A molecular genetic approach for forensic animal species identification

Pyrosequencing: Current forensic methodology and future applications-a review

The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.

Post-Mortem Dental Profile as a Powerful Tool in Animal Forensic Investigations—A Review

Veterinary forensics is becoming more important in our society as a result of the growing demand for investigations related to crimes against animals or investigations of criminal deaths caused by animals. A veterinarian may participate as an expert witness or may be required to give forensic assistance, by providing knowledge of the specialty to establish a complete picture of the involvement of an animal and allowing the Courts to reach a verdict. By applying diverse dental profiling techniques, not only can species, sex, age-at-death, and body size of an animal be estimated, but also data about their geographical origin (provenance) and the post-mortem interval. This review concentrates on the dental techniques that use the characteristics of teeth as a means of identification of freshly deceased and skeletonised animals. Furthermore, this highlights the information that can be extracted about the animal from the post-mortem dental profile.

Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds

Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.

Morphometric variation in wolves and golden jackal in India (Mammalia, Carnivora)

Species of Canis (Carnivora, Canidae) have similar morphology and distinguishing sympatric species is challenging. We present data on morphometry of skull, body and hair of three wild Canis species that occur in India, which include two wolves (Indian wolf, Canislupuspallipes; and Himalayan wolf, Canishimalayensis) and the golden jackal (Canisaureus). A total of 20 cranial and six body measurements and microscopic characteristics of guard hair were analysed, using multivariate ordination to differentiate between species. Cranial measures of the Himalayan wolves were found to be the largest followed by Indian wolves and golden jackals. However, many measures overlapped amongst the three species. Two Principal Components each, for body measures and cranial measures, explained 86 and 91% of the variation in the data, respectively. These Components discriminated the two wolves from golden jackals, but could not distinguish between wolves. Hair medullary patterns were simple and wide type, whereas hair cuticular patterns showed crenate scale margins, near scale distance and irregular wavey scale patterns for all Canis taxa and were not useful to distinguish species. Data reported in this study further contribute to the existing global data on wild canids for a holistic understanding of the variation within the genus and show that distinguishing between all sympatric species from morphology alone may not be possible.

Comparative evaluation of different human dental tissues and alveolar bone for DNA quantity and quality for forensic investigation

In this study, the efficacy of dental tissues (cementum, dentine and pulp) and alveolar bone as a potential source of DNA was tested in terms of the quality and quantity using nuclear and mitochondrial markers for forensic investigation.This study found dentine as the best source of DNA with only 5.36% imbalanced (PHR<0.7) heterozygous loci. Pulp showed the highest quantity of DNA but exhibited 22.3% imbalanced (PHR<0.7) heterozygous loci. Cementum with highest (46.67%) heterozygote imbalance proved to be the last choice as a source of DNA. Alveolar bone exhibited the second-highest total yield of DNA/mg of tissue. All Global Filer™ STR loci were amplified in 70% samples of fresh alveolar bone whereas for 30% samples, only partial profile was generated along with successful sex determination. All the dental tissues and alveolar bone samples amplified non STR markers (D-loop, Cytochrome Oxidase I, SRY, AMEL). Of the alveolar bones from archival samples, one sample exhibited full STR profile whereas other alveolar bone samples gave partial profiles. This study substantiates alveolar bone as an alternate source of nuclear and mitochondrial DNA.

Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting

BACKGROUND

Biomolecular methods for species identification are increasingly being utilised in the study of changing environments, both at the microscopic and macroscopic levels. High-throughput peptide mass fingerprinting has been largely applied to bacterial identification, but increasingly used to identify archaeological and palaeontological skeletal material to yield information on past environments and human-animal interaction. However, as applications move away from predominantly domesticate and the more abundant wild fauna to a much wider range of less common taxa that do not yet have genetically-derived sequence information, robust methods of species identification and biomarker selection need to be determined.

RESULTS

Here we developed a supervised machine learning algorithm for classifying the species of ancient remains based on collagen fingerprinting. The aim was to minimise requirements on prior knowledge of known species while yielding satisfactory sensitivity and specificity. The algorithm uses iterations of a modified random forest classifier with a similarity scoring system to expand its identified samples. We tested it on a set of 6805 spectra and found that a high level of accuracy can be achieved with a training set of five identified specimens per taxon.

