Hostname: page-component-586b7cd67f-2brh9 Total loading time: 0 Render date: 2024-11-24T11:18:37.413Z Has data issue: false hasContentIssue false
  • English
  • Français

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae)

Published online by Cambridge University Press:  20 April 2011

LACEY L. KNOWLES  and
PAVEL B. KLIMOV
LACEY L. KNOWLES*
Affiliation:
University of Michigan, Department of Ecology and Evolutionary Biology, Museum of Zoology, 1109 Geddes Ave., Ann Arbor, Michigan 48109-1079, USA
PAVEL B. KLIMOV*
Affiliation:
University of Michigan, Department of Ecology and Evolutionary Biology, Museum of Zoology, 1109 Geddes Ave., Ann Arbor, Michigan 48109-1079, USA
*
*Corresponding authors: University of Michigan, Museum of Zoology 1109 Geddes Ave., Ann Arbor, Michigan 48109-1079USA. LLK: Phone: (734) 763-5603. Fax: (734) 763-4080. E-mail: [email protected]. PBK: Phone: (734) 763-4354. Fax: (734) 763-4080. E-mail: [email protected]
*Corresponding authors: University of Michigan, Museum of Zoology 1109 Geddes Ave., Ann Arbor, Michigan 48109-1079USA. LLK: Phone: (734) 763-5603. Fax: (734) 763-4080. E-mail: [email protected]. PBK: Phone: (734) 763-4354. Fax: (734) 763-4080. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Summary

With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference – species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates – a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.

