The identification of elephant ivory evidences of illegal trade with mitochondrial cytochrome b gene and hypervariable D-loop region

Lee, Eun-jung; Lee, Yang‐Han; Moon, Sangook; Kim, Nam-ye; Kim, Soonhee; Yang, Moon-Sik; Choi, Dongho; Han, Myunsoo

doi:10.1016/j.jflm.2012.06.014

Cited by 25 publications

(8 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Mitochondria contain compacted genes simplified by introns removal and little duplication, so the regions between genes are very short. The partial cytochrome b and hypervariable D-loop region in mt-DNA has been used in species identification for forensic evidence and particularly suitable for the genetic analysis for population and related taxa (Lee et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus)

Wibowo

Widiyanti

Asvan³

et al. 2021

Biodiversitas

View full text Add to dashboard Cite

Abstract. Wibowo DS, Widiyanti R, Asvan M, Restanti PD, Wijayanto H. 2021. Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus). Biodiversitas 22: 1063-1068. Sumatran elephant is the only subspecies of Asian elephants that receives a critically endangered status from the International Union for Conservation and Nature Resources (IUCN). Identifying the genetic marker of Sumatran elephants is, therefore, important for their conservation. This study aimed to identify the Sumatran elephant based on specific mitochondrial DNA markers of the Cytochrome c oxidase subunit II (COX2) gene. It is an exploratory research considering the limited data and research about the genetic, especially the COX2 of Sumatran elephant (Elephas maximus sumatranus). Forward and reverse sequencing of PCR products was conducted using the primary COX2 from Sumatran elephant samples. The results of the subsequent gene sequencing were aligned with the sequences of other Asian elephants from Genbank using Clustal W software and analyzed using the MEGA program version 6.06. The analysis of genetic distance based on COX2 constituent nucleotides calculated with Kimura’s two-parameter method showed that the genetic distance between Elephas maximus sumatranus and Elephas maximus outside of Sumatra was 0.25%. The phylogenetic trees analyzed using the maximum-likelihood based on nucleotide sequences showed a high homogeneity. The ratio of Elephas maximus sumatranus with Elephas maximus shows levels of nucleotide mutations which are nine nucleotides and four nucleotides. These results indicated that the COX2 gene could not identify the individual species of Sumatran elephant because of the high intraspecies homogeneity, but it detected the interspecies divergence clustered in Asian elephant clade.

show abstract

Section: Introductionmentioning

confidence: 99%

Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus)

Wibowo

Widiyanti

Asvan³

et al. 2021

Biodiversitas

View full text Add to dashboard Cite

show abstract

Section: Methodsmentioning

confidence: 99%

“…Indeed, due to hybridization, some savanna elephants carry the mitochondrial DNA originally found in forest elephants (Ishida et al, 2013; Ishida, Demeke, et al, 2011). In practice, two mitochondrial fragments of 331 and 33 base pairs (bp) of the D‐loop region were targeted with the primer pairs AFDL3/AFDL4 (Eggert et al, 2002; Lee et al, 2013) and Ele‐CytbF1/Ele‐CytbR1 (Cappellini et al, 2014), respectively. One additional mitochondrial fragment of 116 bp of the cytochrome b gene was targeted with the primer pair L15123/H15240 (Ngatia et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

Tracking the origin of worked elephant ivory of a medieval chess piece from Belgium through analysis of ancient DNA

Goffette

Gonzalez

Vanmechelen

et al. 2021

Intl J of Osteoarchaeology

View full text Add to dashboard Cite

The morphological identification of raw biological material used to produce archeological artifacts is sometimes difficult or even impossible. In recent years, newly developed biochemical techniques have allowed more reliable identification of exploited animal species, even for otherwise taxonomically undiagnostic fragments, and thus can help pinpoint the geographical origin of the raw material.However, in addition to being costly, these techniques involve destructive sampling. This explains why they are rarely applied to archeological artifacts, especially those made of precious, imported raw material or those representing intact works of art. Here, we analyzed the ancient DNA (aDNA) of a medieval chess piece made of ivory of unknown origin, recovered from a medieval settlement in Jambes (Namur), Belgium. This chess piece was broken during excavation. We took this unfortunate event as an opportunity to perform aDNA extraction, to try to answer three questions: (1) What Proboscidean species does the ivory come from?; (2) Can we establish the geographic origin of the ivory more precisely?; and (3) Does doing so help our understanding of (part of) the trade route followed by the ivory? We sequenced two short fragments of the mitochondrial genome and compared them with publicly available DNA data. This enabled the identification of the raw material as an African elephant (genus Loxodonta). Although the results cannot exclude that the ivory comes from a forest elephant, the recovered DNA sequence is currently found only among savanna elephant DNA records. The ivory likely originates from an eastern or southern African country and was therefore probably transported along the African trade route passing through the Swahili Corridor. However, the precise itinerary followed by this ivory from the African shore of the Mediterranean Sea to Europe, and then to the archeological site from which it was recovered, remains unknown. Such identification contributes to documenting past trade networks and long-distance exchange.

show abstract

“…However, thus far SSR is the most widely used technology in elephant molecular analysis, for resolving phylogenetic relationships 12 , 21 , 39 , 63 – 66 , population structure and social organization 5 , 37 , 41 , 67 – 71 , illegal poaching and ivory trade 19 , 72 – 76 , ecology and conservation 23 , 27 , 28 , 77 – 79 , distribution and behavior 24 and sex determination 73 , 77 , 80 – 82 . While the early SSR studies were based on PCR amplification followed by polyacrylamide gel electrophoresis and silver staining 55 , 83 , later studies utilized relatively advanced technologies such as fragment analysis or capillary electrophoresis 19 , 40 , 52 , 84 – 86 .…”

Section: Introductionmentioning

confidence: 99%

Revisiting traditional SSR based methodologies available for elephant genetic studies

Marasinghe¹,

Nilanthi²,

Hathurusinghe

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants’ dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.

show abstract

The identification of elephant ivory evidences of illegal trade with mitochondrial cytochrome b gene and hypervariable D-loop region

Cited by 25 publications

References 16 publications

Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus)

Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus)

Tracking the origin of worked elephant ivory of a medieval chess piece from Belgium through analysis of ancient DNA

Revisiting traditional SSR based methodologies available for elephant genetic studies

Contact Info

Product

Resources

About