CONCLUSIONS

This method consistently achieves higher accuracy than two-dimensional principal component analysis and similar accuracy with hierarchical clustering using optimised parameters, which greatly reduces requirements for human input. Within the vertebrata, we demonstrate that this method was able to achieve the taxonomic resolution of family or sub-family level whereas the genus- or species-level identification may require manual interpretation or further experiments. In addition, it also identifies additional species biomarkers than those previously published.

Evaluating the role of Pleistocene refugia, rivers and environmental variation in the diversification of central African duikers (genera Cephalophus and Philantomba)

Background

This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species (Cephalophus dorsalis, C. callipygus and Philantomba monticola). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci.

Results

Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola. The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation.

Conclusions

Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species’ capacity to adapt to environmental change.

Electronic supplementary material

The online version of this article (10.1186/s12862-017-1054-4) contains supplementary material, which is available to authorized users.

Advances in the Knowledge about Kidney Decellularization and Repopulation

End-stage renal disease (ESRD) is characterized by the progressive deterioration of renal function that may compromise different tissues and organs. The major treatment indicated for patients with ESRD is kidney transplantation. However, the shortage of available organs, as well as the high rate of organ rejection, supports the need for new therapies. Thus, the implementation of tissue bioengineering to organ regeneration has emerged as an alternative to traditional organ transplantation. Decellularization of organs with chemical, physical, and/or biological agents generates natural scaffolds, which can serve as basis for tissue reconstruction. The recellularization of these scaffolds with different cell sources, such as stem cells or adult differentiated cells, can provide an organ with functionality and no immune response after in vivo transplantation on the host. Several studies have focused on improving these techniques, but until now, there is no optimal decellularization method for the kidney available yet. Herein, an overview of the current literature for kidney decellularization and whole-organ recellularization is presented, addressing the pros and cons of the actual techniques already developed, the methods adopted to evaluate the efficacy of the procedures, and the challenges to be overcome in order to achieve an optimal protocol.

Genetic diversity of the Tibetan antelope (Pantholops hodgsonii) population of Ladakh, India, its relationship with other populations and conservation implications

BACKGROUND

The Tibetan antelope (Pantholops hodgsonii), or chiru, is an endangered antelope, distributed in China [Xinjiang, Xizang, Qinghai, Zhuolaihu Lake (Breeding habitat)], and India (Aksai Chin and Ladakh). There is a global demand for the species prized wool, which is used in weaving shahtoosh shawls. Over the years, the population of the Tibetan antelope has drastically declined from more than a million to a few thousand individuals, mainly due to poaching. Field studies undertaken in Ladakh, India also indicated winter migration of the population to Tibet. Migration between winter and calving habitats is well established to be female-biased across the Qinghai Tibetan Plateau (QTP). For effective conservation planning, genetic characterization is considered the best way to understand the likely impact of threats for ensuring the long-term viability of the population. In this regard, genetic characteristics of all Chinese populations are well-studied using mitochondrial and microsatellite markers, but information is lacking for the Indian population. Therefore, using the control region marker, we document for the first time the genetic variation of the Indian population of the Tibetan antelope, the extent of migration and its relationships with other populations of China.

RESULTS

The partial fragment of control region (259 bp) marker was successfully amplified in 30 Tibetan antelope samples that were collected from the Chang Chenmo Valley in eastern Ladakh, India. We also retrieved control region sequences (n = 88) available in the public domain from GenBank of different Chinese populations. Low levels of nucleotide (π; 0.004) and haplotype (hd; 0.543) diversity were observed in the Indian population when compared to Chinese populations (π = 0.01357-0.02048 and hd = 0.889-0.986). Commonly used indices (Tajima's D and Fu's Fs) were analyzed for inferring the demographic history of the Indian populations, and all values were negative indicating population expansion or demographic equilibrium, though nonsignificant. We observed five haplotypes in the Indian population, and these were not reported in previously studied populations of QTP. Bayesian-based phylogenetic analysis indicates the presence of four clades, however, the posterior probability support for three of these clades is weak (<0.5). Of these, the Indian population formed a distinct clade, whereas the Chinese populations exhibited shared haplotypes, and no geographic structure was observed. Median-joining network analysis was conducted for 46 haplotypes in the overall population, except the samples from India which showed a star-like topology. The Indian population is separated by one median vector from the Chinese population.

