Skip to main content

Lineage Markers and Their Applications in Forensic DNA Analysis

  • Chapter
  • First Online:
Advances in Forensic Biology and Genetics

Abstract

Lineage markers can be inherited uniparentally, such as the mitochondrial genome—from mother to child, the Y-chromosome—from father to son, or the X-chromosome when passed from mother to son, or diparentally, such as the X-chromosomes passed from mother and father to daughter. While these markers are not individualizing, they are able to determine kinship, identify missing persons through familial testing, and separate male and female DNA samples in instances of sexual assault. For this reason, these unique markers have become a standard assessment in many forensic cases. Here, we discuss the most common lineage markers, their characteristics, and their forensic value and limitations.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+
from $39.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
eBook
USD 199.00
Price excludes VAT (USA)
Hardcover Book
USD 249.99
Price excludes VAT (USA)

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Abdulazeez AB, Aziz IH, Farhan MM (2020) X-chromosome markers used in deficiency of paternity case. Ind J Forensic Med Toxicol 14:789–793

    Google Scholar 

  • Alonso A, Barrio PA, Müller P, Köcher S, Berger B, Martin P, Bodner M, Willuweit S, Parson W, Roewer L (2018) Current state-of-art of STR sequencing in forensic genetics. Electrophoresis 39:2655–2668

    Article  CAS  PubMed  Google Scholar 

  • Alwi AR, Mahat NA, Salleh FM, Ishar SM, Kamaluddin MR, Rashid MRA (2023) Applications of X-chromosome short tandem repeats for human identification: a review. JTLS

    Google Scholar 

  • Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314

    Article  PubMed  PubMed Central  Google Scholar 

  • Anderson S, Bankier AT, Barrell BG, De Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465

    Article  CAS  PubMed  Google Scholar 

  • Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147–147

    Article  CAS  PubMed  Google Scholar 

  • Annis S, Fleischmann Z, Khrapko M, Franco M, Wasko K, Woods D, Kunz WS, Ellis P, Khrapko K (2019) Quasi-Mendelian paternal inheritance of mitochondrial DNA: A notorious artifact, or anticipated behavior? Proc Natl Acad Sci 116:14797–14798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anslinger K, Bayer B (2019) New strategies in the field of mixture deconvolution single cell STR profiling. Forensic Sci Int Genet Suppl Ser 7:259–261

    Article  Google Scholar 

  • Awadalla P, Eyre-Walker A, Smith JM (1999) Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286:2524–2525

    Article  CAS  PubMed  Google Scholar 

  • Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, Van Duijn K, Vermeulen M, Brauer S (2010) Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 87:341–353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, Vermeulen M, De Knijff P, Kayser M (2012) A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRS for differentiating male relatives and paternal lineages. Forensic Sci Int Genet 6:208–218

    Article  CAS  PubMed  Google Scholar 

  • Ballard D, Winkler-Galicki J, Wesoły J (2020) Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects. Int J Leg Med 134:1291–1303

    Article  Google Scholar 

  • Bandelt H-J, Dür A (2007) Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. Mol Phylogenet Evol 42:256–271

    Article  CAS  PubMed  Google Scholar 

  • Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V (2002) The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71:1150–1160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Basta M, Pandya AM (2020) Genetics, X-linked inheritance. StatPearls

    Google Scholar 

  • Behar DM, Van Oven M, Rosset S, Metspalu M, Loogväli E-L, Silva NM, Kivisild T, Torroni A, Villems R (2012) A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90:675–684

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brandstätter A, Sänger T, Lutz-Bonengel S, Parson W, Béraud-Colomb E, Wen B, Kong QP, Bravi CM, Bandelt HJ (2005) Phantom mutation hotspots in human mitochondrial DNA. Electrophoresis 26:3414–3429

    Article  PubMed  Google Scholar 

  • Brenner CH, Weir BS (2003) Issues and strategies in the DNA identification of World Trade Center victims. Theor Popul Biol 63:173–178

