Vascular Plants in ATBI Database Suitable for MaxEnt SDM Modeling

This afternoon I have established a few facts concerning plants in the Smokies.

The ATBI database (available to me on public server) has 432 vascular plant species for which there are 30 or more occurrence records.

This is out of 2001 entries – although the ATBI database reports “1643 species” for subkingdom Tracheobionta. So, 432/2001 is about 21% species that have 30 or more records.

The SEElab already has maps for 225 plant species. (SeeLab-Plants-Mod)

I combined the SEElab plant list (n=225) with the ATBI vascular plants list of more than 30 records (n=432), then filtered for unique records based on scientific name.

This yielded a total of 257 scientific names, suggesting there are 257 plant species from the ATBI database that have NOT been modeled by SEElab.

I have attached this data in the .csv file, “Vasc-Plant-Unique.” Perhaps this is the roughly 257 species Keith Langdon mentioned to me on the phone?

I don’t yet have access to the Nautilus supercomputer so initial runs would need to be done on a PC. I can make my documentation for running individual models on a PC by doing these first runs.

With the refined list of ~257 plant species, is there a preference for particular species or species assemblages?

If there is no preference for a particular plant species (out of those that have the requisite number of 30 or more records) I could just do some species modelling for Hemlock forests, as there is literature available for me to reference and it is interesting to look at potential community impacts from the HWA.

I’m having some trouble forwarding the .csv file to NPS staff (filtering, probably a security risk).

And, WordPress is not letting me upload any file other than a Microsoft .xls file. This is poor data management practice; I should archive a plain text or .csv file. So, my solution for the time being is that I believe I will paste the plain text here:

Saving the file on my local machine:

