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Liu J, Zheng Y, Zheng X, Li T, Wei R, Du W, Wang Z. Development and validation of a novel 30-plex STR assay for canine individual identification and parentage testing. Forensic Sci Int Genet 2024; 71:103056. [PMID: 38678763 DOI: 10.1016/j.fsigen.2024.103056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Domestic dogs are helpers in outdoor human work and companions for families; thus, individual canine identification and parentage testing are crucial in certain fields, including forensics and breeding programs. In this study, a six-dye fluorescent labeling multiplex amplification system containing 29 canine short tandem repeats (STRs) and the sex-determining marker DAmel was developed. The system was called the Tronfo Canine 30-plex STR Kit and was further validated according to the Scientific Working Group on DNA Analysis Methods and the Organization of Scientific Area Committees for Wildlife Forensics guidelines, including tests for PCR conditions, precision, species specificity, sensitivity, stability, repeatability and reproducibility, a population study, and a study of 16 paternity test cases. The results indicated that the novel canine STR assay was accurate, specific, reproducible, stable, and robust. Complete profiles were obtained with 31.25 pg of canine DNA. Additionally, 500 unrelated canine individuals were investigated using this novel system, and the combined power of discrimination and exclusion values were 0.999999999999999999 and 0.999996451039850, respectively. These results suggest that the Tronfo Canine 30-plex STR Kit is highly polymorphic, informative, and suitable for individual canine identification and parentage testing.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yangyang Zheng
- Guangdong Homy Genetics Incorporation, Foshan 528000, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Tao Li
- Nanchang Police Dog Base of the Ministry of Public Security, Nanchang 330000, China
| | - Rongxing Wei
- Nanchang Police Dog Base of the Ministry of Public Security, Nanchang 330000, China
| | - Weian Du
- Guangdong Homy Genetics Incorporation, Foshan 528000, China.
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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2
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Di Nunzio M, Della Valle A, Serino A, Corrado F, Di Nunzio C. How the forensic multidisciplinary approach can solve a fatal dog pack attack. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00746-8. [PMID: 37940786 DOI: 10.1007/s12024-023-00746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
The authors present the case of a 61-year-old man found dead in an agricultural plot. The first investigation of the scene revealed the corpse laid face up in a spot of partially dried blood, next to an olive tree. His face, arms, legs, and abdomen showed signs of severe contusion and laceration of dogs' bite wounds. Next to the victim, an olives bin had been found overturned on the ground. A multi-disciplinary approach, including crime scene analysis, autopsy findings, veterinary animals review, odontologist bite mark study, and forensic genetics DNA correlations, was performed. The present case is a documented watchdogs lethal pack attack and provides an example of how to recognize the more active participants thanks to their odontological alterations. It could be considered the first described dog pack attack case solved by dysgnathia alteration. Comparisons between the dental casts obtained from the dogs and the inflicted wounds were made, resulting in positive correlations between the injuries and the dental arches from two of the six involved dogs, thanks to dental abnormalities and DNA founding. The victim's clothes were also compared with the dogs' dental casts, confirming that they were the most active participants during the pack attack. Dogs' DNA was finally matched with saliva traces found on victim's clothes and skin bite marks.
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Affiliation(s)
| | | | - A Serino
- Hospital of Caserta, Caserta, Italy
| | - F Corrado
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - C Di Nunzio
- CEINGE, Napoli, Italy
- Università Degli Studi Di Napoli Federico II, Napoli, Italy
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3
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Harper CK. Poaching Forensics: Animal Victims in the Courtroom. Annu Rev Anim Biosci 2023; 11:269-286. [PMID: 36790886 DOI: 10.1146/annurev-animal-070722-084803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.
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Affiliation(s)
- Cindy K Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa;
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4
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Identification of volatile organic compounds in muscle tissues of different species based on Headspace-Gas-Chromatography Ion-Mobility Spectrometry. Leg Med (Tokyo) 2022; 59:102132. [DOI: 10.1016/j.legalmed.2022.102132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/23/2022]
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5
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Luttman AM, Komine M, Thaiwong T, Carpenter T, Ewart SL, Kiupel M, Langohr IM, Venta PJ. Development of a 17-Plex of Penta- and Tetra-Nucleotide Microsatellites for DNA Profiling and Paternity Testing in Horses. Front Vet Sci 2022; 9:861623. [PMID: 35464354 PMCID: PMC9021955 DOI: 10.3389/fvets.2022.861623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Tetranucleotide and pentanucleotide short tandem repeat (hereafter termed tetraSTR and pentaSTR) polymorphisms have properties that make them desirable for DNA profiling and paternity testing. However, certain species, such as the horse, have far fewer tetraSTRs than other species and for this reason dinucleotide STRs (diSTRs) have become the standard for DNA profiling in horses, despite being less desirable for technical reasons. During our testing of a series of candidate genes as potentially underlying a heritable condition characterized by megaesophagus in the Friesian horse breed, we found that good tetraSTRs do exist in horses but, as expected, at a much lower frequency than in other species, e.g., dogs and humans. Using a series of efficient methods developed in our laboratory for the production of multiplexed tetraSTRs in other species, we identified a set of tetra- and pentaSTRs that we developed into a 17-plex panel for the horse, plus a sex-identifying marker near the amelogenin gene. These markers were tested in 128 horses representing 16 breeds as well as crossbred horses, and we found that these markers have useful genetic variability. Average observed heterozygosities (Ho) ranged from 0.53 to 0.89 for the individual markers (0.66 average Ho for all markers), and 0.62-0.82 for expected heterozygosity (He) within breeds (0.72 average He for all markers). The probability of identity (PI) within breeds for which 10 or more samples were available was at least 1.1 x 10−11, and the PI among siblings (PIsib) was 1.5 x 10−5. Stutter was ≤ 11% (average stutter for all markers combined was 6.9%) compared to the more than 30% typically seen with diSTRs. We predict that it will be possible to develop accurate allelic ladders for this multiplex panel that will make cross-laboratory comparisons easier and will also improve DNA profiling accuracy. Although we were only able to exclude candidate genes for Friesian horse megaesophagus with no unexcluded genes that are possibly causative at this point in time, the study helped us to refine the methods used to develop better tetraSTR multiplexed panels for species such as the horse that have a low frequency of tetraSTRs.
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Affiliation(s)
- Andrea M. Luttman
- Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Genetics and Genomic Sciences, Michigan State University, East Lansing, MI, United States
| | - Misa Komine
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Tuddow Thaiwong
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- *Correspondence: Tuddow Thaiwong
| | - Tyler Carpenter
- Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI, United States
| | - Susan L. Ewart
- Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Matti Kiupel
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Ingeborg M. Langohr
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Patrick J. Venta
- Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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6
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Raymond PW, Velie BD, Wade CM. Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels. Anim Genet 2021; 53:247-263. [PMID: 34963196 DOI: 10.1111/age.13165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022]
Abstract
This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.
