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13 - Molecular data in systematics: a promise fulfilled, a future beckoning

Published online by Cambridge University Press:  05 July 2016

By
Ward C. Wheeler  and
Gonzalo Giribet
Edited by
David Williams ,
Michael Schmitt  and
Quentin Wheeler
David Williams
Affiliation:
Natural History Museum, London
Michael Schmitt
Affiliation:
Ernst-Moritz-Arndt-Universität Greifswald, Germany
Quentin Wheeler
Affiliation:
State University of New York
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The Future of Phylogenetic Systematics
The Legacy of Willi Hennig
 , pp. 329 - 343
Publisher: Cambridge University Press
Print publication year: 2016

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References

Altenhoff, A.M., Gil, M., Gonnet, G.H. and Dessimoz, C. (2013). Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS One, 8, e53786.CrossRefGoogle ScholarPubMed
Altenhoff, A.M., Schneider, A., Gonnet, G.H. and Dessimoz, C. (2011). OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Research, 39, D289–D294.CrossRefGoogle ScholarPubMed
Andrade, S.C.S., Montenegro, H., Strand, M., et al. (2014). A transcriptomic approach to ribbon worm systematics (Nemertea): resolving the Pilidiophora problem. Molecular Biology and Evolution, 31, 3206–3215.CrossRefGoogle ScholarPubMed
Andrade, S.C.S., Novo, M., Kawauchi, G.Y., Worsaae, K., Pleijel, F., Giribet, G. and Rouse, G.W. (2015). Articulating the “archiannelids”: A phylogenomic approach to annelid relationships with emphasis on meiofaunal taxa. Molecular Biology and Evolution, 32, 2860–2875.CrossRefGoogle Scholar
Arcila, D., Pyron, R.A., Tyler, J.C., Ortí, G. and Betancur-R, R. (2015). An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Molecular Phylogenetics and Evolution, 82, 131–145.CrossRefGoogle ScholarPubMed
Boussau, B., Szollosi, G.J., Duret, L., et al. (2013). Genome-scale coestimation of species and gene trees. Genome Research, 23, 323–330.CrossRefGoogle ScholarPubMed
Cannon, J.T., Kocot, K.M., Waits, D.S., et al. (2014). Phylogenomic resolution of the hemichordate and echinoderm clade. Current Biology 24, 2827–2832.CrossRefGoogle ScholarPubMed
Clark, A.G., Eisen, M.B., Smith, D.R., et al. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203–218.Google ScholarPubMed
Clarke, J.A. and Boyd, C.A. (2015). Methods for the quantitative comparison of molecular estimates of clade age and the fossil record. Systematic Biology, 64, 25–41.CrossRefGoogle ScholarPubMed
Clouse, R.M. and Wheeler, W.C. (2014). Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates. Zootaxa, 3814, 177–201.CrossRefGoogle Scholar
Cooper, A., Lalueza-Fox, C., Anderson, S., et al. (2001). Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature, 409, 704–707.CrossRefGoogle ScholarPubMed
Dahdul, W.M., Lundberg, J.G., Midford, P.E., et al. (2010). The teleost anatomy ontology: Anatomical representation for the genomics age. Systematic Biology, 59, 369–383.CrossRefGoogle ScholarPubMed
Deans, A.R., Lewis, S.E., Huala, E., et al. (2015). Finding our way through phenotypes. PLoS Biology, 13, e1002033.CrossRefGoogle ScholarPubMed
Delsuc, F., Brinkmann, H., Chourrout, D. and Philippe, H. (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439, 965–968.CrossRefGoogle Scholar
Dikow, R.B. (2011). Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae). BMC Genomics, 12, 237.CrossRefGoogle ScholarPubMed
Donoghue, P.C. and Benton, M.J. (2007). Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends in Ecology and Evolution, 22, 424–431.CrossRefGoogle ScholarPubMed
Dunn, C.W., Hejnol, A., Matus, D.Q., et al. (2008). Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, 745–749.CrossRefGoogle ScholarPubMed
Dunn, C.W., Howison, M. and Zapata, F. (2013). Agalma: an automated phylogenomics workflow. BMC Bioinformatics, 14, 330.CrossRefGoogle ScholarPubMed
