Overview Molecular data play a key role in phylogenetic and molecular evolution inferences. Mammalian genomics and systematics provides us with a clear example, with several open evolutionary questions now able to be answered. However, molecular studies have until present used only a handful of standard markers and have not attempted to utilise the information contained within the increasingly large pool of mammalian genome sequences. The identification and utilisation of potentially new informative markers from this comparative genomics pool can help to further resolve the mammalian phylogenetic tree, and better understand the evolutionary dynamics of genes.

Description The EnsEMBL database was used to decide on a set of 1-to-1 orthologous markers from those mammalian genomes available. Exons of reasonable length for further amplification from genomic DNA and sequencing in additional species were then selected. For phylogenomic purposes, CoDing Sequences (CDSs) were also collected. The phylogenetic utility and the evolutionary characteristics of these candidate markers were then evaluated using a homemade bioinformatics pipeline. The resulting OrthoMaM database can be interrogated through this website. The current OrthoMaM release (v7) is based on EnsEMBL v65. It now includes 6,611 exons and 13,111 CDS alignments for up to 39 species.

If you use OrthoMam, please cite:

• OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics. Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M. & Douzery E. J. P. BMC Evolutionary Biology 7 : 241, 2007.

The following works have used and cited OrthoMaM

• 23. Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents. L. Loss-Oliveira, B. O. Aguiar and C. G. Schrago Evolutionary Bioinformatics 8: 127-137 ,2012.
• 22. Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. N. Laguette, N. Rahm, B. Sobhian, C. Chable-Bessia, J. Münch, J. Snoeck, D. Sauter, W. M. Switzer, W. Heneine, F. Kirchhoff, F. Delsuc, A. Telenti and M. Benkirane. Cell Host Microbe 11: 205-217, 2012.
• 21. Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. W. L. S. Li and A. J. Drummond. Mol. Biol. Evol. 29: 751-761, 2012.
• 20. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals. X. Zhou, S. Xu, J. Xu, B. Chen, K. Zhou and G. Yang. Syst. Biol. 61: 150-164, 2011.
• 19. MACSE: Multiple Alignment of Coding SEequences accounting for frameshifts and stop codons. V. Ranwez, S. Harispe, F. Delsuc and E. J. P. Douzery. PLoS One 6: e22594, 2011.
• 18. PhyDesign: an online application for profiling phylogenetic informativeness. F. López-Giráldez and J. P. Townsend. BMC Evol. Biol. 11: 152, 2011.
• 17. Phylogenomic analyses and improved resolution of Cetartiodactyla. X. Zhou, S. Xu, Y. Yang, K. Zhou and G. Yang. Mol. Phylogenet. Evol. 61: 255-264, 2011.
• 16. Morphology, molecular phylogeny, and taxonomic inconsistencies in the study of Bradypus sloths (Pilosa: Bradypodidae). N. de Moraes-Barros, J. A. B. Silva and J. S. Morgante. J. Mammal. 92: 86-100, 2011.
• 15. Developing a series of conservative anchor markers and their application to phylogenomics of Laurasiatherian mammals. X. Zhou, S. Xu, P. Zhang and G. Yang. Mol. Ecol. Resources 11: 134-140, 2011.
• 14. Protein structural modularity and robustness are associated with evolvability M. M. Rorick and G. P. Wagner. Genome Biol. Evol. 3: 456-475, 2011.
• 13. Novel intron markers to study the phylogeny of closely related mammalian species. J. Igea, J. Juste and J. Castresana. BMC Evol. Biol. 10: 369, 2010.
• 12. Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses. R. Makowsky, C. L. Cox, C. Roelke and P. T. Chippindale. Mol. Phylogenet. Evol. 57: 485-494, 2010.
• 11. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. J. Romiguier, V. Ranwez, E. J. P. Douzery and N. Galtier. Genome Res. 20: 1001-1009, 2010.
• 10. SuperTriplets: A triplet-based supertree approach to molecular systematics and phylogenomics. V. Ranwez, A. Criscuolo and E. J. P. Douzery. Bioinformatics 26: i115-i123, 2010.
• 09. An evolutionary genome scan for longevity-related natural selection in mammals. R. W. Jobson, B. Nabholz and N. Galtier. Mol. Biol. Evol. 27: 840-847, 2010.
• 08. The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes. F. Cruz, J. Roux and M. Robinson-Rechavi. BMC Genomics 10: 619, 2009.
• 07. Covariation of branch lengths in phylogenies of functionally related genes. W. L. S. Li and A. G. Rodrigo. PLoS ONE 4: e8487, 2009.
• 06. Computer-assisted automatic classifications, storage, queries and functional assignments of orthologs and in-paralogs proteins. D. Thybert, S. Avner, C. Lucchetti-Miganeh and F. Barloy-Hubler. Curr. Bioinformatics 4: 129-140, 2009.
• 05. PhyloExplorer: a web server to validate, explore and query phylogenetic trees. V. Ranwez, N. Clairon, F. Delsuc, S. Pourali, N. Auberval, S. Diser and V. Berry. BMC Evol. Biol. 9: 108, 2009.
• 04. Reviews in comparative genomic research based on orthologs. Z.-X. Pan, D. Xu, J.-B. Zhang, F. Lin, B.-J. Wu and H.-L. Liu. Hereditas (Beijing) 31: 457-463, 2009.
• 03. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. N. Galtier, L. Duret, S. Glémin and V. Ranwez. Trends Genet. 25: 1-5, 2009.
• 02. IDEA: Interactive Display for Evolutionary Analyses. A. Egan, A. Mahurkar, J. Crabtree, J. H. Badger, J. M. Carlton and J. C. Silva. BMC Bioinformatics 9: 524, 2008.
• 01. PhySIC_IST: cleaning source trees to infer more informative supertrees. C. Scornavacca, V. Berry, V. Lefort, E. J. P. Douzery and V. Ranwez. BMC BioInformatics 9: 413, 2008.