CONCLUSIONS

The present study revealed the presence of different sub-clades in the Bayesian phylogenetic tree and five new haplotypes only in the Indian population or sampling location. Furthermore, in the phylogenetic tree, Indian haplotypes of Tibetan antelopes were clustered with the haplotype reported in the Chinese population of the Xinjiang region. Median-joining network analysis showed shared haplotypes pattern in all populations of QTP except the samples from India which showed new haplotypes. Given the presence of low nucleotide and haplotype diversity in eastern Ladakh populations and limited information available for populations of the western side in its range, we suggest to include genetic studies of Tibetan antelope populations around Aksai Chin (Fig. 1) under the proposed transboundary agenda between India and China and assess relationships with other populations. Such understanding would enable the planning of conservation strategies for ensuring long-term survival of westernmost populations in its range, and if required, it would establish connectivity with the other populations.

Artefactual incised wounds due to postmortem predation by the Sri Lankan water monitor (kabaragoya)

Monitor lizards are large reptilian animals mostly seen around water based habitats. Sri Lanka has an endemic water monitor lizard called the kabaragoya (Varanus salvator salvator) which is perhaps the most common large animal scavenger in the country. Scavenging by the kabaragoya can result in postmortem incised injuries which are caused by their sharp pointed claws as they grip or crawl over a dead body. The author presents four cases where these claw marks raised significant medicolegal issues. In one case of a young female they mimicked defense injuries that might be seen in a person that was killed with heavy sharp weapon trauma to the head. In another case, claw marks on the face raised homicidal allegations in an immersion death following intoxication. In a case of suicidal drowning these injuries simulated self-inflicted cuts. The fourth case shows how claw marks complicated the investigation of a dismembered upper limb. Kabaragoya claw marks are mostly seen in decomposed and macerated bodies recovered from water. Injuries are mostly superficial and limited to skin and soft tissues. Bony injuries are not seen. Awareness of the creature's scavenging habits and careful analysis of the appearance and distribution of the injuries is essential to differentiate claw marks from sharp weapon trauma.

Mummified remains from the Archaeological Museum in Zagreb, Croatia - Reviewing peculiarities and limitations of human and non-human radiological identification and analysis in mummified remains

Forensic protocols and medico-legal techniques are increasingly being employed in investigations of museological material. The final findings of such investigations may reveal interesting facts on historical figures, customs and habits, as well as provide meaningful data for forensic use. Herein we present a case review where forensic experts were requested to identify taxonomic affinities, stage of preservation and provide skeletal analysis of mummified non-human archaeological remains, and verify whether two mummified hands are human or not. The manuscript offers a short review on the process and particularities of radiological species identification, the impact of post-mortem changes in the analysis and imaging of mummified remains as well as the macroscopical interpretation of trauma, pathology and authenticity in mummified remains, which can all turn useful when dealing with forensic cases.

Identificação espécie-específica de carnes e produtos cárneos de origem bubalina e bovina pela técnica de PCR-RFLP

Para avaliar a viabilidade da metodologia da Reação em Cadeia da Polimerase associada com o Polimorfismo de Fragmentos de DNA (PCR-RFLP) na identificação de fraude intencional e contaminação acidental em produtos cárneos de origem bubalina, in natura e processados, foram testadas amostras puras e amostras de carnes com misturas controladas, produzidas em laboratório, com adição de 1%, 5%, 10% e 50% de carne bovina em carne de búfalo, homogeneizada crua e em amostras autoclavada. Foram comparados, ainda, diferentes métodos de extração, usando um kit comercial e a técnica clássica, utilizando fenol/clorofórmio. O resultado estatístico foi obtido por tabela de contingência, analisada pelo teste do qui-quadrado (χ2) e do exato de Fisher. A especificidade encontrada foi altamente significativa (P<0,0001). Observou-se também sensibilidade altamente significativa nas diluições a partir de 10% (P<0,0001). A técnica tem alta especificidade e sensibilidade para detectar até mesmo contaminação de 1%, mas a repetibilidade desse resultado impede a aplicação oficial desse método para a inspeção de contaminação acidental, sendo recomendada somente para inspeção de fraude a partir de 10% de substituição. Em carnes autoclavadas, a eficácia do teste é menor. A técnica pode ser empregada para certificação de produto específico (selo de identidade de espécie).

