A database of Orthologous Mammalian Markers

New release v9 is available (April 2015) !

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.
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 (v9) is based on EnsEMBL v79. It now includes 7349 exons and 14526 CDS alignments for up to 43 species.
If you use OrthoMam, please cite one of these references:
  • Original paper - 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.
  • Database update - OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. Douzery E. J. P., Scornavacca C., Romiguier J., Belkhir K., Galtier N., Delsuc F. & Ranwez V. Molecular Biology and Evolution, 31 (7) : 1923-1928, 2014.
The following works have used and cited OrthoMaM
  • 62. Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers. Blanco I, Kuchenbaecker K, Cuadras D, Wang X, Barrowdale D, de Garibay GR, et al. PLoS ONE 10(4), 2015.
  • 61. A new method for estimating species age supports the coexistence of malaria parasites and their mammalian hosts. J. C. Silva, A. Egan, C. Arze, J. L. Spouge and D. G. Harris. Mol. Biol. Evol.: 2015.
  • 60. Naked but not hairless: the pitfalls of analyses of molecular adaptation based on few genome sequence comparisons. F. Delsuc and M. K. Tilak. Genome Biol. Evol. 7: 768-774, 2015.
  • 59. Gene expression, chromosome heterogeneity and the fast-X effect in mammals. L. P. Nguyen, N. Galtier and B. Nabholz. Biol Lett. 11: 20150010, 2015.
  • 58. A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. K. L. Ilves and H. Lopez-Fernandez. Mol. Ecol. Resour. 14: 802-11, 2014.
  • 57. Practical performance of tree comparison metrics. M. K. Kuhner and J. Yamato. Syst. Biol. 64: 205-14, 2014.
  • 56. Population genomics of eusocial insects: the costs of a vertebrate-like effective population size. J. Romiguier, J. Lourenco, P. Gayral, N. Faivre, L. A. Weinert, S. Ravel, M. Ballenghien, V. Cahais, A. Bernard, E. Loire, L. Keller and N. Galtier. J. Evol. Biol. 27: 593-603, 2014.
  • 55. Phylostratigraphic bias creates spurious patterns of genome evolution. B. A. Moyers and J. Zhang. Mol. Biol. Evol. 32: 258-67, 2014.
  • 54. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. J. Gatesy and M. S. Springer. Mol. Phylogenet. Evol. 80: 231-66, 2014.
  • 53. Performance of genomic data sets on the estimation of the divergence time of New World and Old World anthropoids. C. G. Schrago and C. M. Voloch. Genet. Mol. Res. 13: 1425-37, 2014.
  • 52. Monte Carlo algorithms for Brownian phylogenetic models. B. Horvilleur and N. Lartillot. Bioinformatics 30: 3020-8, 2014.
  • 51. Indel reliability in indel-based phylogenetic inference. H. Ashkenazy, O. Cohen, T. Pupko and D. Huchon. Genome Biol. Evol. 6: 3199-209, 2014.
  • 50. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. H. C. Lanier, H. Huang and L. L. Knowles. Mol. Phylogenet. Evol. 70: 112-9, 2014.
  • 49. Eyes underground: regression of visual protein networks in subterranean mammals. C. A. Emerling and M. S. Springer. Mol. Phylogenet. Evol. 78: 260-70, 2014.
  • 48. Development of rapidly evolving intron markers to estimate multilocus species trees of rodents. A. Rodriguez-Prieto, J. Igea and J. Castresana. PLoS One 9: e96032, 2014.
  • 47. Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates. B. Mello and C. G. Schrago. Evol. Bioinform. Online 10: 79-85, 2014.
  • 46. Alignment errors strongly impact likelihood-based tests for comparing topologies. E. L. Karin, E. Susko and T. Pupko. Mol. Biol. Evol. 31: 3057-3067, 2014.
  • 45. Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). F. Botero-Castro, M. K. Tilak, F. Justy, F. Catzeflis, F. Delsuc and E. J. Douzery. Mol. Phylogenet. Evol. 69: 728-39, 2013.
  • 44. Genome-wide signatures of convergent evolution in echolocating mammals. J. Parker, G. Tsagkogeorga, J. A. Cotton, Y. Liu, P. Provero, E. Stupka and S. J. Rossiter. Nature 502: 228-31, 2013.