    Article  CAS  PubMed  Google Scholar 

  • Bromham L, Eyre-Walker A, Smith NH, Smith JM (2003) Mitochondrial Steve: paternal inheritance of mitochondria in humans. Trends Ecol Evol 18:2–4

    Article  Google Scholar 

  • Buckleton JS, Krawczak M, Weir BS (2011) The interpretation of lineage markers in forensic DNA testing. Forensic Sci Int Genet 5:78–83

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Budowle B, Wilson MR, Dizinno JA, Stauffer C, Fasano MA, Holland MM, Monson KL (1999) Mitochondrial DNA regions HVI and HVII population data. Forensic Sci Int 103:23–35

    Article  CAS  PubMed  Google Scholar 

  • Budowle B, Allard MW, Wilson MR, Chakraborty R (2003) Forensics and mitochondrial DNA: applications, debates, and foundations. Annu Rev Genomics Hum Genet 4:119–141

    Article  CAS  PubMed  Google Scholar 

  • Burr SP, Chinnery PF (2020) Heredity and segregation of mtDNA. Elsevier, The Human Mitochondrial Genome

    Book  Google Scholar 

  • Calacal GC, Delfin FC, Tan MMM, Roewer L, Magtanong DL, Lara MC, De Ungria MCA (2005) Identification of exhumed remains of fire tragedy victims using conventional methods and autosomal/Y-chromosomal short tandem repeat DNA profiling. Am J Forensic Med Pathol 26:285–291

    Article  PubMed  Google Scholar 

  • Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325:31–36

    Article  CAS  PubMed  Google Scholar 

  • Claerhout S, Van Der Haegen M, Vangeel L, Larmuseau MH, Decorte R (2019) A game of hide and seq: identification of parallel Y-STR evolution in deep-rooting pedigrees. Eur J Hum Genet 27:637–646

    Article  CAS  PubMed  Google Scholar 

  • Coble MD, Loreille OM, Wadhams MJ, Edson SM, Maynard K, Meyer CE, Niederstätter H, Berger C, Berger B, Falsetti AB (2009) Mystery solved: the identification of the two missing Romanov children using DNA analysis. PloS One 4:e4838

    Article  PubMed  PubMed Central  Google Scholar 

  • D’aurelio M, Gajewski CD, Lin MT, Mauck WM, Shao LZ, Lenaz G, Moraes CT, Manfredi G (2004) Heterologous mitochondrial DNA recombination in human cells. Hum Mol Genet 13:3171–3179

    Article  PubMed  Google Scholar 

  • Dayama G, Emery SB, Kidd JM, Mills RE (2014) The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res 42:12640–12649

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Cario R, Kura A, Gori AM, Pepe G, Giusti B (2020) Sanger validation of high-throughput sequencing in genetic diagnosis: still the best practice? Front Genet 11:592588

    Article  PubMed  PubMed Central  Google Scholar 

  • De Knijff P (2022) On the forensic use of Y-chromosome polymorphisms. Genes 13:898

    Article  PubMed  PubMed Central  Google Scholar 

  • Diegoli TM (2015) Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 18:140–151

    Article  CAS  PubMed  Google Scholar 

  • Edelmann J, Lessig R, Klintschar M, Szibor R (2004) Advantages of X-chromosomal microsatellites in deficiency paternity testing: presentation of cases. International Congress Series, vol 1261. Elsevier, pp 257–259

    Google Scholar 

  • Eduardoff M, Xavier C, Strobl C, Casas-Vargas A, Parson W (2017) Optimized mtDNA control region primer extension capture analysis for forensically relevant samples and highly compromised mtDNA of different age and origin. Genes 8:237

    Article  PubMed  PubMed Central  Google Scholar 

  • Eichmann C, Parson W (2008) ‘Mitominis’: multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples. Int J Leg Med 122:385–388

    Article  Google Scholar 

  • Elson JL, Andrews RM, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (2001) Analysis of European mtDNAs for recombination. Am J Hum Genet 68:145–153

