, il ne serait pas absurde de se questionner en quoi elles sont intéressantes : permettent-elles une meilleure prédiction ? Sont-elles plus faciles à exploiter, à expliquer ? Pour répondre à de telles questions

A. Albrechtsen, T. Sand-korneliussen, I. Moltke, T. Van-overseem-hansen, F. C. Nielsen et al., Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium, Genet. Epidemiol, vol.33, issue.3, pp.266-274, 2009.

A. Auton, K. Bryc, A. R. Boyko, K. E. Lohmueller, J. Novembre et al., Global distribution of genomic diversity underscores rich complex history of continental human populations, Genome Res, vol.19, issue.5, pp.795-803, 2009.

S. J. Baird, A Simulation Study of Multilocus Clines, Evolution, vol.49, issue.6, pp.1038-1045, 1995.

F. Ball and V. T. Et-stefanov, Evaluation of identity-by-descent probabilities for half-sibs on continuous genome, Mathematical Biosciences, vol.196, issue.2, pp.215-225, 2005.

L. Beckmann, C. Fischer, M. Obreiter, M. Rabes, and J. Et-chang-claude, Haplotype-sharing analysis using Mantel statistics for combined genetic effects, BMC Genetics, vol.6, issue.1, pp.1-5, 2005.

D. J. Begun, A. K. Holloway, K. Stevens, L. W. Hillier, Y. Poh et al.,

M. W. , Population Genomics : Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans, PLOS Biology, vol.5, issue.11, p.310, 2007.

S. Behjati and P. S. Et-tarpey, What is next generation sequencing ?', Archives of Disease in Childhood, vol.98, pp.236-238, 2013.

T. Bersaglieri, P. C. Sabeti, N. Patterson, T. Vanderploeg, S. F. Schaffner et al., Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene, The American Journal of Human Genetics, vol.74, issue.6, pp.1111-1120, 2004.

H. Bickeböller and E. A. Et-thompson, Distribution of Genome Shared IBD by Half-Sibs : Approximation by the Poisson Clumping Heuristic, Theoretical Population Biology, vol.50, issue.1, pp.66-90, 1996.

H. Bickeböller and E. A. Et-thompson, The Probability Distribution of the Amount of an Individual's Genome Surviving to the Following Generation, Genetics, vol.143, issue.2, pp.1043-1049, 1996.

E. M. Blue, C. Y. Cheung, C. G. Glazner, M. P. Conomos, and S. M. Lewis,

S. Sverdlov, Identity-by-descent graphs offer a flexible framework for imputation and both linkage and association analyses, BMC Proceedings, vol.8, p.19, 2014.

S. Boitard and P. Et-loisel, Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation, Theoretical Population Biology, vol.71, issue.3, pp.380-391, 2007.

M. Bonhomme, C. Chevalet, B. Servin, S. Boitard, J. Abdallah et al., Detecting Selection in Population Trees : The Lewontin and Krakauer Test Extended, Genetics, vol.186, issue.1, pp.241-262, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00842515

M. Bosse, H. Megens, O. Madsen, Y. Paudel, L. A. Frantz et al., Regions of Homozygosity in the Porcine Genome : Consequence of Demography and the Recombination Landscape, PLOS Genet, vol.8, issue.11, p.1003100, 2012.

B. L. Browning and S. R. Browning, Efficient multilocus association testing for whole genome association studies using localized haplotype clustering, Genet. Epidemiol, vol.31, issue.5, pp.365-375, 2007.

B. L. Browning and S. R. Browning, A Fast, Powerful Method for Detecting Identity by Descent, The American Journal of Human Genetics, vol.88, issue.2, pp.173-182, 2011.

B. L. Browning and S. R. Browning, Detecting Identity by Descent and Estimating Genotype Error Rates in Sequence Data, The American Journal of Human Genetics, vol.93, issue.5, pp.840-851, 2013.

B. L. Browning and S. R. Browning, Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data, Genetics, vol.194, issue.2, pp.459-471, 2013.

S. Browning and B. L. Et-browning, On Reducing the Statespace of Hidden Markov Models for the Identity by Descent Process, Theoretical Population Biology, vol.62, issue.1, pp.1-8, 2002.

S. R. Browning, Estimation of Pairwise Identity by Descent From BIBLIOGRAPHIE Dense Genetic Marker Data in a Population Sample of Haplotypes, Genetics, vol.178, issue.4, pp.2123-2132, 2008.

S. R. Browning and B. L. Browning, Identity by Descent Between Distant Relatives : Detection and Applications, Annual Review of Genetics, vol.46, issue.1, pp.617-633, 2012.

