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Figure 6 | BMC Evolutionary Biology

Figure 6

From: The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene

Figure 6

A phylogenetic tree of ELP / CTI and the CTI -like bovine PTI , STI and TKDP1 , 2 , 3 , 4 and 5 family. The evolutionary relationship between the protein-coding regions of the marsupial ELP, eutherian CTI and bovine TKDP1-5, PTI and STI transcripts was determined by maximum likelihood analysis using a molecular clock assumption. The bovine SLPI transcript was used as an outgroup (data not shown). Two main groups were formed: 1. mammalian ELP/CTI and 2. bovine CTI, PTI and the TKDPs. Numbers at branch points indicate confidence levels as determined by bootstrap values (100 replicates). Phylogenetic trees were produced with Phylip software version 3.69. Transcripts were aligned with MUSCLE and boostrapped values generated with SEQBOOT. Maximum likelihood trees were generated with DNAMLK using a transition/transversion ratio of 1.34, a Gamma distribution shape of 1.39 with 5 Hidden Markov Model categories, global rearrangements and with a randomised input order jumbled once. The protein-coding regions of the following transcripts were used in the analysis: ELP/CTI, tammar [GenBank: JN191338], fat-tailed dunnart [GenBank: JN191339], stripe-faced dunnart [GenBank: AC186006], koala [GenBank: JN191337] opossum [GenBank: JN191340], brushtail possum, cow [GenBank: JN191341], dog [GenBank: JN191342], cat [GenBank: BK008083], pig [Ensembl: F1SD34_PIG (ENSSSCT00000008098)], Giant panda [GenBank: BK008084], and Common bottlenose dolphin [GenBank: BK008086], and the following bovine transcripts: PTI [GenBank: NM_001001554], STI [GenBank: NM_205786], TKDP1 [GenBank: NM_205776], TKDP2 [GenBank: NM_001012683], TKDP3 [GenBank: XM_584746], TKDP4 [GenBank: NM_205775], and TKDP5 [GenBank: XM_614808] and SLPI [GenBank: NM_001098865].

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