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  • Print publication year: 2016
  • Online publication date: July 2016

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

Altenhoff, A.M., Gil, M., Gonnet, G.H. and Dessimoz, C. (2013). Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS One, 8, e53786.
Altenhoff, A.M., Schneider, A., Gonnet, G.H. and Dessimoz, C. (2011). OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Research, 39, D289D294.
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, 32063215.
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.
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, 131145.
Boussau, B., Szollosi, G.J., Duret, L., et al. (2013). Genome-scale coestimation of species and gene trees. Genome Research, 23, 323330.
Cannon, J.T., Kocot, K.M., Waits, D.S., et al. (2014). Phylogenomic resolution of the hemichordate and echinoderm clade. Current Biology 24, 28272832.
Clark, A.G., Eisen, M.B., Smith, D.R., et al. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203218.
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, 2541.
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, 177201.
Cooper, A., Lalueza-Fox, C., Anderson, S., et al. (2001). Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature, 409, 704707.
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, 369383.
Deans, A.R., Lewis, S.E., Huala, E., et al. (2015). Finding our way through phenotypes. PLoS Biology, 13, e1002033.
Delsuc, F., Brinkmann, H., Chourrout, D. and Philippe, H. (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439, 965968.
Dikow, R.B. (2011). Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae). BMC Genomics, 12, 237.
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, 424431.
Dunn, C.W., Hejnol, A., Matus, D.Q., et al. (2008). Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, 745749.
Dunn, C.W., Howison, M. and Zapata, F. (2013). Agalma: an automated phylogenomics workflow. BMC Bioinformatics, 14, 330.
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.
Fernández, R., Hormiga, G. and Giribet, G. (2014a). Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers, Current Biology, 24, 17721777.
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, 15001513.
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.
Freedman, A.H., Gronau, I., Schweizer, R.M., et al. (2014). Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics, 10, e1004016.
Frost, D.R., Grant, T., Faivovich, J., et al. (2006). The amphibian tree of life. Bulletin of the American Museum of Natural History, 297, 1370.
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, 17.
Giribet, G. (2015). Morphology should not be forgotten in the era of genomics – a phylogenetic perspective. Zoologischer Anzeiger, 256, 96–103.
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, 485501.
Giribet, G., McIntyre, E., Christian, E., et al. (2014). The first phylogenetic analysis of Palpigradi (Arachnida) – the most enigmatic arthropod order. Invertebrate Systematics, 28, 350360.
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.
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.
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, 42614270.
Heled, J. and Drummond, A.J. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570580.
Hennig, W. (1950). Grundzüge einer Theorie der phylogenetischen Systematik. Berlin: Deutscher Zentralverlag.
Hennig, W. (1966). Phylogenetic Systematics. Urbana: University of Illinois Press.
Kemp, C. (2015). The endangered dead. Nature, 518, 292294.
Kocot, K.M., Cannon, J.T., Todt, C., et al. (2011). Phylogenomics reveals deep molluscan relationships. Nature, 447, 452456.
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, 429435.
Laumer, C.E., Hejnol, A. and Giribet, G. (2015). Nuclear genomic signals of the “microturbellarian” roots of platyhelminth evolutionary innovation. eLife 4, e05503.
Lee, E.K., Cibrian-Jaramillo, A., Kolokotronis, S.-O., et al. (2011). A functional phylogenomic view of the seed plants. PLoS Genetics, 7, e1002411.
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, 174183.
Lemmon, A.R., Emme, S.A. and Lemmon, E.M. (2012). Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, 61, 727744.
Liu, L., Pearl, D.K., Brumfield, R.T. and Edwards, S.V. (2008). Estimating species trees using multiple-allele DNA sequence data. Evolution, 62, 20802091.
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.
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, 320328.
Mamanova, L., Coffey, A.J., Scott, C.E., et al. (2010). Target-enrichment strategies for next-generation sequencing. Nature Methods, 7, 111118.
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, 526538.
Meyer, M., Kircher, M., Gansauge, M.T., et al. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222226.
Misof, B., Liu, S., Meusemann, K., et al. (2014). Phylogenomics resolves the timing and pattern of insect evolution. Science, 346, 763767.
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, 301313.
Nakhleh, L. (2013). Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology and Evolution, 28, 719728.
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. 89118.
Nosenko, T., Schreiber, F., Adamska, M., et al. (2013). Deep metazoan phylogeny: when different genes tell different stories. Molecular Phylogenetics and Evolution, 67, 223233.
Parham, J.F., Donoghue, P.C.J., Bell, C.J., et al. (2012). Best practices for justifying fossil calibrations. Systematic Biology, 61, 346359.
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.
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, 17401752.
Pyron, R.A. (2011). Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60, 466481.
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, 283294.
Richter, S., Loesel, R., Purschke, G., et al. (2010). Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. Frontiers in Zoology, 7, 29.
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.
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, 11021120.
Rokas, A., Krüger, D. and Carroll, S.B. (2005). Animal evolution and the molecular signature of radiations compressed in time. Science, 310, 19331938.
Salichos, L. and Rokas, A. (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 497, 327331.
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, 6788.
Sharma, P.P. and Giribet, G. (2014). A revised dated phylogeny of the arachnid order Opiliones. Frontiers in Genetics, 5, 255.
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, 29632984.
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, 8395.
Smith, S., Wilson, N.G., Goetz, F., et al. (2011). Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature, 480, 364367.
Smith, S.A. and Dunn, C.W. (2008). Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics, 24, 715716.
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.
Steel, M. and Penny, D. (2004). Two further links between MP and ML under the poisson model. Applied Mathematics Letters, 17, 785790.
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.
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, 581607.
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.
Weigert, A., Helm, C., Meyer, M., et al. (2014). Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution, 31, 13911401.
Wheeler, W.C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology, 44, 321331.
Wheeler, W.C. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics, 12, 19.
Wheeler, W.C. (2005). Alignment, dynamic homology, and optimization. In Parsimony, phylogeny, and genomics, ed. Albert, V.A.. Oxford: Oxford University Press, pp. 7180.
Wheeler, W.C. (2012). Systematics: A Course of Lectures. Chichester: Wiley-Blackwell.
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, 264284.
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, 919932.
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.
Zhan, S., Zhang, W., Niitepõld, K., et al. (2014). The genetics of monarch butterfly migration and warning colouration. Nature, 514, 317321.
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.
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. 233260.
Ziegler, A., Ogurreck, M., Steinke, T., et al. (2010). Opportunities and challenges for digital morphology. Biology Direct, 5, 45.