Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania

Population genetic structure and historical demography of the population of forest elephants in Côte d'Ivoire

The population of forest elephant (Loxodonta cyclotis) has continuously declined in Côte d'Ivoire and, the remaining population largely consists of subpopulations that are fragmented and isolated. No data actually exist on the level of genetic diversity and population genetic structure of current forest elephant populations in Côte d'Ivoire. In this sense, determining genetic diversity and the underlying mechanisms of population differentiation is crucial for the initiation of effective conservation management. A total of 158 dung samples of forest elephants were collected at stage 1 of decompositions (dung pile intact, very fresh) in three Classified Forests (CF) (Bossématié, Dassioko and Port-Gauthier) in Côte d'Ivoire. A total of 101 sequences of the mitochondrial DNA control region measuring 600 base pair and 26 haplotypes were obtained. A haplotypic diversity ranging from 0.655 ± 0.050 at Bossématié and 0.859 ± 0.088 at Port Gauthier was obtained. Fifteen (15) out of 26 haplotypes observed were singletons and only the Dassioko and Port Gauthier CFs shared the same haplotypes. The strong genetic connectivity between forest elephant populations of the Dassioko and Port Gauthier CFs is supported by the grouping of these populations into a single cluster by Bayesian analysis. Although populations of L. cyclotis exhibit relatively high genetic diversity, habitat fragmentation could affect the genetic variability of current populations. Urgent measures including the reinforcement/establishment of genetic corridors and the strengthening of protection measures need to be undertaken to save the remaining populations of forest elephants in Côte d'Ivoire.

Continent-wide genomic analysis of the African buffalo (Syncerus caffer)

The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided little support for the currently described four subspecies. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.

Modelling elephant corridors over two decades reveals opportunities for conserving connectivity across a large protected area network

Protected area (PA) connectivity is pivotal for the persistence of wide-ranging wildlife species, but is challenged by habitat loss and fragmentation. We analyzed habitat suitability and connectivity for the African elephant (Loxodonta africana) across PAs in south-western Tanzania in 2000, 2010, and 2019. We quantified land-use changes through remote sensing data; estimated habitat suitability through aerial survey data, remotely sensed variables and ensemble species distribution models; modelled least-cost corridors; identified the relative importance of each corridor for the connectivity of the PA network and potential bottlenecks over time through circuit theory; and validated corridors through local ecological knowledge and ground wildlife surveys. From 2000 to 2019, cropland increased from 7% to 13% in the region, with an average expansion of 634 km2 per year. Distance from cropland influenced elephant distribution models the most. Despite cropland expansion, the locations of the modelled elephant corridors (n = 10) remained similar throughout the survey period. Based on local ecological knowledge, nine of the modelled corridors were active, whereas one modelled corridor had been inactive since the 1970s. Based on circuit theory, we prioritize three corridors for PA connectivity. Key indicators of corridor quality varied over time, whereas elephant movement through some corridors appears to have become costlier over time. Our results suggest that, over the past two decades, functional connectivity across the surveyed landscape has largely persisted. Beyond providing crucial information for spatial prioritization of conservation actions, our approach highlights the importance of modeling functional connectivity over time and verifying corridor models with ground-truthed data.

Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania

The Masai giraffe has experienced a population decline from 70,000 to 35,000 in the past three decades and was declared an endangered subspecies by the IUCN in 2019. The remaining number of Masai giraffe are geographically separated by the steep cliffs of the Gregory Rift escarpments (GRE) in Tanzania and Kenya dividing them into two populations, one west and one east of the GRE. The cliffs of the GRE are formidable barriers to east-west dispersal and gene flow and the few remaining natural corridors through the GRE are occupied by human settlements. To assess the impact of the GRE on Masai giraffe gene flow, we examined whole genome sequences of nuclear and mitochondrial DNA (mtDNA) variation in populations located east (Tarangire ecosystem) and west (Serengeti ecosystem) of the GRE in northern Tanzania. Evidence from mtDNA variation, which measures female-mediated gene flow, suggests that females have not migrated across the GRE between populations in the Serengeti and Tarangire ecosystems in the past ~289,000 years. The analysis of nuclear DNA variation compared to mtDNA DNA variation suggests that male-mediated gene flow across the GRE has occurred more recently but stopped a few thousand years ago. Our findings show that Masai giraffes are split into two populations and fulfill the criteria for designation as distinct evolutionary significant units (ESUs), which we denote as western Masai giraffe and eastern Masai giraffe. While establishing giraffe dispersal corridors across the GRE is impractical, conservation efforts should be focused on maintaining connectivity among populations within each of these two populations. The importance of these efforts is heightened by our finding that the inbreeding coefficients are high in some of these Masai giraffe populations, which could result in inbreeding depression in the small and fragmented populations.

Land Use/Cover Change Reduces Elephant Habitat Suitability in the Wami Mbiki–Saadani Wildlife Corridor, Tanzania

Wildlife corridors are critical for maintaining the viability of isolated wildlife populations and conserving ecosystem functionality. Anthropogenic pressure has negatively impacted wildlife habitats, particularly in corridors between protected areas, but few studies have yet quantitatively assessed habitat changes and corresponding wildlife presence. We quantified land use/land cover and human–elephant conflict trends over the past two decades in the Wami Mbiki–Saadani (WMS) wildlife corridor, Tanzania, using RS and GIS combined with human–wildlife conflict reports. We designed landscape metrics and habitat suitability models for the African savanna elephant (Loxodonta africana) as a large mammal key species in the WMS ecosystem. Our results showed that forest cover, a highly suitable habitat for elephants, decreased by 3.0% between 1998 and 2008 and 20.3% between 2008 and 2018. Overall, the highly suitable habitat for elephants decreased by 22.4% from 1998 to 2018, when it was scarcely available and when small fragmented patches dominated the unprotected parts of the corridor. Our findings revealed that large mammalian habitat conservation requires approaches beyond habitat-loss detection and must consider other facets of landscape patterns. We suggest strengthening elephant habitat conservation through community conservation awareness, wildlife corridor mapping, and restoration practices to ensure a sustainable pathway to human–wildlife coexistence.