First, the existence of a star phylogeny consisting of three distinct, but closely related, lineages with no relationship to geography (Figure 5) demonstrates rapid expansion in the evolutionarily recent past [54], and is could be the result of recolonization by animals from throughout the range.
Additionally, a smaller phylogeny consisting of just human and opossum class I genes and the mouse Mill genes was also inferred by maximum likelihood (Additional file 1: Figure S3).
A new clade is formed in the agt1 phylogeny, consisting of P. cerrateae, P. sp. Pe411, P. pugnicaudex, and P. chutanka.
Our Ig3 phylogeny consisted of 290 arthropod exons, ranging from 102 to 132 bp in length, and the Ig7 phylogeny consisted of 219 arthropod exons, ranging from 243 to 312 bp in length.
The matrix used to construct the phylogeny consisted of 97 UCOS contigs with combined length of 20,438 nucleotides.
The overall CHIKV phylogeny consisted of all 188 near-complete or complete genome CHIKV sequences available in the NT database as of March 2015.
The EBOV phylogeny consisted of the newly MiSeq- and nanopore-sequenced Ebola strain Lomela-LokoliaB11 from the 2014 DRC outbreak [ 17], as well as other representative EBOV strains, including strains from the 2014 2015 West African outbreak [ 8, 35].
The resulting phylogeny identified a large clade consisting of the 12 B73 Meg genes and one of the sorghum Meg homologs (SbMeg1), separated from Meg14 and the other sorghum homolog (SbMeg2) with strong statistical support.
A recent phylogeny indicates that the genus Alloteropsis occurs within a clade consisting of both C3 and C4 species (Christin et al., 2008).
This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs.
