Differentiation of two South African otter species ( Aonyx capensis and Lutra maculicollis ) from spraint based on partial CytB primer sets

Madisha, M. Thabang; Ponsonby, D.; Schwaibold, Ute; Kotzé, Antoinette; Jansen, Raymond; Brettschneider, Helene; Dalton, Desiré L.

doi:10.1016/j.gecco.2015.05.001

Cited by 7 publications

(5 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…They were successful in amplifying DNA from ~50% of the spraint samples (A.-P. Pazil, personal communication) to ascertain species. The amplification of short (<300 bp) fragments of mitochondrial DNA is reported to produce higher amplification success rates (Madisha et al, 2015;Shih et al, 2017).…”

Section: Conservation Geneticsmentioning

confidence: 99%

“…Roadkills of the hairy-nosed otter have been reported near peat swamp forests in Perak, Pahang (Sebastian, 1995), and more recently in Northern Selangor, Malaysia (Tan, 2015;Woo, 2021). The presence of the Eurasian otter in Malaysia is highly uncertain and limited to just two records from the northern part of the peninsula (Miller, 1900;Mohd-Azlan & Sharma, 2006) and one from Borneo (Phillipps & Phillipps, 2016) Species identification by DNA analysis of scat samples has relied mainly on the amplification of mitochondrial DNA sequences, such as the control and 16s rRNA regions (e.g., Mills et al, 2000) cytochrome b gene (e.g., Hsieh et al, 2001;Madisha et al, 2015) and mitochondrial D-loop region (Bozarth et al, 2010). DNA from noninvasive sources such as hair and feces usually contain only trace amounts of low-quality fragmented DNA, which degrades further with time, resulting in amplification failure in old decayed samples (Shih et al, 2017;Waits & Paetkau, 2005).…”

Section: Conservation Geneticsmentioning

confidence: 99%

“…Species identification by DNA analysis of scat samples has relied mainly on the amplification of mitochondrial DNA sequences, such as the control and 16s rRNA regions (e.g., Mills et al, 2000 ) cytochrome b gene (e.g., Hsieh et al, 2001 ; Madisha et al, 2015 ) and mitochondrial D‐loop region (Bozarth et al, 2010 ). DNA from noninvasive sources such as hair and feces usually contain only trace amounts of low‐quality fragmented DNA, which degrades further with time, resulting in amplification failure in old decayed samples (Shih et al, 2017 ; Waits & Paetkau, 2005 ).…”

Section: Introductionmentioning

confidence: 99%

“…Pazil, personal communication) to ascertain species. The amplification of short (<300 bp) fragments of mitochondrial DNA is reported to produce higher amplification success rates (Madisha et al, 2015 ; Shih et al, 2017 ). PCR amplification of mitochondrial fragments has been successfully combined with restriction‐fragment‐length polymorphisms (PCR‐RFLP) analysis to distinguish among closely related taxa (e.g., Bidlack et al, 2007 ; Cossíos & Angers, 2006 ; Hansen & Jacobsen, 1999 ; Mukherjee et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR‐RFLP analysis

Sharma

Chee‐Yoong

Kannan

et al. 2022

Ecology and Evolution

View full text Add to dashboard Cite

Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth‐coated otter, Asian small‐clawed otter, and hairy‐nosed otter have been reliably reported as residents. We designed a replicable and cost‐efficient PCR‐RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR‐RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D‐loop region and a 300‐bp fragment of the mt ND4 gene using primer sets TanaD, TanaD‐Mod, and OTR‐ND4, respectively. Amplification products were digested with restriction enzymes to generate species‐specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD‐Mod primer amplifying DNA from all 33 spraints. TanaD and OTR‐ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD‐Mod provided the expected species‐specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR‐ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR‐ND4 primer–enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD‐Mod (455 USD). We suggest the use of both OTR‐ND4 and TanaD‐Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR‐RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.

show abstract

Section: Conservation Geneticsmentioning

confidence: 99%

Section: Conservation Geneticsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR‐RFLP analysis

Sharma

Chee‐Yoong

Kannan

et al. 2022

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…27 Species identification was conducted using developed partial CytB primers. 28 A homology search was done on all sequences obtained using the BlastN function on the US National Center for Biotechnology Information (NCBI) online database. Control sample DNA for A. capensis and H. maculicollis was extracted from reference tissue samples obtained from the South African National Zoological Gardens Biomaterials Bank (Biobank).…”

Section: Dna Extraction and Species Identificationmentioning

confidence: 99%

Genetic diversity of African clawless otters (Aonyx capensis) occurring in urbanised areas of Gauteng, South Africa

Ponsonby¹,

Madisha²,

Schwaibold³

et al. 2019

S. Afr. J. Sci.

Self Cite

View full text Add to dashboard Cite

Genetic diversity is the basis of the evolutionary potential of species to respond to environmental changes. However, restricting the movement of species can result in populations becoming less connected which can reduce gene flow and can subsequently result in a loss of genetic diversity. Urban expansion can lead to the fragmentation of habitats which affects the ability of species to move freely between areas. In this study, the genetic diversity of the African clawless otter (Aonyx capensis) in Gauteng (South Africa) was assessed using non-invasive sampling techniques. DNA was extracted from spraint (faecal) samples collected along nine rivers and genotyped using 10 microsatellites to assess population structure and genetic diversity. Samples were grouped based on locality and by catchment to determine whether isolated subpopulations exist. Genetic diversity of A. capensis in Gauteng was found to be low (mean observed heterozygosity (Ho)=0.309). Analysis of genetic structure provides support for the otter populations being panmictic with high gene flow between populations from different rivers. Results from the study indicate that the movement of A. capensis is not affected by physical barriers in urbanised areas. However, because the genetic diversity of the species in the study area is low, these animals may not be able to cope with future environmental changes.

show abstract

Increased population density and behavioural flexibility of African clawless otters (Aonyx capensis) in specific anthropogenic environments

et al. 2020

View full text Add to dashboard Cite

Differentiation of two South African otter species ( Aonyx capensis and Lutra maculicollis ) from spraint based on partial CytB primer sets

Cited by 7 publications

References 21 publications

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR‐RFLP analysis

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR‐RFLP analysis

Genetic diversity of African clawless otters (Aonyx capensis) occurring in urbanised areas of Gauteng, South Africa

Increased population density and behavioural flexibility of African clawless otters (Aonyx capensis) in specific anthropogenic environments

Contact Info

Product

Resources

About