    Article  CAS  PubMed  Google Scholar 

  • Feng L, Xu C, Zeng X, Zhang H, Yang F, Li W, Tu Z, Li C, Hu L (2014) Y-chromosomal haplotyping of single sperm cells isolated from semen mixtures–a successful identification of three perpetrators in a multi-suspect sexual assault case. Croat Med J 55:537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Forster L, Forster P, Lutz-Bonengel S, Willkomm H, Brinkmann B (2002) Natural radioactivity and human mitochondrial DNA mutations. Proc Natl Acad Sci 99:13950–13954

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Frascarelli C, Zanetti N, Nasca A, Izzo R, Lamperti C, Lamantea E, Legati A, Ghezzi D (2023) Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions. Front Genet 14:1089956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galtier N, Enard D, Radondy Y, Bazin E, Belkhir K (2006) Mutation hot spots in mammalian mitochondrial DNA. Genome Res 16:215–222

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ge J, Budowle B (2021) Forensic investigation approaches of searching relatives in DNA databases. J Forensic Sci 66:430–443

    Article  CAS  PubMed  Google Scholar 

  • Giles RE, Blanc H, Cann HM, Wallace DC (1980) Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci 77:6715–6719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, Evett I, Hagelberg E, Sullivan K (1994) Identification of the remains of the Romanov family by DNA analysis. Nat Genet 6:130–135

    Article  CAS  PubMed  Google Scholar 

  • Gomes C, Magalhães M, Alves C, Amorim A, Pinto N, Gusmão L (2012) Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs. Int J Leg Med 126:917–921

    Article  Google Scholar 

  • Gomes I, Pinto N, Antão-Sousa S, Gomes V, Gusmão L, Amorim A (2020) Twenty years later: a comprehensive review of the X chromosome use in forensic genetics. Front Genet 11:568094

    Article  Google Scholar 

  • Gray MW (2012) Mitochondrial evolution. Cold Spring Harb Perspect Biol 4:a011403

    Article  PubMed  PubMed Central  Google Scholar 

  • Gray A (2021) DNA-nanopore technology: a human perspective. Emerg Top Life Sci 5:455–463

    Article  CAS  PubMed  Google Scholar 

  • Greenberg BD, Newbold JE, Sugino A (1983) Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA. Gene 21:33–49

    Article  CAS  PubMed  Google Scholar 

  • Guideline R.V (n.d.) Scientific working group on DNA analysis methods (SWGDAM), vol 6. Forensic Science Communications

    Google Scholar 

  • Haas C, Shved N, Rühli FJ, Papageorgopoulou C, Purps J, Geppert M, Willuweit S, Roewer L, Krawczak M (2013) Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596–1639). Forensic Sci Int Genet 7:610–617

    Article  CAS  PubMed  Google Scholar 

  • Hall CL, Zascavage RR, Sedlazeck F, Planz JV (2020) Potential applications of nanopore sequencing for forensic analysis. Forensic Sci Rev 32:23–54

    CAS  PubMed  Google Scholar 

  • Han J-P, Yang F, Xu C, Wei Y-L, Zhao X-C, Hu L, Ye J, Li C-X (2014) A new strategy for sperm isolation and STR typing from multi-donor sperm mixtures. Forensic Sci Int Genet 13:239–246

    Article  CAS  PubMed  Google Scholar 

  • Hashiguchi K, Bohr VA, De Souza-Pinto NC (2004) Oxidative stress and mitochondrial DNA repair: implications for NRTIs induced DNA damage. Mitochondrion 4:215–222

    Article  CAS  PubMed  Google Scholar 

  • Hazkani-Covo E, Zeller RM, Martin W (2010) Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet 6:e1000834

    Article  PubMed  PubMed Central  Google Scholar 

  • Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu S-F (2021) Human mitochondrial control region and mtgenome: design and forensic validation of NGS multiplexes, sequencing and analytical software. Genes 12:599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howell N, Elson JL, Howell C, Turnbull DM (2007) Relative rates of evolution in the coding and control regions of African mtDNAs. Mol Biol Evol 24:2213–2221

    Article  CAS  PubMed  Google Scholar 

  • Huffman K, Hanson E, Ballantyne J (2023) Y-STR mixture deconvolution by single-cell analysis. J Forensic Sci 68:275–288

    Article  CAS  PubMed  Google Scholar 

  • Ingman M, Gyllensten U (2007) Rate variation between mitochondrial domains and adaptive evolution in humans. Hum Mol Genet 16:2281–2287

    Article  CAS  PubMed  Google Scholar 

  • Ivanov PL, Wadhams MJ, Roby RK, Holland MM, Weedn VW, Parsons TJ (1996) Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nat Genet 12:417–420

    Article  CAS  PubMed  Google Scholar 

  • Jackson A, Jackson J, Mountain H, Brearley D (2016) Forensic Science, 4th edn. Pearson Education

    Google Scholar 

  • Jobling MA, Tyler-Smith C (2017) Human Y-chromosome variation in the genome-sequencing era. Nat Rev Genet 18:485–497

    Article  CAS  PubMed  Google Scholar 

  • Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A (2006) The role of selection in the evolution of human mitochondrial genomes. Genetics 172:373–387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kong Q-P, Bandelt H-J, Sun C, Yao Y-G, Salas A, Achilli A, Wang C-Y, Zhong L, Zhu C-L, Wu S-F (2006) Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15:2076–2086

    Article  CAS  PubMed  Google Scholar 

  • Kraytsberg Y, Schwartz M, Brown TA, Ebralidse K, Kunz WS, Clayton DA, Vissing J, Khrapko K (2004) Recombination of human mitochondrial DNA. Science 304:981

    Article  CAS  PubMed  Google Scholar 

  • Kühlbrandt W (2015) Structure and function of mitochondrial membrane protein complexes. BMC Biol 13:1–11

    Article  Google Scholar 

  • Lee SR, Han J (2017) Mitochondrial nucleoid: shield and switch of the mitochondrial genome. Oxid Med Cell Longev 2017

    Google Scholar 

  • Liu G, Zheng Y, Wu Q, Feng T, Xia Y, Chen D, Ren L, Bai X, Li Q, Chen D (2023) Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application. Int J Leg Med 137:1693–1703

    Article  Google Scholar 

  • Logsdon GA, Vollger MR, Eichler EE (2020) Long-read human genome sequencing and its applications. Nat Rev Genet 21:597–614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434–439

    Article  CAS  PubMed  Google Scholar 

  • Luo S, Valencia CA, Zhang J, Lee N-C, Slone J, Gui B, Wang X, Li Z, Dell S, Brown J (2018) Biparental inheritance of mitochondrial DNA in humans. Proc Natl Acad Sci 115:13039–13044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lutz-Bonengel S, Parson W (2019) No further evidence for paternal leakage of mitochondrial DNA in humans yet. Proc Natl Acad Sci 116:1821–1822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lyons EA, Scheible MK, Sturk-Andreaggi K, Irwin JA, Just RS (2013) A high-throughput Sanger strategy for human mitochondrial genome sequencing. BMC Genomics 14:1–16

    Article  Google Scholar 

  • Malyarchuk BA, Rogozin IB, Berikov VB, Derenko MV (2002) Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region. Hum Genet 111:46–53

    Article  CAS  PubMed  Google Scholar 

  • Malyarchuk B, Grzybowski T, Derenko M, Perkova M, Vanecek T, Lazur J, Gomolcák P, Tsybovsky I (2008) Mitochondrial DNA phylogeny in eastern and western Slavs. Mol Biol Evol 25:1651–1658

    Article  CAS  PubMed  Google Scholar 

  • McElhoe JA, Holland MM, Makova KD, Su MS-W, Paul IM, Baker CH, Faith SA, Young B (2014) Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Sci Int Genet 13:20–29

    Google Scholar 

  • McElhoe JA, Addesso A, Young B, Holland MM (2024) A new tool for probabilistic assessment of MPS data associated with mtDNA mixtures. Genes 15:194

    Google Scholar 

  • Mellars P (2006) A new radiocarbon revolution and the dispersal of modern humans in Eurasia. Nature 439:931–935

    Article  CAS  PubMed  Google Scholar 

  • Nass MM, Nass S (1963) Intramitochondrial fibers with DNA characteristics: I. Fixation and electron staining reactions. J Cell Biol 19:593–611

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nicholls TJ, Gustafsson CM (2018) Separating and segregating the human mitochondrial genome. Trends Biochem Sci 43:869–881

    Article  CAS  PubMed  Google Scholar 

  • Ogden R, Vasiljevic N, Prost S (2021) Nanopore sequencing in non-human forensic genetics. Emerg Top Life Sci 5:465–473

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Olivieri A, Achilli A, Pala M, Battaglia V, Fornarino S, Al-Zahery N, Scozzari R, Cruciani F, Behar DM, Dugoujon J-M (2006) The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314:1767–1770

    Article  CAS  PubMed  Google Scholar 

  • Parson W, Dür A (2007) EMPOP—a forensic mtDNA database. Forensic Sci Int Genet 1:88–92

    Article  PubMed  Google Scholar 

  • Parson W, Brandstätter A, Alonso A, Brandt N, Brinkmann B, Carracedo A, Corach D, Froment O, Furac I, Grzybowski T (2004) The EDNAP mitochondrial DNA population database (Empop) collaborative exercises: organisation, results and perspectives. Forensic Sci Int 139:215–226

    Article  CAS  PubMed  Google Scholar 

  • Parson W, Fendt L, Ballard D, Børsting C, Brinkmann B, Carracedo Á, Carvalho M, Coble MD, Real FC, Desmyter S (2008) Identification of West Eurasian mitochondrial haplogroups by mtDNA SNP screening: Results of the 2006–2007 EDNAP collaborative exercise. Forensic Sci Int Genet 2:61–68

    Article  PubMed  Google Scholar 

  • Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S (2013) Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet 7:543–549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parson W, Huber G, Moreno L, Madel M-B, Brandhagen MD, Nagl S, Xavier C, Eduardoff M, Callaghan TC, Irwin JA (2015) Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples. Forensic Sci Int Genet 15:8–15

    Article  CAS  PubMed  Google Scholar 

  • Peck MA, Brandhagen MD, Marshall C, Diegoli TM, Irwin JA, Sturk-Andreaggi K (2016) Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq. Forensic Sci Int Genet 24:103–111

    Article  CAS  PubMed  Google Scholar 

  • Pervez MT, Abbas SH, Moustafa MF, Aslam N, Shah SSM (2022) A comprehensive review of performance of next-generation sequencing platforms. Biomed Res Int 2022

    Google Scholar 

  • Pilli E, Berti A (2021) Forensic DNA analysis: technological development and innovative applications. CRC Press

    Book  Google Scholar 

  • Pollard MO, Gurdasani D, Mentzer AJ, Porter T, Sandhu MS (2018) Long reads: their purpose and place. Hum Mol Genet 27:R234–R241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prinz M, Boll K, Baum H, Shaler B (1997) Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci Int 85:209–218

    Article  CAS  PubMed  Google Scholar 

  • Quintana-Murci L, Fellous M (2001) The human Y chromosome: the biological role of a “functional wasteland”. Biomed Res Int 1:18–24

    Article  CAS  Google Scholar 

  • Ralf A, Lubach D, Kousouri N, Winkler C, Schulz I, Roewer L, Purps J, Lessig R, Krajewski P, Ploski R (2020) Identification and characterization of novel rapidly mutating Y-chromosomal short tandem repeat markers. Hum Mutat 41:1680–1696

    Article  CAS  PubMed  Google Scholar 

  • Ralf A, Zandstra D, Weiler N, Van Ijcken WF, Sijen T, Kayser M (2021) RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates. Forensic Sci Int Genet 55:102595