Ebersberger, I., Strauss, S. and von Haeseler, A. (2009). HaMStR: Profile hidden markov model based search for orthologs in ESTs. BMC Evolutionary Biology, 9, 157.CrossRefGoogle ScholarPubMed
Fernández, R., Hormiga, G. and Giribet, G. (2014a). Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers, Current Biology, 24, 1772–1777.CrossRefGoogle ScholarPubMed
Fernández, R., Laumer, C.E., Vahtera, V., et al. (2014b). Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Molecular Biology and Evolution, 31, 1500–1513.CrossRefGoogle ScholarPubMed
Francis, W.R., Christianson, L.M., Kiko, R., et al. (2013). A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genomics, 14, 167.CrossRefGoogle ScholarPubMed
Freedman, A.H., Gronau, I., Schweizer, R.M., et al. (2014). Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics, 10, e1004016.CrossRefGoogle ScholarPubMed
Frost, D.R., Grant, T., Faivovich, J., et al. (2006). The amphibian tree of life. Bulletin of the American Museum of Natural History, 297, 1–370.CrossRefGoogle Scholar
Garwood, R.J., Sharma, P.P., Dunlop, J.A. and Giribet, G. (2014). A new stem group Palaeozoic harvestman revealed through integration of phylogenetics and development. Current Biology, 24, 1–7.CrossRefGoogle Scholar
Giribet, G. (2015). Morphology should not be forgotten in the era of genomics – a phylogenetic perspective. Zoologischer Anzeiger, 256, 96–103.CrossRefGoogle Scholar
Giribet, G. and Edgecombe, G.D. (2013). Stable phylogenetic patterns in scutigeromorph centipedes (Myriapoda: Chilopoda: Scutigeromorpha): dating the diversification of an ancient lineage of terrestrial arthropods. Invertebrate Systematics, 27, 485–501.CrossRefGoogle Scholar
Giribet, G., McIntyre, E., Christian, E., et al. (2014). The first phylogenetic analysis of Palpigradi (Arachnida) – the most enigmatic arthropod order. Invertebrate Systematics, 28, 350–360.CrossRefGoogle Scholar
González, V.L., Andrade, S.C.S., Bieler, R., et al. (2015). A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proceedings of the Royal Society, B Biological Science, 282, 2014.2332.Google ScholarPubMed
Gravel, S., Zakharia, F., Moreno-Estrada, A., et al. (2013). Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genetics, 9, e1004023.CrossRefGoogle ScholarPubMed
Hejnol, A., Obst, M., Stamatakis, A., , M., , O., et al. (2009). Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society, B Biological Science, 276, 4261–4270.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
Hennig, W. (1950). Grundzüge einer Theorie der phylogenetischen Systematik. Berlin: Deutscher Zentralverlag.Google Scholar
Hennig, W. (1966). Phylogenetic Systematics. Urbana: University of Illinois Press.Google Scholar
Kemp, C. (2015). The endangered dead. Nature, 518, 292–294.CrossRefGoogle ScholarPubMed
Kocot, K.M., Cannon, J.T., Todt, C., et al. (2011). Phylogenomics reveals deep molluscan relationships. Nature, 447, 452–456.CrossRefGoogle Scholar
Kocot, K.M., Citarella, M.R., Moroz, L.L. and Halanych, K.M. (2013). PhyloTreePruner: A phylogenetic tree-based approach for selection of orthologous sequences for phylogenomics. Evolutionary Bioinformics, 9, 429–435.Google ScholarPubMed
Laumer, C.E., Hejnol, A. and Giribet, G. (2015). Nuclear genomic signals of the “microturbellarian” roots of platyhelminth evolutionary innovation. eLife 4, e05503.CrossRefGoogle ScholarPubMed
Lee, E.K., Cibrian-Jaramillo, A., Kolokotronis, S.-O., et al. (2011). A functional phylogenomic view of the seed plants. PLoS Genetics, 7, e1002411.CrossRefGoogle ScholarPubMed
Lemer, S., Kawauchi, G.Y., Andrade, S.C.S., et al. (2015). Re-evaluating the phylogeny of Sipuncula through transcriptomics. Molecular Phylogenetics and Evolution, 83, 174–183.CrossRefGoogle ScholarPubMed
