Who are the elephants living in the hybridization zone? How genetics may guide conservation to better protect endangered elephants

Bonnald, Julie; Utge, José; Kuhner, Mary K.; Wasser, Samuel K.; Asalu, Edward; Okimat, John Paul; Krief, Sabrina

doi:10.1016/j.gecco.2021.e01917

Cited by 7 publications

(9 citation statements)

References 52 publications

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“…When applied to a set of 1,408 videos recorded in Sebitoli, in the hybridization area in Uganda, these criteria produced three groups of phenotypes using an unsupervised K -means approach (the expected savannah and forest phenotypes and a third group, present in 51.1% of the videos). This third group could correspond to hybrid individuals, whose presence had been noted previously in the south of our study area (Mondol et al, 2015; Bonnald et al, 2021).…”

Section: Discussionsupporting

confidence: 73%

Phenotypical characterization of African savannah and forest elephants, with special emphasis on hybrids: the case of Kibale National Park, Uganda

Bonnald

Cornette

Pichard

et al. 2022

Oryx

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The IUCN now recognizes the savannah Loxodonta africana and forest Loxodonta cyclotis elephants to be separate species. Despite ecological, behavioural and morphological differences, and different habitat ranges, genetic studies confirm that the two species and hybrids coexist in forest–savannah ecotones. However, the hybrid phenotypes have not yet been described. In this survey we examined whether the phenotypes of the two species and of hybrids can be distinguished. In the first step, we used a machine learning algorithm (K-nearest neighbours) to compare 296 reference images of African elephants from five forest areas and six savannah areas where hybrids have not been recorded, confirming that six morphological criteria can be used to distinguish the species with more than 90% confidence. In the second step, we analysed 1,408 videos of elephants from 14 camera traps in Sebitoli, in Kibale National Park, Uganda, part of the main hybridization area. We used a multiple correspondence analysis and a species assignment key, highlighting the presence of three categories of phenotypes. Compared to the savannah and forest phenotypes (36.8 and 12.1%, respectively), the intermediate phenotypes, which could include hybrids, were more frequent (51.1%). Further studies combining morphology and genetics of the same individuals will be necessary to refine this species assignment key to characterize phenotypes confidently. This non-invasive, fast and inexpensive phenotypical-based method could be a valuable tool for conservation programmes.

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Section: Discussionsupporting

confidence: 73%

Phenotypical characterization of African savannah and forest elephants, with special emphasis on hybrids: the case of Kibale National Park, Uganda

Bonnald

Cornette

Pichard

et al. 2022

Oryx

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“…However, there are unresolved patterns (e.g., the positioning of the Mozambique elephants, Figure 3 ) that would need to be further explored through a comparison of Dataset 3 to continent-wide genomic data, although beyond the scope of the current study with its primary focus on fecal DNA sample collection and analysis. The generation of genome-wide data from fecal samples may enable other broad-scale genomic questions to be addressed, for example, the evolutionary history of elephants and other species, and estimation of the age of inter-species hybridization zones ( Tonzo et al, 2020 ; Bonnald et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…Elephants ( L. africana ) are ideal candidates for testing a non-invasive approach because invasive sampling can be unsafe and expensive ( Jacobson et al, 1988 ; Kock et al, 1993 ), and they occur across very large and sometimes difficult to access geographic areas ( Gray et al, 2014 ). Non-invasive samples have been used extensively to study elephants, e.g., to establish relatedness and demography ( Munshi-South, 2011 ), investigate hybridization between forest and savanna elephants ( Bonnald et al, 2021 ), study population structure and gene flow ( de Flamingh et al, 2018 ), and estimate population size ( Gray et al, 2014 ). We used samples from zoo individuals to investigate DNA content and preservation relative to dung freshness.…”

Section: Introductionmentioning

confidence: 99%

Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

et al. 2023

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Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.

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“…However, there are unresolved patterns (e.g., the positioning of the Mozambique elephants, Figure 3) that would need to be further explored through a comparison of Dataset 3 to continent-wide genomic data, although beyond the scope of the current study with its primary focus is on reporting a method for fecal DNA sample analysis. The possibility of generating genome-wide data from fecal samples may also shed light on other broad-scale genomic questions, for example, the evolutionary history of elephants and other species, and estimation of the age of inter-species hybridization zones (Tonzo et al, 2020; Bonnald et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Elephants are ideal candidates for testing a non-invasive approach because invasive collection of their samples can be unsafe and expensive (Jacobson et al, 1988;Kock et al, 1993), and they occur across very large and sometimes difficult to access geographic areas (Gray et al, 2014). Non-invasive samples have been used extensively to study elephants, e.g., to establish relatedness and demography (Munshi-South, 2011), investigate hybridization between forest and savanna elephants (Bonnald et al, 2021), study population structure and gene flow (de Flamingh et al, 2018), and estimate population size (Gray et al, 2014). We used samples from zoo individuals to investigate DNA content and preservation relative to dung freshness and verified the practicality and effectiveness of our pipeline in free-ranging elephants from five localities in South Africa.…”

Section: Introductionmentioning

confidence: 99%

Non-invasive fecal DNA yields whole genome and metagenomic data for species conservation

Flamingh

Ishida

Pečnerová

et al. 2022

Preprint

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Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, and/or dangerous species. Integrating genomic techniques that use non-invasive biological samples with advances in computational approaches can benefit and inform wildlife conservation and management. Here we present a molecular pipeline that uses non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at 6X coverage) and metagenomic sequences, combining in a novel fashion widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome and/or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated by this pipeline was demonstrated by the application of genome-scale analysis and metagenomics to zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses generated compositional taxon classifications that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of our approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular pipeline presented here extends applications beyond what has previously been shown for target-enriched datasets and contributes towards the expansion and application of genomic techniques to conservation science and practice.

show abstract

Who are the elephants living in the hybridization zone? How genetics may guide conservation to better protect endangered elephants

Cited by 7 publications

References 52 publications

Phenotypical characterization of African savannah and forest elephants, with special emphasis on hybrids: the case of Kibale National Park, Uganda

Phenotypical characterization of African savannah and forest elephants, with special emphasis on hybrids: the case of Kibale National Park, Uganda

Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

Non-invasive fecal DNA yields whole genome and metagenomic data for species conservation

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