Abstract
The functional constraint imposed on exonic sequences increases marker universality and improves sequence alignment accuracy, yet introns have been favoured recently in Avian Tree of Life studies because of the increased sequence coverage that would be required to yield similar resolving power with exons. In this study, we address this shortcoming by developing a pipeline to identify a large number of exonic markers from five avian genomes. Markers were targeted to maximize phylogenetic informativeness and to exclude multi-copy genes. We demonstrate the universality of these markers by testing a portion of them on a taxonomically diverse assemblage of avian specimens.
Zusammenfassung
Einhundert neue Exon-Markergene für Phylogenieuntersuchungen bei Vögeln
Eukaryotische Gene bestehen aus proteincodierenden Exons und nicht-codierenden Introns. Da die Nucleotidsequenzen von Exons funktionellen Zwängen unterliegen, eignen sie sich gut als Markergene, da sie universell sind und sich einfacher alignieren lassen. Bislang wurden eher Intronsequenzen genutzt, so z.B. in “Avian Tree of Life” Untersuchungen, da sie bereits in größerer Menge vorliegen. Ausgehend von fünf Vogelgenomuntersuchungen wurde in dieser Arbeit eine große Anzahl von Exon-Markern identifiziert. Die Markergene wurden unter dem Aspekt ausgesucht, ob sie phylogenetisch informativ sind und nicht in mehrfachen Kopien im Genom vorkommen. 100 Exonmarker wurden anhand einer repräsentativen Auswahl von Vogelarten überprüft, ob die zugehörigen PCR-Primer universell einsetzbar sind.
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References
Brown JW, Payne RB, Mindell DP (2007) Nuclear DNA does not reconcile “rocks” and “clocks” in Neoaves: a comment on Ericson et al. Biol Lett 3:257–259. doi:10.1038/nature03150
Chojnowski JL, Kimball RT, Braun EL (2008) Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene 410:89–96. doi:10.1016/j.gene.2007.11.016
Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881–10890. doi:10.1093/nar/16.22.10881
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. doi:10.1093/nar/gkh340
Ericson PGP, Anderson CL, Ohlson JI et al (2006) Diversification of Neoaves: integration of molecular sequence data and fossils. Biol Lett 2:543–547. doi:10.1098/rsbl2006.0523
Fain MG, Houde P (2004) Parallel radiations in the primary clades of birds. Evolution 58:2558–2573. doi:10.1554/04-235
Flicek P, Amode MR, Barrell D et al (2012) Ensembl 2012. Nucleic Acids Res 40:D84–D90. doi:10.1093/nar/gkr991
Fong JJ, Fujita MK (2011) Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata. Mol Phylogenet Evol 61:300–307. doi:10.1016/j.ympev.2011.06.016
Fredslund J, Schauser L, Madsen LH et al (2005) PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. Nucleic Acids Res 33:W516–W520. doi:10.1093/nar/gki425
Hackett SJ, Kimball RT, Reddy S et al (2008) A phylogenomic study of birds reveals their evolutionary history. Science 320:1763–1768. doi:10.1126/science.1157704
Haider S, Ballester B, Smedley D et al (2009) BioMart Central Portal—unified access to biological data. Nucleic Acids Res 37:W23–W27. doi:10.1093/nar/gkp265
Hedges SB, Dudley J, Kumar S (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971–2972. doi:10.1093/bioinformatics/btl505
Holmes I, Durbin R (1998) Dynamic programming alignment accuracy. J Comput Biol 5:493–504. doi:10.1089/cmb.1998.5.493
Hughes CE, Eastwood RJ, Bailey CD (2006) From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Phil Trans R Soc Lond B 361:211–225. doi:10.1098/rstb2005.1735
Jetz W, Thomas GH, Joy JB et al (2012) The global diversity of birds in space and time. Nature 491:444–448. doi:10.1038/nature11631
Kalendar R, Lee D, Schulman AH (2011) Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 98:137–144. doi:10.1016/j.ygeno.2011.04.009
Kimball RT, Braun EL, Barker FK et al (2009) A well-tested set of primers to amplify regions spread across the avian genome. Mol Phylogenet Evol 50:654–660. doi:10.1016/j.ympev.2008.11.018
Leaché AD, Rannala B (2011) The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol 60:126–137. doi:10.1093/sysbio/syq073
Liu K, Linder CR, Warnow T (2010) Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Curr 2:RRN1198. doi:10.1371/currents.RRN1198
López-Giráldez F, Townsend JP (2011) PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol Biol 11:152. doi:10.1186/1471-2148-11-152
McCormack JE, Harvey MG, Faircloth BC et al (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 8:e54848. doi:10.1371/journal.pone.0054848
Murphy WJ, Eizirik E, Johnson WE et al (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409:614–618. doi:10.1038/35054550
Parker J, Tsagkogeorga G, Cotton JA et al (2013) Genome-wide signatures of convergent evolution in echolocating mammals. Nature 502:228–231. doi:10.1038/nature12511
Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676–679. doi:10.1093/bioinformatics/bti079
Rokas A, Holland PWH (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15:454–459. doi:10.1016/S0169-5347(00)01967-4
Shapiro LH, Dumbacher JP (2001) Adenylate kinase intron 5: a new nuclear locus for avian systematics. Auk 118:248–255. doi:10.1642/0004-8038(2001)118[0248:AKIANN]2.0.CO;2
Smedley D, Haider S, Ballester B et al (2009) BioMart—biological queries made easy. BMC Genom 10:22. doi:10.1186/1471-2164-10-22
Song S, Liu L, Edwards SV, Wu S (2012) Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. PNAS 109:14942–14947. doi:10.1073/pnas.1211733109
Townsend JP (2007) Profiling phylogenetic informativeness. Syst Biol 56:222–231. doi:10.1080/10635150701311362
Acknowledgments
This work was funded by the Natural Sciences and Engineering Research Council of Canada via a post-doctoral fellowship to KCRK and a grant to AJB. We thank Oliver Haddrath for providing general assistance in the laboratory. All tissue samples were supplied by the Royal Ontario Museum.
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Kerr, K.C.R., Cloutier, A. & Baker, A.J. One hundred new universal exonic markers for birds developed from a genomic pipeline. J Ornithol 155, 561–569 (2014). https://doi.org/10.1007/s10336-014-1041-0
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DOI: https://doi.org/10.1007/s10336-014-1041-0