Mitigation of human-wildlife-conflict in Masai Mara, Kenya

[ES]La interacción negativa entre los humanos y los animales salvajes o conflictos humanos fauna (HWC) es un problema emergente de conservación a nivel mundial. Aunque los seres humanos, el ganado y la fauna silvestre sufren de estas interacciones las investigaciones realizadas sobre HWC se han centrado en los efectos negativos de la HWC en los seres humanos, pero muy pocos estudios se han centrado en los efectos negativos de la HWC sobre las especies de la fauna silvestre. Aunque se han propuesto muchas estrategias de mitigación de HWC, pocos estudios han evaluado su eficacia. Del mismo modo, se han hecho muchos trabajos de investigación de enfermedades zoonóticas, pero no hay estudios sobre la influencia de la migración de larga distancia de herbívoros grandes en la epidemiología del parásito o la diversidad y el intercambio de parásitos entre los ñus y ganado. Este trabajo examina los efectos de HWC sobre las especies de vida silvestre en particular elefantes. Se investiga la gestión de HWC a través de translocaciones y los factores que influyen en sus resultados. Por último, el papel de la migración de los ñus de larga distancia sobre la prevalencia del parásito y la diversidad de esta especie se examinará con el objetivo de identificar los parásitos compartidos con el ganado. Los resultados pondrán de relieve la naturaleza de HWC y sus estrategias de mitigación[EN]Negative interaction between humans and wild animals or wildlife human conflicts (HWC) is an emerging conservation issue globally. Although humans, their livestock and wildlife suffer from these interactions research conducted on HWC has focused on the negative effects of HWC on humans but very few studies have focused on the negative effects of HWC on wildlife species. Although many HWC mitigation strategies have been proposed, few studies have evaluated their effectiveness. Similarly, much work has been done zoonotic disease research, but no studies have been done on the influence of long distance migration by large herbivores on parasite epidemiology or diversity and parasite sharing between wildebeest and livestock. This work examine the effects of HWC on wildlife species particularly elephants. The management of HWC through translocations and the factors influencing its’ outcomes is investigated. Finally, the role of long distance wildebeest migration on parasite prevalence and diversity in this species will be examined with the goal of identifying parasites shared with livestock. Results will highlight the nature of HWC and its mitigation strategies.Tesis Univ. Jaén. Departamento de Biología Experimental, leída el 7 de octubre de 201

The antigen recognition portion of African buffalo class I MHC is highly polymorphic, consistent with a complex pathogen challenge environment, and the 3’ region suggests distinct haplotype configurations

African buffalo (Syncerus caffer) have been distinct from the Auroch lineage leading to domestic cattle for 5 million years, and are reservoirs of multiple pathogens, that affect introduced domestic cattle. To date, there has been no analysis of the class I MHC locus in African buffalo. We present the first data on African buffalo class I MHC, which demonstrates that gene and predicted protein coding sequences are approximately 86–87% similar to that of African domestic cattle in the peptide binding region. The study also shows concordance in the distribution of codons with elevated posterior probabilities of positive selection in the buffalo class I MHC and known antigen binding sites in cattle. Overall, the diversity in buffalo class I sequences appears greater than that in cattle, perhaps related to a more complex pathogen challenge environment in Africa. However, application of NetMHCpan suggested broad clustering of peptide binding specificities between buffalo and cattle. Furthermore, in the case of at least 20 alleles, critical peptide-binding residues appear to be conserved with those of cattle, including at secondary anchor residues. Alleles with six different length transmembrane regions were detected. This preliminary analysis suggests that like cattle, but unlike most other mammals, African buffalo appears to exhibit configuration (haplotype) variation in which the loci are expressed in distinct combinations

A practical guideline to remote biopsy darting of wildebeests for genetic sampling

The use of biopsy darts for remote collection of tissue samples from free-ranging terrestrial and aquatic animal species has gained popularity in the recent past. The success of darting is very important since scientists may not have many chances to re-dart the same animal, especially with the free-ranging elusive wildlife species. We used wildebeest (Connochaetes taurinus) as a model to estimate the optimum shooting distance, pressure and the shot part of the body through which a researcher can optimize the success and amount of tissue collected from similar wild land mammalian species. Wildebeests were darted at six categories of distances ranging between 10 and 45 m and dart gun pressures of 5–14 millibar. The number of failed darts increased by increasing the darting distance: 0% (10 m), 0% (20 m), 6% (30 m), 20% (35 m), 71% (40 m), and 67% (45 m). There was a notable effect of the distances on the amount of tissue collected 20 m offered the best results. Dart gun pressure had no effect on the amount of tissue samples obtained. The amount of tissue obtained from successful darts was the same whether the animal was darted on the shoulder or thigh. In this paper, we present a practical guideline for remote biopsy darting of wildebeest to obtain optimum amount of tissue samples, which could be generalized for similar wild land mammalian species