S. R. Browning and B. L. Browning, Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent, The American Journal of Human Genetics, vol.97, issue.3, pp.404-418, 2015.

S. R. Browning and E. A. Et-thompson, Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies, Genetics, vol.190, issue.4, pp.1521-1531, 2012.

A. Caballero and M. A. Et-toro, Interrelations between effective population size and other pedigree tools for the management of conserved populations, Genetics Research, vol.75, issue.03, pp.331-343, 2000.

C. Cannings, The Identity by Descent Process along the Chromosome, Human Heredity, vol.56, issue.1-3, pp.126-130, 2003.

S. Carmi, P. F. Palamara, V. Vacic, T. Lencz, A. Darvasi et al., The Variance of Identity-by-Descent Sharing in the Wright-Fisher Model, Genetics, vol.193, issue.3, pp.911-928, 2013.

S. Carmi, P. R. Wilton, J. Wakeley, and I. Et-pe'er, A renewal theory approach to IBD sharing, Theoretical population biology 97, pp.35-48, 2014.
DOI : 10.1016/j.tpb.2014.08.002

URL : http://europepmc.org/articles/pmc4179929?pdf=render

N. H. Chapman and E. A. Et-thompson, The effect of population history on the lengths of ancestral chromosome segments, Genetics, vol.162, issue.1, pp.449-458, 2002.

N. H. Chapman and E. A. Et-thompson, The Effect of Population History on the Lengths of Ancestral Chromosome Segments, Genetics, vol.162, issue.1, pp.449-458, 2002.

N. H. Chapman and E. A. Et-thompson, A model for the length of tracts of identity by descent in finite random mating populations', Theor Popul Biol, vol.64, issue.2, pp.141-150, 2003.

C. Charlier, F. Farnir, P. Berzi, P. Vanmanshoven, B. Brouwers et al., Identity-by-descent mapping of recessive traits in livestock : application to map the bovine syndactyly locus to chromosome 15, Genome Res, vol.6, issue.7, pp.580-589, 1996.

X. Chen, Z. Ma, and Y. Et-wang, Markov jump processes in modeling coalescent with recombination, Ann. Statist, vol.42, issue.4, pp.1361-1393, 2014.
DOI : 10.1214/14-aos1227

URL : https://doi.org/10.1214/14-aos1227

R. Cheng, J. Z. Ma, F. A. Wright, S. Lin, X. Gao et al., Nonparametric Disequilibrium Mapping of Functional Sites Using Haplotypes of Multiple Tightly Linked Single-Nucleotide Polymorphism Markers, Genetics, vol.164, issue.3, pp.1175-1187, 2003.

A. G. Clark, The role of haplotypes in candidate gene studies, Genetic Epidemiology, vol.27, issue.4, pp.321-333, 2004.

G. Cobbs, Renewal Process Approach to the Theory of Genetic Linkage : Case of No Chromatid Interference, Genetics, vol.89, issue.3, pp.563-581, 1978.

F. Coppieters, K. Van-schil, M. Bauwens, H. Verdin, A. De-jaegher et al., Identity-by-descent-guided mutation analysis and exome sequencing in consanguineous families reveals unusual clinical and molecular findings in retinal dystrophy, Genet Med, vol.16, issue.9, pp.671-680, 2014.

D. R. Cox, Renewal Theory, 1962.

I. Curik, M. Feren?akovi?, and J. Et-sölkner, Inbreeding and runs of homozygosity : A possible solution to an old problem, Livestock Science, vol.166, pp.26-34, 2014.

D. Debouzie, La notion de population en dynamique et génétique des populations, Natures Sciences Sociétés, vol.7, issue.4, pp.19-26, 1999.

K. P. Donnelly, The probability that related individuals share some section of genome identical by descent, Theoretical Population Biology, vol.23, issue.1, pp.34-63, 1983.

M. C. Double, R. Peakall, N. R. Beck, A. Cockburn, and M. Et-sorenson, Dispersal, philopatry, and infidelity : dissecting local genetic structure in superb fairy-wrens (malurus cyaneus), Evolution, vol.59, issue.3, pp.625-635, 2005.
DOI : 10.1554/04-166

A. J. Drummond, M. A. Suchard, D. Xie, and A. Et-rambaut, Bayesian phylogenetics with BEAUti and the BEAST 1, Molecular biology and evolution, vol.29, issue.7, pp.1969-1973, 2012.
DOI : 10.1093/molbev/mss075

URL : https://academic.oup.com/mbe/article-pdf/29/8/1969/13648091/mss075.pdf

C. Durrant and A. P. Et-morris, Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data, BMC Genetics, vol.6, issue.1, pp.1-5, 2005.

