Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies

Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea

Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.

Lost at sea: determining geographic origins of illegally traded green sea turtles (Chelonia mydas) rescued on Hainan Island, China

Abstract ContextGreen sea turtles are threatened by exploitation for food and medicine markets, with Asian populations facing the heaviest pressures. Sea turtle confiscations that happen out at sea can give a general area that poachers are targeting, but it can be difficult to determine the impact on specific nesting rookeries. Previous studies circumvented this difficulty by using genetic markers to identify nesting rookery origins of confiscated green turtles. AimsTo determine the impact on nesting rookeries from the illegal harvesting of green sea turtles by Hainan fishermen and describe the genetic diversity of the Paracel Islands’ green sea turtle population. MethodsIn the present study, we sequenced 384bp of mitochondrial DNA control region from 85 illegally traded green sea turtles rescued on Hainan Island, China, to investigate their population of origin. For reference-source data, we used previously published mtDNA haplotype data from rookeries from Australasian waters and mtDNA haplotype data from 16 newly collected samples from the Paracel Islands in the South China Sea, a previously unsampled area. Key resultsTen and four mtDNA haplotypes, all being reported before, were detected from the Hainan confiscation and Paracel Islands rookery respectively. However, CmP19, an infrequent haplotype that has been found only in 10 green sea turtles previously, made up ~45% of our rescued samples and ~62% of the Paracel Islands sample, suggesting a potential association between CmP19 and the Paracel Island rookery. Haplotype diversity of the rescued green sea turtles was relatively high (h=0.7143±0.04), whereas nucleotide diversity was relatively low (π=0.0031±0.00), compared with other rookeries. Mixed-stock analysis suggested that the rookeries in the Paracel Islands (~57%) and the Sulu Sea (~29%) are experiencing the greatest impact from illegal harvesting by fishermen from Hainan and neighbouring countries. ConclusionsThe Paracel Islands population contains a unique genetic makeup compared with other studied rookeries, particularly the high frequency of the previously rare CmP19 haplotype. The current harvesting of green sea turtles by Hainan fishermen affects not only protected local populations (Paracel Islands), but also distant populations (Sulu Sea) in protected international waters. ImplicationsEstablishment of a large-scale Sea Turtle Nature Reserve in the South China Sea, including a special law enforcement team to monitor this National Marine Park, needs to be top priority to help curb illegal harvesting. The Paracel Islands represents a newly defined population, and conservation measures need to be taken immediately to preserve this distinct population.

Wildlife forensics in battle against veneration frauds in Uttarakhand, India: identification of protected Indian monitor lizard in items available in the local market under the name of Hatha Jodi

Certain articles of worship are commonly sold in Uttarakhand, India by the name Hatha Jodi, a root of a rare plant found only in a few parts of central India. The present work provides genetic proof that the Hatha Jodi sold in three local markets of Uttarakhand contained material from the Varanus species, species protected under the Indian Wildlife (Protection) Act, 1972. A total of eight samples were bought, two each from the local markets in Haridwar and Rishikesh, three from Dehradun and one from an online source (Amazon). The initial inspection confirmed that two of the samples were made of plastic material. Therefore only the other six samples were subjected to DNA analysis. DNA sequences were successfully obtained and matched with reference sequences available in NCBI Genbank database through BLAST search tool for species identification. All the six samples matched 100% with the Indian monitor lizard. The findings indicate how commercialization and the wildlife trade are playing a role in decline of the population of the Indian monitor lizard. If strong protection measures are not taken as soon as possible, the Indian monitor lizards will go Extinct very soon. Therefore, we suggest that the Government and Wildlife enforcement agencies take serious action against the illegal articles available in the local markets of Uttarakhand under the name Hatha Jodi. Further, the government needs to take legal action against offenders in other states in which the product is available for sale.

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing

The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform [corrected]. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.

Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing

Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 96,188 (29.63%) putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (F_IS >0) and low values of H_obs, which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future.

Forensic genetics and genomics: Much more than just a human affair

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.

