Dataset.md

PlantPhylomoji Dataset

The plant phylomoji dataset features the following plant species and character information:

Name	Emoji	Emoji_text_code	Species	Family	n	gs
Apple	🍎	apple	Malus domestica	Rosaceae	17	0.75
Avocado	🥑	avocado	Persea americana	Lauraceae	12	0.92
Bamboo	🎋	tanabata_tree	Phyllostachys sp.	Poaceae	24	2.4
Banana	🍌	banana	Musa x paradisiaca	Musaceae	11	0.68
Carrot	🥕	carrot	Daucus carota	Apiaceae	9	0.47
Cherry	🍒	cherries	Prunus avium	Rosaceae	8	0.43
Chestnut	🌰	chestnut	Castanea dentata	Fagaceae	12	0.98
Chili Pepper	🌶️	hot_pepper	Capsicum annuum	Solanaceae	12	3.16
Chocolate	🍫	chocolate_bar	Theobroma cacao	Malvaceae	10	0.4
Clover	☘️	shamrock	Trifolium sp.	Fabaceae	14	0.73
Corn	🌽	corn	Zea mays	Poaceae	10	2.7
Cucumber	🥒	cucumber	Cucumis sativus	Cucurbitaceae	7	0.9
Daisy	🌼	blossom	Bellis perennis	Asteraceae	9	1.58
Eggplant	🍆	eggplant	Solanum melongena	Solanaceae	12	1
Fern	🌿	herb	Mickelia sp.	Dryopteridaceae	NA	NA
Grapes	🍇	grapes	Vitis vinifera	Vitaceae	19	0.4
Hibiscus	🌺	hibiscus	Hibiscus rosa-sinensis	Malvaceae	40	2.37
Japanese Cherry	🌸	cherry_blossom	Prunus x yedoensis	Rosaceae	16	0.55
Kiwi	🥝	kiwi_fruit	Actinidia deliciosa	Actinidiaceae	87	2.2
Lemon	🍋	lemon	Citrus × limon	Rutaceae	9	0.4
Maple	🍁	maple_leaf	Acer sp.	Sapindaceae	13	0.71
Melon	🍈	melon	Cucumis melo	Cucurbitaceae	12	1
Olive	🍸️	cocktail	Olea europaea	Oleaceae	23	1.95
Palm	🌴	palm_tree	Cocos nucifera	Arecaceae	16	2.8
Peach	🍑	peach	Prunus persica	Rosaceae	8	0.3
Peanuts	🥜	peanuts	Arachis hypogaea	Fabaceae	20	2.87
Pear	🍐	pear	Pyrus malus	Rosaceae	17	0.62
Pine	🌲	evergreen_tree	Pinus sp.	Pinaceae	NA	NA
Pineapple	🍍	pineapple	Ananas comosus	Bromeliaceae	25	0.55
Potato	🥔	potato	Solanum tuberosum	Solanaceae	24	0.89
Pumpkin	🎃	jack_o_lantern	Cucurbita maxima	Cucurbitaceae	20	0.46
Rice	🌾	ear_of_rice	Oryza sativa	Poaceae	12	0.5
Rose	🌹	rose	Rosa sp	Rosaceae	7	0.76
Saguaro	🌵	cactus	Carnegiea gigantea	Cactaceae	11	1.44
Strawberry	🍓	strawberry	Fragaria vesca	Rosaceae	7	0.25
Sunflower	🌻	sunflower	Helianthus annuus	Asteraceae	17	3.67
Sweet potato	🍠	sweet_potato	Ipomoea batatas	Convolvulaceae	45	2.3
Tangerine	🍊	tangerine	Citrus reticulata	Rutaceae	9	0.47
Tobacco	🚬	smoking	Nicotiana tabacum	Solanaceae	24	5.18
Tomato	🍅	tomato	Solanum lycopersicum	Solanaceae	12	1.06
Tulip	🌷	tulip	Tulipa sp.	Liliaceae	12	15.13
Water Clover	🍀	four_leaf_clover	Marsilea sp.	Marsileaceae	NA	NA
Watermelon	🍉	watermelon	Citrullus lanatus	Cucurbitaceae	11	0.5

Haploid chromosome number (n) and Genome Size (gs) from Escudero & Wendel 2020.