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Affiliation(s)
- Patrick W Raymond
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brandon D Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Claire M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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7
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Lee M, Hwang IK, Jung JY, Kim JY, Chang M, Moon S. Construction of an in-house allelic ladder for Canine Genotypes™ Panel 2.1 Kit. J Forensic Sci 2021; 66:2362-2368. [PMID: 34296771 DOI: 10.1111/1556-4029.14812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022]
Abstract
Dogs (Canis lupus familiaris) are among the most common companion animals in the Republic of Korea. Recently, there have been many criminal cases of dog cruelty, injury, and theft, among others. This has increased the importance of dog-related biological evidence at crime scenes. The National Forensic Service of the Republic of Korea conducts short tandem repeat (STR) analysis using the Thermo Scientific Canine Genotypes™ Panel 2.1 Kit (Canine Kit) to identify individual dogs through forensic analysis. The Canine Kit was developed as a forensic STR kit for the identification of individual dogs. However, an allelic ladder was neither developed nor included in the commercial kit, leaving an issue of accurate genotyping. Primer details for the 18 markers used in the Canine Kit are proprietary information, and thus, unavailable to end-users. In this study, an allelic ladder was constructed with 160 fragments by combining 158 fragments of STR alleles obtained by nested PCR and two fragments artificially obtained from the sex-determination marker. By including the new allelic ladder in analysis of samples amplified with the Canine Kit, the accuracy and reliability of data analysis were improved. Application of this allelic ladder would be helpful for interlaboratory data sharing and standardization of canine genotype databases.
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Affiliation(s)
- Minji Lee
- Forensic DNA Division, National Forensic Service, Wonju, Korea
| | - In Kwan Hwang
- Forensic DNA Division, National Forensic Service, Wonju, Korea
| | - Ju Yeon Jung
- Forensic DNA Division, National Forensic Service, Wonju, Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju, Korea
| | - Miwha Chang
- Forensic DNA Division, National Forensic Service, Wonju, Korea
| | - Seohyun Moon
- Forensic DNA Division, National Forensic Service, Wonju, Korea
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8
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Kanthaswamy S, Brendel T, Cancela L, Andrade de Oliveira DA, Brenig B, Cons C, Crespi JA, Dajbychová M, Feldl A, Itoh T, Landi V, Martinez A, Natonek-Wisniewska M, Oldt RF, Radko A, Ramírez O, Rodellar C, Ruiz-Girón M, Schikorski D, Turba ME, Giovambatista G. An inter-laboratory study of DNA-based identity, parentage and species testing in animal forensic genetics. Forensic Sci Res 2021; 7:708-713. [PMID: 36817240 PMCID: PMC9930802 DOI: 10.1080/20961790.2021.1886679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The probative value of animal forensic genetic evidence relies on laboratory accuracy and reliability. Inter-laboratory comparisons allow laboratories to evaluate their performance on specific tests and analyses and to continue to monitor their output. The International Society for Animal Genetics (ISAG) administered animal forensic comparison tests (AFCTs) in 2016 and 2018 to assess the limitations and capabilities of laboratories offering forensic identification, parentage and species determination services. The AFCTs revealed that analyses of low DNA template concentrations (≤300 pg/µL) constitute a significant challenge that has prevented many laboratories from reporting correct identification and parentage results. Moreover, a lack of familiarity with species testing protocols, interpretation guidelines and representative databases prevented over a quarter of the participating laboratories from submitting correct species determination results. Several laboratories showed improvement in their genotyping accuracy over time. However, the use of forensically validated standards, such as a standard forensic short tandem repeat (STR) kit, preferably with an allelic ladder, and stricter guidelines for STR typing, may have prevented some common issues from occurring, such as genotyping inaccuracies, missing data, elevated stutter products and loading errors. The AFCTs underscore the importance of conducting routine forensic comparison tests to allow laboratories to compare results from each other. Laboratories should keep improving their scientific and technical capabilities and continuously evaluate their personnel's proficiency in critical techniques such as low copy number (LCN) analysis and species testing. Although this is the first time that the ISAG has conducted comparison tests for forensic testing, findings from these AFCTs may serve as the foundation for continuous improvements of the overall quality of animal forensic genetic testing.
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Affiliation(s)
- Sreetharan Kanthaswamy
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA,California National Primate Research Center, University of California, Davis, CA, USA,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Torsten Brendel
- Eurofins Genomics Europe Applied Genomics GmbH, Ebersberg, Germany
| | | | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Goettingen, Goettingen, Germany
| | - Carmen Cons
- Facultad de Veterinaria, Laboratorio de Genética Bioquímica (LAGENBIO), Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Julian A. Crespi
- Facultad de Ciencias Veterinarias UNLP, IGEVET – Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina
| | | | - Andreas Feldl
- Eurofins Genomics Europe Applied Genomics GmbH, Ebersberg, Germany
| | - Tomohito Itoh
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan (LIAJ), Maebashi, Japan
| | - Vincenzo Landi
- Department of Veterinary Medicine, Animal Breeding and Genetics, University of Bari “Aldo Moro”, Valenzano, Italy
| | - Amparo Martinez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | | | - Robert F. Oldt
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA,California National Primate Research Center, University of California, Davis, CA, USA,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Anna Radko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | | | - Clementina Rodellar
- Facultad de Veterinaria, Laboratorio de Genética Bioquímica (LAGENBIO), Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Manuel Ruiz-Girón
- Laboratorio de Biología Molecular y Genómica, Hispalis Biolab S.L.U., Seville, Spain
| | | | | | - Guillermo Giovambatista
- Facultad de Ciencias Veterinarias UNLP, IGEVET – Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina,CONTACT Guillermo Giovambatista
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9
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Berger C, Heinrich J, Berger B, Hecht W, Parson W. Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs. Genes (Basel) 2021; 12:genes12060908. [PMID: 34208207 PMCID: PMC8230911 DOI: 10.3390/genes12060908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.