J. Y. Dutheil, G. Ganapathy, A. Hobolth, T. Mailund, M. K. Uyenoyama et al.,

M. H. Schierup, Ancestral Population Genomics : The Coalescent Hidden Markov Model Approach, Genetics, vol.183, issue.1, pp.259-274, 2009.

J. Eriksson, G. Larson, U. Gunnarsson, B. Bed'hom, and M. Tixier-boichard,

L. Strömstedt, Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken, PLOS Genet, vol.4, issue.2, p.1000010, 2008.

A. Eyre-walker, Do mitochondria recombine in humans ?, Philosophical Transactions of the Royal Society B : Biological Sciences, vol.355, pp.1573-1580, 1403.

M. Fagny, E. Patin, D. Enard, L. B. Barreiro, L. Quintana-murci et al., Exploring the Occurrence of Classic Selective Sweeps in Humans Using Whole-Genome Sequencing Data Sets, Mol Biol Evol, vol.31, issue.7, pp.1850-1868, 2014.

D. Falush, M. Stephens, and J. K. Et-pritchard, Inference of Population Structure Using Multilocus Genotype Data : Linked Loci and Correlated Allele Frequencies, Genetics, vol.164, issue.4, pp.1567-1587, 2003.

M. I. Fariello, S. Boitard, H. Naya, M. Sancristobal, and B. Et-servin, Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations, Genetics, vol.193, issue.3, pp.929-941, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00842696

A. Ferrer-admetlla, C. Leuenberger, J. D. Jensen, and D. Et-wegmann, An Approximate Markov Model for the Wright Fisher Diffusion and Its Application to Time Series Data, Genetics, vol.203, issue.2, pp.831-846, 2016.

A. Ferrer-admetlla, M. Liang, T. Korneliussen, and R. Et-nielsen, On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure, Mol Biol Evol, vol.31, issue.5, pp.1275-1291, 2014.

R. A. Fisher, The theory of inbreeding, vol.120, p.pp, 1949.

R. A. Fisher, A Fuller Theory of "Junctions" in Inbreeding, 1954.

R. A. Fisher, An Algebraically Exact Examination of Junction Formation and Transmission in Parent-offspring Inbreeding, 1959.

I. R. Franklin, The distribution of the proportion of the genome which is homozygous by descent in inbred individuals, Theoretical Population Biology, vol.11, issue.1, pp.60-80, 1977.

A. H. Freedman, R. M. Schweizer, D. O. Vecchyo, .. Han, E. Davis et al.,

I. Gronau, Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs', PLOS Genet, vol.12, issue.3, p.1005851, 2016.

S. B. Gabriel, The Structure of Haplotype Blocks in the Human Genome, Science, vol.296, issue.5576, pp.2225-2229, 2002.

S. Garte, Locus-specific genetic diversity between human populations : An analysis of the literature', Am. J. Hum. Biol, vol.15, issue.6, pp.814-823, 2003.

H. Gauvin, C. Moreau, J. Lefebvre, C. Laprise, H. Vézina et al., Genome-wide patterns of identity-by-descent sharing in the French Canadian founder population, Eur J Hum Genet, vol.22, issue.6, pp.814-821, 2014.

A. P. Ghosh, Backward and forward equations for diffusion processes, Wiley Encyclopedia of Operations Research and Management Science (EORMS), 2010.

F. Gibson and P. Et-froguel, Genetics of the APM1 Locus and Its Contribution to Type 2 Diabetes Susceptibility in French Caucasians, Diabetes, vol.53, issue.11, pp.2977-2983, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00174502

J. L. Gittleman and M. Et-kot, Adaptation : Statistics and a Null Model for Estimating Phylogenetic Effects, Syst Biol, vol.39, issue.3, pp.227-241, 1990.

G. B. Golding and C. Et-strobeck, Linkage disequilibrium in a finite population that is partially selfing, Genetics, vol.94, issue.3, pp.777-789, 1980.

I. Goldringer and T. Et-bataillon, On the Distribution of Temporal Variations in Allele Frequency, Genetics, vol.168, issue.1, pp.563-568, 2004.

Z. Gompert, T. L. Parchman, and C. A. Et-buerkle, Philosophical Transactions of the Royal Society of London B, vol.367, pp.439-450, 1587.

E. González-tortuero, J. Rusek, I. Maayan, A. Petrusek, L. Piálek et al., Genetic diversity of two Daphnia-infecting microsporidian parasites, based on sequence variation in the internal transcribed spacer region, Parasites & Vectors, vol.9, p.293, 2016.

S. Gutiérrez, L. González-cerón, A. Montoya, M. A. Sandoval, M. E. Tórres et al., Genetic structure of Plasmodium vivax in Nicaragua, a country in the control phase, based on the carboxyl terminal region of the merozoite surface protein-1, Infection, Genetics and Evolution, vol.40, pp.324-330, 2016.

