Conflicts between separate phylogenies based on different genes can be observed on several genomic levels: when comparing phylogenies based on different genomes (e.g. organellar vs. nuclear), different genes or different copies of a gene (either alleles or paralogues), or even different parts of one gene.
Trees based on different types of genome distance have been popularized in the study of archaic humans as a way to determine their genetic similarity to different hominins [ 66, 67].
Most studies aiming at the discovery of CNV regions have made use of genome-wide approaches based on different array-based comparative genomic hybridisation (aCGH) and comparative genomic intensity (aCGI) platforms, and have provided partial evidences of their nature, real size and/or population distribution.
An alternative explanation based on different evolutionary rates of genome segments has been proposed [ 42, 59].
More recently, phylogenetic analyses based on different regions of the genome have shown that WNV isolates form two well-supported lineages (19, 31, 32).
Since the network reconstruction process is organism specific and is based on different datasets such as annotated genome sequence, high-throughput network-wide datasets and bibliomic data on the detailed properties of individual network components [ 15], it is not easy for biologists to efficiently construct the integrated cellular network by traditional genetic/molecular manipulation.
Most of the deep nodes are still uncertain, mainly due to low support values as well as some incongruence between analyses based on different data sets (complete mitochondrial genomes versus individual genes -18S, 28S, 16S, CO1), these two issues being obviously related.
Therefore, sets of T pigs were selected from the entire population based on different criteria for dense genotyping (or whole-genome sequencing).
The ML trees based on the different genome search methods (1 and 2) were largely the same.