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Affiliation(s)
- Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Correspondence: ; Tel.: +43-512-9003-70640
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35390 Giessen, Germany;
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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10
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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11
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A reference allelic ladder for Western Capercaillie (Tetrao urogallus) and Black Grouse (Tetrao tetrix) enables linking grouse genetic data across studies. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractRapid anthropogenic climate change and progressing habitat degradation are considered top threats to biodiversity. The employment of demanding umbrella species as indicators for ecosystem health is a popular and cost-effective strategy that facilitates continuous monitoring and evaluation within a long-term conservation management scheme. The Western Capercaillie (Tetrao urogallus) and the Black Grouse (Tetrao tetrix) are both considered viable candidates due to their extensive habitat requirements, the possibility for conservative, non-invasive sampling, and their broad popular appeal. Regional population surveys based on genetic data from Short Sequence Repeat (SSR) analysis are being conducted throughout the Palearctic. However, to ensure reliable comparability among laboratories, standardization is required. Here, we report a catalogue of fifty fully characterized reference alleles from twelve SSR loci and the construction of a customizable allelic ladder for genotyping and individualization in Western Capercaillie and Black Grouse. This methodological improvement will help to cost-efficiently generate and collate supraregional data from different grouse surveys and thereby contribute to conservation management. Reference alleles and ladders can be obtained on demand.
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12
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Cui W, Jin X, Guo Y, Chen C, Zhang W, Wang Y, Lan J, Zhu B. Development and Validation of a Novel Five-Dye Short Tandem Repeat Panel for Forensic Identification of 11 Species. Front Genet 2020; 11:1005. [PMID: 33193588 PMCID: PMC7541953 DOI: 10.3389/fgene.2020.01005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/06/2020] [Indexed: 01/16/2023] Open
Abstract
Species identification of unknown biological samples is of fundamental importance for forensic applications, especially in crime detection, poaching, and illegal trade of endangered animals as well as meat fraud. In this study, a novel panel was developed to simultaneously identify 10 different animal species (Gallus domesticus, Anas platyrhynchos domesticus, Ovis aries, Sus scrofa domesticus, Bos taurus, Equus caballus, Columba livia domestica, Rattus norvegicus, Mus musculus, and Canis lupus familiaris) and human beings by amplifying 22 short tandem repeat (STR) loci in a multiplex PCR using a set of five fluorescently labeled dyes. This novel 22-STR panel was validated by optimization of PCR conditions as well as species specificity, sensitivity, reproducibility, precision, DNA mixture, and tissue/organ consistency. The results of developmental validation showed that the 22-STR loci achieved high species specificity among 10 animal species and human beings, and the sensitivity of this panel was 0.09 ng. This 22-STR panel identified different meats in mixed samples, and the minimum detected mixture ratio in the current test was 10% (0.1 ng/1 ng). This sensitive, accurate, and specific 22-STR panel can be used for forensic species identification and the detection of meat fraud and adulteration.
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Affiliation(s)
- Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Use of Microsatellites in Genetic Diversity Assessment, Parentage Testing and Individual Identification of the Kangal Shepherd Dog. ACTA VET-BEOGRAD 2020. [DOI: 10.2478/acve-2020-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Abstract
The Kangal Shepherd Dog is considered the most common dog breed of Turkish origin. This study investigated variations in ten autosomal microsatellite markers (PEZ01, PEZ03, PEZ05, PEZ06, PEZ08, PEZ12, PEZ20, FHC2010, FHC2054 and FHC2079) for the purposes of genetic diversity assessment of the Kangal breed. In addition, the use of markers was assessed in parentage testing and individual identification within the Kangal breed. The microsatellite markers were typed in 51 Kangal dogs. The total number of alleles in the study population was 69. The mean number of alleles per locus was 6.9, and varied from four (FHC2079) to 12 (PEZ12). The polymorphic information content (PIC) ranged from 0.52 (FHC2079) to 0.87 (PEZ12), with the mean value for all loci of 0.717. Power of exclusion (PE) in 10 microsatellites investigated varied between 0.143 (FHC2054) and 0.472 (PEZ08) per locus. In order to determine the efficiency of using microsatellites for individual identification in the Kangal breed, power of discrimination (PD) and matching probability (MP) were calculated for each microsatellite marker. The panel achieved high combined MP (6.77 × 10-10) and high combined PD value of 99.99999%. The obtained results may contribute to further recognition of the Kangal breed, and confirm that the investigated microsatellites enable a reliable parentage testing and individual identification of the breed.
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14
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Dormontt E, Jardine D, van Dijk KJ, Dunker B, Dixon R, Hipkins V, Tobe S, Linacre A, Lowe A. Forensic validation of a SNP and INDEL panel for individualisation of timber from bigleaf maple (Acer macrophyllum Pursch). Forensic Sci Int Genet 2020; 46:102252. [DOI: 10.1016/j.fsigen.2020.102252] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/22/2019] [Accepted: 01/19/2020] [Indexed: 10/25/2022]
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15
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Nonhuman forensic genetics. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Berger B, Heinrich J, Niederstätter H, Hecht W, Morf N, Hellmann A, Rohleder U, Schleenbecker U, Berger C, Parson W. Forensic characterization and statistical considerations of the CaDNAP 13-STR panel in 1,184 domestic dogs from Germany, Austria, and Switzerland. Forensic Sci Int Genet 2019; 42:90-98. [PMID: 31277051 DOI: 10.1016/j.fsigen.2019.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 12/13/2022]
Abstract
Crime scene samples originating from domestic dogs such as hair, blood, or saliva can be probative as possible transfer evidence in human crime and in dog attack cases. In the majority of such cases canine DNA identification using short tandem repeat (STR) analysis is the method of choice, which demands, among others, a systematic survey of allele frequency data in the relevant dog populations. A set of 13 highly polymorphic canine STR markers was used to analyze samples of 1,184 dogs (including 967 purebred dogs) from the so-called DACH countries (Germany, Austria, Switzerland). This CaDNAP 13-STR panel has previously been validated for canine identification in a forensic context. Here, we present robust estimates of allele frequencies, which are essential to assess the weight of the evidence by estimating the probability of a matching DNA profile within the dog population under question, e.g. in the form of a random match probability (RMP). The geographical provenance of the tested dogs showed a negligible influence on the observed genotype variation. Therefore, we combined the STR data from all three countries into a single dog population sample (DPS). In contrast, pronounced genetic differentiation between dog breeds was found by principal component analysis and sub-structure analysis with the STRUCTURE software. These findings entailed the need to account for the effects of DPS breed composition on allele frequency estimates. A possible strategy, which was favored here, relies on collecting a DPS that is guided by the breed composition of the relevant dog population. In total, dogs from 166 different breeds were included in our DPS, 64 of them including at least 5 individuals (n = 771 dogs). Sampling reflected the abundance of breeds in the DACH countries with the following being the most common ones: German Shepherds (population frequency: 14.3%), Dachshunds (5.9%), Labrador Retrievers (3.9%), and Golden Retrievers (3.2%). The pedigree listing of the purebred dogs in our DPS ranked German Shepherds (DPS frequency 8.5%) first, followed by Labrador Retrievers (3.9%), Golden Retrievers (3%), and Dachshunds (2.5%). RMP values based on overall allele frequencies and accounting for substructure using FST between breeds ranged between 10-13 and 10-14 and represent a conservative approach of RMP assessment.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nadja Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Andreas Hellmann
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | - Udo Rohleder
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | | | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
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17
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Isukapatla AR, Sinha M, Pulamagatta V, Chandrasekar A, Ahirwar B. Genetic Architecture of Southeast-coastal Indian tribal populations: A Y-chromosomal phylogenetic analysis. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2019. [DOI: 10.1186/s41935-019-0132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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18
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Moore MK, Frazier K. Humans Are Animals, Too: Critical Commonalities and Differences Between Human and Wildlife Forensic Genetics. J Forensic Sci 2019; 64:1603-1621. [DOI: 10.1111/1556-4029.14066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/10/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- M. Katherine Moore
- Forensic Laboratory Conservation Biology Division Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration 219 Fort Johnson Road Charleston SC29412
| | - Kim Frazier
- Wyoming Game and Fish Wildlife Forensic and Fish Health Laboratory 1212 South Adams Street Laramie WY 82070
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19
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Zenke P, Egyed B, Kovács G, Pádár Z. Implementation of genetic based individualization of White stork (Ciconia ciconia) in forensic casework. Forensic Sci Int Genet 2019; 40:e245-e247. [PMID: 30744983 DOI: 10.1016/j.fsigen.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Petra Zenke
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, Hungary
| | - Balázs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Kovács
- Research Centre for Forensic Sciences and Criminology, University Széchenyi István, Győr, Hungary
| | - Zsolt Pádár
- Department of Forensic Medicine, Medical School, University of Pécs, 7624 Szigeti út 12. Hungary.