M. W. Hahn, Accurate Inference and Estimation in Population Genomics, Mol Biol Evol, vol.23, issue.5, pp.911-918, 2006.

M. W. Hahn, Toward a Selection Theory of Molecular Evolution, Evolution, vol.62, issue.2, pp.255-265, 2008.

J. Haldane, The combination of linkage values, and the calculation of distances between the loci of linked factors, Genetics, vol.8, pp.299-309, 1919.

J. B. Haldane and C. H. Et-waddington, Inbreeding and linkage, Genetics, vol.16, issue.4, p.357, 1931.

K. Harris and R. Et-nielsen, Inferring demographic history from a spectrum of shared haplotype lengths, PLoS Genet, vol.9, issue.6, p.1003521, 2013.

K. Harris, S. Sheehan, J. A. Kamm, and Y. S. Song, Decoding coalescent hidden Markov models in linear time, Research in Computational Molecular Biology, pp.100-114, 2014.

D. L. Hartl, A. G. Clark, and A. G. Clark, Principles of population genetics, vol.116, 1997.

B. J. Hayes, M. E. Goddard, and . Et, Prediction of total genetic value using genome-wide dense marker maps, Genetics, vol.157, issue.4, pp.1819-1829, 2001.

B. J. Hayes, P. M. Visscher, and M. E. Goddard, Increased accuracy of artificial selection by using the realized relationship matrix, Genetics Research, vol.91, issue.01, p.47, 2009.

B. J. Hayes, P. M. Visscher, H. C. Mcpartlan, and M. E. Goddard, Novel multilocus measure of linkage disequilibrium to estimate past effective population size, Genome Research, vol.13, issue.4, pp.635-643, 2003.

P. W. Hedrick and R. C. Lacy, Measuring Relatedness between Inbred Individuals, J Hered, vol.106, issue.1, pp.20-25, 2015.

S. Hellmig, S. Mascheretti, J. Renz, H. Frenzel, F. Jelschen et al., Haplotype analysis of the CD11 gene cluster in patients with chronic Helicobacter pylori infection and gastric ulcer disease, Tissue Antigens, vol.65, issue.3, pp.271-274, 2005.

W. G. Hill and J. Et-hernández-sánchez, Prediction of Multilocus Identity-by-Descent, Genetics, vol.176, issue.4, pp.2307-2315, 2007.

W. Hill and B. Et-weir, Variation in actual relationship as a consequence of Mendelian sampling and linkage, Genetics research, vol.93, issue.1, pp.47-64, 2011.

P. A. Hohenlohe, P. C. Phillips, and W. A. Et-cresko, Int J Plant Sci, vol.171, issue.9, pp.1059-1071, 2010.

X. Hu, F. C. Yeh, and Z. Wang, Structural Genomics : Correlation Blocks, Population Structure, and Genome Architecture', Curr Genomics, vol.12, issue.1, pp.55-70, 2011.
DOI : 10.2174/138920211794520141

URL : http://europepmc.org/articles/pmc3129043?pdf=render

X. Hu, F. C. Yeh, and Z. Wang, Structural Genomics : Correlation Blocks, Population Structure, and Genome Architecture', Curr Genomics, vol.12, issue.1, pp.55-70, 2011.
DOI : 10.2174/138920211794520141

URL : http://europepmc.org/articles/pmc3129043?pdf=render

H. Innan, B. Padhukasahasram, and M. Et-nordborg, The Pattern of Polymorphism on Human Chromosome 21, Genome Res, vol.13, issue.6a, pp.1158-1168, 2003.

V. K. Iyengar, H. K. Reeve, and T. Et-eisner, Paternal inheritance of a female moth's mating preference, Nature, vol.419, issue.6909, pp.830-832, 2002.
DOI : 10.1038/nature01027

S. E. Johnston, C. Bérénos, J. Slate, and J. M. Et-pemberton, Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries), Genetics, vol.203, issue.1, pp.583-598, 2016.

N. L. Kaplan, T. Darden, and R. R. Et-hudson, The coalescent process in models with selection, Genetics, vol.120, issue.3, pp.819-829, 1988.
DOI : 10.1017/s0016672300029074

N. L. Kaplan, R. R. Hudson, and C. H. Langley, The "hitchhiking effect" revisited, Genetics, vol.123, issue.4, pp.887-899, 1989.

M. Kardos, A. Qvarnström, and H. Et-ellegren, Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in, 2017.

, Ficedula Flycatcher Genome Sequences', Genetics p. genetics.116, 198861.

