Microsatellite repeat motif and amplicon length affect amplification success of degraded faecal DNA

Flamingh, Alida de; Sole, Catherine L.; Aarde, Rudi J. van

doi:10.1007/s12686-014-0160-5

Cited by 6 publications

(2 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, microsatellite genotype errors are often associated with degraded DNA amplification, e.g. null allele or false allele amplification (de Flamingh et al, 2014;Taberlet et al, 1999). Combined these factors resulted in fewer individuals being genotyped for nDNA than mtDNA.…”

Section: Data Generationmentioning

confidence: 99%

Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa

2017

Self Cite

View full text Add to dashboard Cite

African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in Kruger National Park (South Africa) to populations in nearby countries (Botswana, Mozambique, Zambia and Zimbabwe). We used a 446 base pair mitochondrial DNA (mtDNA) control region fragment (141 individuals) and 9 nuclear DNA (nDNA) microsatellite markers (69 individuals) to investigate phylogenetic relationships and gene flow among elephant populations. The mtDNA and nDNA phylogeographic patterns were incongruent, with mtDNA patterns likely reflecting the effects of ancient female migrations, with patterns persisting due to female philopatry, and nDNA patterns likely reflecting male-mediated dispersal. Kruger elephant heterozygosity and differentiation were examined, and were not consistent with genetic isolation, a depleted gene pool or a strong founder effect. Mitochondrial DNA geographic patterns suggested that the Kruger population was founded by elephants from areas both north and south of Kruger, or has been augmented through migration from more than one geographic source. We discuss our findings in light of the need for conservation initiatives that aim at maintaining or restoring connectivity among populations. Such initiatives may provide a sustainable, self-regulating management approach for elephants in southern Africa while maintaining genetic diversity within and gene flow between Kruger Park and nearby regions.

show abstract

Section: Data Generationmentioning

confidence: 99%

Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa

2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…A total of 142 samples were collected and genotyped for 9 highly variable nuclear DNA microsatellite loci (de Flamingh et al, (2018); SI Table 1). Sample collection, DNA extraction procedures, and microsatellite amplification are detailed in de Flamingh et al (2018), and genotype errors were quantified as described in de Flamingh et al (2014). Heterozygous genotypes were replicated at least four times, and homozygous genotypes were replicated at least three times.…”

Section: Elephant Genetic Datamentioning

confidence: 99%

Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants

de Flamingh,

Alexander,

Perrin-Stowe

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes.

show abstract

Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants

de Flamingh,

Alexander,

Perrin-Stowe

et al. 2024

Biodivers Conserv

View full text Add to dashboard Cite

Microsatellite repeat motif and amplicon length affect amplification success of degraded faecal DNA

Cited by 6 publications

References 7 publications

Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa

Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa

Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants

Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants

Contact Info

Product

Resources

About