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Example Datasets

For analysis of ecological interactions, SuchTree is distributed with a curated collection of several different co-phylogenetic relationships gathered from the literature. Additionally, a collection of simulated interactions with various properties, along with an annotated notebook for generating them, is also included. Interactions are registered in a JSON object (data/studies.json).

For convenience, I've given each dataset a short name (e.g., 'gopher-louse') suitable for labeling in plots.

If you are aware of any publications with this type of data, please let me know! A pull request would be the ideal way to make sure you get some credit for telling me about it, but an email or a message on social media would be perfectly fine.

If you use any of these datasets in your work, please cite the original authors as listed below. If you use SuchTree to analyze the data, please cite the SuchTree paper.

Host/Parasite

  • gopher-louse Hafner, M.S. & Nadler, S.A. 1988. Phylogenetic trees support the coevolution of parasites and their hosts. Nature 332: 258-259)
  • dove-louse Dale H. Clayton, Sarah E. Bush, Brad M. Goates, and Kevin P. Johnson. 2003. Host defense reinforces host–parasite cospeciation. PNAS.
  • sedge-smut Escudero, Marcial. 2015. Phylogenetic congruence of parasitic smut fungi (Anthracoidea, Anthracoideaceae) and their host plants (Carex, Cyperaceae): Cospeciation or host-shift speciation? American journal of botany.
  • fish-worm Maarten P. M. Vanhove, Antoine Pariselle, Maarten Van Steenberge, Joost A. M. Raeymaekers, Pascal I. Hablützel, Céline Gillardin, Bart Hellemans, Floris C. Breman, Stephan Koblmüller, Christian Sturmbauer, Jos Snoeks, Filip A. M. Volckaert & Tine Huyse. 2015. Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites, Scientific Reports.

Plant/Pollinator (visitor) interactions

These were originally collected by Enrico Rezende et al. :

Enrico L. Rezende, Jessica E. Lavabre, Paulo R. Guimarães, Pedro Jordano & Jordi Bascompte "Non-random coextinctions in phylogenetically structured mutualistic networks," Nature, 2007

