify relatedness of workers in colonies to test the hypothesis that competitively dominant ants reach large colony sizes due to polygyny, that is, the presence of multiple egg-laying queens in a single colony. We find that variation in polygyny is not associated with competitive ability; in fact, the most dominant species, unexpectedly, showed little evidence of polygyny. We also use these markers to investigate variation in mating behavior among the ant species and find that different species vary in the number of males fathering the offspring of each colony. Finally, we show that the nature of polygyny varies between the two commonly polygynous species, Crematogaster mimosae and Tetraponera penzigi: in C. mimosae, queens in the same colony are often related, while this is not the case for T. penzigi. These results shed light on factors influencing the evolution of species coexistence in an ant-plant mutualism, as well as demonstrating the effectiveness of RADseq-derived SNPs for parentage analysis.