Lemmon, A.R., Emme, S.A. and Lemmon, E.M. (2012). Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, 61, 727–744.CrossRefGoogle ScholarPubMed
Liu, L., Pearl, D.K., Brumfield, R.T. and Edwards, S.V. (2008). Estimating species trees using multiple-allele DNA sequence data. Evolution, 62, 2080–2091.CrossRefGoogle ScholarPubMed
Liu, L., Yu, L. and Edwards, S.V. (2010). A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology, 10, 302.CrossRefGoogle ScholarPubMed
Liu, L., Yu, L.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
Mamanova, L., Coffey, A.J., Scott, C.E., et al. (2010). Target-enrichment strategies for next-generation sequencing. Nature Methods, 7, 111–118.CrossRefGoogle ScholarPubMed
McCormack, J.E., Hird, S.M., Zellmer, A.J., Carstens, B.C. and Brumfield, R.T. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66, 526–538.CrossRefGoogle ScholarPubMed
Meyer, M., Kircher, M., Gansauge, M.T., et al. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222–226.CrossRefGoogle ScholarPubMed
Misof, B., Liu, S., Meusemann, K., et al. (2014). Phylogenomics resolves the timing and pattern of insect evolution. Science, 346, 763–767.CrossRefGoogle ScholarPubMed
Murienne, J., Edgecombe, G.D. and Giribet, G. (2010). Including secondary structure, fossils and molecular dating in the centipede tree of life. Molecular Phylogenetics and Evolution, 57, 301–313.CrossRefGoogle ScholarPubMed
Nakhleh, L. (2013). Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology and Evolution, 28, 719–728.CrossRefGoogle ScholarPubMed
Norell, M.A. (1992). Taxic origin and temporal diversity: the effect of phylogeny. In Extinction and phylogeny, ed. Novacek, M.J. and Wheeler, Q.D.. New York: Columbia University Press pp. 89–118.Google Scholar
Nosenko, T., Schreiber, F., Adamska, M., et al. (2013). Deep metazoan phylogeny: when different genes tell different stories. Molecular Phylogenetics and Evolution, 67, 223–233.CrossRefGoogle ScholarPubMed
Parham, J.F., Donoghue, P.C.J., Bell, C.J., et al. (2012). Best practices for justifying fossil calibrations. Systematic Biology, 61, 346–359.CrossRefGoogle ScholarPubMed
Peloso, P.L.V., Frost, D.R., Richards, S.J., et al. (2016). The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae). Cladistics, 32, 113–140.Google Scholar
Philippe, H., Snell, E.A., Bapteste, E., et al. (2004). Phylogenomics of eukaryotes: impact of missing data on large alignments. Molecular Biology and Evolution, 21, 1740–1752.CrossRefGoogle ScholarPubMed
Pyron, R.A. (2011). Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60, 466–481.CrossRefGoogle ScholarPubMed
Ramírez, M.J., Coddington, J.A., Maddison, W.P., et al. (2007). Linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology, 56, 283–294.CrossRefGoogle ScholarPubMed
Richter, S., Loesel, R., Purschke, G., et al. (2010). Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. Frontiers in Zoology, 7, 29.CrossRefGoogle ScholarPubMed
Riesgo, A., Andrade, S.C.S., Sharma, P.P., et al. (2012). Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Frontiers in Zoology, 9, 33.CrossRefGoogle ScholarPubMed
Riesgo, A., Farrar, N., Windsor, P.J., Giribet, G. and Leys, S.P. (2014). The analysis of eight transcriptomes from all Porifera classes reveals surprising genetic complexity in sponges. Molecular Biology and Evolution, 31, 1102–1120.CrossRefGoogle ScholarPubMed
Rokas, A., Krüger, D. and Carroll, S.B. (2005). Animal evolution and the molecular signature of radiations compressed in time. Science, 310, 1933–1938.CrossRefGoogle ScholarPubMed
Salichos, L. and Rokas, A. (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 497, 327–331.CrossRefGoogle ScholarPubMed
Seltmann, K.C., Yoder, M.J., Mikó, I., et al. (2012). A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research, 27, 67–88.Google Scholar