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20
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Kanthaswamy S, Oldt RF, Montes M, Falak A. Comparing two commercial domestic dog (Canis familiaris
) STR genotyping kits for forensic identity calculations in a mixed-breed dog population sample. Anim Genet 2018; 50:105-111. [DOI: 10.1111/age.12758] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2018] [Indexed: 11/26/2022]
Affiliation(s)
- S. Kanthaswamy
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale AZ 85306 USA
- California National Primate Research Center; University of California; One Shields Ave Davis CA 95616 USA
- Evolutionary Biology Graduate Program; School of Life Sciences; Arizona State University; Tempe AZ 85281 USA
| | - R. F. Oldt
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale AZ 85306 USA
- Evolutionary Biology Graduate Program; School of Life Sciences; Arizona State University; Tempe AZ 85281 USA
| | - M. Montes
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale AZ 85306 USA
| | - A. Falak
- School of Mathematics and Natural Sciences; Arizona State University (ASU) at the West Campus; Glendale AZ 85306 USA
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21
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Berger B, Berger C, Heinrich J, Niederstätter H, Hecht W, Hellmann A, Rohleder U, Schleenbecker U, Morf N, Freire-Aradas A, McNevin D, Phillips C, Parson W. Dog breed affiliation with a forensically validated canine STR set. Forensic Sci Int Genet 2018; 37:126-134. [PMID: 30149287 DOI: 10.1016/j.fsigen.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/23/2018] [Accepted: 08/11/2018] [Indexed: 11/28/2022]
Abstract
We tested a panel of 13 highly polymorphic canine short tandem repeat (STR) markers for dog breed assignment using 392 dog samples from the 23 most popular breeds in Austria, Germany, and Switzerland. This STR panel had originally been selected for canine identification. The dog breeds sampled in this study featured a population frequency ≥1% and accounted for nearly 57% of the entire pedigree dog population in these three countries. Breed selection was based on a survey comprising records for nearly 1.9 million purebred dogs belonging to more than 500 different breeds. To derive breed membership from STR genotypes, a range of algorithms were used. These methods included discriminant analysis of principal components (DAPC), STRUCTURE, GeneClass2, and the adegenet package for R. STRUCTURE analyses suggested 21 distinct genetic clusters. Differentiation between most breeds was clearly discernable. Fourteen of 23 breeds (61%) exhibited maximum mean cluster membership proportions of more than 0.70 with a highest value of 0.90 found for Cavalier King Charles Spaniels. Dogs of only 6 breeds (26%) failed to consistently show only one major cluster. The DAPC method yielded the best assignment results in all 23 declared breeds with 97.5% assignment success. The frequency-based assignment test also provided a high success rate of 87%. These results indicate the potential viability of dog breed prediction using a well-established and sensitive set of 13 canine STR markers intended for forensic routine use.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University, Giessen, Germany
| | - Andreas Hellmann
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | - Udo Rohleder
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | | | - Nadja Morf
- Institute of Legal Medicine, University of Zürich, Switzerland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Australia
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.
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22
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Wesselink M, Dragutinović A, Noordhoek JW, Bergwerff L, Kuiper I. DNA typing of birch: Development of a forensic STR system for Betula pendula and Betula pubescens. Forensic Sci Int Genet 2018; 35:70-81. [DOI: 10.1016/j.fsigen.2018.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 03/01/2018] [Accepted: 04/02/2018] [Indexed: 11/26/2022]
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23
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Investigating the population structure and genetic differentiation of livestock guard dog breeds. Animal 2018; 12:2009-2016. [PMID: 29331165 DOI: 10.1017/s1751731117003573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.
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24
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Ciampolini R, Cecchi F, Spinetti I, Rocchi A, Biscarini F. The use of genetic markers to estimate relationships between dogs in the course of criminal investigations. BMC Res Notes 2017; 10:414. [PMID: 28818115 PMCID: PMC5561628 DOI: 10.1186/s13104-017-2722-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/29/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Attacks on humans by dogs in a pack, though uncommon, do happen, and result in severe, sometimes fatal, injuries. We describe the role that canine genetic markers played during the investigation of a fatal dog-pack attack involving a 50-year-old male truck driver in a parking lot in Tuscany (Italy). Using canine specific STR genetic markers, the local authorities, in the course of their investigations, reconstructed the genetic relationships between the dogs that caused the deadly aggression and other dogs belonging to the owner of the parking who, at the moment of the aggression, was located in another region of Italy. RESULTS From a Bayesian clustering algorithm, the most likely number of clusters was two. The average relatedness among the dogs responsible for the aggression was higher than the average relatedness among the other dogs or between the two groups. Taken together, all these results indicate that the two groups of dogs are clearly distinct. Genetic relationships showed that the two groups of dogs were not related. It was therefore unlikely that the murderous dogs belonged to the owner of the parking lot who, on grounds of this and additional evidence, was eventually acquitted.