  • 43. Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. F. Lopez-Giraldez, A. H. Moeller and J. P. Townsend. Biomed Res. Int. 2013: 621604, 2013.
  • 42. Adaptive evolution of the osmoregulation-related genes in cetaceans during secondary aquatic adaptation. S. Xu, Y. Yang, X. Zhou, J. Xu, K. Zhou and G. Yang. BMC Evol. Biol. 13: 189, 2013.
  • 41. Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses. V. R. Perovic. J. Math. Chem. 51: 2238-2255, 2013.
  • 40. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. J. Romiguier, V. Ranwez, F. Delsuc, N. Galtier and E. J. P. Douzery. Mol. Biol. Evol. 30: 2134-2144, 2013.
  • 39. Evolution of functional genes in cetaceans driven by natural selection on a phylogenetic and population level. A. E. Moura, A. Natoli, E. Rogan and A. R. Hoelzel. Evol. Biol. 40: 341-354, 2013.
  • 38. Efficient newly designed primers for the amplification and sequencing of bird mitochondrial genomes. S. A. Amer, M. M. Ahmed and M. Shobrak. Biosci. Biotechnol. Biochem. 77: 577-581, 2013.
  • 37. Conventional simulation of biological sequences leads to a biased assessment of multi-loci phylogenetic analysis. B. O. Aguiar and C. G. Schrago. Evol. Bioinformatics 9: 317-325, 2013.
  • 36. The precision of the hominid timescale estimated by relaxed clock methods. C. G. Schrago and C. M. Voloch. J. Evol. Biol. 26: 746-755, 2013.
  • 35. Bayesian selection of nucleotide substitution models and their site assignments. C.-H. Wu, M. A. Suchard and A. J. Drummond. Mol. Biol. Evol. 30: 669-688, 2013.
  • 34. Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes. N. Lartillot. Mol. Biol. Evol. 30: 489-502, 2013.
  • 33. High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes. B. Nabholz, H. Ellegren and J. B. W. Wolf. Mol. Biol. Evol. 30: 272-284, 2013.
  • 32. Genomic evidence for large, long-lived ancestors to placental mammals. J. Romiguier, V. Ranwez, E. J. P. Douzery and N. Galtier. Mol. Biol. Evol. 30: 5-13, 2013.
  • 31. Combining multiple autosomal introns for studying shallow phylogeny and taxonomy of Laurasiatherian mammals: Application to the tribe Bovini (Cetartiodactyla, Bovidae). A. Hassanin, J. An, A. Ropiquet, T. T. Nguyen and A. Couloux. Mol. Phylogenet. Evol. 66: 766-775, 2013.
  • 30. E value cutoff and eukaryotic genome content phylogenetics. J. A. Rosenfeld and R. DeSalle. Mol. Phylogenet. Evol 63: 342-350, 2012.
  • 29. EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies. C. Li, J.-J. M. Riethoven and G. J. P. Naylor. Mol. Ecol. Res. 12: 967-971, 2012.
  • 28. A method to find longevity-selected positions in the mammalian proteome. J. Semeiks and N. V. Grishin. PLoS One 7: e38595, 2012.
  • 27. ALG11  a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene. F. Belinky, A. Szitenberg, I. Goldfarb, T. Feldstein, G. Wörheide, M. Ilan and D. Huchon. Mol. Phylogenet. Evol. 63: 702-713, 2012.
  • 26. Impact of the partitioning scheme on divergence times inferred from mammalian genomic data sets. C. M. Voloch and C. G. Schrago. Evol. Bioinformatics 8: 207-218, 2012.
  • 25. Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. J. Romiguier, E. Figuet, N. Galtier, E. J. P. Douzery, B. Boussau, J. Y. Dutheil and V. Ranwez. PLoS One 7: e33852, 2012.
  • 24. Comprehensive primer design for analysis of population genetics in non-sequenced organisms. A. Tezuka, N. Matsushima, Y. Nemoto, H. D. Akashi, M. Kawata and T. Makino. PLoS ONE 7: e32314, 2012.
  • 23. 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.
  • 22. Testing synchrony in historical biogeography: the case of New World primates and Hystricognathi rodents. L. Loss-Oliveira, B. O. Aguiar and C. Schrago. Evol. Bioinformatics 8: 127137, 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, 2012.
  • 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.