Abstract
Most of the length of the Y chromosome escapes recombination with the X chromosome and is strictly paternally inherited. This has profound evolutionary implications and provides (together with the matrilineal mitochondrial DNA) unique tools in human population genetics. Absence of recombination implies that a most parsimonious tree can be easily constructed from SNPs and other slowly mutating polymorphisms. The main branches of this tree, called haplogroups, have distinct geographic distributions and can be used to trace human migrations. Faster evolving polymorphisms, such as microsatellites provide readily time estimates for these migrations and other demographic events. Beyond sets of predefined polymorphism, sequencing of most of the non-recombining portion of the Y chromosome has yielded an accurate picture of the global evolution of this chromosome. Combining the Y chromosome with mitochondrial DNA has revealed sex-specific migrations, particularly in the Colonial period. Since surnames are also patrilineally inherited in many populations, the analysis of Y chromosome variation within surnames has shed light on the dynamics of surnames in populations, but has also contributed to the investigation of notorious lineages, such as the Columbus, Bourbons, and Draculs. However, it also raises the possibility of predicting a surname from an anonymous sample, which may be an important tool in forensic genetics but raises also privacy concerns for participants in genetic studies.
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References
Adams SM, King TE, Bosch E, Jobling MA (2006) The case of the unreliable SNP: recurrent back-mutation of Y-chromosomal marker P25 through gene conversion. Forensic Sci Int 159:14–20
Adams SM, Bosch E, Balaresque PL et al (2008) The genetic legacy of religious diversity and intolerance: paternal lineages of Christians, Jews, and Muslims in the Iberian Peninsula. Am J Hum Genet 83:725–736
Alonso S, Flores C, Cabrera V et al (2005) The place of the Basques in the European Y-chromosome diversity landscape. Eur J Hum Genet 13:1293–1302
Arredi B, Poloni ES, Paracchini S et al (2004) A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 75:338–345
Athey TW (2005) Haplogroup prediction from Y-STR values using an allele- frequency approach. J Genet Geneal 1:1–7
Bachtrog D (2013) Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat Rev Genet 14:113–124
Balaresque P, Bowden GR, Adams SM et al (2010) A predominantly neolithic origin for European paternal lineages. PLoS Biol 8:e1000285
Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL (1997) An apportionment of human DNA diversity. Proc Natl Acad Sci USA 94:4516–4519
Batini C, Ferri G, Destro-Bisol G et al (2011) Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Mol Biol Evol 28:2603–2613
Battaggia C, Anagnostou P, Boschi I et al (2012) Detecting sex-biased gene flow in African-Americans through the analysis of intra- and inter-population variation at mitochondrial DNA and Y- chromosome microsatellites. Balk J Med Genet 15:7–14
Berniell-Lee G, Plaza S, Bosch E et al (2008) Admixture and sexual bias in the population settlement of La Reunion Island (Indian Ocean). Am J Phys Anthropol 136:100–107
Berniell-Lee G, Calafell F, Bosch E et al (2009) Genetic and demographic implications of the bantu expansion: insights from human paternal lineages. Mol Biol Evol 26:1581–1589
Bosch E, Calafell F, Santos FR et al (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65:1623–1638
Bosch E, Calafell F, Comas D et al (2001) High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula. Am J Hum Genet 68:1019–1029
Bosch E, Calafell F, Rosser ZH et al (2003) High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis. Hum Genet 112:353–363
Bouzekri N, Taylor PG, Hammer MF, Jobling MA (1998) Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1 (DYF155S1). Hum Mol Genet 7:643–653
Calafell F, Comas D, Bertranpetit J (2002) Why names. Genome Res 12:219–221
Cann R, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325:31–36
Charlier P, Olalde I, Sole N et al (2013) Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both kings of France). Forensic Sci Int 226:38–40. https://doi.org/10.1016/j.forsciint.2012.11.018
Corach D, Lao O, Bobillo C et al (2010) Inferring continental ancestry of argentineans from autosomal, Y-chromosomal and mitochondrial DNA. Ann Hum Genet 74:65–76
Cruciani F, La Fratta R, Santolamazza P et al (2004) Phylogeographic analysis of haplogroup E3b (E-M215) y chromosomes reveals multiple migratory events within and out of Africa. Am J Hum Genet 74:1014–1022
Cruciani F, La Fratta R, Torroni A et al (2006) Molecular dissection of the Y chromosome haplogroup E-M78 (E3b1a): a posteriori evaluation of a microsatellite-network-based approach through six new biallelic markers. Hum Mutat 27:831–832