S. Karlin and H. E. Et-taylor, A Second Course in Stochastic Processes, 1981.

Y. Kim and R. Et-nielsen, Linkage Disequilibrium as a Signature of Selective Sweeps, Genetics, vol.167, issue.3, pp.1513-1524, 2004.

Y. Kim and W. Et-stephan, Detecting a Local Signature of Genetic Hitchhiking Along a Recombining Chromosome, Genetics, vol.160, issue.2, pp.765-777, 2002.

U. Knief, B. Kempenaers, and W. Et-forstmeier, Meiotic recombination shapes precision of pedigree-and marker-based estimates of inbreeding, Heredity, vol.118, issue.3, pp.239-248, 2017.

M. J. Lercher, A. O. Urrutia, and L. D. Hurst, Clustering of housekeeping genes provides a unified model of gene order in the human genome, Nat Genet, vol.31, issue.2, pp.180-183, 2002.

A. Leutenegger, B. Prum, E. Génin, C. Verny, A. Lemainque et al., Estimation of the Inbreeding Coefficient through Use of Genomic Data, The American Journal of Human Genetics, vol.73, issue.3, pp.516-523, 2003.

A. A. Levy and M. Et-feldman, Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization, Biological Journal of the Linnean Society, vol.82, issue.4, pp.607-613, 2004.

R. C. Lewontin and J. Et-krakauer, Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms, Genetics, vol.74, issue.1, pp.175-195, 1973.

C. Li, X. Wang, H. Cai, Y. Fu, Y. Luan et al., Molecular microevolution and epigenetic patterns of the long non-coding gene H19 show its potential function in pig domestication and breed divergence, BMC Evolutionary Biology, vol.16, p.87, 2016.

X. Li, Y. Jian, C. Xie, J. Wu, Y. Xu et al., Fast diffusion of domesticated maize to temperate zones, 2017.

Y. Li, W. Sung, and J. J. Et-liu, Association Mapping via Regularized Regression Analysis of Single-Nucleotide-Polymorphism Haplotypes in Variable-Sized Sliding Windows, The American Journal of Human Genetics, vol.80, issue.4, pp.705-715, 2007.

M. Liang and R. Et-nielsen, The Lengths of Admixture Tracts, Genetics, vol.197, issue.3, pp.953-967, 2014.

P. Librado and J. Et-rozas, DnaSP v5 : a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.

S. Lin, A. Chakravarti, and D. J. Et-cutler, Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies, Nat Genet, vol.36, issue.11, pp.1181-1188, 2004.

C. Lo, A. C. Lossie, T. Liang, Y. Liu, X. Xuei et al., High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model', PLOS Genet, vol.12, issue.8, p.1006178, 2016.

N. Mantel, The Detection of Disease Clustering and a Generalized Regression Approach, Cancer Res, vol.27, issue.2, pp.209-220, 1967.

E. R. Mardis, The impact of next-generation sequencing technology on genetics, Trends in Genetics, vol.24, issue.3, pp.133-141, 2008.

K. Markianos, E. Bischoff, C. Mitri, W. M. Guelbeogo, A. Gneme et al., Genetic Structure of a Local Population of the Anopheles gambiae Complex in Burkina Faso, PLOS ONE, vol.11, issue.1, p.145308, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02008317

O. C. Martin, Two-and Three-Locus Tests for Linkage Analysis Using Recombinant Inbred Lines, Genetics, vol.173, issue.1, pp.451-459, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00081006

O. C. Martin and F. Et-hospital, Distribution of Parental Genome Blocks in Recombinant Inbred Lines, Genetics, vol.189, issue.2, pp.645-654, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000534

R. A. Mathias, P. Gao, J. L. Goldstein, A. F. Wilson, E. W. Pugh et al.,

P. Harris, A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q, BMC Genetics, vol.7, issue.1, p.38, 2006.

R. Mcquillan, A. Leutenegger, R. Abdel-rahman, C. S. Franklin, M. Pericic et al., Runs of Homozygosity in European Populations, The American Journal of Human Genetics, vol.83, issue.3, pp.359-372, 2008.

G. A. Mcvean and N. J. Et-cardin, Approximating the coalescent with recombination, Philosophical Transactions of the Royal Society B : Biological Sciences, vol.360, pp.1387-1393, 1459.

Z. Meng, D. V. Zaykin, C. Xu, M. Wagner, and M. G. Et-ehm, Selection of Genetic Markers for Association Analyses, Using Linkage Disequilibrium and Haplotypes, The American Journal of Human Genetics, vol.73, issue.1, pp.115-130, 2003.

T. M. Meuwissen and M. E. Goddard, Prediction of identity by descent probabilities from marker-haplotypes, Genetics Selection Evolution, vol.33, issue.6, pp.605-634, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00894392

R. S. Meyer, J. Y. Choi, M. Sanches, A. Plessis, J. M. Flowers et al., Domestication history and geographical adaptation inferred from a SNP map of African rice, 2016.

M. S. , On Nei and Roychoudhury's Sampling Variances of Heterozygosity and Genetic Distance, Genetics, vol.80, issue.1, pp.223-226, 1975.

M. Mondal, F. Casals, T. Xu, G. M. Dall'olio, M. Pybus et al., Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation, 2016.

R. C. Moore and M. H. Stevens, Local Patterns of Nucleotide Polymorphism Are Highly Variable in the Selfing Species Arabidopsis thaliana, J Mol Evol, vol.66, issue.2, p.116, 2008.

J. C. Mueller and C. Et-andreoli, Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity, Bioinformatics, vol.20, issue.5, pp.786-787, 2004.

H. Muranty, V. Jorge, C. Bastien, C. Lepoittevin, L. Bouffier et al., Potential for marker-assisted selection for forest tree breeding : lessons from 20 years of MAS in crops, Tree Genetics & Genomes, vol.10, issue.6, pp.1491-1510, 2014.

T. Nakajima, S. Wooding, T. Sakagami, M. Emi, K. Tokunaga et al., Natural Selection and Population History in the Human Angiotensinogen Gene (AGT) : 736 Complete AGT Sequences in Chromosomes from Around the World, The American Journal of Human Genetics, vol.74, issue.5, pp.898-916, 2004.

M. Nei and A. K. Et-roychoudhury, Sampling variances of heterozygosity and genetic distance, Genetics, vol.76, issue.2, pp.379-390, 1974.

R. Nielsen, Statistical tests of selective neutrality in the age of genomics, Heredity, vol.86, issue.6, pp.641-647, 2001.

J. Ohashi, I. Naka, J. Patarapotikul, H. Hananantachai, G. Brittenham et al., Extended Linkage Disequilibrium Surrounding the Hemoglobin E Variant Due to Malarial Selection, The American Journal of Human Genetics, vol.74, issue.6, pp.1198-1208, 2004.

T. K. Oleksyk, K. Zhao, F. M. Vega, D. A. Gilbert, S. J. O'brien et al., Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations, PLOS ONE, vol.3, issue.3, p.1712, 2008.

T. Paape, P. Zhou, A. Branca, R. Briskine, N. Young et al., Fine scale population recombination rates, hotspots and correlates of recombination in the Medicago truncatula genome, Genome Biol Evol p, p.46, 2012.

P. F. Palamara, Population genetics of identity by descent, 2014.

P. F. Palamara, T. Lencz, A. Darvasi, and I. Et-pe'er, Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History, The American Journal of Human Genetics, vol.91, issue.5, pp.809-822, 2012.

D. S. Park, Y. Baran, F. Hormozdiari, C. Eng, D. G. Torgerson et al., PIGS : improved estimates of identity-by-descent probabilities by probabilistic IBD graph sampling, BMC Bioinformatics, vol.16, issue.5, pp.1-12, 2015.

P. Paschou, Y. Feng, A. J. Pakstis, W. C. Speed, M. M. Demille et al., Indications of Linkage and Association of Gilles de la Tourette Syndrome in Two Independent Family Samples : 17q25 Is a Putative Susceptibility Region, The American Journal of Human Genetics, vol.75, issue.4, pp.545-560, 2004.

T. Pemberton, D. Absher, M. Feldman, R. Myers, N. Rosenberg et al., Genomic Patterns of Homozygosity in Worldwide Human Populations, The American Journal of Human Genetics, vol.91, issue.2, pp.275-292, 2012.

J. K. Pritchard, M. Stephens, and P. Et-donnelly, Inference of Population Structure Using Multilocus Genotype Data, Genetics, vol.155, issue.2, pp.945-959, 2000.

F. Rodolphe, J. Martin, and E. Et-della-chiesa, Theoretical description of chromosome architecture after multiple back-crossing, Theoretical Population Biology, vol.73, issue.2, pp.289-299, 2008.

A. R. Rogers, How population growth affects linkage disequilibrium, Genetics, vol.197, issue.4, pp.1329-1341, 2014.

J. A. Ross, D. C. Koboldt, J. E. Staisch, H. M. Chamberlin, B. P. Gupta et al., Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination, PLOS Genetics, vol.7, issue.7, p.1002174, 2011.

F. Rousset, Inbreeding and relatedness coefficients : what do they measure ?, Heredity, vol.88, issue.5, pp.371-380, 2002.
URL : https://hal.archives-ouvertes.fr/halsde-00341658

J. Rozas and R. Et-rozas, DnaSP version 3 : an integrated program for molecular population genetics and molecular evolution analysis, Bioinformatics, vol.15, issue.2, pp.174-175, 1999.

P. C. Sabeti, D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter et al., Detecting recent positive selection in the human genome from haplotype structure', Nature, vol.419, issue.6909, p.832, 2002.

R. M. Sahasrabudhe, P. Lott, C. Ruiz-ponte, M. Teixeira, and . Et-carvajal,

L. G. Carmona, Abstract 1281 : Identification of novel susceptibility genes in familial gastric cancer using next generation sequencing and identity-by-descent mapping, Cancer Res, vol.74, pp.1281-1281, 2014.

E. Santiago and A. Et-caballero, Variation After a Selective Sweep in a Subdivided Population, Genetics, vol.169, issue.1, pp.475-483, 2005.

C. Schlötterer, A Microsatellite-Based Multilocus Screen for the Identification of Local Selective Sweeps, Genetics, vol.160, issue.2, pp.753-763, 2002.

C. Schlötterer, Hitchhiking mapping-functional genomics from the population genetics perspective, Trends in Genetics, vol.19, issue.1, pp.32-38, 2003.

C. Schlötterer and D. Et-dieringer, A Novel Test Statistic for the Identification of Local Selective Sweeps Based on Microsatellite Gene Diversity, 2013.

K. Schmid and Z. Et-yang, The Trouble with Sliding Windows and the Selective Pressure in BRCA1, PLOS ONE, vol.3, issue.11, p.3746, 2008.

N. J. Schork, Extended multipoint identity-by-descent analysis of human quantitative traits : efficiency, power, and modeling considerations, Am J Hum Genet, vol.53, issue.6, pp.1306-1319, 1993.

W. Sellars, Empiricism and the philosophy of mind', Minnesota studies in the philosophy of science 1(19), pp.253-329, 1956.

N. Shah, H. Hirakawa, S. Kusakabe, N. Sandal, J. Stougaard et al., High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines, DNA Res p, p.33, 2016.

L. Skipper, K. Wilkes, M. Toft, M. Baker, S. Lincoln et al., Linkage Disequilibrium and Association of MAPT H1 in Parkinson Disease, The American Journal of Human Genetics, vol.75, issue.4, pp.669-677, 2004.

D. Smirnov, A. Bruzel, M. Morley, and V. G. Et-cheung, Direct IBD mapping : identical-by-descent mapping without genotyping, Genomics, vol.83, issue.2, pp.335-345, 2004.

P. E. Smouse and R. Et-peakall, Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure, Heredity, vol.82, issue.5, pp.561-573, 1999.

R. S. Spielman, R. E. Mcginnis, and W. J. Et-ewens, Transmission test for linkage disequilibrium : the insulin gene region and insulin-dependent diabetes mellitus (IDDM), American journal of human genetics, vol.52, issue.3, p.506, 1993.

J. Stainton, B. Charlesworth, C. Haley, A. Kranis, K. Watson et al., Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens, J. Anim. Breed. Genet, 2016.

P. Stam, The distribution of the fraction of the genome identical by descent in finite random mating populations', Genetics Research, vol.35, issue.02, pp.131-155, 1980.

J. Staples, D. Qiao, M. Cho, E. Silverman, D. Nickerson et al., PRIMUS : Rapid Reconstruction of Pedigrees from Genome-wide Estimates of Identity by Descent, The American Journal of Human Genetics, vol.95, issue.5, pp.553-564, 2014.

V. T. Stefanov, Distribution of genome shared identical by descent by two individuals in grandparent-type relationship, Genetics, vol.156, issue.3, pp.1403-1410, 2000.

J. R. Stinchcombe and H. E. Hoekstra, Combining population genomics and quantitative genetics : finding the genes underlying ecologically important traits, Heredity, vol.100, issue.2, pp.158-170, 2007.

K. N. Stölting, R. Nipper, D. Lindtke, C. Caseys, S. Waeber et al., Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species, Molecular Ecology, vol.22, issue.3, pp.842-855, 2013.

J. A. Sved, The covariance of heterozygosity as a measure of linkage disequilibrium between blocks of linked and unlinked sites in Hapmap, Genetics Research, vol.93, issue.04, pp.285-290, 2011.

Z. Szpiech, J. Xu, T. Pemberton, W. Peng, S. Zöllner et al., Long Runs of Homozygosity Are Enriched for Deleterious Variation', Am J Hum Genet, vol.93, issue.1, pp.90-102, 2013.

