Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

BMC Bioinformatics

Table 1 Statistics of extant and ancestral genomes in the drosophila dataset.

Extant species	genes	adjacencies	coverage
melanogaster	6410	6402	47%
simulans	7195	6750	50%
sechellia	7551	7261	48%
erecta	6961	6910	49%
yacuba	7313	7058	49%
ananassae	6558	6459	47%
pseudoobscura	7280	7007	48%
persimilis	7361	7025	47%
willistoni	6236	6063	43%
mojavensis	6484	6403	48%
virilis	6512	6437	48%
grimsawi	6538	6220	46%
Ancestral species	genes	adjacencies > 0.9	genes with more than 2 adjacencies
ANC1	8054	7164	578
ANC2	8364	5422	164
ANC3	8696	7529	1348
ANC4	9455	3746	113
ANC5	7564	5021	160
ANC6	7242	6117	58
ANC7	6677	6184	210
ANC8	6954	5777	413
ANC9	8816	2872	47
ANC10	8026	2360	24
ANC11	7157	2030	3

Column "genes" is the number of genes in the dataset. Column "coverage" is the proportion of the genes in the dataset to the total number of genes annotated in Ensembl. Column "adjacencies" is the number of adjacencies in an extant genome or adjacencies in ancestral genomes with a posterior probability > 0.9. Column "genes with more than 2 adjacencies" is the number of genes involved in more than 2 adjacencies of posterior probability > 0.9. This value is reported only for ancestral genomes, as in extant all genes have 0, 1 or 2 neighbors by definition.

ISSN: 1471-2105