Despite the revolution brought by phylogenomics, accurately reconstructing the Tree of Life remains a challenge due to discordance between gene and species histories. These incongruences arise from biological processes like incomplete lineage sorting (ILS). The multispecies coalescent (MSC) model, a cornerstone for species tree inference, accounts for ILS but assumes strict orthology, no recombination within loci, and free recombination between loci. The multispecies network coalescent (MSNC) extends the MSC to accommodate diploid hybridization, but real biological complexities often require further refinement.

This thesis addresses these limitations by investigating the impact of MSC assumption violations on phylogenetic inference. We explore three key areas: (1) the potential of utilizing paralogs for species tree reconstruction, (2) the influence of recombination on population parameter estimation, and (3) the effectiveness of existing gene tree correction methods. We then introduce two novel methods, MPAllopp and Polyphest, specifically designed to infer phylogenetic networks that account for both ILS and polyploidy, a prevalent phenomenon in evolution. These methods are validated through extensive simulations and real data analyses.

Overall, this thesis contributes to enhancing the accuracy of phylogenetic inference by critically evaluating existing methods and developing novel approaches that can handle the complexities of real-world data.