A new subspecies identification and population study of the Asian small-clawed otter (Aonyx cinereus) in Malay Peninsula and southern Thailand based on fecal DNA method

Three species of otter can be found throughout Malay Peninsula: Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata. In this study, we focused on the A. cinereus population that ranges from the southern and the east coast to the northern regions of Malay Peninsula up to southern Thailand to review the relationships between the populations based on the mitochondrial D-loop region. Forty-eight samples from six populations were recognized as Johor, Perak, Terengganu, Kelantan, Ranong, and Thale Noi. Among the 48 samples, 33 were identified as A. cinereus, seven as L. sumatrana, and eight as L. perspicillata. Phylogenetically, two subclades formed for A. cinereus. The first subclade grouped all Malay Peninsula samples except for samples from Kelantan, and the second subclade grouped Kelantan samples with Thai sample. Genetic distance analysis supported the close relationships between Thai and Kelantan samples compared to the samples from Terengganu and the other Malaysian states. A minimum-spanning network showed that Kelantan and Thailand formed a haplogroup distinct from the other populations. Our results show that Thai subspecies A. cinereus may have migrated to Kelantan from Thai mainland. We also suggest the classification of a new subspecies from Malay Peninsula, the small-clawed otter named A. cinereus kecilensis.

DNA barcode through cytochrome b gene information of mtDNA in native chicken strains

This study was carried out to figure out the potentiality of a cytochrome b gene as a barcoding tool in discriminating native chicken strains and other Gallus gallus species. We performed PCR amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The results revealed that all Saudi chicken strains were identical to each other but when compared with other species of Gallus the differences were exciting. The phylogenetic tree revealed that there were seven clusters represented for native strains and were clustered together especially in black strain and dark brown ones. The results have confirmed that using cytochrome b gene to discriminate between Saudi chicken strains and other species of G. gallus fowl was a very sufficient tool. Moreover, we can consider short fragment of cytochrome b gene of mtDNA as a universal DNA barcode region. It was a much more accurate and efficient tool to discriminate interspecies than intraspecies. We think it needs more studies to confirm this concept, and we have to apply that tool for many species of vertebrate and invertebrate as well.

Extração de DNA e avaliação da composição espécie-específica de queijos

Foram testados três métodos de extração de DNA em amostras de queijo, com o objetivo de identificar uma técnica eficiente para extração de DNA em amostras com várias limitações, como alto teor de gordura, alto grau de degradação do DNA e grande concentração de impurezas. A técnica que faz uso do tiocianato de guanidina mostrou-se mais adequada para identificação de adição intencional não declarada de leite bovino em queijos bubalinos, podendo ser empregada para certificação de produto específico (selo de Identidade de Espécie).

Application of STR markers in wildlife forensic casework involving Australian black-cockatoos (Calyptorhynchus spp.)

Parrots and cockatoos are highly prized aviary birds and the demands for such species has fuelled their illegal trade and harvest from the wild. Here we report on three forensic case studies involving black-cockatoos (Calyptorhynchus spp.) endemic to Australia. These cases involve suspected poaching and illegal killing of endangered red- and white-tailed black-cockatoos. Through the prior development of 20 polymorphic microsatellite loci and population databases for white- and red-tailed black-cockatoos, the tools are available to conduct high-resolution paternity and individual identity testing. In one case, we matched a red-tailed black-cockatoo nestling to a tree hollow from which it was poached through the use of DNA from eggshell recovered from the nest. For the second case, we utilized our provenance population database (nest sites), and identified the kinship and geographic origin of a white-tailed black-cockatoo, which was illegally harvested from the wild. The third case determined the number individual white-tailed black-cockatoos allegedly shot at a fruit grower's orchard from body part remains. These genetic investigations highlight the significance and statistical confidence of DNA profiling and associated databases for endangered taxa, such as exotic birds. Our cockatoo population databases are the first of their kind in Australia, and demonstrate the efficacy of such approaches to identify such illegal activity. With a robust set of genetic markers and methodologies in place, we aim to broaden our population databases to include other cockatoo species of conservation concern.