I'm looking to populate this table with more data. If you have data to contribute, please send me an email.

Download dataset table: plantphylomoji.csv

Strict tree

This is the original tree. The parenthetical phylogeny includes Mangoes and Lettuce.

( 🌲,( 🥑,(( 🌷, ( 🌴, ( 🍌, ( 🍍, ( 🌽, ( 🎋, 🌾 )))))),(( 🍇, ((( 🥜, ☘️), ((( 🌹, 🍓 ), (( 🍎, 🍐 ), ( 🍑, (🌸, 🍒) ))), ( 🌰, ( 🎃, ( 🍉, ( 🥒, 🍈)))))), (( 🌺, 🥦 ), (( 🍊, 🍋 ), ( 🍁, 🥭))))),( 🌵, ( 🥝, (( 🍠, ( 🌶️, (🍆, ( 🥔, 🍅)))), ( 🥕,( 🥬, ( 🌻, 🌼)))))))))

Complete tree

This tree includes emojis of plant byproducts, and other emojis with an unclear ID. 🍀= Marsilea, 🍫 = Theobroma and 🚬 = Nicotiana

(( 🌿, 🍀),( 🌲,( 🥑,(( 🌷, ( 🌴, ( 🍌, ( 🍍, ( 🌽, ( 🎋, 🌾 )))))),(( 🍇, ((( 🥜, ☘️), ((( 🌹, 🍓 ), (( 🍎, 🍐 ), ( 🍑, ( 🌸, 🍒) ))), ( 🌰, ( 🎃, ( 🍉, ( 🥒, 🍈)))))), ((🥦, ( 🌺, 🍫)), (( 🍊, 🍋 ), (🍁,🥭))))),( 🌵, ( 🥝,(( 🍸️, ( 🍠, ( 🚬,( 🌶️, ( 🍆, ( 🥔, 🍅)))))), ( 🥕,( 🥬, ( 🌻, 🌼))))))))))

Ultrametric tree

Topology and edge lengths based on Phylomaker (Jin & Qian 2019) See: phylomoji_phylomaker.R

Download ultrametric tree file:plantphylomoji_ultrametric.tree

• Mickelia sp and Musa x paradisiaca are missing from this set

Additional trees include:

Superasterids tree

( 🌵, ( 🥝, (( 🍠, ( 🌶️, ( 🍆, ( 🥔, 🍅)))), ( 🥕,( 🌻, 🌼)))))

Solanales tree

( 🍠, ( 🌶️, ( 🍆, ( 🥔, 🍅)))))

See all the additional trees at: plantphylomoji_vectors.txt

References:

Chase, M. W., Christenhusz, M. J. M., Fay, M. F., Byng, J. W., Judd, W. S., Soltis, D. E., ... & Stevens, P. F. (2016). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society, 181(1), 1-20.

Escudero, M., & Wendel, J. F. The grand sweep of chromosomal evolution in angiosperms. New Phytologist. doi: 10.1111/nph.16668.

Jin, Y., & Qian, H. (2019). V. PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography, 42(8), 1353-1359.

Kocyan, A., Zhang, L. B., Schaefer, H., & Renner, S. S. (2007). A multi-locus chloroplast phylogeny for the Cucurbitaceae and its implications for character evolution and classification. Molecular phylogenetics and evolution, 44(2), 553-577.

Qian, H., & Jin, Y. (2016). An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. Journal of Plant Ecology, 9(2), 233-239.

Särkinen, T., Bohs, L., Olmstead, R.G. et al. A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evol Biol 13, 214 (2013). https://doi.org/10.1186/1471-2148-13-214.

Soreng, R. J., Peterson, P. M., Romaschenko, K., Davidse, G., Teisher, J. K., Clark, L. G., ... & Zuloaga, F. O. (2017). A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications. Journal of Systematics and Evolution, 55(4), 259-290.

Xiang, Y., Huang, C. H., Hu, Y., Wen, J., Li, S., Yi, T., ... & Ma, H. (2017). Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication. Molecular Biology and Evolution, 34(2), 262-281.

Yu, Guangchuang, David Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 2017. “Ggtree: An R Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data.” Methods in Ecology and Evolution 8 (1): 28–36. doi:10.1111⁄2041-210X.12628.