As most nodes in the ML tree were poorly supported, it is not clear whether some abnormal branching patterns in the cytosolic HSP70 tree are simply due to the lack of informative sites or other factors (e.g., incomplete lineage sorting, horizontal gene transfer, paralogy) that can lead to discordance between the gene and the species trees.
This need arises from the possibility of incomplete lineage sorting, horizontal gene transfer, introgression and population fragmentation effects [ 24].
Such discordance may arise from incomplete lineage sorting, horizontal gene transfer or hybridization, and was observed in our data set when using classical phylogenomics methods such as superalignment strategy or consensus supertree methods.
Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny.
Reasons for the incongruence are manifold, e.g., different inheritance pathways, divergent selection pressures, and most prominent, incomplete lineage sorting and horizontal gene flow (e.g. [ 4, 5]).
Therefore we recommend the use of this marker as an addition to mitochondrial markers (like COI ) in order to prevent erroneous estimation of species trees caused by introgressive hybridization, incomplete lineage sorting or horizontal gene transfer.
This is termed phylogenetic incongruence, and may arise from a methodological failure of the inference process or from biological processes, such as horizontal gene transfer, incomplete lineage sorting, and introgression.
Processes such as incomplete lineage sorting, recombination, and horizontal transfer can cause discord among gene and species trees, masking true evolutionary relationships among closely related taxa [ 11].
We anticipated that some genes would provide conflicting phylogenetic signals due to horizontal gene transfer, incomplete lineage sorting, or other factors in their evolutionary history.
Species tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete lineage sorting (ILS), and horizontal gene transfer (HGT).
