Identification of a forensic case using microscopy and forensically informative nucleotide sequencing (FINS): a case study of small Indian civet (Viverricula indica)

Fourier transform infrared spectroscopy and chemometrics for the discrimination of animal fur types

Rapid and reliable animal fur identification has remained a challenge for customs inspection. The accurate distinction between fur types has a significant meaning in implementing the correct tariff policy. A variety of analytical methods have been applied to work on distinguishing animal fur types, with tools of microscopy, molecular testing, mass spectrometry, Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy. In this research, the capability of attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) combined with pattern recognition methods was investigated for the discrimination of animal fur in six types. This work was to explore the non-destructive application of ATR-FTIR technique in discriminant analysis of animal fur. All spectra were collected by ATR-FTIR of the wavenumber ranging from 4000 to 650 cm^-1. Data pretreatments included moving average smoothing and multiplicative scatter correction (MSC). Four supervised classification algorithms were chosen to categorize the types of fur: soft independent modeling of class analogy (SIMCA), principal component analysis linear discriminant analysis (PCA-LDA), partial least squares discriminant analysis (PLS-DA), least squares support vector machine (LS-SVM). PLS-DA and LS-SVM were both effective approaches, with a 100% classification accuracy rate. The accuracy of PCA-LDA and SIMCA was 98.33% and 99.44%, respectively. Furthermore, LS-SVM model obtained using Monte-Carlo sampling method also obtained 100% prediction accuracy, while all other methods produced misclassification. LS-SVM corrected the non-linearities for the animal fur FTIR data but also remarkably improved the prediction performance level. The results of this study revealed that the combination of ATR-FTIR and chemometrics has a huge potential for animal fur discrimination.

A Fast PCR Test for the Simultaneous Identification of Species and Gender in Horses, Donkeys, Mules and Hinnies

Having considered that the current methods are costly and time-consuming, we designed an only 3 pairs primer-based PCR test to accurately identify the species and gender in horses, donkeys, mules and hinnies. Through a thorough sequence comparison between horse and donkey's highly similar genomes, and a vast amount of preliminary confirmation, we found that three fragments, CNGB3 gene on an autosome, displacement loop region on mitochondrial DNA and SRY genes on chromosome Y, within these equine DNA, are enough to enable us achieving our goal. The PCR test described here would be an economical, fast and accurate alternative for the most commonly-used methods, polymerase chain reaction-restriction fragment length polymorphism, microsatellite assay, and sequencing.

Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome

Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004-0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225-0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.

A Wildlife Forensic Study for the Species Identification of Indian Blackbuck through Forensically Informative Nucleotide Sequencing (FINS)

Identification of exhibits obtained in wildlife cases usually presents challenging tasks for the forensic science investigators. This study describes a casework, where a degraded tissue sample was recovered from pathology department LUVAS University Hisar, Haryana to resolve the identity of the questioned sample. The mitochondrial DNA region of the questioned sample was amplified and sequenced using universal primers of cytochrome b gene to determine the forensically informative nucleotide sites to find the species identity. The obtained sequencing results were compared with the most homologous sequences extracting from NCBI-GenBank database and a phylogenetic tree was done with the aligned sequences to determine the species identity with strong bootstrap support. The informative sites generated revealed that the degree of sequence similarity showed maximum homology (100%) with the sequence obtained from the database. Based on the FINS analysis the recovered sample related to Antilope cervicapra (family Bovidae).

Follow-up on the characterization of peptidic markers in hair and fur for the identification of common North American species

RATIONALE

Species identification of hair is routinely done by microscopic analysis. Following previous studies that used protein analysis to characterize species markers in hair and wool, the present work aims at covering a larger number of species and to ultimately offer a method for rapid hair identification in forensics and archaeology.

METHODS

Hair is mostly made of alpha-keratins; these proteins have only been sequenced in a handful of species and most animal families are under-represented. Using a methodology developed for the characterization of peptidic markers in tissues such as bone (peptide mass fingerprinting or PMF) and commonly applied on collagen, hair from common North American fur-bearing species was analyzed by MALDI-TOF-MS to obtain peptidic profiles.

