R: Thirty datasets with inapplicable data

inapplicable.datasets {TreeSearch}

R Documentation

Thirty datasets with inapplicable data

Description

These are the datasets used to evaluate the behaviour of the inapplicable algorithm in Brazeau et al. (2019). The name of each item corresponds to the datasets listed below. Datasets are sorted into two subsets, each sorted alphabetically; the first subset comprise simpler datasets with faster processing times. inapplicable.datasets provide the data in the matrix format generated by read.nexus.data(); inapplicable.phyData are in phyDat format. inapplicable.trees lists for each dataset a sample of up to 50 trees obtained by tree search under each inapplicable treatment, named accordingly. inapplicable.citations is a named character vector specifying the source of each dataset.

Usage

inapplicable.datasets

inapplicable.phyData

inapplicable.trees

inapplicable.citations

Format

An object of class list of length 30.

An object of class list of length 31.

An object of class character of length 30.

Source

Subset one (faster processing):

Agnarsson2004: AGNARSSON, I. 2004. Morphological phylogeny of cobweb spiders and their relatives (Araneae, Araneoidea, Theridiidae). Zoological Journal of the Linnean Society, 141, 447–626.
Capa2011: CAPA, M., HUTCHINGS, P., AGUADO, M. T. and BOTT, N. J. 2011. Phylogeny of Sabellidae (Annelida) and relationships with other taxa inferred from morphology and multiple genes. Cladistics, 27, 449–469.
DeAssis2011: DE ASSIS, J. E. and CHRISTOFFERSEN, M. L. 2011. Phylogenetic relationships within Maldanidae (Capitellida, Annelida), based on morphological characters. Systematics and Biodiversity, 9, 233–245.
OLeary1999: O'LEARY, M. A. and GEISLER, J. H. 1999. The position of Cetacea within Mammalia: phylogenetic analysis of morphological data from extinct and extant taxa. Systematic Biology, 48, 455–490.
Rousset2004: ROUSSET, V., ROUSE, G. W., SIDDALL, M. E., TILLIER, A. and PLEIJEL, F. 2004. The phylogenetic position of Siboglinidae (Annelida) inferred from 18S rRNA, 28S rRNA and morphological data. Cladistics, 20, 518–533.
Sano2011: SANO, M. and AKIMOTO, S.-I. 2011. Morphological phylogeny of gall-forming aphids of the tribe Eriosomatini (Aphididae: Eriosomatinae). Systematic Entomology, 36, 607–627.
Sansom2010: SANSOM, R. S., FREEDMAN, K., GABBOTT, S. E., ALDRIDGE, R. J. and PURNELL, M. A. 2010. Taphonomy and affinity of an enigmatic Silurian vertebrate, Jamoytius kerwoodi White. Palaeontology, 53, 1393–1409.
Schulze2007: SCHULZE, A., CUTLER, E. B. and GIRIBET, G. 2007. Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology. Molecular Phylogenetics and Evolution, 42, 171–92.
Shultz2007: SHULTZ, J. W. 2007. A phylogenetic analysis of the arachnid orders based on morphological characters. Zoological Journal of the Linnean Society, 150, 221–265.
Wetterer2000: WETTERER, A. L., ROCKKMAN, M. V. and SIMMONS, N. B. 2000. Phylogeny of phyllostomid bats (Mammalia: Chiroptera): data from diverse morphological systems, sex chromosomes, and restriction sites. Bulletin of the American Museum of Natural History, 248, 1–200.
Wills2012: WILLS, M. A., GERBER, S., RUTA, M. and HUGHES, M. 2012. The disparity of priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data. Journal of Evolutionary Biology, 25, 2056–2076.

Subset two (longer processing times):