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Affiliation(s)
- Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, Università di Pisa, V.le delle Piagge 2, 56124, Pisa, Italy
| | - Francesca Cecchi
- Dipartimento di Scienze Veterinarie, Università di Pisa, V.le delle Piagge 2, 56124, Pisa, Italy
| | - Isabella Spinetti
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell'Area Clinica, Università di Pisa, Via Savi 10, 56126, Pisa, Italy
| | - Anna Rocchi
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell'Area Clinica, Università di Pisa, Via Savi 10, 56126, Pisa, Italy
| | - Filippo Biscarini
- CNR-IBBA, Via Bassini 15, 20133, Milano, Italy. .,Division of Infection & Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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25
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26
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de Groot M, van Haeringen WA. An evaluation of the International Society for Animal Genetics recommended parentage and identification panel for the domestic pigeon (Columba livia domestica
). Anim Genet 2017; 48:431-435. [DOI: 10.1111/age.12555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- M. de Groot
- VHLGenetics; Agro Business Park 100 NL 6708 PW Wageningen The Netherlands
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27
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Canu A, Mattioli L, Santini A, Apollonio M, Scandura M. ‘Video-scats’: combining camera trapping and non-invasive genotyping to assess individual identity and hybrid status in gray wolf. WILDLIFE BIOLOGY 2017. [DOI: 10.2981/wlb.00355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Antonio Canu
- A. Canu, M. Apollonio and M. Scandura , Dept. of Science for Nature and Environmental Resources, Univ. of Sassari, Via Muroni 25, IT-07100 Sassari, Italy. AC also at: C.I.R.Se.M.A.F. Firenze, Italy
| | - Luca Mattioli
- L. Mattioli, Regione Toscana, Settore Attività Faunistico Venatoria, Pesca Dilettantistica, Pesca in Mare, Arezzo, Italy
| | | | - Marco Apollonio
- A. Canu, M. Apollonio and M. Scandura , Dept. of Science for Nature and Environmental Resources, Univ. of Sassari, Via Muroni 25, IT-07100 Sassari, Italy. AC also at: C.I.R.Se.M.A.F. Firenze, Italy
| | - Massimo Scandura
- A. Canu, M. Apollonio and M. Scandura , Dept. of Science for Nature and Environmental Resources, Univ. of Sassari, Via Muroni 25, IT-07100 Sassari, Italy. AC also at: C.I.R.Se.M.A.F. Firenze, Italy
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28
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Trophic overlap between wolves and free-ranging wolf×dog hybrids in the Apennine Mountains, Italy. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2016.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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29
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Rajpoot A, Kumar VP, Bahuguna A, Kumar D. Forensically informative nucleotide sequencing (FINS) for the first time authentication of Indian Varanus species: implication in wildlife forensics and conservation. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:892-900. [PMID: 27838947 DOI: 10.1080/24701394.2016.1202943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
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.
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Affiliation(s)
- Ankita Rajpoot
- a Molecular Systematic Laboratory , Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Ved Prakash Kumar
- b Forensic and Conservation Genetic Cell , Wildlife Institute of India , Dehradun , Uttarakhand , India.,c Department of Zoology , Veer Kunwar Singh University , Arrah , Bihar , India
| | - Archana Bahuguna
- a Molecular Systematic Laboratory , Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Dhyanendra Kumar
- c Department of Zoology , Veer Kunwar Singh University , Arrah , Bihar , India
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Zenke P, Egyed B, Pádár Z, Kovács G. Increasing relevance of non-human genetics in Hungarian forensic practice. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Rahimi-Mianji G, Nejati-Javaremi A, Farhadi A. Genetic diversity, parentage verification, and genetic bottlenecks evaluation in iranian turkmen horse1. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415090082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Kanthaswamy S. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges. Anim Genet 2015; 46:473-84. [DOI: 10.1111/age.12335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 01/09/2023]
Affiliation(s)
- S. Kanthaswamy
- School of Mathematical and Natural Sciences; Arizona State University (ASU) at the West Campus; 4701 W Thunderbird Road Glendale AZ 85306-4908 USA
- California National Primate Research Center; University of California; Davis CA 95616 USA
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Rogberg-Muñoz A, Wei S, Ripoli MV, Guo BL, Carino MH, Lirón JP, Prando AJ, Vaca RJA, Peral-García P, Wei YM, Giovambattista G. Effectiveness of a 95 SNP panel for the screening of breed label fraud in the Chinese meat market. Meat Sci 2015; 111:47-52. [PMID: 26334371 DOI: 10.1016/j.meatsci.2015.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/13/2015] [Accepted: 08/19/2015] [Indexed: 10/23/2022]
Abstract
Breed assignment has proved to be useful to control meat trade and protect the value of special productions. Meat-related frauds have been detected in China; therefore, 95 SNPs selected from the ISAG core panel were evaluated to develop an automated and technologically updated tool to screen breed label fraud in the Chinese meat market. A total of 271 animals from four Chinese yellow cattle (CYC) populations, six Bos taurus breeds, two Bos indicus and one composite were used. The allocation test distinguished European, Japanese and Zebu breeds, and two Chinese genetic components. It correctly allocated Japanese Black, Zebu and British breeds in 100, 90 and 89% of samples, respectively. CYC evidenced the Zebu, Holstein and Limousin introgression. The test did not detect CYC components in any of the 25 samples from Argentinean butchers. The method could be useful to certify Angus, Hereford and Japanese Black meat, but a modification in the panel would be needed to differentiate other breeds.
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Affiliation(s)
- A Rogberg-Muñoz
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina; Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos AiresArgentina
| | - S Wei
- Key Laboratory of Agro-Products Processing and Quality Control, Ministry of Agriculture, Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences, P.O. Box 5109, Beijing 100193, P.R. of China
| | - M V Ripoli
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - B L Guo
- Key Laboratory of Agro-Products Processing and Quality Control, Ministry of Agriculture, Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences, P.O. Box 5109, Beijing 100193, P.R. of China
| | - M H Carino
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - J P Lirón
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - A J Prando
- Cátedra de Zootecnia, Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - R J A Vaca
- Cátedra de Zootecnia, Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - P Peral-García
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Y M Wei
- Key Laboratory of Agro-Products Processing and Quality Control, Ministry of Agriculture, Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agricultural Sciences, P.O. Box 5109, Beijing 100193, P.R. of China
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.
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Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers. Animal 2015; 9:1921-8. [PMID: 26245492 DOI: 10.1017/s1751731115001561] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.