  • arr1 Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation. Amer. J. Bot. 69:82-97.
  • arr2 Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation. Amer. J. Bot. 69:82-97.
  • arr3 Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation. Amer. J. Bot. 69:82-97.
  • bahe Barrett, S. C. H., and K. Helenurm. 1987. The Reproductive-Biology of Boreal Forest Herbs.1. Breeding Systems and Pollination. Canadian Journal of Botany 65:2036-2046.
  • cllo Clements, R. E., and F. L. Long. 1923, Experimental pollination. An outline of the ecology of flowers and insects. Washington, D.C., USA, Carnegie Institute of Washington.
  • dihi Dicks, LV, Corbet, SA and Pywell, RF 2002. Compartmentalization in plant–insect flower visitor webs. J. Anim. Ecol. 71: 32–43
  • dish Dicks, LV, Corbet, SA and Pywell, RF 2002. Compartmentalization in plant–insect flower visitor webs. J. Anim. Ecol. 71: 32–43
  • dupo Dupont YL, Hansen DM and Olesen JM 2003 Structure of a plant-flower-visitor network in the high-altitude sub-alpine desert of Tenerife, Canary Islands. Ecography 26:301-310
  • eol Elberling, H., and J. M. Olesen. 1999. The structure of a high latitude plant-flower visitor system: the dominance of flies. Ecography 22:314-323.
  • eolz Elberling & Olesen unpubl.
  • eski Eskildsen et al. unpubl.
  • herr Herrera, J. 1988 Pollination relatioships in southern spanish mediterranean shrublands. Journal of Ecology 76: 274-287.
  • hock Hocking, B. 1968. Insect-flower associations in the high Arctic with special reference to nectar. Oikos 19:359-388.
  • inpk Inouye, D. W., and G. H. Pyke. 1988. Pollination biology in the Snowy Mountains of Australia: comparisons with montane Colorado, USA. Australian Journal of Ecology 13:191-210.
  • kevn Kevan P. G. 1970. High Arctic insect-flower relations: The interrelationships of arthropods and flowers at Lake Hazen, Ellesmere Island, Northwest Territories, Canada. Ph.D. thesis, University of Alberta, Edmonton, 399 pp.
  • kt90 Kato, M., Kakutani, T., Inoue, T. and Itino, T. (1990). Insect-flower relationship in the primary beech forest of Ashu, Kyoto: An overview of the flowering phenology and the seasonal pattern of insect visits. Contrib. Biol. Lab., Kyoto, Univ., 27, 309-375.
  • med1 Medan, D., N. H. Montaldo, M. Devoto, A. Mantese, V. Vasellati, and N. H. Bartoloni. 2002. Plant-pollinator relationships at two altitudes in the Andes of Mendoza, Argentina. Arctic Antarctic and Alpine Research 34:233-241.
  • med2 Medan, D., N. H. Montaldo, M. Devoto, A. Mantese, V. Vasellati, and N. H. Bartoloni. 2002. Plant-pollinator relationships at two altitudes in the Andes of Mendoza, Argentina. Arctic Antarctic and Alpine Research 34:233-241.
  • memm Memmott J. 1999. The structure of a plant-pollinator food web. Ecology Letters 2:276-280.
  • moma Mosquin, T., and J. E. H. Martin. 1967. Observations on the pollination biology of plants on Melville Island, N.W.T., Canada. Canadian Field Naturalist 81:201-205.
  • mott Motten, A. F. 1982. Pollination Ecology of the Spring Wildflower Community in the Deciduous Forests of Piedmont North Carolina. Doctoral Dissertation thesis, Duke University, Duhram, North Carolina, USA; Motten, A. F. 1986. Pollination ecology of the spring wildflower community of a temperate deciduous forest. Ecological Monographs 56:21-42.
  • mull McMullen 1993
  • oflo Olesen unpubl.
  • ofst Olesen unpubl.
  • olau Olesen unpubl.
  • olle Ollerton, J., S. D. Johnson, L. Cranmer, and S. Kellie. 2003. The pollination ecology of an assemblage of grassland asclepiads in South Africa. Annals of Botany 92:807-834.
  • perc Percival, M. 1974. Floral ecology of coastal scrub in sotheast Jamaica. Biotropica, 6, 104-129.
  • prap Primack, R.B. 1983. Insect pollination in the New Zealand mountain flora. New Zealand J. Bot. 21, 317-333, AB.
  • prca Primack, R.B. 1983. Insect pollination in the New Zealand mountain flora. New Zealand J. Bot. 21, 317-333. Cass
  • prcg Primack, R.B. 1983. Insect pollination in the New Zealand mountain flora. New Zealand J. Bot. 21, 317-333. Craigieb.
  • ptnd Petanidou, T. 1991. Pollination ecology in a phryganic ecosystem. Unp. PhD. Thesis, Aristotelian University, Thessaloniki.
  • rabr Ramirez, N., and Y. Brito. 1992. Pollination Biology in a Palm Swamp Community in the Venezuelan Central Plains. Botanical Journal of the Linnean Society 110:277-302.
  • rmrz Ramirez, N. 1989. Biología de polinización en una comunidad arbustiva tropical de la alta Guyana Venezolana. Biotropica 21, 319-330.
  • schm Schemske, D. W., M. F. Willson, M. N. Melampy, L. J. Miller, L. Verner, K. M. Schemske, and L. B. Best. 1978. Flowering Ecology of Some Spring Woodland Herbs. Ecology 59:351-366.
  • smal Small, E. 1976. Insect pollinators of the Mer Bleue peat bog of Ottawa. Canadian Field Naturalist 90:22-28.
  • smra Smith-Ramírez C., P. Martinez, M. Nuñez, C. González and J. J. Armesto 2005 Diversity, flower visitation frequency and generalism of pollinators in temperate rain forests of Chiloé Island,Chile. Botanical Journal of the Linnean Society, 2005, 147, 399–416.