Species identification of the Northern shrimp (Pandalus borealis) by polymerase chain reaction-restriction fragment length polymorphism and proteomic analysis

Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belong to the superfamily Penaeoidea, which include the families Penaeidae and Solenoceridae, and 11 other crustacean species, including prawns, shrimps, lobsters, and crabs. For this purpose, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was designed based on the amplification of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial regions using the primers 16S-CruF and 16S-CruR. The 966-bp PCR products were produced and cleaved with the restriction enzymes AluI, TaqI, and HinfI, which provided species-specific restriction patterns. In addition, a proteomic approach, based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-ion trap (ESI-IT) mass spectrometry, was used to identify and characterize new P. borealis-specific peptides that could be useful as potential markers of this species in protein-based detection methods. To our knowledge, this is the first time a molecular method has been successfully applied to identify a wide range of prawn and shrimp species, including P. borealis, for either whole individuals or processed products. However, validation of the methods proposed here is required by applying them to a larger sample of individuals from different populations and geographic origins in order to avoid mainly false-negative results.

South American camelid illegal traffic detection by means of molecular markers

South American camelids comprise the wild species guanaco and vicuña and their respective domestic relatives llama and alpaca. The aim of the present study was to determine by DNA analysis to which of these species belong a herd of camelids confiscated from a llama breeder but alleged to be alpacas by the prosecution, and to evaluate the usefulness of mitochondrial and autosomal DNA markers to solve judicial cases involving camelid taxa. Cytochrome b and cytochrome oxidase I mitochondrial genes and 7 STR were analyzed in 25 confiscated samples. Mitochondrial results were inconclusive because 18 of the sequestered samples presented haplotypes that corresponded to the guanaco haplogroup and the remaining seven belonged to a vicuña linage. Microsatellite data of casework samples and llama reference samples revealed different genetic profiles by the presence of private alleles at two microsatellites suggesting that the confiscated animals could be alpaca, or at least alpaca hybrids instead of pure llama.

Discrimination between human and animal DNA: application of a duplex polymerase chain reaction to forensic identification

Identification of a report's species is one of the basic analyses in forensic laboratories. The authors report the case of 6 bone fragments recovered in a wooded area, which were not attributable to 1 animal species on the basis of morphologic examination. The aim of this study was to develop a duplex polymerase chain reaction (PCR) to discriminate human and animal origin of bone fragments. The method is based on the PCR amplification of cytochrome b and a 16S ribosomal mitochondrial DNA fragment, which has never been tested up to now. Our protocol combines a single-round PCR with direct visualization of amplicons in agarose gel, without sequencing analysis of the PCR products. The presence of a single band (359 bp) indicates a nonhuman origin of the sample, whereas 2 bands (157 and 359 bp) indicate a human biologic sample.This method revealed to be useful for forensic purposes because the 16S ribosomal mitochondrial DNA is a small human-specific fragment that is easily amplifiable even with degraded DNA from biologic materials such as old bones.

Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling

BACKGROUND

The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets.

METHODOLOGY/PRINCIPAL FINDINGS

We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279-modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively.

CONCLUSIONS/SIGNIFICANCE

Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.

Mitochondrial DNA sequencing of cat hair: an informative forensic tool

Approximately 81.7 million cats are in 37.5 million U.S. households. Shed fur can be criminal evidence because of transfer to victims, suspects, and/or their belongings. To improve cat hairs as forensic evidence, the mtDNA control region from single hairs, with and without root tags, was sequenced. A dataset of a 402-bp control region segment from 174 random-bred cats representing four U.S. geographic areas was generated to determine the informativeness of the mtDNA region. Thirty-two mtDNA mitotypes were observed ranging in frequencies from 0.6-27%. Four common types occurred in all populations. Low heteroplasmy, 1.7%, was determined. Unique mitotypes were found in 18 individuals, 10.3% of the population studied. The calculated discrimination power implied that 8.3 of 10 randomly selected individuals can be excluded by this region. The genetic characteristics of the region and the generated dataset support the use of this cat mtDNA region in forensic applications.

Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene

Species identification techniques commonly utilized in Australian Forensic Science laboratories are gel immunodifussion antigen antibody reactions and hair comparison analysis. Both of these techniques have significant limitations and should be considered indicative opinion based tests. The Barcode of Life Initiative aims to sequence a section of DNA (~648 base pairs) for the Cytochrome Oxidase I mitochondrial gene (COI) in all living species on Earth, with the data generated being uploaded to the Barcode of Life Database (BOLD) which can then be used for species identification. The COI gene therefore offers forensics scientists an opportunity to use the marker to analyze unknown samples and compare sequences generated in BOLD. Once sequences from enough species are on the database, it is anticipated that routine identification of an unknown species may be possible. However, most forensic laboratories are not yet suited to this type of analysis and do not have the expertise to fully interpret the implications of matches and non matches involving a poorly sampled taxa (for example where there are cryptic species) and in providing the required opinion evidence. Currently, the use of BOLD is limited by the number of relevant species held in the database and the quality assurance and regulation of sequences that are there. In this paper, the COI methodology and BOLD are tested on a selection of introduced and Australian mammals in a forensic environment as the first step necessary in the implementation of this approach in the Australian context. Our data indicates that the COI methodology performs well on distinct species but needs further exploration when identifying more closely related species. It is evident from our study that changes will be required to implement DNA based wildlife forensics using the BOLD approach for forensic applications and recommendations are made for the future adoption of this technology into forensic laboratories.

