OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
Vincent Ranwez,Vincent Ranwez,Frédéric Delsuc,Frédéric Delsuc,Sylvie Ranwez,Khalid Belkhir,Khalid Belkhir,Marie-Ka Tilak,Marie-Ka Tilak,Emmanuel J. P. Douzery,Emmanuel J. P. Douzery +10 more
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TLDR
The resulting OrthoMaM (Orthologous Mammalian Markers) database is expected to be useful for further resolving the phylogenetic tree of placental mammals and for better understanding the evolutionary dynamics of their genomes, i.e., the forces that shaped coding sequences in terms of selective constraints.Abstract:
Molecular sequence data have become the standard in modern day phylogenetics. In particular, several long-standing questions of mammalian evolutionary history have been recently resolved thanks to the use of molecular characters. Yet, most studies have focused on only a handful of standard markers. The availability of an ever increasing number of whole genome sequences is a golden mine for modern systematics. Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels. The EnsEMBL database was used to determine a set of orthologous genes from 12 available complete mammalian genomes. As targets for possible amplification and sequencing in additional taxa, more than 3,000 exons of length > 400 bp have been selected, among which 118, 368, 608, and 674 are respectively retrieved for 12, 11, 10, and 9 species. A bioinformatic pipeline has been developed to provide evolutionary descriptors for these candidate markers in order to assess their potential phylogenetic utility. The resulting OrthoMaM (Orthologous Mammalian Markers) database can be queried and alignments can be downloaded through a dedicated web interface http://kimura.univ-montp2.fr/orthomam
. The importance of marker choice in phylogenetic studies has long been stressed. Our database centered on complete genome information now makes possible to select promising markers to a given phylogenetic question or a systematic framework by querying a number of evolutionary descriptors. The usefulness of the database is illustrated with two biological examples. First, two potentially useful markers were identified for rodent systematics based on relevant evolutionary parameters and sequenced in additional species. Second, a complete, gapless 94 kb supermatrix of 118 orthologous exons was assembled for 12 mammals. Phylogenetic analyses using probabilistic methods unambiguously supported the new placental phylogeny by retrieving the monophyly of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria. Muroid rodents thus do not represent a basal placental lineage as it was mistakenly reasserted in some recent phylogenomic analyses based on fewer taxa. We expect the OrthoMaM database to be useful for further resolving the phylogenetic tree of placental mammals and for better understanding the evolutionary dynamics of their genomes, i.e., the forces that shaped coding sequences in terms of selective constraints.read more
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GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
TL;DR: It is shown that GUIDANCE2 outperforms all previously developed methodologies to detect unreliable MSA regions and provides a set of alternative MSAs which can be useful for downstream analyses.
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MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
TL;DR: The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons).
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Genome-wide signatures of convergent evolution in echolocating mammals
Joe Parker,Georgia Tsagkogeorga,James Cotton,James Cotton,Yuan Liu,Paolo Provero,Paolo Provero,Elia Stupka,Stephen J. Rossiter +8 more
TL;DR: This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
Scott V. Edwards,Zhenxiang Xi,Axel Janke,Brant C. Faircloth,John E. McCormack,Travis C. Glenn,Bojian Zhong,Shaoyuan Wu,Emily Moriarty Lemmon,Alan R. Lemmon,Adam D. Leaché,Liang Liu,Charles C. Davis +12 more
TL;DR: Many of S&G's criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is aSpecial case of emerging network models in phylogenomics.
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
John Gatesy,Mark S. Springer +1 more
TL;DR: It is suggested that inaccurate gene trees that imply unrealistically deep coalescences debilitate shortcut coalescence analyses of the placental dataset, and a critical conundrum is outlined that challenges the general utility of shortcuts coalescence methods at deep phylogenetic scales.
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