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Santos MM, Maia LL, Nobre DM, Oliveira Neto JF, Garcia TR, Lage MCGR, de Melo MIV, Viana WS, Palhares MS, da Silva Filho JM, Santos RL, Valle GR. Sex ratio of equine offspring is affected by the ages of the mare and stallion. Theriogenology 2015; 84:1238-45. [PMID: 26234461 DOI: 10.1016/j.theriogenology.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/30/2015] [Accepted: 07/01/2015] [Indexed: 11/26/2022]
Abstract
The aim of this study was to determine the influence of parental age on the sex ratio of offspring in horses. Two trials were performed. In the first trial, the data from a randomly obtained population with a 1:1 sex ratio of 59,950 Mangalarga Marchador horses born in Brazil from 1990 to 2011 were analyzed. The sex ratios of the offspring were compared among groups according to the mare and the stallion ages (from 3 to 25 years). In the first step of the analysis, the mares and stallions were grouped according to age in 5-year intervals. In the second step, the groups were based on the parental age gap at conception. In the third step, the group of the mares and stallions with similar ages from the second step was subdivided, and the different parental age subgroups that were divided into 5-year intervals were compared. In the fourth step, the sex ratio of the offspring was determined according to the ages of the mares and the stallions at conception. The second trial was based on the data from 253 horses of several breeds that were born after natural gestation into a herd from 1989 to 2010, and the offspring of groups that were younger or older than 15 years were compared. The data from both trials were analyzed using a chi-square test (P ≤ 0.01 for the first trial; and P ≤ 0.05 for the second trial) for the comparisons of the sex ratios. In the first trial, the Spearman test (P ≤ 0.01) was used to verify the correlations between the parental age and the offspring sex ratio. In the first trial, the offspring sex ratio decreased as the mare or stallion age increased, and the decrease was more marked for the mares than for the stallions. In the second trial, the mares older than 15 years had more fillies than the younger mares, but the stallion age had no effect on the sex of the offspring. The first trial, with a large number of horses, revealed the pattern of the distribution of the sex ratios of offspring according to the parental age in horses, whereas the second trial, with a more restricted number of horses, confirmed the influence of the age of the mare on the offspring sex ratio. We concluded that the parental age affected the offspring sex ratio in horses and that this effect was stronger for the mares than for the stallions.
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Affiliation(s)
- Marianna Machado Santos
- Departamento de Medicina Veterinária, Pontifícia Universidade Católica de Minas Gerais, Betim, Minas Gerais, Brazil
| | - Leonardo Lara Maia
- Departamento de Medicina Veterinária, Pontifícia Universidade Católica de Minas Gerais, Betim, Minas Gerais, Brazil
| | - Daniel Magalhães Nobre
- Escola de Medicina, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - José Ferraz Oliveira Neto
- Associação Brasileira dos Criadores do Cavalo Mangalarga Marchador, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago Rezende Garcia
- Associação Brasileira dos Criadores do Cavalo Mangalarga Marchador, Belo Horizonte, Minas Gerais, Brazil
| | - Maria Coeli Gomes Reis Lage
- Departamento de Medicina Veterinária, Pontifícia Universidade Católica de Minas Gerais, Betim, Minas Gerais, Brazil
| | - Maria Isabel Vaz de Melo
- Departamento de Medicina Veterinária, Pontifícia Universidade Católica de Minas Gerais, Betim, Minas Gerais, Brazil
| | - Walmir Santos Viana
- Regimento de Cavalaria Alferes Tiradentes, Polícia Militar do Estado de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maristela Silveira Palhares
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - José Monteiro da Silva Filho
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Renato Lima Santos
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Guilherme Ribeiro Valle
- Departamento de Medicina Veterinária, Pontifícia Universidade Católica de Minas Gerais, Betim, Minas Gerais, Brazil.
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Spadaro A, Ream K, Braham C, Webb KM. Local mitochondrial DNA haplotype databases needed for domestic dog populations that have experienced founder effect. Forensic Sci Int 2015; 248:113-8. [PMID: 25612881 DOI: 10.1016/j.forsciint.2014.12.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/19/2014] [Accepted: 12/27/2014] [Indexed: 10/24/2022]
Abstract
Biological material from pets is often collected as evidence from crime scenes. Due to sample type and quality, mitochondrial DNA (mtDNA) is frequently evaluated to identify the potential contributor. MtDNA has a lower discriminatory power than nuclear DNA with multiple individuals in a population potentially carrying the same mtDNA sequence, or haplotype. The frequency distribution of mtDNA haplotypes in a population must be known in order to determine the evidentiary value of a match between crime scene evidence and the potential contributor of the biological material. This is especially important in geographic areas that include remote and/or isolated populations where founder effect may have lead to a decrease in genetic diversity and a non-random distribution of haplotypes relative to the population at large. Here we compared the haplotype diversity in dogs from the noncontiguous states of Alaska and Hawaii relative to the contiguous United States (US). We report a greater proportion of dogs carrying an A haplotype in Alaska relative to any other US population. Significant variation in the distribution of haplotype frequencies was discovered when comparing the haplotype diversity of dogs in Hawaii to that of the continental US. Each of these regions exhibits reduced genetic diversity relative to the contiguous US, likely due to founder effect. We recommend that specific databases be created to accurately represent the mitochondrial haplotype diversity in these remote areas. Furthermore, our work demonstrates the importance of local surveys for populations that may have experienced found effect.
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Affiliation(s)
- Amanda Spadaro
- Department of Biology, Allegheny College, Meadville, PA, United States
| | - Kelsey Ream
- Department of Natural Resources and Environmental Science, University of Illinois, Urbana, IL, United States
| | - Caitlyn Braham
- Department of Graduate Studies, John Carroll University, University Heights, OH, United States
| | - Kristen M Webb
- Department of Biology, Allegheny College, Meadville, PA, United States.
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Molecular identification of python species: development and validation of a novel assay for forensic investigations. Forensic Sci Int Genet 2014; 16:64-70. [PMID: 25541013 DOI: 10.1016/j.fsigen.2014.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question.
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38
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Kanthaswamy S, Smith DG. Genetic and ethnohistoric evidence suggest current Native American population datasets in the FBI's CODIS Database Are Not Sufficiently Representative. Forensic Sci Int Genet 2014; 13:e13-5. [DOI: 10.1016/j.fsigen.2014.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/12/2014] [Accepted: 05/09/2014] [Indexed: 11/27/2022]
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Santos S, Oliveira M, Amorim A, van Asch B. A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers. Electrophoresis 2014; 35:3201-7. [PMID: 25146979 DOI: 10.1002/elps.201400107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/07/2022]
Abstract
The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.