Sharma, P.P. and Giribet, G. (2014). A revised dated phylogeny of the arachnid order Opiliones. Frontiers in Genetics, 5, 255.CrossRefGoogle ScholarPubMed
Sharma, P.P., Kaluziak, S., Pérez-Porro, A.R., et al. (2014). Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal. Molecular Biology and Evolution, 31, 2963–2984.CrossRefGoogle ScholarPubMed
Smith, B.T., Harvey, M.G., Faircloth, B.C., Glenn, T.C. and Brumfield, R.T. (2014). Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Systematic Biology, 63, 83–95.CrossRefGoogle ScholarPubMed
Smith, S., Wilson, N.G., Goetz, F., et al. (2011). Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature, 480, 364–367.CrossRefGoogle ScholarPubMed
Smith, S.A. and Dunn, C.W. (2008). Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics, 24, 715–716.CrossRefGoogle ScholarPubMed
Spitzer, M., Lorkowski, S., Cullen, P., Sczyrba, A. and Fuellen, G. (2006). IsoSVM–distinguishing isoforms and paralogs on the protein level. BMC Bioinformatics, 7, 110.CrossRefGoogle ScholarPubMed
Steel, M. and Penny, D. (2004). Two further links between MP and ML under the poisson model. Applied Mathematics Letters, 17, 785–790.CrossRefGoogle Scholar
Tonini, J., Moore, A., Stern, D., Shcheglovitova, M. and Orti, G. (2015). Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLoS Currents Tree of Life, 7.Google Scholar
Tuffley, C. and Steel, M. (1997). Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bulletin of Mathematical Biology, 59, 581–607.CrossRefGoogle Scholar
Vogt, L., Grobe, P., Quast, B. and Bartolomaeus, T. (2012). Accommodating ontologies to biological reality – top- level categories of cumulative-constitutively organized material entities. PLoS One, 7, e30004.CrossRefGoogle ScholarPubMed
Weigert, A., Helm, C., Meyer, M., et al. (2014). Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution, 31, 1391–1401.CrossRefGoogle ScholarPubMed
Wheeler, W.C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology, 44, 321–331.CrossRefGoogle Scholar
Wheeler, W.C. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics, 12, 1–9.CrossRefGoogle Scholar
Wheeler, W.C. (2005). Alignment, dynamic homology, and optimization. In Parsimony, phylogeny, and genomics, ed. Albert, V.A.. Oxford: Oxford University Press, pp. 71–80.Google Scholar
Wheeler, W.C. (2012). Systematics: A Course of Lectures. Chichester: Wiley-Blackwell.CrossRefGoogle Scholar
Wood, H.M., Matzke, N.J., Gillespie, R.G. and Griswold, C.E. (2013). Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Systematic Biology, 62, 264–284.CrossRefGoogle ScholarPubMed
Xi, Z.X., Liu, L., Rest, J.S. and Davis, C.C. (2014). Coalescent versus concatenation methods and the placement of amborella as sister to water lilies. Systematic Biology, 63, 919–932.CrossRefGoogle ScholarPubMed
Zapata, F., Wilson, N.G., Howison, M., et al. (2014). Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proceedings of the Royal Society, B Biological Science, 281, 2014.1739.Google ScholarPubMed
Zhan, S., Zhang, W., Niitepõld, K., et al. (2014). The genetics of monarch butterfly migration and warning colouration. Nature, 514, 317–321.CrossRefGoogle ScholarPubMed
Ziegler, A., Faber, C., Mueller, S. and Bartolomaeus, T. (2008). Systematic comparison and reconstruction of sea urchin (Echinoidea) internal anatomy: a novel approach using magnetic resonance imaging. BMC Biology, 6, 33.CrossRefGoogle ScholarPubMed
Ziegler, A. and Menze, B.H. (2013). Accelerated acquisition, visualization, and analysis of zoo-anatomical data. In Computation for Humanity, eds Zander, J. and Mosterman, P.J.. Information Technology to Advance Society, Boca Raton: CRC Press, pp. 233–260.Google Scholar
Ziegler, A., Ogurreck, M., Steinke, T., et al. (2010). Opportunities and challenges for digital morphology. Biology Direct, 5, 45.CrossRefGoogle ScholarPubMed

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