Dataset Information

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis).

ABSTRACT: The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6-5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop-raiding versus noncrop-raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.

SUBMITTER: Budd K

PROVIDER: S-EPMC7319146 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis).

Budd Kris K Gunn Joe C JC Finch Tabitha T Klymus Katy K Sitati Noah N Eggert Lori S LS

Ecology and evolution 20200518 12

The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6-5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome compos ...[more]

PMID: 32607180

Similar Datasets

Project description:Crop damage by forest elephants (Loxodonta africana cyclotis) and the resulting human-elephant conflict are issues of great concern for both the conservation of the species and the protection of rural livelihoods in Central Africa. Addressing these problems requires identifying the factors that facilitate or impede crop-raiding by forest elephants. Yet to date, the environmental or anthropogenic factors that influence the occurrence and intensity of crop-raiding by forest elephants are largely unknown. We used a multivariate approach to investigate conditions under which forest elephants raid some fields and not others in the buffer zone of Monts de Cristal National Park (MCNP), Gabon. We first interviewed 121 farmers from 11 villages situated within 10 km of MCNP regarding the occurrence of elephant crop-raiding of their fields. We then collected data on 39 explanatory variables to characterize the agricultural fields. Of these, the most important predictors of elephant raid occurrence of crop damage were presence of fruit trees, elephant deterrents (scarecrows, fire, wire string fences and empty barrels), and field topography. We secondly assessed the effect of stage of crop growth, presence of fruit trees, field topography and presence of elephant deterrents on crop-raiding occurrence and intensity by counting raids and measuring areas of crop damage every week in 17 plantations over 19 weeks in the most elephant-impacted zone of the study area. We found that fruit presence and stage of crop growth led to more intense damage to crops, whereas local deterrents did not inhibit raiding events and crop damage by elephants. We report a tradeoff between non-timber forest products (NTFP) services and crop-raiding by elephants. We show for the first time that steep topography impedes elephant damage to crops with no raids recorded in fields with surrounding slopes greater than 25%. We discuss whether farming on steep fields could be used as a strategy for mitigating crop-raiding to favor human-elephant coexistence and enhance elephant conservation.

Project description:Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals sampled in 2015 and 2017. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. In northern Tanzania, elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean F ST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean A R = 9.96), heterozygosity (mean µH E = 0.73), and effective population sizes (mean N e = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.

Project description:Accurate counts of animals are critical for prioritizing conservation efforts. Past research, however, suggests that observers on aerial surveys may fail to detect all individuals of the target species present in the survey area. Such errors could bias population estimates low and confound trend estimation. We used two approaches to assess the accuracy of aerial surveys for African savanna elephants (Loxodonta africana) in northern Botswana. First, we used double-observer sampling, in which two observers make observations on the same herds, to estimate detectability of elephants and determine what variables affect it. Second, we compared total counts, a complete survey of the entire study area, against sample counts, in which only a portion of the study area is sampled. Total counts are often considered a complete census, so comparing total counts against sample counts can help to determine if sample counts are underestimating elephant numbers. We estimated that observers detected only 76% ± SE of 2% of elephant herds and 87 ± 1% of individual elephants present in survey strips. Detectability increased strongly with elephant herd size. Out of the four observers used in total, one observer had a lower detection probability than the other three, and detectability was higher in the rear row of seats than the front. The habitat immediately adjacent to animals also affected detectability, with detection more likely in more open habitats. Total counts were not statistically distinguishable from sample counts. Because, however, the double-observer samples revealed that observers missed 13% of elephants, we conclude that total counts may be undercounting elephants as well. These results suggest that elephant population estimates from both sample and total counts are biased low. Because factors such as observer and habitat affected detectability of elephants, comparisons of elephant populations across time or space may be confounded. We encourage survey teams to incorporate detectability analysis in all aerial surveys for mammals.

Project description:BackgroundThe increasing human population and global intensification of agriculture have had a major impact on the world's natural ecosystems and caused devastating effects on populations of mega-herbivores such as the African savanna elephants, through habitat reduction and fragmentation and increased human-animal conflict. Animals with vast home ranges are forced into increasingly smaller geographical areas, often restricted by fencing or encroaching anthropogenic activities, resulting in huge pressures on these areas to meet the animals' resource needs. This can present a nutritional challenge and cause animals to adapt their movement patterns to meet their dietary needs for specific minerals, potentially causing human-animal conflict. The aim of this review is to consolidate understanding of nutritional drivers for animal movement, especially that of African savanna elephants and focus the direction of future research. Peer reviewed literature available was generally geographically specific and studies conducted on isolated populations of individual species. African savanna elephants have the capacity to extensively alter the landscape and have been more greatly studied than other herbivores, making them a good example species to use for this review. Alongside this, their movement choices, potentially linked with nutritional drivers could be applicable to a range of other species. Relevant case study examples of other herbivores moving based on nutritional needs are discussed.MethodsThree databases were searched in this review: Scopus, Web of Science and Google Scholar, using identified search terms. Inclusion and exclusion criteria were determined and applied as required. Additional grey literature was reviewed as appropriate.ResultsInitial searches yielded 1,870 records prior to application of inclusion and exclusion criteria. A less detailed review of grey literature, and additional peer-reviewed literature which did not meet the inclusion criteria but was deemed relevant by the authors was also conducted to ensure thorough coverage of the subject.DiscussionA review of peer reviewed literature was undertaken to examine nutritional drivers for African elephant movement, exploring documented examples from free-ranging African savanna elephants and, where relevant, other herbivore species. This could help inform prediction or mitigation of human-elephant conflict, potentially when animals move according to nutritional needs, and related drivers for this movement. In addition, appropriate grey literature was included to capture current research.

Dataset Information

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis).

Publications

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (<i>Loxodonta africana</i>) and forest elephants (<i>L. cyclotis</i>).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets