A genome-scale investigation of incongruence in culicidae mosquitoes

Genome Biology and Evolution

Volumn 7, Issue 12, 2015, Pages 3463-3471

  Wang, Yuyu ^a,b   Zhou, Xiaofan ^b   Yang, Ding ^a   Rokas, Antonis ^b  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b VANDERBILT UNIVERSITY   (United States)

Author keywords

Bipartition; Bootstrap support (BS); Gene tree; Internode certainty (IC); Maximum likelihood

Indexed keywords

ANIMAL; ANOPHELES; CLASSIFICATION; GENETIC SELECTION; GENETICS; INSECT GENOME; PHYLOGENY;

ANIMALS; ANOPHELES; GENOME, INSECT; PHYLOGENY; SELECTION, GENETIC;

EID: 84982091017     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv235     Document Type: Article

References (35)

1. Arensburger P, et al. 2010. Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science 330:86-88.
2. Besansky NJ, et al. 1994. Molecular phylogeny of the Anopheles gambiae complex suggests genetic introgression between principalmalaria vectors. Proc Natl Acad Sci U S A. 91:6885-6888.
3. Betancur-R R, Naylor G, OrtíG. 2014. Conserved genes, sampling error, and phylogenomic inference. Syst Biol. 63:257-262.
4. Capella-Gutierrez S, Silla-Martinez J, Gabaldon T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973.
5. Chen M, Liang D, Zhang P. 2015. Selecting question-specific genes to reduce incongruence in phylogenomics: a case study of jawed vertebrate backbone phylogeny. Syst Biol. 64:1104-1120.
6. Clark AG, Messer PW. 2015. Conundrum of jumbled mosquito genomes. Science 347:27-28.
7. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 24:332-340.
8. Dell'Ampio E, et al. 2014. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol. 31:239-249.
9. Faircloth BC, et al. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol. 61:717-726.
10. Fontaine MC, et al. 2015. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347:1258524.
11. Galtier N, Daubin V. 2008. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc B Biol Sci. 363:4023-4029.
12. Hess J, Goldman N. 2011. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PLoS ONE 6:e22783.
13. Hittinger CT, JohnstonM, Tossberg JT, Rokas A. 2010. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci U S A. 107:1476-1481.
14. Holt RA, et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129-149.
15. Jarvis ED, et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331.
16. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet 22:225-231.
17. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
18. Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61:727-744.
19. Liu L, Yu L, Pearl DK, Edwards SV. 2009. Estimating species phylogenies using coalescence times among sequences. Syst Biol. 58:468-477.
20. Marinotti O, et al. 2013. The Genome of Anopheles darling, the main neotropical malaria vector. Nucleic Acids Res. 41:7387-7400.
21. Mirarab S, Warnow T. 2015. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31:i44-i52.
22. Nater A, Burri R, Kawakami T, Smeds L, Ellegren H. 2015. Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst Biol. 64:1000-1017.
23. Neafsey DE, et al. 2015. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 347:1258522.
24. Nene V, et al. 2007. Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316:1718-1723.
25. Robinson DR, Foulds LR. 1981. Comparison of phylogenetic trees. Math Biosci 53:131-147.
26. Rokas A, Abbot P. 2009. Harnessing genomics for evolutionary insights. Trends Ecol Evol. 24:192-200.
27. Romiguier J, Ranwez V, Delsuc F, Galtier N, Douzery EJP. 2013. Less is more in mammalian phylogenomics: AT-rich genesminimize tree conflicts and unravel the root of placental mammals. Mol Biol Evol. 30:2134-2144.
28. Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327-331.
29. Salichos L, Stamatakis A, Rokas A. 2014. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol. 31:1261-1271.
30. Song S, Liu L, Edwards SV, Wu S. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci U S A. 109:14942-14947.
31. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313.
32. Suh A, Smeds L, Ellegren H. 2015. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol. 13:e1002224.
33. Suyama M, Torrents D, Bork P. 2006. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34:609-612.
34. Wickett NJ, et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A. 111:E4859-E4868.
35. Zhong B, Liu L, Yan Z, Penny D. 2013. Origin of land plants using the multispecies coalescent model. Trends Plant Sci. 18:492-495.