İki birey arasındaki benzerlik; populasyon genetiği, kantitatif genetik, davranışsal ekoloji ve sosyobiyoloji çalışmalarının merkezinde yer almaktadır. Bireyler arasındaki benzerlik katsayısı, bilinen bir soyağacından hesaplanabilmektedir. Ancak, soyağacı bilgilerinin yokluğunda bu katsayı genetik belirteçler kullanılarak tahmin edilmektedir. Başka bir deyişle genetik belirteçler, ataları bilinmeyen bireyler için benzerliğin tahmin edilmesine izin vermektedir. Birtakım tahmin ediciler kullanılarak genetik belirteç verisinden benzerlik tahmin edilebilmektedir. Bu tahmin ediciler, populasyondaki genetik yapının bilinmemesinden dolayı, çiftleşmelerin/evliliklerin büyük oranda rastgele olduğu şeklinde kritik bir varsayıma sahiptir. Ancak, gerçek dünyada populasyonlara ait genetik yapının oluşmasında rastgele olmayan çiftleşmelerin/evliliklerin de söz konusu olmasından dolayı bu varsayım sık sık ihlal edilmektedir. Genetik belirteçlerin hızla gelişmesi ile birçok tahmin etme yöntemi öne sürülmüştür. Farklı varsayımlar kullanılarak geliştirilen ve her biri farklı koşullar altında değişen etkinliklere sahip olan bir dizi tahmin edici bulunmaktadır. Bu tahmin edicilerden hiçbiri tek başına, tüm çalışmaların gerekliliklerini yerine getirememektedir. Populasyonun yapısına göre hangi yöntemin kullanılması gerektiğinin belirlenebilmesi için çok sayıda çalışma yapılması gerekmektedir. Bu çalışmanın amacı, Lynch (1988), Li ve ark. (1993) ile Wang (2002) tarafından geliştirilen benzerlik indeksi, Queller ve Goodnight (1989) tarafından geliştirilen regresyon tabanlı tahmin yöntemi ile Lynch ve Ritland (1999) tarafından geliştirilen regresyon tabanlı moment tahmin yöntemi olarak bilinen dört farklı benzerlik yöntemini tanıtmaktır.
Anahtar Kelimeler: Moleküler belirteçler; genetik benzerlik; popülasyon genetiği
Pairwise relatedness is central to studies of population genetics, quantitative genetics, behavioral ecology, and sociobiology. The relatedness coefficient between individuals can be calculated from a known pedigree. In the absence of pedigree information, this coefficient can be estimated by using genetic markers. In other words, genetic markers allow the estimation of relatedness for individuals with unknown ancestors. Relatedness can be estimated from genetic marker data using a number of estimators. These estimators, however, make the critical assumption of a large random mating population, since the genetic structures are unknown. The assumption is frequently violated in the real world where nonrandom mating usually lead to genetic structures. With the rapid development of genetic markers, quite a few estimation methods have been proposed. There are a number of estimators that have been developed using different assumptions, each with varying efficiencies under different conditions. A single estimator cannot fulfill the requirements of all studies. A large number of studies are required to determine which method should be used according to the structure of the population. The objective of this study is to introduce four different relatedness methods: the similarity index (Lynch, 1988; Li et al. 1993), and Wang (2002), a regression based estimator (Queller and Goodnight, 1989), and a regression based method of moments estimator (Lynch and Ritland, 1999).
Keywords: Molecular markers; genetic relatedness; population genetics
- Pinto N, Gusmao L, Egeland T, Amorim A. Estimating relatedness with no prior specification of any genealogy: the role of the X-chromosome. Forensic Sci Int Genet Suppl Ser. 2013;4(1):e252-3. [Crossref]
- Conomos MP, Reiner AP, Weir BS, Thornton TA. Model-free estimation of recent genetic relatedness. Am J Hum Genet. 2016;98(1):127-48. [Crossref] [PubMed] [PMC]
- Weir BS, Goudet J. A unified characterization of population structure and relatedness. Genetics. 2017;206(4):2085-103. [Crossref] [PubMed] [PMC]
- Sethuraman A. Estimating genetic relatedness in admixed populations. G3 (Bethesda). 2018;8(10):3203-20. [Crossref] [PubMed] [PMC]
- Crow J, Kimura M. An Introduction to Population Genetics Theory. 1st ed. New-York: Harper and Row Publishers, Inc.; 1970. p.235-80.