RESULTS

Alpha-keratin peptides that are typically dominant on peptide mass profiles of hair were chosen as markers. Matching peaks were identified for each species tested and compared to known sequences from related organisms whenever possible. The markers were used to create a flowchart to narrow down identification to the family level.

CONCLUSIONS

The methodology was developed on a limited numbers of markers chosen for their variability and reliability on the peptide mass fingerprint. In the absence of genetic sequences, this strategy is a quick way to compare species from a common geographic origin. The work presented here was focused on North American species but could be applied to other animal families.

Forensically informative nucleotide sequencing (FINS) for the first time authentication of Indian Varanus species: implication in wildlife forensics and conservation

Monitor lizards are Varanus species widely distributed, endangered reptile in the IUCN red data list. In India, based on the morphological and ecological characteristic, it is divided into four species viz. Bengal monitor lizard, Yellow monitor lizard, Desert monitor lizard and Water monitor lizard. These four species listed as Schedule I species in Indian Wildlife (Protection) Act 1972. This paper first attempt to present Forensically Informative Nucleotide Sequencing (FINS) for the Indian Varanus based on three mitochondrial genes. The molecular framework will be useful for the identification of Indian Varanus species and trade products derived from monitors and as such, have important applications for wildlife management and conservation. Here, we used known 14 individual skin pieces of four species of monitor lizards; the partial fragment of three mitochondrial genes (Cyt b, 12S rRNA, and 16S rRNA) were amplified for genetic study. In Cyt b, 12S rRNA and 16s rRNA, we observed, 5, 5 and 4 Haplotypes; 71, 69, and 43 Variables sites; 90, 89, and 50 Parsimony Informative sites within four species of Indian monitor lizards, respectively. Despite it, the nucleotide composition was T 26.4, C 32.8, A 29.2 and G11.6; T 18.8, C 29.7, A 34.0 and G 17.5; T 21.7, C 27.3, A 32.5 and G 18.5 in Cyt b, 12S rRNA and 16S rRNA, respectively. The neighbor joining phylogenetic tree and maximum parsimony tree of three mitochondrial genes, showed similar results and reveal that, there are two major clades are present in Indian monitor lizards.

Forensic animal DNA analysis using economical two-step direct PCR

Wildlife forensic DNA analysis by amplification of a mitochondrial locus followed by DNA sequencing is routine, yet suffers from being costly and time-consuming. To address these disadvantages we report on a low-cost two-step direct PCR assay to efficiently analyze 12 forensically relevant mammalian sample types without DNA extraction. A cytochrome oxidase I degenerate-universal primer pair was designed and validated for the developed assay. The 12 sample types, which included bone, horn, feces, and urine, were amplified successfully by the assay using a pre-direct PCR dilution protocol. The average amplification success rate was as high as 92.5 % (n = 350), with an average PCR product concentration of 220.71 ± 180.84 ng/μL. Differences in amplification success rate and PCR product quantity between sample types were observed; however, most samples provided high quality sequences, permitting a 100 % nucleotide similarity to their respective species via BLAST database queries. The combination of PBS and Phire(®) Hot Start II DNA polymerase gave comparable amplification success rate and amplicon quantity with the proprietary commercial kits (P > 0.05, n = 350) but at considerably lower cost. The stability of the assay was tested by successfully amplifying samples that had been stored for up to 12 months. Our data indicate that this low-cost two-step direct amplification assay has the potential to be a valuable tool for the forensic DNA community.

Forensically informative nucleotide sequencing (FINS) for the authentication of Chinese medicinal materials

Chinese medicinal materials may be authenticated by molecular identification. As a definitive approach to molecular identification of medicinal materials, forensically informative nucleotide sequencing (FINS) comprises four steps, namely (1) DNA extraction from biological samples, (2) selection and amplification of a specific DNA fragment, (3) determination of the sequence of the amplified DNA fragment and (4) cladistic analysis of the sample DNA sequence against a DNA database. Success of the FINS identification depends on the selection of DNA region and reference species. This article describes the techniques and applications of FINS for authenticating Chinese medicinal materials.