On the potential of using peculiarities of the protein intrinsic disorder distribution in mitochondrial cytochrome b to identify the source of animal meats

This study was conducted to identify the source of animal meat based on the peculiarities of protein intrinsic disorder distribution in mitochondrial cytochrome b (mtCyt-b). The analysis revealed that animal and avian species can be discriminated based on the proportions of the two groups of residues, Leu+Ile, and Ser+Pro+Ala, in the amino acid sequences of their mtCyt-b. Although levels of the overall intrinsic disorder in mtCyt-b is not very high, the peculiarities of disorder distribution within the sequences of mtCyt-b from different species varies in a rather specific way. In fact, positions and intensities of disorder/flexibility "signals" in the corresponding disorder profiles are relatively unique for avian and animal species. Therefore, it is possible to devise a set of simple rules based on the peculiarities of disorder profiles of their mtCyt-b proteins to discriminate among species. This intrinsic disorder-based analysis represents a new technique that could be used to provide a promising solution for identification of the source of meats.

Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions

The hypervariable region I (HVRI) is persistently used to discern haplotypes, to distinguish geographic subpopulations, and to infer taxonomy in a range of organisms. Numerous studies have highlighted greater heterogeneity elsewhere in the mitochondrial DNA control region, however-particularly, in some species, in other understudied hypervariable regions. To assess the abundance and utility of such potential variations in orang-utans, we characterised 36 complete control-region haplotypes, of which 13 were of Sumatran and 23 of Bornean maternal ancestry, and compared polymorphisms within these and within shorter HVRI segments predominantly analysed in prior phylogenetic studies of Sumatran (~385 bp) and Bornean (~323 bp) orang-utans. We amplified the complete control region in a single PCR that proved successful even with highly degraded, non-invasive samples. By using species-specific primers to produce a single large amplicon (~1600 bp) comprising flanking coding regions, our method also serves to better avoid amplification of nuclear mitochondrial insertions (numts). We found the number, length and position of hypervariable regions is inconsistent between orang-utan species, and that prior definitions of the HVRI were haphazard. Polymorphisms occurring outside the predominantly analysed segments were phylogeographically informative in isolation, and could be used to assign haplotypes to comparable clades concordant with geographic subpopulations. The predominantly analysed segments could discern only up to 76% of all haplotypes, highlighting the forensic utility of complete control-region sequences. In the face of declining sequencing costs and our proven application to poor-quality DNA extracts, we see no reason to ever amplify only specific 'hypervariable regions' in any taxa, particularly as their lengths and positions are inconsistent and cannot be reliably defined-yet this strategy predominates widely. Given their greater utility and consistency, we instead advocate analysis of complete control-region sequences in future studies, where any shorter segment might otherwise have proven the region of choice.

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.

Complete mitochondrial genome of a wild Alashan Red Deer (Cervus elaphus alxaicus)

The complete mitochondrial genome of a wild red deer from Helan Mountain, China was sequenced and annotated newly. The total length of the mitochondrial genome is 16,428 bp, with a base composition of 33.3% A, 28.8% T, 24.4% C and 13.5% G, and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region.

DNA barcode based wildlife forensics for resolving the origin of claw samples using a novel primer cocktail

Excessive wildlife hunting for commercial purposes can have negative impacts on biodiversity and may result in species extinction. To ensure compliance with legal statutes, forensic identification approaches relying on molecular markers may be used to identify the species of origin of animal material from hairs, claw, blood, bone, or meat. Using this approach, DNA sequences from the COI "barcoding" gene have been used to identify material from a number of domesticated animal species. However, many wild species of carnivores still present great challenges in generating COI barcodes using standard "universal" primer pairs. In the work presented here, the mitochondrial COI gene was successfully amplified using a novel primer cocktail, and the products were sequenced to determine the species of twenty one unknown samples of claw material collected as part of forensic wildlife case investigations. Sixteen of the unknown samples were recognized to have originated from either Panthera leo or P. pardus individuals. The remaining five samples could be identified only to the family level due to the absence of reference animal sequences. This is the first report on the use of COI sequences for the identification of P. pardus and P. leo from claw samples as part of forensic investigations in India. The study also highlights the need for adequate reference material to aid in the resolution of suspected cases of illegal wildlife harvesting.

The control of mtDNA replication during differentiation and development

BACKGROUND

Mitochondrial DNA (mtDNA) is important for energy production as it encodes some of the key genes of electron transfer chain, where the majority of cellular energy is generated through oxidative phosphorylation (OXPHOS). MtDNA replication is mediated by nuclear DNA-encoded proteins or enzymes, which translocate to the mitochondria, and is strictly regulated throughout development. It starts with approximately 200 copies in each primordial germ cell and these copies undergo expansion and restriction events at various stages of development.