DNA typing in wildlife crime: recent developments in species identification

Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.

Using species-specific repeat and PCR-RFLP in typing of DNA derived from blood of human and animal species

Species determination of tissue specimens, including blood, is an important component of forensic analysis to distinguish human from animal remains. DNA markers based on a method of species-specific PCR and amplifying the 359-base pair (bp) fragment of the mitochondrially encoded cytochrome-b gene and then digestion with the TaqI restriction enzyme were developed for detection and discrimination of human, cattle, buffalo, horse, sheep, pig, dog, cat and chicken blood samples. The results reveal that PCR-amplification of the gene encoding the species-specific repeat (SSR) region generated 603 bp in cattle and buffalo, 221 bp in horse, 374 bp in sheep, <or=100 bp in pig, 808 bp in dog, 672 bp in cat and 50 bp in chicken. Restriction analysis of the amplified 359-bp portion of the cytochrome-b gene using the TaqI restriction enzyme results in species-specific restriction fragment length polymorphism (RFLP) between buffalo, cattle and human. Two different bands were generated in buffalo (191 and 168 bp) and human (209 and 150 bp), with no digestion in cattle (359 bp). Cytochrome-b is a highly conserved region and consequently a good molecular marker for diagnostic studies. Therefore, the two complementary techniques, SSR-PCR and PCR-RFLP, could be used successfully as routine methods in forensics for sensitive, rapid, simple and inexpensive identification of the species in bloodstains.

Molecular identification of Indian crocodile species: PCR-RFLP method for forensic authentication*

South East Asian countries are known for illegal poaching and trade of crocodiles clandestinely, to be used in skin, medicinal, and cosmetic industries. Besides crocodiles being listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora, India has its Wildlife Protection Act, 1972 for conservation of crocodile species. Hitherto, lack of any rapid and reliable technique for examinations of crocodile-based crime exhibits such as skin, bones, etc. has been a major problem for an effective promulgation of law on illegal trade. DNA-based identification of species using PCR-RFLP technique for an apt identification of all the three Indian crocodile species namely, Crocodylus porosus, Crocodylus palustris and Gavialis gangeticus is presented here. A 628 bp segment of cytochrome b gene was amplified using novel primers followed by restriction digestion with three enzymes i.e., HaeIII, MboI, and MwoI, separately and in combination. The technique has produced a species-specific pattern for identifying the three crocodile species individually, which fulfills the requirement for its forensic application. It is expected that the technique will prove handy in identification of all the three Indian crocodile species and strengthen conservation efforts.

Simple and sensitive method for identification of human DNA by allele-specific polymerase chain reaction of FOXP2

The forkhead box P2 (FOXP2) gene is specifically involved in speech and language development in humans. The sequence is well conserved among many vertebrate species but has accumulated amino acid changes in the human lineage. The aim of this study was to develop a simple method to discriminate between human and nonhuman vertebrate DNA in forensic specimens by amplification of a human-specific genomic region. In the present study, we designed an allele-specific polymerase chain reaction (PCR) using primers to amplify smaller than 70-bp regions of FOXP2 to identify DNA as being of human or nonhuman, including ape, origin. PCR amplification was also successfully performed using fluorescence-labeled primers, and this method allows a single PCR reaction with a genomic DNA sample as small as 0.01 ng. This system also identified the presence of human DNA in two blood stains stored for 20 and 38 years. The results suggested the potential usefulness of FOXP2 as an identifier of human DNA in forensic samples.