Keywords

Acarigene treefeather mitespinnatus-groupProctophyllodesspecies tree
Type
Research Article
Information
Parasitology , Volume 138 , Special Issue 13: Systematics as a cornerstone of parasitology , November 2011 , pp. 1750 - 1759
Copyright
Copyright © Cambridge University Press 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Atyeo, W. T. and Braasch, N. L. (1966). The feather mite genus Proctophyllodes (Sarcoptiformes: Proctophyllodidae). Bulletin of the University of Nebraska State Museum 5, 1–354.Google Scholar
Badek, A., Dabert, M., Mironov, S. V. and Dabert, J. (2008). A new species of the genus Proctophyllodes (Analgoidea: Proctophyllodidae) from Cetti's warbler Cettia cetti (Passeriformes: Sylviidae) with DNA Barcode Data. Annales Zoologici 58, 397–402.CrossRefGoogle Scholar
Belfiore, N. M., Liu, L. and Moritz, C. (2008). Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Systematic Biology 57, 294–310.CrossRefGoogle ScholarPubMed
Blanco, G., Seoane, J. and de la Puente, J. (1999). Showiness, non-parasitic symbionts, and nutritional condition in a passerine bird. Annales Zoologici Fennici 36, 83–91.Google Scholar
Brumfield, R. T., Liu, L., Lum, D. E. and Edwards, S. V. (2008). Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Systematic Biology 57, 719–731.CrossRefGoogle ScholarPubMed
Cannone, J., Subramanian, S., Schnare, M., Collett, J., D'Souza, L., Du, Y., Feng, B., Lin, N., Madabusi, L., Muller, K., Pande, N., Shang, Z., Yu, N. and Gutell, R. (2002). The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2.CrossRefGoogle ScholarPubMed
Carstens, B. C. and Knowles, L. L. (2007). Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology 56, 400–411.CrossRefGoogle ScholarPubMed
Cranston, K. A., Hurwitz, B., Ware, D., Stein, L. and Wing, R. A. (2009). Species trees from highly incongruent gene trees in rice. Systematic Biology 58, 489–500.CrossRefGoogle ScholarPubMed
Degnan, J. H. and Rosenberg, N. A. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution 24, 332–340.CrossRefGoogle ScholarPubMed
Degnan, J. H. and Salter, L. A. (2005). Gene tree distributions under the coalescent process. Evolution 59, 24–37.Google ScholarPubMed
Drummond, A. J. and Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7, 214.CrossRefGoogle ScholarPubMed
Eckert, A. J. and Carstens, B. C. (2008). Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Molecular Phylogenetics and Evolution 49, 832–842.CrossRefGoogle ScholarPubMed
Edwards, S. V., Liu, L. and Pearl, D. K. (2007). High-resolution species trees without concatenation. Proceedings of the National Academy of Sciences, USA 104, 5936–5941.CrossRefGoogle ScholarPubMed
Felsenstein, J. (2004). Inferring Phylogenies, Sinauer Associates, Sunderland, MA, USA.Google Scholar
Gillespie, J. J., Johnston, J. S., Cannone, J. J. and Gutell, R. R. (2006). Characteristics of the nuclear (18S, 5·8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Insect Molecular Biology 15, 657–686.CrossRefGoogle ScholarPubMed
Hartup, B. K., Stott-Messick, B., Guzy, M. and Ley, D. H. (2004). Health survey of house finches (Carpodacus mexicanus) from Wisconsin. Avian Diseases 48, 84–90.CrossRefGoogle ScholarPubMed
Heled, J. and Drummond, A. J. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27, 570–580.CrossRefGoogle ScholarPubMed
Huang, H., He, Q., Kubatko, L. S. and Knowles, L. L. (2010). Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Systematic Biology 59, 573–583.CrossRefGoogle ScholarPubMed
Huang, H. and Knowles, L. L. (2009). What is the danger of the anomaly zone for empirical phylogenetics? Systematic Biology 58, 527–536.CrossRefGoogle ScholarPubMed
Joly, S., McLenachan, P. A. and Lockhart, P. J. (2009). A statistical approach for distinguishing hybridization and incomplete lineage sorting. American Naturalist 174, E54–E70.CrossRefGoogle ScholarPubMed
Klimov, P. B. and OConnor, B. M. (2008). Origin and higher-level relationships of psoroptidian mites (Acari: Astigmata: Psoroptidia): evidence from three nuclear genes. Molecular Phylogenetics and Evolution 47, 1135–1156.CrossRefGoogle ScholarPubMed
Knowles, L. L. (2009). Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Systematic Biology 58, 463–467.CrossRefGoogle ScholarPubMed
Knowles, L. L. (2010). Sampling strategies for species-tree estimation. In Estimating Species Trees: Practical and Theoretical Aspects (ed. Knowles, L. L. and Kubatko, L. S.), Wiley-Blackwell, Hoboken, NJ, USA.Google Scholar
Knowles, L. L. and Chan, Y.-H. (2008). Resolving species phylogenies of recent evolutionary radiations. Annals of the Missouri Botanical Garden 95, 224–231.CrossRefGoogle Scholar
Knowles, L. L. and Kubatko, L. S. (2010). Estimating species trees: an introduction to concepts and models. In Estimating Species Trees: Practical and Theoretical Aspects (ed. Knowles, L. L. and Kubatko, L. S.), pp. 1–12. Wiley-Blackwell, Hoboken, NJ, USA.Google Scholar
Kubatko, L. and Degnan, J. (2007). Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56, 17–24.CrossRefGoogle ScholarPubMed
Kubatko, L. S. and Gibbs, H. L. (2010). Estimating species relationships and taxon distinctiveness in Sistrurus rattlesnakes using multi-locus data. In Estimating Species Trees: Practical and Theoretical Aspects (ed. Knowles, L. L. and Kubatko, L. S.), pp. 193–206. Wiley-Blackwell, Hoboken, NJ, USA.Google Scholar
Linnen, C. (2010). Species-tree estimation for complex divergence Histories: A case study in Neodiprion sawflies. In Estimating Species Trees: Practical and Theoretical Aspects (ed. Knowles, L. L. and Kubatko, L. S.), pp. 145–192. Wiley-Blackwell, Hoboken, NJ, USA.Google Scholar
Liu, L. and Pearl, D. K. (2007). Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56, 504–514.CrossRefGoogle ScholarPubMed
Liu, L., Yu, L., Kubatko, L., Pearl, D. K. and Edwards, S. V. (2009). Coalescent methods for estimating phylogenetic trees. Molecular Phylogenetics and Evolution 53, 320–328.CrossRefGoogle ScholarPubMed
Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology 46, 523–536.CrossRefGoogle Scholar
Maddison, W. P. and Knowles, L. L. (2006). Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55, 21–30.CrossRefGoogle ScholarPubMed
Mathews, D. H., Sabina, J., Zuker, M. and Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology 288, 911–940.CrossRefGoogle ScholarPubMed
McCormack, J. E., Heled, J., Delaney, K. S., Peterson, A. T. and Knowles, L. L. (2010). Calibrating divergence times on species trees versus gene trees: Implications for speciation history of Aphelocoma jays. Evolution 65, 184–202.CrossRefGoogle Scholar
McCormack, J. E., Huang, H. and Knowles, L. L. (2009). Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Systematic Biology 58, 501–508.CrossRefGoogle ScholarPubMed
Mossel, E. and Roch, S. (2010). Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACM Transactions on Computational Biology and Bioinformatics 7, 166–171.CrossRefGoogle ScholarPubMed
Mossel, E. and Vigoda, E. (2005). Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309, 2207–2209.CrossRefGoogle Scholar
Oneal, E., Otte, D. and Knowles, L. L. (2010). Testing for biogeographic mechanisms promoting divergence in Caribbean crickets (genus Amphiacusta). Journal of Biogeography 37, 530–540.CrossRefGoogle Scholar
Posada, D. and Buckley, T. R. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53, 793–808.CrossRefGoogle ScholarPubMed
Rambaut, A. (2009). FigTree. Available online at http://tree.bio.ed.ac.uk/software/figtree/.Google Scholar
Rambaut, A. and Drummond, A. J. (2009). Tracer v1.5. Available from http://beast.bio.ed.ac.uk/Tracer.Google Scholar
Takahata, N. (1989). Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122, 957–966.CrossRefGoogle ScholarPubMed
Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31, 3406–3415.CrossRefGoogle ScholarPubMed
Supplementary material: PDF

Knowles Supplementary Material

Knowles Supplementary Material

Download Knowles Supplementary Material(PDF)
PDF 107.5 KB