Frugivory interactions

  • bair Baird, J.W. 1980. The selection and use of fruit by birds in an eastern forest. Wilson Bulletin 92: 63-73.
  • beeh Beehler, B. 1983. Frugivory and polygamy in birds of paradise. Auk, 100: 1-12.
  • cacg Carlo et al. 2003. Avian fruit preferences across a Puerto Rican forested landscape: pattern consistency and implications for seed removal. Oecologia 134: 119-131
  • caci Carlo et al. 2003. Avian fruit preferences across a Puerto Rican forested landscape: pattern consistency and implications for seed removal. Oecologia 134: 119-131
  • caco Carlo et al. 2003. Avian fruit preferences across a Puerto Rican forested landscape: pattern consistency and implications for seed removal. Oecologia 134: 119-131
  • cafr Carlo et al. 2003. Avian fruit preferences across a Puerto Rican forested landscape: pattern consistency and implications for seed removal. Oecologia 134: 119-131
  • crom Crome, F.H.J. 1975. The ecology of fruit pigeons in tropical Northern Queensland. Australian Journal of Wildlife Research, 2: 155-185.
  • fros Frost, P.G.H. 1980. Fruit-frugivore interactions in a South African coastal dune forest. Pages 1179-1184 in: R. Noring (ed.). Acta XVII Congresus Internationalis Ornithologici, Deutsches Ornithologische Gessenshaft, Berlin.
  • gen1 Galetti, M., Pizo, M.A. 1996. Fruit eating birds in a forest fragment in southeastern Brazil. Ararajuba, Revista Brasileira de Ornitologia, 4: 71-79.
  • gen2 Galetti, M., Pizo, M.A. 1996. Fruit eating birds in a forest fragment in southeastern Brazil. Ararajuba, Revista Brasileira de Ornitologia, 4: 71-79.
  • hamm Hammann, A. & Curio, B. 1999. Interactions among frugivores and fleshy fruit trees in a Philippine submontane rainforest
  • hrat Jordano P. 1985. El ciclo anual de los paseriformes frugívoros en el matorral mediterráneo del sur de España: importancia de su invernada y variaciones interanuales. Ardeola, 32, 69-94.
  • kant Kantak, G.E. 1979. Observations on some fruit-eating birds in Mexico. Auk, 96: 183-186.
  • lamb Lambert F. 1989. Fig-eating by birds in a Malaysian lowland rain forest. J. Trop. Ecol., 5, 401-412.
  • lope Tutin, C.E.G., Ham, R.M., White, L.J.T., Harrison, M.J.S. 1997. The primate community of the Lopé Reserve, Gabon: diets, responses to fruit scarcity, and effects on biomass. American Journal of Primatology, 42: 1-24.
  • mack Mack, AL and Wright, DD. 1996. Notes on occurrence and feeding of birds at Crater Mountain Biological Research Station, Papua New Guinea. Emu 96: 89-101.
  • mont Wheelwright, N.T., Haber, W.A., Murray, K.G., Guindon, C. 1984. Tropical fruit-eating birds and their food plants: a survey of a Costa Rican lower montane forest. Biotropica, 16: 173-192.
  • ncor P. Jordano, unpubl.
  • nnog P. Jordano, unpubl.
  • sapf Noma, N. 1997. Annual fluctuations of sapfruits production and synchronization within and inter species in a warm temperate forest on Yakushima Island, Japan. Tropics, 6: 441-449.
  • snow Snow, B.K., Snow, D.W. 1971. The feeding ecology of tanagers and honeycreepers in Trinidad. Auk, 88: 291-322.
  • wes Silva, W.R., P. De Marco, E. Hasui, and V.S.M. Gomes, 2002. Patterns of fruit-frugivores interactions in two Atlantic Forest bird communities of South-eastern Brazil: implications for conservation. Pp. 423-435. In: D.J. Levey, W.R. Silva and M. Galetti (eds.) Seed dispersal and frugivory: ecology, evolution and conservation. Wallinford: CAB International.
  • wyth Snow B.K. & Snow D.W. 1988. Birds and berries, Calton, England.