Feline mitochondrial DNA sampling for forensic analysis: when enough is enough!

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing

Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.

The Revolution of Animal Genomics in Forensic Sciences

Nowadays, the coexistence between humans and domestic animals (especially dogs and cats) has become a common scenario of daily life. Consequently, during a forensic investigation in civil or criminal cases, the biological material from a domestic animal could be considered "evidence" by law enforcement agencies. Animal genomics offers an important contribution in attacks and episodes of property destruction or in a crime scene where the non-human biological material is linked to the victim or perpetrator. However, only a few animal genetics laboratories in the world are able to carry out a valid forensic analysis, adhering to standards and guidelines that ensure the admissibility of data before a court of law. Today, forensic sciences focus on animal genetics considering all domestic species through the analysis of STRs (short tandem repeats) and autosomal and mitochondrial DNA SNPs (single nucleotide polymorphisms). However, the application of these molecular markers to wildlife seems to have gradually gained a strong relevance, aiming to tackle illegal traffic, avoid the loss of biodiversity, and protect endangered species. The development of third-generation sequencing technologies has glimmered new possibilities by bringing "the laboratory into the field", with a reduction of both the enormous cost management of samples and the degradation of the biological material.

Application of a mitochondrial DNA control region frequency database for UK domestic cats

DNA variation in 402bp of the mitochondrial control region flanked by repeat sequences RS2 and RS3 was evaluated by Sanger sequencing in 152 English domestic cats, in order to determine the significance of matching DNA sequences between hairs found with a victim's body and the suspect's pet cat. Whilst 95% of English cats possessed one of the twelve globally widespread mitotypes, four new variants were observed, the most common of which (2% frequency) was shared with the evidential samples. No significant difference in mitotype frequency was seen between 32 individuals from the locality of the crime and 120 additional cats from the rest of England, suggesting a lack of local population structure. However, significant differences were observed in comparison with frequencies in other countries, including the closely neighbouring Netherlands, highlighting the importance of appropriate genetic databases when determining the evidential significance of mitochondrial DNA evidence.

A new view on the European feline population from mtDNA analysis in Polish domestic cats

Domestic cats from Eastern Europe have been poorly represented in studies on mitochondrial DNA diversity for forensic purposes until now. The aim of the present study was to contribute to closing this gap. The genetic structure and the origin of a cat population in Poland were examined against the background of human migrations over the centuries. One hundred and eighty-one cats from animal shelters in seven cities were genotyped. Twenty-one mtDNA haplotypes were found, with only one haplotype present in each of the populations, at an average frequency of 63.54%, and 13 haplotypes being found only in single populations. The analysis revealed the unexpectedly high frequency of haplotype PL02, in previous studies observed only in single cats. Differences in the number of the haplotypes, from four to eight, were observed among the shelters. The findings are discussed with regard to a world-wide database of feline sequences and to the complicated history of Poland. The study underscores the necessity of creating local databases of haplotypes that are of high evidentiary value to the forensic investigations conducted in a given country.

Integrating the Forensic Sciences in Wildlife Case Investigations

The application of medical knowledge to the purpose of law is the foundation of forensic pathology. A forensic postmortem examination often involves the expertise of multiple scientific disciplines to reconstruct the full story surrounding the death of an animal. Wildlife poses additional challenges in forensic investigations due to little or no associated history, and the disruptive effects of decomposition. To illustrate the multidisciplinary nature of wildlife forensic medicine, the authors outline a case of secondary pentobarbital/phenytoin toxicosis in a bald eagle ( Haliaeetus leucocephalus). The eagle was the single fatality in a group of 8 birds that fed on euthanized domestic cat remains that had been improperly disposed of in a landfill. Cooperation between responding law enforcement officers, pathologists, and other forensic scientists led to the successful diagnosis and resolution of the case.

Establishing a database of Canadian feline mitotypes for forensic use

Hair shed by pet animals is often found and collected as evidence from crime scenes. Due to limitations such as small amount and low quality, mitochondrial DNA (mtDNA) is often the only type of DNA that can be used for linking the hair to a potential contributor. mtDNA has lower discriminatory power than nuclear DNA because multiple, unrelated individuals within a population can have the same mtDNA sequence, or mitotype. Therefore, to determine the evidentiary value of a match between crime scene evidence and a suspected contributor, the frequency of the mitotype must be known within the regional population. While mitotype frequencies have been determined for the United States' cat population, the frequencies are unknown for the Canadian cat population. Given the countries' close proximity and similar human settlement patterns, these populations may be homogenous, meaning a single, regional database may be used for estimating cat population mitotype frequencies. Here we determined the mitotype frequencies of the Canadian cat population and compared them to the United States' cat population. The two cat populations are statistically homogenous, however mitotype B6 was found in high frequency in Canada and extremely low frequency in the United States, meaning a single database would not be appropriate for North America. Furthermore, this work calls attention to these local spikes in frequency of otherwise rare mitotypes, instances of which exist around the world and have the potential to misrepresent the evidentiary value of matches compared to a regional database.