Cruciani F, Trombetta B, Massaia A et al (2011) A revised root for the human y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa. Am J Hum Genet 88:814–818
Dorit R, Akashi H, Gilbert W (1995) Absence of polymorphism at the ZFY locus on the human Y chromosome. Science 268:1183–1185
Dupanloup I, Pereira L, Bertorelle G et al (2003) A recent shift from polygyny to monogamy in humans is suggested by the analysis of worldwide Y-chromosome diversity. J Mol Evol 57:85–97
Durbin RM, Abecasis GR, Altshuler DL et al (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073
Flores C, Maca-Meyer N, Perez JA et al (2003) A predominant European ancestry of paternal lineages from canary islanders. Ann Hum Genet 67:138–152
Francalacci P, Morelli L, Angius A et al (2013) Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341:565–569
Gitschier J (2009) Inferential genotyping of Y chromosomes in latter-day saints founders and comparison to Utah samples in the HapMap project. Am J Hum Genet 84:251–258
Gonzalez AM, Brehm A, Perez JA et al (2003) Mitochondrial DNA affinities at the Atlantic fringe of Europe. Am J Phys Anthropol 120:391–404
Guerra DC, Perez CF, Izaguirre MH et al (2011) Gender differences in ancestral contribution and admixture in Venezuelan populations. Hum Biol 83:345–361
Gymrek M, McGuire AL, Golan D et al (2013) Identifying personal genomes by surname inference. Science 339:321–324
Hammer MF, Karafet TM, Redd AJ et al (2001) Hierarchical patterns of global human Y-chromosome. Diversity 18:1189–1203
Hammer MF, Behar DM, Karafet TM et al (2009) Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood. Hum Genet 126:707–717
Helgason A, Sigureth ardottir S, Gulcher JR et al (2000a) mtDNA and the origin of the Icelanders: deciphering signals of recent population history. Am J Hum Genet 66:999–1016
Helgason A, Sigureth ardottir S, Nicholson J et al (2000b) Estimating Scandinavian and Gaelic ancestry in the male settlers of Iceland. Am J Hum Genet 67:697–717
Hurles ME, Sykes BC, Jobling MA, Forster P (2005) The dual origin of the Malagasy in island Southeast Asia and East Africa: evidence from maternal and paternal lineages. Am J Hum Genet 76:894–901
Jakubiczka S, Arnemann J, Cooke HJ et al (1989) A search for restriction fragment length polymorphism on the human Y chromosome. Hum Genet 84:86–88
Jobling MA, Tyler-Smith C (1995) Fathers and sons: the Y chromosome and. Hum Evol 11:449–456
Jorde LB, Watkins WS, Bamshad MJ et al (2000) The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet 66:979–988
Karafet TM, Mendez FL, Meilerman MB et al (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838
King TE, Jobling MA (2009a) Founders, drift, and infidelity: the relationship between Y chromosome diversity and patrilineal surnames. Mol Biol Evol 26:1093–1102
King TE, Jobling MA (2009b) What’s in a name? Y chromosomes, surnames and the genetic genealogy revolution. Trends Genet 25:351–360
King TE, Bowden GR, Balaresque PL et al (2007) Thomas Jefferson’s Y chromosome belongs to a rare European lineage. Am J Phys Anthropol 132:584–589
Lahn BT, Page DC (1997) Functional coherence of the human Y chromosome. Science 278:675–680
Lahn BT, Page DC (1999) Four evolutionary strata on the human X chromosome. Science 286:964–967
Lalueza-Fox C, Gigli E, Bini C et al (2011) Genetic analysis of the presumptive blood from Louis XVI, King of France. Forensic Sci Int Genet 5:459–463. https://doi.org/10.1016/j.fsigen.2010.09.007
Lao O, Vallone PM, Coble MD et al (2010) Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA. Hum Mutat 31:1875–1893
Larmuseau MH, Delorme P, Germain P et al (2013) Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings. Eur J Hum Genet 22(5):681–687
Larmuseau MHD, Vanderheyden N, Van Geystelen A et al (2014) Recent radiation within Y-chromosomal Haplogroup R-M269 resulted in high Y-STR haplotype resemblance. Ann Hum Genet 78:92–103. https://doi.org/10.1111/ahg.12050
Lucotte G, Ngo NY (1985) p49F, a highly polymorphic probe that detects TaqI RFLPs on the human Y chromosome. Nucleic Acids Res 13:8285
Malaspina P, Persichetti F, Novelletto A et al (1990) The human Y chromosome shows a low level of DNA polymorphism. Ann Hum Genet 54:297–305
Martinez-Cruz B, Ioana M, Calafell F et al (2012) Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings. PLoS One 7:e41803. https://doi.org/10.1371/journal.pone.0041803
Martínez-González LJ, Martínez-Espín E, Álvarez JC et al (2012) Surname and Y chromosome in southern Europe: a case study with Colom/Colombo. Eur J Hum Genet 20:211–216. https://doi.org/10.1038/ejhg.2011.162
McEvoy B, Bradley DG (2006) Y-chromosomes and the extent of patrilineal ancestry in Irish surnames. Hum Genet 119:212–219
McEvoy B, Brady C, Moore LT, Bradley DG (2006) The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis. Eur J Hum Genet 14:1288–1294
