Haplotype convergence is rare, due to the sheer odds involved of two unrelated individuals independently evolving exactly the same genetic sequence in the site of interest. Thus, haplotypes are shared mainly between very closely related individuals, as the genetic information in two related individuals will be much more similar than between unrelated individuals. Substitution bias further increases the likelihood of haplotype convergence, as this increases the probability of mutations occurring at the same site. Sequences may also diverge from the same original sequence and then revert, converging in this manner. Convergence through convergent evolution in two unrelated groups is much less common, as derived traits may arise through dramatically different pathways.
Erroneously determining two individuals do be identical due to haplotype convergence becomes much less likely when more genetic markers are tested, since that would require a larger amount of extremely rare coincidences. With modern high-throughput sequencing approaches, sequencing a large set of markers, or even the entire genome, is much more feasible and greatly minimizes these issues.
In some regions, due to low diversity in the Y-STR gene (often used to study surname origin), haplotype convergence may confuse analyses, concluding unrelated individuals to be very closely related.
Similarly, a study of New World mitochondrial DNA haplogroups observed that similarities in haplotypes between Native Americans and Asians were a result of the hypervariability of the HVSI region in mitochondrial DNA, rather than common ancestry.
As an example of haplotype convergence due to convergent evolution in more distantly related groups, threespine stickleback in blackwater environments similar to that of the ancient bluefin killifish and black bream independently evolved the same haplotype in the SWS2 gene, which promotes better eyesight in those conditions.
- Brenner, Charles H. (2014-01-01). "Understanding Y haplotype matching probability". Forensic Science International: Genetics. 8 (1): 233–243. doi:10.1016/j.fsigen.2013.10.007. PMID 24315614.
- Malhi, Ripan S.; Eshleman, Jason A.; Greenberg, Jonathan A.; Weiss, Deborah A.; Shook, Beth A. Schultz; Kaestle, Frederika A.; Lorenz, Joseph G.; Kemp, Brian M.; Johnson, John R. (2002-04-01). "The Structure of Diversity within New World Mitochondrial DNA Haplogroups: Implications for the Prehistory of North America". The American Journal of Human Genetics. 70 (4): 905–919. doi:10.1086/339690.
- Cairns, J.; Foster, P. L. (August 1991). "Adaptive Reversion of a Frameshift Mutation in Escherichia Coli". Genetics. 128 (4): 695–701. ISSN 0016-6731. PMC 1204544. PMID 1916241.
- Brenner, Charles H. (2014). "Understanding Y haplotype matching probability". Forensic Science International: Genetics. 8 (1): 233–243. doi:10.1016/j.fsigen.2013.10.007. PMID 24315614.
- Stern, David L. (2013). "The genetic causes of convergent evolution". Nature Reviews Genetics. 14 (11): 751–764. doi:10.1038/nrg3483. ISSN 1471-0064. PMID 24105273.
- "Common haplotypes". ancestry.com. 14 December 2006. Retrieved 28 March 2012.[better source needed]
- Blair, C.; Murphy, R. W. (2011-01-01). "Recent Trends in Molecular Phylogenetic Analysis: Where to Next?". Journal of Heredity. 102 (1): 130–138. doi:10.1093/jhered/esq092. ISSN 0022-1503.
- Solé-Morata, Neus; Villaescusa, Patricia; García-Fernández, Carla; Font-Porterias, Neus; Illescas, María José; Valverde, Laura; Tassi, Francesca; Ghirotto, Silvia; Férec, Claude (2017-08-04). "Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ". Scientific Reports. 7 (1). doi:10.1038/s41598-017-07710-x. ISSN 2045-2322.
- Marques, David A.; Taylor, John S.; Jones, Felicity C.; Palma, Federica Di; Kingsley, David M.; Reimchen, Thomas E. (2017-04-11). "Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments". PLOS Biology. 15 (4): e2001627. doi:10.1371/journal.pbio.2001627. ISSN 1545-7885.