    Article  CAS  PubMed  Google Scholar 

  • Richards MB, Macaulay VA, Bandelt H-J, Sykes BC (1998) Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet 62:241–260

    Article  CAS  PubMed  Google Scholar 

  • Roewer L (2009) Y chromosome STR typing in crime casework. Forensic Sci Med Pathol 5:77–84

    Article  CAS  PubMed  Google Scholar 

  • Roewer L (2019) Y-chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. Wiley Interdiscip Rev Forensic Sci 1:e1336

    Article  Google Scholar 

  • Roewer L, Amemann J, Spurr N, Grzeschik K-H, Epplen J (1992) Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts. Hum Genet 89:389–394

    Article  CAS  PubMed  Google Scholar 

  • Salas A, Carracedo A, Macaulay V, Richards M, Bandelt H-J (2005) A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun 335:891–899

    Article  CAS  PubMed  Google Scholar 

  • Sanger F (1981) Determination of nucleotide sequences in DNA. Science 214:1205–1210

    Article  CAS  PubMed  Google Scholar 

  • Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441–448

    Article  CAS  PubMed  Google Scholar 

  • Schwartz M, Vissing J (2002) Paternal inheritance of mitochondrial DNA. N Engl J Med 347:576–580

    Article  PubMed  Google Scholar 

  • Schwartz M, Vissing J (2004) No evidence for paternal inheritance of mtDNA in patients with sporadic mtDNA mutations. J Neurol Sci 218:99–101

    Article  CAS  PubMed  Google Scholar 

  • Sharma N, Pasala MS, Prakash A (2019) Mitochondrial DNA: Epigenetics and environment. Environ Mol Mutagen 60:668–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sibille I, Duverneuil C, De La Grandmaison GL, Guerrouache K, Teissiere F, Durigon M, De Mazancourt P (2002) Y-STR DNA amplification as biological evidence in sexually assaulted female victims with no cytological detection of spermatozoa. Forensic Sci Int 125:212–216

    Article  CAS  PubMed  Google Scholar 

  • Slatko BE, Gardner AF, Ausubel FM (2018) Overview of next-generation sequencing technologies. Curr Protoc Mol Biol 122:e59

    Article  PubMed  PubMed Central  Google Scholar 

  • Stoneking M, Melton T, Nott J, Barritt S, Roby R, Holland M, Weedn V, Gill P, Kimpton C, Aliston-Greiner R (1995) Establishing the identity of Anna Anderson Manahan. Nat Genet 9:9–10

    Article  CAS  PubMed  Google Scholar 

  • Stringer CB, Andrews P (1988) Genetic and fossil evidence for the origin of modern humans. Science 239:1263–1268

    Article  CAS  PubMed  Google Scholar 

  • Taylor RW, Turnbull DM (2005) Mitochondrial DNA mutations in human disease. Nat Rev Genet 6:389–402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taylor RW, Mcdonnell MT, Blakely EL, Chinnery PF, Taylor GA, Howell N, Zeviani M, Briem E, Carrara F, Turnbull DM (2003) Genotypes from patients indicate no paternal mitochondrial DNA contribution. Ann Neurol 54:521–524

    Article  CAS  PubMed  Google Scholar 

  • Technologies O.N. Nanopore sequencing accuracy [Online]. Available: https://nanoporetech.com/platform/accuracy. Accessed 4 Feb 2024

  • Templeton JE, Brotherton PM, Llamas B, Soubrier J, Haak W, Cooper A, Austin JJ (2013) DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification. Investigative Genet 4:1–13

    Article  Google Scholar 

  • Tillmar AO, Kling D, Butler JM, Parson W, Prinz M, Schneider PM, Egeland T, Gusmão L (2017) DNA Commission of the International Society for Forensic Genetics (ISFG): Guidelines on the use of X-STRs in kinship analysis. Forensic Sci Int Genet 29:269–275