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Affiliation(s)
- Sara Santos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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Bao F, Wells JD. Population genetic structure of an invasive forensically important insect. Electrophoresis 2014; 35:3193-200. [PMID: 24934687 DOI: 10.1002/elps.201400108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/15/2014] [Accepted: 06/11/2014] [Indexed: 11/12/2022]
Abstract
The forensic utility of an insect can depend in part on its population structure. Although some native North American species have been characterized in this fashion, information is lacking for species that were introduced from elsewhere and that might have lower genetic diversity and less geographic differentiation. We surveyed Chrysomya megacephala, an Asian fly present in the continental USA since the 1980s. Amplified Fragment Length Polymorphism profiles were generated from adult insects collected across Florida and in Mobile, Alabama. Analysis of Molecular Variance on 151 polymorphic loci found significant but very small variation among samples. STRUCTURE and principal coordinate analyses produced the same two clusters in the population, consistent with C. megacephala in Florida having originated from two separate source populations. A weak negative correlation between genetic and geographic distances probably reflected the geographic arrangement of the genetic clusters. A positive relative relatedness coefficient for each sample indicated that flies arriving at a bait within a short time were likely to be close relatives, consistent with the earlier results for native North American carrion flies. However, genetic diversity estimated for the introduced Florida C. megacephala was lower than for native species or for published data on Malaysian C. megacephala, perhaps reflecting the genetic effects of being introduced to a new geographic region. Genetic assignment, a method that has been proposed as a way to infer corpse postmortem relocation, was much less successful for C. megacephala compared to the native species, possibly reflecting a history of admixture.
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Affiliation(s)
- Fanchen Bao
- Department of Biological Sciences and International Forensic Research Institute, Florida International University, Miami, FL, USA
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The risks of using “species-specific” PCR assays in wildlife research: The case of red fox (Vulpes vulpes) identification in Tasmania. Forensic Sci Int Genet 2014; 11:e9-11. [DOI: 10.1016/j.fsigen.2014.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/21/2022]
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Schury N, Schleenbecker U, Hellmann AP. Forensic animal DNA typing: Allele nomenclature and standardization of 14 feline STR markers. Forensic Sci Int Genet 2014; 12:42-59. [PMID: 24893348 DOI: 10.1016/j.fsigen.2014.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/29/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022]
Abstract
Since the domestic cat (Felis catus) has become one of the most popular pets and owners usually develop a close relationship to their cats, it is necessary to take traces of cats into account for forensic casework. For this purpose feline short tandem (STR) repeat markers have been investigated in several earlier studies, but no detailed description of sequence data, allelic variations or a repeat-based nomenclature is available. The aim of the study was to provide a suggestion for the allele nomenclature of 14 cat STR markers according to the recommendations of the International Society for Forensic Genetics (ISFG) for human DNA typing and to present a standardized system for a secure DNA typing of samples. Samples of 122 unrelated cats from a local animal shelter and private owners in Germany were used to generate a population database with allele frequencies and to analyze the tandemly repeated sequence variations within the alleles of each STR marker. These markers could be grouped into two STR classes: simple repeat STRs and complex STRs (some with the supplement highly complex), consisting of di- and tetranucleotide repeat motifs. After analyzing the repeat structure and elaborating a repeat based nomenclature, allelic ladders of common and rarely occurring alleles for each marker were designed to enable accurate typing of alleles that differ in fragment length and to facilitate data exchange.
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Affiliation(s)
- N Schury
- Bundeskriminalamt, Forensic Science Institute, KT32, Äppelallee 45, 65203 Wiesbaden, Germany; Johannes Gutenberg University Mainz, Institute of Legal Medicine - Medical University, Molecular Biology, Am Pulverturm 3, 55131 Mainz, Germany
| | - U Schleenbecker
- Bundeskriminalamt, Forensic Science Institute, KT32, Äppelallee 45, 65203 Wiesbaden, Germany
| | - A P Hellmann
- Bundeskriminalamt, Forensic Science Institute, KT32, Äppelallee 45, 65203 Wiesbaden, Germany.
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Tridico S, Houck M, Kirkbride KP, Smith M, Yates B. Morphological identification of animal hairs: Myths and misconceptions, possibilities and pitfalls. Forensic Sci Int 2014; 238:101-7. [DOI: 10.1016/j.forsciint.2014.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
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Chen JW, Uboh CE, Soma LR, You Y, Jiang Z, Li X, Guan F, Liu Y. Identification of sample donor by 24-plex short tandem repeat in a post-race equine plasma containing dexamethasone. SPRINGERPLUS 2014; 3:94. [PMID: 24600547 PMCID: PMC3935034 DOI: 10.1186/2193-1801-3-94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/14/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Animal sport such as horseracing is tainted with drug abuse as are human sports. Treatment of racehorses on race day with therapeutic medications in most cases is banned, and thus, it is essential to monitor the illicit use of drugs in the racing horse to maintain integrity of racing, ensure fair competition and protect the health, safety and welfare of the horse, jockeys and drivers. In the event of a dispute over the identity of the sample donor, if the regulator can provide evidence that the DNA genotype profile of the post-race sample matched that of the alleged donor, then the potential drug violation case might be easily resolved without legal challenges. CASE DESCRIPTION We present a case study of a racehorse sample that tested positive for dexamethasone in a post-race plasma sample in Pennsylvania (PA) but the result was challenged by the trainer of the horse. Dexamethasone is a synthetic glucocorticoid widely used in the management of musculoskeletal problems in horses but its presence in the horse during competition is banned by the PA Racing Commissions. The presence of dexamethasone in the post-competition plasma sample was confirmed using liquid chromatography-tandem mass spectrometry. However, this finding was challenged by the trainer of the horse alleging that the post-race sample was not collected from his/her horse and thus petitioned the Commission to be absolved of any wrong-doing. To resolve the dispute, a DNA test was ordered by the PA Racing Commission to identify the correct donor of the dexamethasone positive sample. For this purpose, a 24-plex short tandem repeat analysis to detect 21 equine markers and three human markers was employed. The results indicated that all the samples tested had identical DNA profiles and thus, it was concluded that the samples were collected from the same horse and that the probability of drawing a false conclusion was approximately zero (1.5 × 10(-15)). CONCLUSIONS The plasma sample confirmed for the presence of dexamethasone was collected from the alleged horse.
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Affiliation(s)
- Jin-Wen Chen
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Cornelius E Uboh
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA ; Pennsylvania Equine Toxicology & Research Center, Department of Chemistry, West Chester University, 220 E Rosedale Avenue, West Chester, PA 19382 USA
| | - Lawrence R Soma
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Youwen You
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Zibin Jiang
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Xiaoqing Li
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Fuyu Guan
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Ying Liu
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
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Johnson RN, Wilson-Wilde L, Linacre A. Current and future directions of DNA in wildlife forensic science. Forensic Sci Int Genet 2013; 10:1-11. [PMID: 24680123 DOI: 10.1016/j.fsigen.2013.12.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/22/2022]
Abstract
Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders; essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Examples are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Centre for Wildlife Genomics, Science and Learning Division, Australian Museum, Sydney, Australia.