- Laporte F, Charcosset A, Mary-Huard T. Estimation of the relatedness coefficients from biallelic markers, application in plant mating designs. Biometrics. 2017;73(3):885-94. [Crossref] [PubMed]
- Blouin MS. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol Evol. 2003;18(10): 503-11. [Crossref]
- Dodds KG, McEwan JC, Brauning R, Anderson RM, van Stijn TC, Kristjánsson T, et al. Construction of relatedness matrices using genotyping-by-sequencing data. BMC Genomics. 2015;16(1):1047. [Crossref] [PubMed] [PMC]
- Rousset F. Inbreeding and relatedness coefficients: what do they measure? Heredity (Edinb). 2002;88(5):371-80. [Crossref] [PubMed]
- Wang J. Pedigrees or markers: which are better in estimating relatedness and inbreeding coefficient? Theor Popul Biol. 2016;107:4-13. [Crossref] [PubMed]
- Speed D, Balding DJ. Relatedness in the post-genomic era: is it still useful? Nat Rev Genet. 2014;16(1):33-44. [Crossref] [PubMed]
- Ackerman MS, Johri P, Spitze K, Xu S, Doak TG, Young K, et al. Estimating seven coefficients of pairwise relatedness using population-genomic data. Genetics. 2017;206(1): 105-18. [Crossref] [PubMed] [PMC]
- Krawczak M. Kinship Testing. Encyclopedia of Life Sciences. John Wiley & Sons; 2010. p.1-6. [Crossref]
- Blouin MS, Parsons M, Lacaille V, Lotz S. Use of microsatellite loci to classify individuals by relatedness. Mol Ecol. 1996;5(3):393-401. [Crossref] [PubMed]
- Hedrick PW, Lacy RC. Measuring relatedness between inbred individuals. J Hered. 2015;106 (1):20-5. [Crossref] [PubMed]
- Wang J. Estimating pairwise relatedness in a small sample of individuals. Heredity (Edinb). 2017;119(5):302-13. [Crossref] [PubMed] [PMC]
- Wang J. An estimator for pairwise relatedness using molecular markers. Genetics. 2002;160 (3):1203-15.
- Oliehoek PA, Windig JJ, van Arendonk JA, Bijma P. Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics. 2006;173(1):483-96. [Crossref] [PubMed] [PMC]
- Milligan BG. Maximum-likelihood estimation of relatedness. Genetics. 2003;163(3):1153-67.
- Wang J. Unbiased relatedness estimation in structured populations. Genetics. 2011;187(3): 887-901. [Crossref] [PubMed] [PMC]
- Konovalov DA, Heg D. Technical Advances: a maximum-likelihood relatedness estimator allowing for negative relatedness values. Mol Ecol Resour. 2008;8(2):256-63. [Crossref] [PubMed]
- Csilléry K, Johnson T, Beraldi D, Clutton-Brock T, Coltman D, Hansson B, et al. Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics. 2006;173(4):2091-101. [Crossref] [PubMed] [PMC]
- Thomas SC. The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philos Trans R Soc Lond B Biol Sci. 2005;360(1459):1457-67. [Crossref] [PubMed] [PMC]
- Ritland K. Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res. 1996;67(2):175-85. [Crossref]
- Shikano T. Estimation of quantitative genetic parameters using marker-inferred relatedness in Japanese flounder: a case study of upward bias. J Hered. 2008;99(2):94-104. [Crossref] [PubMed]
- Queller DC, Goodnight KF. Estimating relatedness using genetic markers. Evolution. 1989;43(2):258-75. [Crossref] [PubMed]
- Lynch M, Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 1999;152(4):1753-66.
- Hardy OJ. Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Mol Ecol. 2003;12(6): 1577-88. [Crossref] [PubMed]
- Lynch M. Estimation of relatedness by DNA fingerprinting. Mol Biol Evol. 1988;5(5):584-99.
- Li CC, Weeks DE, Chakravarti A. Similarity of DNA fingerprints due to chance and relatedness. Hum Hered. 1993;43(1):45-52. [Crossref] [PubMed]
- Bink MC, Anderson AD, van de Weg WE, Thompson EA. Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population. Theor Appl Genet. 2008;117(6):843-55. [Crossref] [PubMed]
- Van de Casteele T, Galbusera P, Matthysen E. A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol. 2001;10(6):1539-49. [Crossref] [PubMed]
- Wang J. Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods. J Evol Biol. 2014;27(3):518-30. [Crossref] [PubMed]
- Weir BS. Genetic Data Analysis II: Methods for Discrete Population Genetic Data. 2nd ed. Sunderland, Mass, USA: Sinauer; 1996. p.445.
- Kardos M, Luikart G, Allendorf FW. Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees. Heredity (Edinb). 2015;115 (1):63-72. [Crossref] [PubMed] [PMC]
- Huang K, Ritland K, Guo S, Shattuck M, Li B. A pairwise relatedness estimator for polyploids. Mol Ecol Resour. 2014;14(4):734-44. [Crossref] [PubMed]
.: İşlem Listesi