Mendez FL, Krahn T, Schrack B et al (2013) An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet 92:454–459
Mendizabal I, Sandoval K, Berniell-Lee G et al (2008) Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. BMC Evol Biol 8:213
Myres NM, Rootsi S, Lin AA et al (2010) A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 19:95–101
Núñez C, Baeta M, Sosa C et al (2010) Reconstructing the population history of Nicaragua by means of mtDNA, Y-chromosome STRs, and autosomal STR markers. Am J Phys Anthropol 143:591–600
Pérez-Lezaun A, Calafell F, Comas D et al (1999) Sex-specific migration patterns in central Asian populations revealed by the analysis of Y-chromosome STRs and mtDNA. Am J Hum Genet 65:208–219
Poznik GD, Henn BM, Yee MC et al (2013) Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341:562–565
Rocca RA, Magoon G, Reynolds DF et al (2012) Discovery of Western European R1b1a2 Y chromosome variants in 1000 genomes project data: an online community approach. PLoS One 7:e41634
Romualdi C, Balding D, Nasidze IS et al (2002) Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 12:602–612
Rootsi S, Magri C, Kivisild T et al (2004) Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe. Am J Hum Genet 75:128–137
Rootsi S, Zhivotovsky LA, Baldovic M et al (2007) A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. Eur J Hum Genet 15:204–211
Rootsi S, Myres NM, Lin AA et al (2012) Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus. Eur J Hum Genet 20:1275–1282
Satta Y, Iwase M (2015) Genes on X and Y chromosomes. In: Evolution of the human genome I. Evolutionary studies. Springer, Tokyo
Schlecht J, Kaplan ME, Barnard K et al (2008) Machine-learning approaches for classifying haplogroup from Y chromosome STR data. PLoS Comput Biol 4:e1000093
Seielstad MT, Hebert JM, Lin AA et al (1994) Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. Hum Mol Genet 3:2159–2161
Seielstad MT, Minch E, Cavalli-Sforza LL (1998) Genetic evidence for a higher female migration rate in humans. Nat Genet 20:278–280
Semino O, Passarino G, Oefner PJ et al (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perpective. Science 290:1155–1159
Semino O, Magri C, Benuzzi G et al (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023–1034
Skorecki K, Selig S, Blazer S et al (1997) Y chromosomes of Jewish priests. Nature 385:32
Soares P, Ermini L, Thomson N et al (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84:740–759
Stefflova K, Dulik MC, Pai AA et al (2009) Evaluation of group genetic ancestry of populations from Philadelphia and Dakar in the context of sex-biased admixture in the Americas. PLoS One 4:e7842
Sykes B, Irven C (2000) Surnames and the Y chromosome. Am J Hum Genet 66:1417–1419
The Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339–348
Thomson R, Pritchard JK, Shen P et al (2000) Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci U S A 97:7360–7365
Tofanelli S, Bertoncini S, Castri L et al (2009) On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages. Mol Biol Evol 26:2109–2124
Torres JB, Doura MB, Keita SO, Kittles RA (2012) Y chromosome lineages in men of west African descent. PLoS One 7:e29687
Torroni A, Chen YS, Semino O et al (1994) mtDNA and Y-chromosome polymorphisms in four native American populations from southern Mexico. Am J Hum Genet 54:303–318
Trombetta B, Cruciani F, Sellitto D, Scozzari R (2011) A new topology of the human Y chromosome haplogroup E1b1 (E-P2) revealed through the use of newly characterized binary polymorphisms. PLoS One 6:e16073
Underhill PA, Jin L, Lin AA et al (1997) Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res 7:996–1005
Underhill PA, Myres NM, Rootsi S et al (2010) Separating the post-glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. Eur J Hum Genet 18:479–484
Van Geystelen A, Decorte R, Larmuseau MH (2013) Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs. Forensic Sci Int Genet 7:573–580
Verdu P, Austerlitz F, Estoup A et al (2009) Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa. Curr Biol 19:312–318
Wei W, Ayub Q, Chen Y et al (2013) A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 23:388–395
Wooding S, Ostler C, Prasad BV et al (2004) Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data. Hum Genet 115:221–229
Zerjal T, Xue Y, Bertorelle G et al (2003) The genetic legacy of the mongols. Am J Hum Genet 72:717–721
Zhong H, Shi H, Qi XB et al (2010) Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 55:428–435
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Calafell, F., Comas, D. (2021). The Y Chromosome. In: Saitou, N. (eds) Evolution of the Human Genome II. Evolutionary Studies. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56904-6_5
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