| | - Linzi Wilson-Wilde
- Australia New Zealand Policing Advisory Agency - National Institute of Forensic Science, Melbourne, Australia
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Bedford Park, Adelaide, Australia
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Ribeca C, Bonfatti V, Cecchinato A, Albera A, Gallo L, Carnier P. Effect of polymorphisms in candidate genes on carcass and meat quality traits in double muscled Piemontese cattle. Meat Sci 2013; 96:1376-83. [PMID: 24361557 DOI: 10.1016/j.meatsci.2013.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/25/2013] [Accepted: 11/26/2013] [Indexed: 11/27/2022]
Abstract
The aim of this study was to investigate the association between 10 candidate genes and carcass weight and conformation, carcass daily gain, and meat quality (pH, color, cooking loss, drip loss and shear force) in 990 double-muscled Piemontese young bulls. Animals were genotyped at each of the following genes: growth hormone, growth hormone receptor, pro-opiomelanocortin, pro-opiomelanocortin class 1 homeobox 1, melanocortin-4 receptor, corticotrophin-releasing hormone, diacylglycerol O-acyltransferase-1, thyroglobulin, carboxypeptidase E and gamma-3 regulatory subunit of the AMP-activated protein kinase. All the investigated SNPs had additive effects which were relevant for at least one of the traits. Relevant associations between the investigated SNPs and carcass weight, carcass daily gain and carcass conformation were detected, whereas associations of SNPs with meat quality were moderate. Results confirmed some of previously reported associations, but diverged for others. Validation in other cattle breeds is required to use these SNPs in gene-assisted selection programs for enhancement of carcass traits and meat quality.
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Affiliation(s)
- C Ribeca
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - V Bonfatti
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.
| | - A Cecchinato
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - A Albera
- Piemontese Cattle Breeders Association (ANABoRaPi), strada Trinità 32/a, Carrù, 12061, Italy
| | - L Gallo
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - P Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
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Validation of two canine STR multiplex-assays following the ISFG recommendations for non-human DNA analysis. Forensic Sci Int Genet 2013; 8:90-100. [PMID: 24315595 DOI: 10.1016/j.fsigen.2013.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/07/2013] [Accepted: 07/01/2013] [Indexed: 11/22/2022]
Abstract
To gain general acceptance forensic DNA testing in animals needs to improve standardization of analysis methods and data interpretation. Recently, the International Society of Forensic Genetics (ISFG) took particular care of this topic by publishing recommendations for forensic non-human DNA analysis following the successful example of human DNA analysis in order to provide a basis for harmonization of the still existing inter-laboratory variability. By following these recommendations we demonstrate the performance of two short tandem repeat (STR) multiplexes for forensic identity testing of canine biological material. Thirteen STRs and two sex-specific markers were selected and validated according to the ISFG guidelines. Population genetic parameters were calculated based on 295 dog samples collected in Austria (124) and Germany (171). A repeat-based nomenclature of the mainly tetrameric STRs and corresponding allelic ladders are presented. All 146 different alleles included in the ladders were sequenced for correct allele calling. Additionally, a canine cell line (DH82-D3167) was evaluated as standard reference material.
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Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species. J Forensic Leg Med 2013; 20:334-8. [DOI: 10.1016/j.jflm.2012.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 07/15/2012] [Accepted: 09/07/2012] [Indexed: 02/07/2023]
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Bonfatti V, Albera A, Carnier P. Genetic associations between daily BW gain and live fleshiness of station-tested young bulls and carcass and meat quality traits of commercial intact males in Piemontese cattle. J Anim Sci 2013; 91:2057-66. [PMID: 23463552 DOI: 10.2527/jas.2012-5386] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to investigate genetic relationships between beef traits of station-tested young bulls and carcass and meat quality traits (MQ) of commercial intact males in Piemontese cattle. Phenotypes for daily gain (DG) and live fleshiness traits (width at withers: WW; shoulder muscularity: SM; loin width: LW; loin thickness: LT; thigh muscularity: TM; thigh profile: TP) and thinness of the shin bone (BT) were available for 3,109 and 2,183 performance-tested young bulls, respectively. Carcass daily gain (CDG), carcass conformation (SEUS), pH at 24 h (pH24h) and 8 d after slaughter (pH8d), lightness (L*), redness (a*), yellowness (b*), hue angle (HA), saturation index (SI), drip loss (DL), cooking loss (CL), and shear force (SF) were assessed for 1,208 commercial intact males. (Co) variance components were estimated in a set of twelve 9-traits analyses using REML and linear animal models including all performance-test traits and 1 carcass or MQ trait at a time. Heritabilities ± SE of beef traits ranged from 0.26 ± 0.03 (LW) to 0.47 ± 0.01 (DG), whereas those of carcass traits and MQ from 0.06 ± 0.03 (CL) to 0.63 ± 0.04 (HA). The genetic correlation (rg) between DG and CDG was 0.75 ± 0.10, indicating that DG, as measured at the test station, is a good indicator of the carcass gain achieved by commercial animals under farms conditions. Daily BW gain of station-tested bulls correlated positively with color traits (from 0.11 ± 0.12 to 0.54 ± 0.09), ph8d (rg ± SE = 0.31 ± 0.11), DL (rg ± SE = 0.29 ± 0.17), and CL (rg ± SE = 0.27 ± 0.18). Live fleshiness of station-tested bulls exhibited genetic correlations with MQ of commercial animals that were positive for L* and b* (from 0.13 ± 0.08 to 0.65 ± 0.14) and negative for pH (from -0.27 ± 0.15 to -0.57 ± 0.11), CL (from -0.16 ± 0.23 to -0.43 ± 0.22), and SF (TM: rg ± SE = -0.31 ± 0.15; TP: rg ± SE = -0.41 ± 0.17). The thinness of the shin bone correlated unfavorably with CDG (rg ± SE = -0.74 ± 0.07) and favorably with SEUS (rg ± SE = 0.65 ± 0.17), CL (rg ± SE = -0.39 ± 0.13), and SF (rg ± SE = -0.32 ± 0.17). The estimated genetic correlations indicate that selection to increase DG, as measured at the test station, exerts moderate adverse effects on MQ. Because selection emphasis is greater for live fleshiness than for DG, the correlated response in MQ and carcass traits is expected to be influenced to a greater extent by selection for muscularity, even though these traits are less heritable than DG.
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Affiliation(s)
- V Bonfatti
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, 35020 Legnaro (PD), Italy
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D’Amato ME, Alechine E, Cloete KW, Davison S, Corach D. Where is the game? Wild meat products authentication in South Africa: a case study. INVESTIGATIVE GENETICS 2013; 4:6. [PMID: 23452350 PMCID: PMC3621286 DOI: 10.1186/2041-2223-4-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/14/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species. RESULTS The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species. CONCLUSIONS The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
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Affiliation(s)
- Maria Eugenia D’Amato
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Evguenia Alechine
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
| | - Kevin Wesley Cloete
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
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