Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.
BACKGROUND
We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant).


RESULTS
We have produced 2000 ESTs (1.2 mega bases) from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects.


CONCLUSIONS
The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.
Kullberg
Morgan
M
Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden. morgan.kullberg@cob.lu.se
Hallström
Björn
B
Arnason
Ulfur
U
Janke
Axel
A
D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D006801:Humans; D008322:Mammals / Q000145:classification / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment
Nature. 2006 Nov 2;444(7115):85-8
17051155
Genetics. 1994 May;137(1):243-56
8056314
J Mol Evol. 1996 Dec;43(6):650-61
8995062
Mol Biol Evol. 2007 Jan;24(1):26-53
17047029
Mol Biol Evol. 1998 Dec;15(12):1637-46
9866199
Nature. 1992 Mar 12;356(6365):121-5
1545862
BMC Biol. 2005 Jan 28;3:2
15679890
Mol Biol Evol. 2005 Apr;22(4):1107-18
15689528
BMC Evol Biol. 2007 Jan 25;7:8
17254354
Mol Biol Evol. 2007 Aug;24(8):1722-30
17494028
PLoS Comput Biol. 2007 Jan 5;3(1):e2
17206860
J Mol Evol. 1991 Feb;32(2):128-44
1901092
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8151-6
12034869
PLoS Biol. 2006 Apr;4(4):e91
16515367
Nature. 2007 Jun 14;447(7146):799-816
17571346
BMC Evol Biol. 2004 Jun 28;4:18
15222900
Mol Biol Evol. 1995 Jul;12(4):546-57
7659011
Mol Biol Evol. 2006 Aug;23(8):1493-503
16751257
Mol Phylogenet Evol. 2005 Nov;37(2):426-41
15935706
PLoS Genet. 2007 Jan 5;3(1):e2
17206863
Mol Biol Evol. 2006 Feb;23(2):268-78
16237206
Cytogenet Genome Res. 2002;96(1-4):20-32
12438776
Bioinformatics. 2001 Aug;17(8):754-5
11524383
Mol Biol Evol. 2004 Feb;21(2):397-403
14660685
Bioinformatics. 2005 May 1;21(9):2104-5
15647292
Mol Biol Evol. 1996 May;13(5):685-90
8676743
Bioinformatics. 2005 Mar;21(6):703-10
15458983
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8
15608197
Mol Biol Evol. 2007 Jan;24(1):6-9
17012374
Mol Biol Evol. 2006 Dec;23(12):2274-8
16971694
Mol Biol Evol. 2004 Sep;21(9):1740-52
15175415
BMC Evol Biol. 2006 Jun 15;6:48
16776834
Mol Biol Evol. 1986 Sep;3(5):418-26
3444411
Syst Biol. 2003 Oct;52(5):696-704
14530136
PLoS One. 2007 Jan 17;2(1):e158
17225861
BMC Bioinformatics. 2002 Oct 25;3:31
12398795
Bioinformatics. 1998;14(9):817-8
9918953
Mol Phylogenet Evol. 2006 Feb;38(2):363-80
16054401
Mol Phylogenet Evol. 2007 Oct;45(1):81-8
17574446
J Mol Evol. 1984;20(1):86-93
6429346
Gene. 2000 Dec 23;259(1-2):177-87
11163975
Comput Appl Biosci. 1997 Oct;13(5):555-6
9367129
Science. 1991 Jun 21;252(5013):1651-6
2047873
Physiol Genomics. 2000 Apr 27;2(3):143-7
11015593
Mol Biol Evol. 2005 Dec;22(12):2472-9
16107592
Mol Phylogenet Evol. 2003 Aug;28(2):186-96
12878458
Science. 2001 Dec 14;294(5550):2348-51
11743200
Physiol Genomics. 2001 Dec 21;7(2):97-104
11773596
Nature. 1981 Aug 6;292(5823):538-40
7254349
J Mol Evol. 1993 Mar;36(3):270-81
8483165
Syst Biol. 2003 Oct;52(5):604-17
14530129
J Mol Evol. 1992 Jun;34(6):493-505
1593642
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417
Genome Res. 2007 Apr;17(4):413-21
17322288
Genome Res. 2003 Sep;13(9):2129-41
12952881
Comput Appl Biosci. 1992 Jun;8(3):275-82
1633570
Anal Biochem. 1987 Apr;162(1):156-9
2440339