Identification of animal species using the partial sequences in the mitochondrial 16S rRNA gene

This study investigated a PCR direct sequencing method for species identification by analyzing partial sequences in the mitochondrial 16S rRNA genes of many animal species amplified with universal primers. Samples from 182 vertebrates and 103 invertebrates were analyzed, and the sequences could be obtained in 182 and 72 species, respectively. The sequence divergence was sufficient to identify the species at the level of genus with the aid of the GenBank database and the BLAST tool. This method could be a powerful tool for animal species identification, especially in forensic cases in which many unknown biological samples should be analyzed.

Forensic species identification based on size variation of mitochondrial DNA hypervariable regions

In this study, two new systems for species identification were developed based on size variation of mitochondrial DNA hypervariable regions among animals: one was a conventional method using non-fluorescent primer sets and agarose gel electrophoresis and the other was an automatic method using fluorescent primer sets and capillary electrophoresis. DNA samples from 18 mammal, four birds, and 19 fish species were amplified using three primer sets specific for mammals, birds, and fishes, respectively. The differences in the sizes of the polymerase chain reaction (PCR) products, ranging from about 350 to 900 bp, permitted us to identify species. These systems were successfully applied to various specimens from several criminal cases. In unknown samples, which were different in size from reference DNA markers, sequencing of the PCR products and subsequent BLAST analysis helped to identify species. Furthermore, the sequence data provided us with information on individuals. Because these species identification methods are very simple, easy, rapid, and exact, they are useful in the field of forensic science.

Restriction fragment length polymorphism of mitochondrial DNA and phylogenetic relationships among five species of Indian freshwater turtles

DNA-based identification of species for phylogenetic analysis as well as forensic identification is widely being carried out with the help of polymerase chain reaction (PCR). In this study, a successful effort has been made to identify 5 species of Indian freshwater turtles, including 3 hard-shell turtles (Geoemydidae), i.e. Kachuga dhongoka, K. kachuga and Geoclemys hamiltoni, and 2 species of soft-shell turtles (Trionychidae), i.e. Aspideretes gangeticus and Lissemys punctata punctata, by using a well-optimized PCR-RFLP method. The analysis of nucleotide sequence variations in the PCR-amplified mitochondrial cyt-b genes (encoding cytochrome b) from the 5 species revealed its usefulness in the taxonomic differentiation of these species. On the basis of cyt-b sequence data and the PCR-RFLP pattern, a phylogeny was developed to resolve the genetic relationships between these species, living in the same habitat type. In comparison, the PCR-RFLP of mitochondrial 16S rDNA genes appeared less decisive in analysing phylogenetic relationships or even in species differentiation. Further, the molecular method (PCR-RFLP) developed here is simple, rapid, reliable and reproducible; hence it can be routinely applied for species identification, essential for conservation and management of endangered chelonian species.

Genetic traceability of livestock products: A review

Traceability is the ability to maintain the identification of animal, or animal products, all along the production chain. It represents an essential tool to safeguard public and animal health and to valorize typical production systems. European food legislation is particularly strict and traceability systems, based on product labeling, have become mandatory in all European countries. However, the implementation of this system does not ensure consumers against fraud. Paper documents can be counterfeit so researchers have focused on the study of genetic traceability systems based on products identification through DNA analysis. In fact DNA is inalterable, detectable in every cell, resistant to heat treatments, and allows for individual, breed or species identification. Even if results are promising, these techniques are too expensive to be converted in routine tests but they could be a trusted tool for verification of suspected fraud. The present review proposes a synthesis of the major advances made in individual, breed, and species genetic identification in the last years, focusing on advantages and disadvantages and on their real future applications for animal productions.

Identification of mammal species using species-specific DNA pyrosequencing

In forensic casework it is highly relevant to be able to deduce the species origin of an unknown biological sample. For such a purpose we have designed and developed an assay for species identification based on DNA sequencing of two short mitochondrial DNA amplicons. In short, partial 12S rRNA and partial 16S rRNA fragments (approximately 100bp) are amplified by PCR followed by direct sequencing using pyrosequencing technique. Due to properties of the chosen targets, the same PCR conditions and primers were used irrespective of the true species of an unknown sample. A total of 28 different mammals present in the European fauna were sequenced both for the partial 12S rRNA and the partial 16S rRNA sequences for accuracy verification. Together the two sequences showed to have a high divergence factor, discriminating almost all mammals. Furthermore, the human reference nucleotide sequences were always at least nine nucleotides different compared to the other sequenced species both at the partial 12S rRNA and the partial 16S rRNA sequences.