Aguado2009: AGUADO, M. T. and SAN MARTIN, G. 2009. Phylogeny of Syllidae (Polychaeta) based on morphological data. Zoologica Scripta, 38, 379–402.
Aria2015: ARIA, C., CARON, J. B. and GAINES, R. 2015. A large new leanchoiliid from the Burgess Shale and the influence of inapplicable states on stem arthropod phylogeny. Palaeontology, 58, 629–660.
Asher2005: ASHER, R. J. and HOFREITER, M. 2006. Tenrec phylogeny and the noninvasive extraction of nuclear DNA. Systematic biology, 55, 181–94.
Baker2009: BAKER, W. J., SAVOLAINEN, V., ASMUSSEN-LANGE, C. B., CHASE, M. W., DRANSFIELD, J., FOREST, F., HARLEY, M. M., UHL, N. W. and WILKINSON, M. 2009. Complete generic-level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches. Systematic Biology, 58, 240–256.
Bouchenak2010: BOUCHENAK-KHELLADI, Y., VERBOOM, G. A., SAVOLAINEN, V. and HODKINSON, T. R. 2010. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time. Botanical Journal of the Linnean Society, 162, 543–557.
Conrad2008: CONRAD, J. L. 2008. Phylogeny And Systematics Of Squamata (Reptilia) Based On Morphology. Bulletin of the American Museum of Natural History, 310, 1–182.
Dikow2009: DIKOW, T. 2009. A phylogenetic hypothesis for Asilidae based on a total evidence analysis of morphological and DNA sequence data (Insecta: Diptera: Brachycera: Asiloidea). Organisms Diversity and Evolution, 9, 165–188.
Eklund2004: EKLUND, H., DOYLE, J. A. and HERENDEEN, P. S. 2004. Morphological phylogenetic analysis of living and fossil Chloranthaceae. International Journal of Plant Sciences, 165, 107–151.
Geisler2001: GEISLER, J. H. 2001. New morphological evidence for the phylogeny of Artiodactyla, Cetacea, and Mesonychidae. American Museum Novitates, 3344, 53.
Giles2015: GILES, S., FRIEDMAN, M. and BRAZEAU, M. D. 2015. Osteichthyan-like cranial conditions in an Early Devonian stem gnathostome. Nature, 520, 82–85.
Griswold1999: GRISWOLD, C. E., CODDINGTON, J. A., PLATNICK, N. I. and FORSTER, R. R. 1999. Towards a phylogeny of entelegyne spiders (Araneae, Araneomorphae, Entelegynae). Journal of Arachnology, 27, 53–63.
Liljeblad2008: LILJEBLAD, J., RONQUIST, F., NIEVES-ALDREY, J. L., FONTAL-CAZALLA, F., ROS-FARRE, P., GAITROS, D. and PUJADE-VILLAR, J. 2008. A fully web-illustrated morphological phylogenetic study of relationships among oak gall wasps and their closest relatives (Hymenoptera: Cynipidae).
Loconte1991: LOCONTE, H. and STEVENSON, D. W. 1991. Cladistics of the Magnoliidae. Cladistics, 7, 267–296.
Longrich2010: LONGRICH, N. R., SANKEY, J. and TANKE, D. 2010. Texacephale langstoni, a new genus of pachycephalosaurid (Dinosauria: Ornithischia) from the upper Campanian Aguja Formation, southern Texas, USA. Cretaceous Research, 31, 274–284.
OMeara2014: O'MEARA, R. N. and THOMPSON, R. S. 2014. Were There Miocene Meridiolestidans? Assessing the phylogenetic placement of Necrolestes patagonensis and the presence of a 40 million year Meridiolestidan ghost lineage. Journal of Mammalian Evolution, 21, 271–284.
Rougier2012: ROUGIER, G. W., WIBLE, J. R., BECK, R. M. D. and APESTEGUIA, S. 2012. The Miocene mammal Necrolestes demonstrates the survival of a Mesozoic nontherian lineage into the late Cenozoic of South America. Proceedings of the National Academy of Sciences, 109, 20053–8.
Sharkey2011: SHARKEY, M. J., CARPENTER, J. M., VILHELMSEN, L., HERATY, J., LILJEBLAD, J., DOWLING, A. P. G., SCHULMEISTER, S., MURRAY, D., DEANS, A. R., RONQUIST, F., KROGMANN, L. and WHEELER, W. C. 2012. Phylogenetic relationships among superfamilies of Hymenoptera. Cladistics, 28, 80–112.
Sundue2010: SUNDUE, M. A., ISLAM, M. B. and RANKER, T. A. 2010. Systematics of Grammitid Ferns (Polypodiaceae): Using Morphology and Plastid Sequence Data to Resolve the Circumscriptions of Melpomene and the Polyphyletic Genera Lellingeria and Terpsichore. Systematic Botany, 35, 701–715.
Vinther2008: VINTHER, J., VAN ROY, P. and BRIGGS, D. E. G. 2008. Machaeridians are Palaeozoic armoured annelids. Nature, 451, 185–188.
Wilson2003: WILSON, G. D. F. and EDGECOMBE, G. D. 2003. The Triassic isopod Protamphisopus wianamattensis (Chilton) and comparison by extant taxa (Crustacea, Phreatoicidea). Journal of Paleontology, 77, 454–470.
Wortley2006: WORTLEY, A. H. and SCOTLAND, R. W. 2006. The effect of combining molecular and morphological data in published phylogenetic analyses. Systematic Biology, 55, 677–685.
Zanol2014: ZANOL, J., HALANYCH, K. M. and FAUCHALD, K. 2014. Reconciling taxonomy and phylogeny in the bristleworm family Eunicidae (Polychaete, Annelida). Zoologica Scripta, 43, 79–100.
Zhu2013: ZHU, M., YU, X., AHLBERG, P. E., CHOO, B., LU, J., QIAO, T., QU, Q., ZHAO, W., JIA, L., BLOM, H. and ZHU, Y. 2013. A Silurian placoderm with osteichthyan-like marginal jaw bones. Nature, 502, 188–193.

References

Brazeau MD, Guillerme T, Smith MR (2019). “An algorithm for morphological phylogenetic analysis with inapplicable data.” Systematic Biology, 68(4), 619–631. doi:10.1093/sysbio/syy083.

Examples

data("inapplicable.datasets", package = "TreeSearch")
names(inapplicable.datasets)

[Package TreeSearch version 1.5.1 Index]