SCOPE OF REVIEW

I describe the patterns of mtDNA replication at key stages of development. I explain that it is essential to regulate mtDNA copy number and to establish the mtDNA set point in order that the mature, specialised cell acquires the appropriate numbers of mtDNA copy to generate sufficient adenosine triphosphate (ATP) through OXPHOS to undertake its specialised function. I discuss how these processes are dependent on the controlled expression of the nuclear-encoded mtDNA-specific replication factors and that this can be modulated by mtDNA haplotypes. I discuss how these events are altered by certain assisted reproductive technologies, some of which have been proposed to prevent the transmission of mutant mtDNA and others to overcome infertility. Furthermore, some of these technologies are predisposed to transmitting two or more populations of mtDNA, which can be extremely harmful.

MAJOR CONCLUSIONS

The failure to regulate mtDNA replication and mtDNA transmission during development is disadvantageous.

GENERAL SIGNIFICANCE

Manipulation of oocytes and embryos can lead to significant implications for the maternal-only transmission of mtDNA. This article is part of a Special Issue entitled Frontiers of mitochondrial research.

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.

DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa

Poaching of wildlife animals for subsistence and commercial purposes has lead to population declines in Africa. In forensic cases, a need exists to identify the species of origin of carcasses, meat or blood. In the study presented here, the mitochondrial COI gene was sequenced to determine the species of unknown samples in three suspect South African forensic wildlife cases. In two cases the unknown samples were identified as originating from domestic cattle (Bos taurus) and in the third case the sample was identified as common reedbuck (Redunca arundinum). This is the first report of the COI sequence of common reedbuck. The study highlights the need for accurate wildlife reference material from each country in order to convict wildlife cases.

Application of DNA forensic techniques for identifying poached guanacos (Lama guanicoe) in Chilean Patagonia*

Guanaco (Lama guanicoe) is a protected and widely distributed ungulate in South America. A poacher, after killing guanacos in Valle Chacabuco, Chilean Patagonia, transported and stored the meat. Samples were retrieved by local police but the suspect argued that the meat was from a horse. Mitochondrial cytochrome b gene (774 pb), 15 loci microsatellites, and SRY gene were used to identify the species, number of animals and their population origin, and the sex of the animals, respectively. Analysis revealed that the samples came from a female (absence of SRY gene) Patagonian guanaco (assignment probability between 0.0075 and 0.0282), and clearly distinguishing it from sympatric ungulates (E-value = 0). Based on the evidence obtained in the field in addition to forensic data, the suspect was convicted of poaching and illegally carrying fire arms. This is the first report of molecular tools being used in forensic investigations of Chilean wildlife indicating its promising future application in guanaco management and conservation.

Sequence characterization and polymerase chain reaction-restriction fragment length polymorphism of the mitochondrial DNA 12S rRNA gene provides a method for species identification of Indian deer

Characterization of species-specific molecular markers and development of a method for identification of Indian deer species is necessary to monitor illegal trade of parts and products for better conservation and management of the endangered species. In this investigation, we characterized the 12S rRNA gene sequence for differentiation of Indian deer species and developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based method for their identification. Universal primers were used for the amplification of the mitochondrial 12S rRNA gene from genomic DNA of chital or spotted deer, hog deer, barking deer, sika deer, musk deer and sambar. PCR products of chital, hog deer and Himalayan musk deer were cloned and sequenced for the first time. Among the Indian deer species, more than 90% similarity was observed in the mitochondrial 12S rRNA gene. The sequences of the above deer species were restriction mapped with the help of Lasergene (DNAstar Inc., Madison, WI, USA). PCR amplicon of these deer species were subjected to restriction digestion with Rsa1, Dde1, Bsr1 and BstSF1 endonucleases that showed a species-specific RFLP pattern. This technique provides a reliable and efficient tool for identification of deer species using a variety of biomaterials.

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.

A forensic STR profiling system for the Eurasian badger: a framework for developing profiling systems for wildlife species

Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (theta) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI(ave)) was 2.18 x 10(-7). This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.

Validation of the barcoding gene COI for use in forensic genetic species identification

The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification.