Résumé
The evolution of gene families is complex, involving gene-level
evolutionary events such as gene duplication, horizontal gene transfer,
and gene loss (DTL), and other processes such as incomplete lineage
sorting (ILS). Because of this, topological differences often exist
between gene trees and species trees. A number of models have been
recently developed to explain these discrepancies, the most realistic of
which attempt to consider both gene-level events and ILS. When unified in
a single model, the interaction between ILS and gene-level events can
cause polymorphism in gene copy number, which we refer to as copy number
hemiplasy (CNH). In this paper we extend the Wright-Fisher process to
include duplications and losses over several species, and show that the
probability of CNH for this process can be significant. We study how well
two unified models --- MLMSC (MultiLocus MultiSpecies Coalescent), which
models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does
not --- approximate the Wright-Fisher process with duplication and loss.
We then study the effect of CNH on gene family evolution by comparing
MLMSC and DLCoal. We generate comparable gene trees under both
models, showing significant differences in various summary statistics;
most importantly, CNH reduces the number of gene copies greatly. If this
is not taken into account, the traditional method of estimating
duplication rates (by counting the number of gene copies) becomes
inaccurate. The simulated gene trees are also used for species tree
inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating
that their accuracy, based on CNH-unaware simulations calibrated on real
data, may have been overestimated.}