T. Meerman, G. J. Van-der-meulen, M. A. Sandkuijl, and L. A. , Perspectives of identity by descent (IBD) mapping in founder populations, Clinical & Experimental Allergy, vol.25, pp.97-102, 1995.

E. A. Thompson, The IBD process along four chromosomes, Theoretical population biology, vol.73, issue.3, pp.369-373, 2008.

E. A. Thompson, Identity by Descent : Variation in Meiosis, Across Genomes, and in Populations, Genetics, vol.194, issue.2, pp.301-326, 2013.

E. A. Thompson and N. H. Et-chapman, Computational Methods for SNPs and Haplotype Inference', number 2983 in 'Lecture Notes in Computer Science, pp.74-83, 2002.

V. Thouzeau, Inférer l'histoire des populations humaines à partir des diversités génétiques et linguistiques, 2017.

M. Tiret and F. Et-hospital, Blocks of chromosomes identical by descent in a population : Models and predictions', PLOS ONE, vol.12, issue.11, p.187416, 2017.

P. M. Visscher, S. E. Medland, M. A. Ferreira, K. I. Morley, G. Zhu et al., Assumption-Free Estimation of Heritability from Genome-Wide Identity-by-Descent Sharing between Full Siblings, PLOS Genet, vol.2, issue.3, p.41, 2006.

R. Vitalis and D. Et-couvet, Estimation of Effective Population Size and Migration Rate From One-and Two-Locus Identity Measures, Genetics, vol.157, issue.2, pp.911-925, 2001.
URL : https://hal.archives-ouvertes.fr/halsde-00342380

K. Walters and C. Et-cannings, The probability density of the total IBD length over a single autosome in unilineal relationships, Theoretical Population Biology, vol.68, issue.1, pp.55-63, 2005.

X. Wang, Y. Long, N. Wang, J. Zou, G. Ding et al., Breeding histories and selection criteria for oilseed rape in Europe and China identified by genome wide pedigree dissection, 2017.

R. S. Waples, A generalized approach for estimating effective population size from temporal changes in allele frequency, Genetics, vol.121, issue.2, pp.379-391, 1989.

B. J. Ward and C. Van-oosterhout, hybridcheck : software for the rapid detection, visualization and dating of recombinant regions in genome sequence data, Mol Ecol Resour, vol.16, issue.2, pp.534-539, 2016.

B. S. Weir, P. J. Avery, and W. G. Hill, Effect of mating structure on variation in inbreeding, Theoretical Population Biology, vol.18, issue.3, pp.396-429, 1980.

B. S. Weir, L. R. Cardon, A. D. Anderson, D. M. Nielsen, and W. G. Hill, Measures of human population structure show heterogeneity among genomic regions, Genome Res, vol.15, issue.11, pp.1468-1476, 2005.

B. S. Weir and W. G. Hill, Effect of mating structure on variation in linkage disequilibrium, Genetics, vol.95, issue.2, pp.477-488, 1980.

B. J. White, M. W. Hahn, M. Pombi, B. J. Cassone, N. F. Lobo et al., Localization of Candidate Regions Maintaining a Common Polymorphic Inversion (2la) in Anopheles gambiae, PLOS Genetics, vol.3, issue.12, p.217, 2007.

E. G. Williamson and M. Et-slatkin, Using maximum likelihood to estimate population size from temporal changes in allele frequencies, Genetics, vol.152, issue.2, pp.755-761, 1999.

C. Wiuf and J. Et-hein, On the Number of Ancestors to a DNA Sequence, Genetics, vol.147, issue.3, pp.1459-1468, 1997.

S. Wright, Systems of Mating. I. the Biometric Relations between Parent and Offspring, Genetics, vol.6, issue.2, pp.111-123, 1921.

S. Wright, Systems of mating. IV. The effects of selection, Genetics, vol.6, issue.2, p.162, 1921.

S. Wright, Systems of mating. V. General considerations, Genetics, vol.6, issue.2, p.167, 1921.

W. Xu and . Meyers, Genetics of complex human diseases : genome screening, association studies and fine mapping, Clinical & Experimental Allergy, vol.28, pp.1-5, 1998.

H. Zhao, R. Pfeiffer, and M. H. Et-gail, Haplotype analysis in population genetics and association studies, Pharmacogenomics, vol.4, issue.2, pp.171-178, 2003.

X. Zheng and B. S. Et-weir, Eigenanalysis of SNP data with an identity by descent interpretation, Theoretical Population Biology, vol.107, pp.65-76, 2016.

J. Ødegård and T. H. Et-meuwissen, Identity-by-descent genomic selection using selective and sparse genotyping, Genetics Selection Evolution, vol.46, p.3, 2014.