In vitro fertilization program in white rhinoceros

The Anthropocene is marked by a dramatic biodiversity decline, particularly affecting the family Rhinocerotidae. Three of five extant species are listed as Critically Endangered (Sumatran, Javan, black rhinoceros), one as Vulnerable (Indian rhinoceros), and only one white rhino (WR) subspecies, the Southern white rhinoceros (SWR), after more than a century of successful protection is currently classified as Near Threatened by the IUCN, while numbers again are declining. Conversely, in 2008, the SWR’s northern counterpart and second WR subspecies, the Northern white rhinoceros (NWR), was declared extinct in the wild. Safeguarding these vanishing keystone species urgently requires new reproductive strategies. We here assess one such strategy, the novel in vitro fertilization program in SWR and – for the first-time NWR – regarding health effects, donor-related, and procedural factors. Over the past 8 years, we performed 65 procedures in 22 white rhinoceros females (20 SWR and 2 NWR) comprising hormonal ovarian stimulation, ovum pick-up (OPU), in vitro oocyte maturation, fertilization, embryo culture, and blastocyst cryopreservation, at an efficiency of 1.0 ± 1.3 blastocysts per OPU, generating 22 NWR, 19 SWR and 10 SWR/NWR hybrid blastocysts for the future generation of live offspring

Influence of massive and long distance migration on parasite epidemiology: Lessons from the great wildebeest migration

Very little is known about the influence of massive and long distance migration on parasite epidemiology. Migration can simultaneously minimize exposure to common parasites in their habitats and increase exposure to novel pathogens from new environments and habitats encountered during migration, while physiological stress during long distance movement can lead to immune suppression, which makes migrants vulnerable to parasites. In this paper, we investigated the diversity, prevalence, parasite load, co-infection patterns and predilection sites of adult gastrointestinal helminths in 130 migrating wildebeests and tested for their relation with animal age, sex and migration time (which also could indicate different migration routes), and compared them with the non-migratory wildebeest. Surprisingly, only four parasite species were found, Oesophagostomum columbianum, Haemonchus placei, Calicophoron raja and Moniezia expansa, which were lower than in non-migratory wildebeest reported in the literature. These parasites were generalists, infecting livestock, and suggests that wildebeest and livestock, because of their interaction during migration, have a cross-infection risk. There was a negative relation between parasites diversity, prevalence and intensity of infection, and host age, which suggests that wildebeests acquire protective immunity against these parasites as they get older. Prevalence and intensity of infection were higher among wildebeest crossing the Mara Bridge (early migrants) compared to those crossing the Serena (late migrants), which suggests that early migrants (or migrants originating from different areas) have varying infection intensities. The prevalence and intensity of infection were higher in males compared to females and may be due to ecological, behavioural, or physiological differences between males and females. Our findings compared to those of previous studies suggest that migration may provide a mechanism to minimize exposure of hosts to common parasites through migratory escape, but this result awaits examination of helminths epidemiology of non-migratory wildebeests from areas of migrant origins. The potential parasitic cross-infection between wildebeests and livestock is a real risk to be taken into account in the management of wildebeest migration corridors.The authors also thank KWS for funding the research, and Sophia Masila for editing the manuscript

Genomic analysis reveals limited hybridization among three giraffe species in Kenya

Background: In the speciation continuum the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species

Genomic analysis reveals limited hybridization among three giraffe species in Kenya

Background: In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species

Data from: Genomic analysis reveals limited hybridization among three giraffe species in Kenya

The data deposited here was generated by and reported in Coimbra et al. (2023). SNP calling and linkage pruning snp_calling_per_species.tar.gz: includes a genotype likelihoods (GL) file estimated with ANGSD for each giraffe species. sampled_ld.tar.gz: contains a random sample of estimated pairwise r2 values for each species used to fit linkage disequilibrium (LD) decay curves. ld_pruned_snps.tar.gz: contains an LD-pruned ANGSD GL file per species. snp_calling_combined.tar.gz: includes a single LD-pruned ANGSD GL file comprising all sampled individuals of the three giraffe species analyzed in this study. Relatedness relatedness.tar.gz: contains the input and output files used with NGSremix to estimate relatedness among giraffe in the dataset. snp_calling_combined_unrelated.tar.gz: includes a single LD-pruned ANGSD GL file comprising all unrelated individuals of the three giraffe species analyzed in this study. Population structure and admixture pcangsd.tar.gz: contains the covariance matrix generated by PCAngsd. ngsadmix.tar.gz: includes run likelihood lists for each K value ranging from 1 to 11, as well as the admixture proportions (stored in '.qopt' files) inferred from the run with the highest log-likelihood for each K in NGSadmix. evaladmix.tar.gz: contains the pairwise correlation of residuals between individuals estimated with evalAdmix for the NGSadmix runs with the highest log-likelihood run for each K. SNP-based phylogenomic inference snp_phylogeny.tar.gz: contains the input PHYLIP file and the IQ-TREE output tree and log files. Phylogeny of mitochondrial genomes mtdna_phylogeny.tar.gz: includes the 13 mitochondrial protein-coding gene alignments, the partitions file, and the IQ-TREE output tree and log files. Inference of migration events admixture_graphs.tar.gz: contains the TreeMix / OrientAGraph input file ('treemix.frq.strat.gz'), the output files for all TreeMix and OrientAGraph runs, and the OptM summary table of TreeMix runs ('optm.tsv'). Test for introgression dsuite_introgression.tar.gz: includes the input VCF, the admixture graph topology reconstructed by OrientAGraph, and the Dsuite output files for the estimation of Patterson's D, f4-ratio, and f-branch statistics. Contemporary migration rates ba3-snps.tar.gz: contains the input and output files for the BA3-SNPs-autotune and BA3-SNPs runs. Demographic reconstruction demographic_inference.tar.gz: includes the SFS files generated with ANGSD and realSFS and the StairwayPlot2 blueprint and output files. Other: metadata.csv: a companion file containing sample information used in conjunction with R scripts to plot the figures in the paper