W. Doolittle, Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2128, 1999.
DOI : 10.1126/science.284.5423.2124

E. Bapteste, L. Van-iersel, A. Janke, S. Kelchner, S. Kelk et al., Networks: expanding evolutionary thinking, Trends in Genetics, vol.29, issue.8, pp.439-441, 2013.
DOI : 10.1016/j.tig.2013.05.007

J. Mallet, Hybrid speciation, Nature, vol.77, issue.7133, pp.279-283, 2007.
DOI : 10.1038/nature05706

A. Nolte and D. Tautz, Understanding the onset of hybrid speciation, Trends in Genetics, vol.26, issue.2, pp.54-58, 2010.
DOI : 10.1016/j.tig.2009.12.001

R. Abbott, D. Albach, S. Ansell, J. Arntzen, S. Baird et al., Hybridization and speciation, Journal of Evolutionary Biology, vol.9, issue.2, pp.229-246, 2013.
DOI : 10.1186/1471-2148-9-83

N. Patterson, P. Moorjani, Y. Luo, S. Mallick, N. Rohland et al., Ancient Admixture in Human History, Genetics, vol.192, issue.3, pp.1065-1093, 2012.
DOI : 10.1534/genetics.112.145037
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522152

J. Pickrell and J. Pritchard, Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data, PLoS Genetics, vol.26, issue.11, p.23166502, 2012.
DOI : 10.1371/journal.pgen.1002967.s016

S. Mallick, H. Li, M. Lipson, I. Mathieson, M. Gymrek et al., The Simons Genome Diversity Project: 300 genomes from 142 diverse populations, Nature, vol.81, issue.7624, pp.201-206, 2016.
DOI : 10.1086/519795
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161557

L. Boto, Horizontal gene transfer in evolution: facts and challenges, Proceedings of the Royal Society B: Biological Sciences, vol.8, issue.2, pp.819-827, 1683.
DOI : 10.1016/0022-5193(65)90083-4
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842723

J. Hotopp, Horizontal gene transfer between bacteria and animals, Trends in Genetics, vol.27, issue.4, pp.157-163, 2011.
DOI : 10.1016/j.tig.2011.01.005

O. Zhaxybayeva and W. Doolittle, Lateral gene transfer, Current Biology, vol.21, issue.7, pp.242-246, 2011.
DOI : 10.1016/j.cub.2011.01.045

D. Posada, K. Crandall, and E. Holmes, Recombination in Evolutionary Genomics, Annual Review of Genetics, vol.36, issue.1, pp.75-97, 2002.
DOI : 10.1146/annurev.genet.36.040202.111115

S. Vuilleumier and S. Bonhoeffer, Contribution of recombination to the evolutionary history of HIV, Current Opinion in HIV and AIDS, vol.10, issue.2, pp.84-89, 2015.
DOI : 10.1097/COH.0000000000000137

M. Rasmussen, M. Hubisz, I. Gronau, and A. Siepel, Genome-wide inference of ancestral recombination graphs):e1004342. https, PLoS Genetics, vol.10, issue.5, p.24831947, 2014.
DOI : 10.1371/journal.pgen.1004342
URL : http://doi.org/10.1371/journal.pgen.1004342

D. Huson, R. Rupp, and C. Scornavacca, Phylogenetic networks: concepts, algorithms and applications, 2010.
DOI : 10.1017/CBO9780511974076

D. Morrison, Introduction to Phylogenetic Networks. RJR Productions, 2011.

D. Bryant and V. Moulton, Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks, Molecular Biology and Evolution, vol.21, issue.2, pp.255-265, 2004.
DOI : 10.1093/molbev/msh018

D. Huson and C. Scornavacca, A Survey of Combinatorial Methods for Phylogenetic Networks, Genome Biology and Evolution, vol.3, issue.0, pp.23-35, 2011.
DOI : 10.1093/gbe/evq077

Y. Yu and L. Nakhleh, A maximum pseudo-likelihood approach for phylogenetic networks, BMC Genomics, vol.16, issue.Suppl 10, p.1, 2015.
DOI : 10.1007/s00285-013-0683-5
URL : http://doi.org/10.1186/1471-2164-16-s10-s10

C. Solís-lemus and C. Ané, Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting):e1005896. https, PLoS Genetics, vol.12, issue.3, p.26950302, 2016.

J. Camin and R. Sokal, A method for deducing branching sequences in phylogeny, Evolution, pp.311-326, 1965.

D. Swofford, G. Olsen, P. Waddell, and D. Hillis, Phylogenetic inference, Molecular systematics, pp.407-514, 1996.

Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Maximum likelihood inference of reticulate evolutionary histories, Proceedings of the National Academy of Sciences, vol.14, issue.46, pp.16448-16453, 2014.
DOI : 10.1371/journal.pcbi.1003649
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246314

K. Huber, S. Linz, V. Moulton, and T. Wu, Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations, Journal of Mathematical Biology, vol.17, issue.6, pp.699-725, 2016.
DOI : 10.1073/pnas.1407950111
URL : https://ueaeprints.uea.ac.uk/54718/1/NNI_Network_JMB_rev.pdf

K. Huber, V. Moulton, and T. Wu, Transforming phylogenetic networks: Moving beyond tree space, Journal of Theoretical Biology, vol.404, pp.30-39, 2016.
DOI : 10.1016/j.jtbi.2016.05.030
URL : http://arxiv.org/abs/1601.01788

L. Nakhleh, Evolutionary phylogenetic networks: models and issues. In: Problem solving handbook in computational biology and bioinformatics, pp.125-158, 2010.
DOI : 10.1007/978-0-387-09760-2_7
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.215.3536

L. Kubatko, Identifying Hybridization Events in the Presence of Coalescence via Model Selection, Systematic Biology, vol.58, issue.5, pp.478-488, 2009.
DOI : 10.1093/sysbio/syp055

H. Park and L. Nakhleh, Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria, BMC Bioinformatics, vol.13, p.12, 2012.

D. Robinson, Comparison of labeled trees with valency three, Journal of Combinatorial Theory, Series B, vol.11, issue.2, pp.105-1190095, 1971.
DOI : 10.1016/0095-8956(71)90020-7

M. Baroni, S. Grünewald, V. Moulton, and C. Semple, Bounding the Number of Hybridisation Events for a Consistent Evolutionary History, Journal of Mathematical Biology, vol.8, issue.2, pp.171-182, 2005.
DOI : 10.1007/s00285-005-0315-9

M. Bordewich and C. Semple, On the Computational Complexity of the Rooted Subtree Prune and Regraft Distance, Annals of Combinatorics, vol.8, issue.4, pp.409-423, 2005.
DOI : 10.1007/s00026-004-0229-z

G. Jin, L. Nakhleh, S. Snir, and T. Tuller, Maximum likelihood of phylogenetic networks, Bioinformatics, vol.22, issue.21, pp.2604-2611, 2006.
DOI : 10.1093/bioinformatics/btl452
URL : https://academic.oup.com/bioinformatics/article-pdf/22/21/2604/698677/btl452.pdf

C. Choy, J. Jansson, K. Sadakane, and W. Sung, Computing the maximum agreement of phylogenetic networks, Theoretical Computer Science, vol.335, issue.1, pp.93-107, 2005.
DOI : 10.1016/j.tcs.2004.12.012

J. Jansson and W. Sung, Inferring a level-1 phylogenetic network from a dense set of rooted triplets, Theoretical Computer Science, vol.363, issue.1, pp.60-68, 2006.
DOI : 10.1016/j.tcs.2006.06.022

M. Fischer, L. Van-iersel, S. Kelk, and C. Scornavacca, On Computing the Maximum Parsimony Score of a Phylogenetic Network, SIAM Journal on Discrete Mathematics, vol.29, issue.1, pp.559-585, 2015.
DOI : 10.1137/140959948

F. Pardi and C. Scornavacca, Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable, PLOS Computational Biology, vol.7, issue.4, pp.1004135-25849429, 2015.
DOI : 10.1371/journal.pcbi.1004135.s001
URL : https://hal.archives-ouvertes.fr/lirmm-01237428

S. Zhu and J. Degnan, Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent, Systematic Biology, 2017.
DOI : 10.1093/sysbio/syw097

G. Jin, L. Nakhleh, S. Snir, and T. Tuller, Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study, Molecular Biology and Evolution, vol.24, issue.1, pp.324-337, 2007.
DOI : 10.1093/molbev/msl163
URL : https://academic.oup.com/mbe/article-pdf/24/1/324/3741380/msl163.pdf

C. Than, D. Ruths, and L. Nakhleh, PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships, BMC Bioinformatics, vol.9, issue.1, pp.322-18662388, 2008.
DOI : 10.1186/1471-2105-9-322
URL : http://doi.org/10.1186/1471-2105-9-322

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.
DOI : 10.1093/bioinformatics/btu033

K. Culik and D. Wood, A note on some tree similarity measures, Information Processing Letters, vol.15, issue.1, pp.39-420020, 1982.
DOI : 10.1016/0020-0190(82)90083-7

M. Li, J. Tromp, and L. Zhang, On the Nearest Neighbour Interchange Distance Between Evolutionary Trees, Journal of Theoretical Biology, vol.182, issue.4, pp.463-467, 1996.
DOI : 10.1006/jtbi.1996.0188
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.190.9281

B. Allen and M. Steel, Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees, Annals of Combinatorics, vol.5, issue.1, pp.1-15, 2001.
DOI : 10.1007/s00026-001-8006-8
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.24.8389

B. Dasgupta, X. He, T. Jiang, M. Li, J. Tromp et al., On computing the nearest neighbor interchange distance, Discrete Mathematical Problems with Medical Applications: DIMACS Workshop Discrete Mathematical Problems with Medical Applications, pp.125-143, 1999.
DOI : 10.1090/dimacs/055/09