    Article  CAS  PubMed  Google Scholar 

  • Tj P (1998) A high observed substitution rate in the human mitochondrial DNA control region. Nat Genet 18:109–110

    Google Scholar 

  • Tokutomi T, Takada Y, Murayama T, Mukaida M, Kanetake J (2009) Real-time PCR method for identification of Asian populations in forensic casework. Leg Med 11:S106–S108

    Article  Google Scholar 

  • Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV, Larsen M, Smith DG, Vullo CM, Wallace DC (1993) Asian affinities and continental radiation of the four founding Native American mtDNAs. Am J Hum Genet 53:563

    CAS  PubMed  PubMed Central  Google Scholar 

  • Umetsu K, Yuasa I (2005) Recent progress in mitochondrial DNA analysis. Leg Med 7:259–262

    Article  CAS  Google Scholar 

  • Van Oven M (2015) PhyloTree Build 17: Growing the human mitochondrial DNA tree. Forensic Sci Int Genet Suppl Ser 5:e392–e394

    Article  Google Scholar 

  • Van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386–E394

    Article  PubMed  Google Scholar 

  • Vissing J (2019) Paternal comeback in mitochondrial DNA inheritance. Proc Natl Acad Sci 116:1475–1476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vollger MR, Logsdon GA, Audano PA, Sulovari A, Porubsky D, Peluso P, Wenger AM, Concepcion GT, Kronenberg ZN, Munson KM (2020) Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Ann Hum Genet 84:125–140

    Article  CAS  PubMed  Google Scholar 

  • Volodko NV, Starikovskaya EB, Mazunin IO, Eltsov NP, Naidenko PV, Wallace DC, Sukernik RI (2008) Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas. Am J Hum Genet 82:1084–1100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Bogenhagen DF (2006) Human mitochondrial DNA nucleoids are linked to protein folding machinery and metabolic enzymes at the mitochondrial inner membrane. J Biol Chem 281:25791–25802

    Article  CAS  PubMed  Google Scholar 

  • Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND (2019) Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol 37:1155–1162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Willuweit S, Roewer L (2015) The new Y chromosome haplotype reference database. Forensic Sci Int Genet 15:43–48

    Article  CAS  PubMed  Google Scholar 

  • Willuweit S, Roewer L, Group I. F. Y. C. U (2007) Y chromosome haplotype reference database (YHRD): update. Forensic Sci Int Genet 1:83–87

    Article  PubMed  Google Scholar 

  • Woods CG, Cox J, Springell K, Hampshire DJ, Mohamed MD, Mckibbin M, Stern R, Raymond FL, Sandford R, Sharif SM (2006) Quantification of homozygosity in consanguineous individuals with autosomal recessive disease. Am J Hum Genet 78:889–896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zascavage RR, Hall CL, Thorson K, Mahmoud M, Sedlazeck FJ, Planz JV (2019a) Approaches to whole mitochondrial genome sequencing on the Oxford Nanopore Minion. Curr Protoc Hum Genet 104:e94

    Article  CAS  PubMed  Google Scholar 

  • Zascavage RR, Thorson K, Planz JV (2019b) Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing. Electrophoresis 40:272–280

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Yu Z, Mo X, Zhao X, Li W, Liu H, Liu C, Wu R, Sun H (2021) Comparative evaluation of autosomal STRs and X-chromosome STRs as a complement of autosomal STRs in kinship testing in Southern Han Chinese. Ann Hum Biol 48:66–69

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Roxanne R. Zascavage.

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2025 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kapema, B., McBroom Henson, K.E., Mello, I., Zascavage, R.R. (2025). Lineage Markers and Their Applications in Forensic DNA Analysis. In: Dash, H.R., Elkins, K.M., Al-Snan, N.R. (eds) Advances in Forensic Biology and Genetics. Springer, Singapore. https://doi.org/10.1007/978-981-96-4585-5_17

Download citation

Keywords

Publish with us

Policies and ethics

Profiles

  1. Bupe Kapema