Documents/NPS-NICS-Practicum/ATBI-vasc-plant-021414/Vasc-Plant-Unique.txt

RecordNo,Kingdom,Class,Order,Family,Taxon,……,Data……………….,Type,Common Name 13413,,,,,Carex brunnescens sphaerostachya,,38,Specimens,Few flowered sedge 13432,,,,,Carex debilis variety,,75,Specimens, 13433,,,,,Carex digitalis,,43,Specimens,sedge 13449,,,,,Carex prasina,,30,Specimens,Drooping sedge 13456,,,,,Carex scabrata,,31,Specimens,Rough sedge 13460,,,,,Carex species,,291,Specimens, 13464,,,,,Carex swanii,,38,Specimens,Swan’s sedge 13471,,,,,Carex virescens,,31,Specimens,sedge 13513,,,,,Agrostis perennans,,42,Specimens,Upland bent 13522,,,,,Andropogon species,,71,Specimens, 13608,,,Ophioglossales,Ophioglossaceae,Botrychium biternatum,,58,Specimens,Southern grape fern 13610,,,,,Botrychium dissectum v. dissectum,,978,Specimens,”Cutleaf grapefern, dissectum” 13611,,,,,Botrychium dissectum v. obliquum,,155,Specimens,”Cutleaf grapefern, obliquum” 13617,,,,,Botrychium species,,38,Specimens, 13625,,,,,Asplenium rhizophyllum,,110,Specimens,Walking-fern spleenwort 13628,,,,,Asplenium trichomanes,,43,Specimens,Maiden-hair spleenwort 13630,,,,Blechnaceae,Woodwardia areolata,,126,Specimens,Netted chain fern 13633,,,,,Pteridium aquilinum,,1058,Specimens,Bracken fern 13634,,,,,Pteridium aquilinum subspecies,,78,Specimens, 13637,,,,,Pteridium aquilinum variety,,89,Specimens, 13638,,,,Dryopteridaceae,Athyrium asplenioides,,64,Specimens, 13639,,,,,Athyrium filix-femina angustum,,306,Specimens,Small northern lady fern 13640,,,,,Athyrium filix-femina asplenioides,,10129,Specimens,Southern lady fern 13648,,,,,Diplazium pycnocarpon,,66,Specimens,Glade fern 13652,,,,,Dryopteris cristata,,401,Specimens,”Crested wood fern,” 13656,,,,,Dryopteris species,,83,Specimens, 13658,,,,,Onoclea sensibilis,,43,Specimens,Sensitive fern 13665,,,,,Osmunda claytoniana,,42,Specimens,Interrupted fern 13666,,,,,Osmunda regalis,,66,Specimens,Royal fern 13669,,,,Polypodiaceae,Pleopeltis polypodioides,,63,Specimens,Resurrection fern 13671,,,,,Polypodium appalachianum,,3307,Specimens, 13768,,,,,Arisaema triphyllum triphyllum,,76,Specimens, 13772,,,Commelinales,Commelinaceae,Commelina communis,,39,Specimens,Common dayflower 13779,,,,,Tradescantia subaspera,,35,Specimens,Spiderwort 13788,,,,,Carex intumescens,,44,Specimens,Intumescent sedge 13794,,,,,Carex laxiflora v. laxiflora,,36,Specimens, 13802,,,,,Carex lurida,,30,Specimens,smaller hop sedge 13805,,,,,Carex nigromarginata,,42,Specimens,Black-margined sedge 13814,,,,,Arundinaria gigantea,,42,Specimens,Cane 13835,,,,,Spiranthes cernua,,38,Specimens,Nodding lady’s tresses 13839,,,,,Spiranthes species,,103,Specimens, 13843,,,,,Triphora trianthophora,,73,Specimens,Nodding Pogonia 13844,,,Liliales,Liliaceae,Trillium undulatum,,85,Specimens,Painted Trillium 13845,,,,,Trillium vaseyi,,35,Specimens,Vasey`s trillium 13863,,,,,Smilax species,,57,Specimens, 13876,,,,,Cypripedium acaule,,37,Specimens,Pink lady’s slipper 13881,,,,Typhaceae,Typha latifolia,,81,Specimens,wideleaf cattail 13887,,,,,Huperzia lucidula,,4103,Specimens,shining Club-moss 13908,,,,,Chaerophyllum tainturieri v. tainturieri,,10010,Specimens,wild chervil 13910,,,,,Cryptotaenia canadensis,,43,Specimens,Honewort 13924,,,,,Sanicula canadensis v. canadensis,,125,Specimens,Canada black snakeroot 13928,,,,,Sanicula smallii,,35,Specimens,small’s black snakeroot 13929,,,,,Sanicula species,,47,Specimens, 13931,,,,,Taenidia integerrima,,31,Specimens,Yellow pimpernel 13932,,,,,Thaspium barbinode,,30,Specimens,meadow-parsnip 13939,,,,,Cinna latifolia,,37,Specimens,woodreed 13944,,,,,Danthonia species,,44,Specimens, 13945,,,,,Danthonia spicata,,35,Specimens,Poverty grass 13950,,,,,Dichanthelium clandestinum,,41,Specimens,Deer-tongue witchgrass 13953,,,,,Dichanthelium dichotomum v. dichotomum,,36,Specimens, 13963,,,,,Dichanthelium species,,96,Specimens, 13976,,,,,Elymus riparius,,105,Specimens,wild rye 13993,,,,,Festuca subverticillata,,31,Specimens,Sheep`s-fescue 13995,,,,,Glyceria nubigena,,123,Specimens,Smoky Mountain Mannagrass 14003,,,,,Lolium arundinaceum,,76,Specimens, 14014,,,,,Muhlenbergia tenuiflora,,43,Specimens,Muhly 14026,,,,,Panicum species,,192,Specimens, 14042,,,,,Poa alsodes,,38,Specimens,wood bluegrass 14052,,,,,Poa species,,47,Specimens, 14055,,,,,Poaceae_genus species,,110,Specimens, 14058,,,,,Schizachyrium scoparium v. scoparium,,167,Specimens, 14087,,,,,Juncus effusus solutus,,37,Specimens,Soft rush 14093,,,,,Juncus tenuis,,103,Specimens,Larger path rush 14099,,,,,Luzula acuminata variety,,34,Specimens, 14110,,,,,Dioscorea quaternata,,221,Specimens,wild yam 14112,,,,,Dioscorea villosa,,47,Specimens, 14131,,,,,Allium tricoccum,,35,Specimens,”Ramps, wild leeks” 14135,,,,,Chamaelirium luteum,,50,Specimens,Fairy wand 14148,,,,,Erythronium umbilicatum umbilicatum,,154,Specimens, 14154,,,,,Lilium michauxii,,43,Specimens,Carolina lily 14157,,,,,Lilium superbum,,157,Specimens,Turk’s cap lily 14161,,,,,Maianthemum racemosum racemosum,,1292,Specimens, 14173,,,,,Polygonatum biflorum v. biflorum,,40,Specimens,Great Solomon’s seal 14175,,,,,Polygonatum biflorum variety,,126,Specimens, 14177,,,,,Polygonatum pubescens,,123,Specimens,hairy Solomon’s seal 14188,,,,,Trillium catesbaei,,78,Specimens,catesby’s trillium 14190,,,,,Trillium erectum,,122,Specimens,Wake robin 14191,,,,,Trillium grandiflorum,,34,Specimens,white trillium 14195,,,,,Trillium species,,80,Specimens, 14200,,,,,Galearis spectabilis,,58,Specimens,Showy orchis 14201,,,,,Goodyera pubescens,,292,Specimens,Downy rattlesnake-plantain 14202,,,,,Goodyera repens,,89,Specimens,Lesser rattlesnake-plantain 14285,,,Fagales,Betulaceae,Alnus serrulata,,111,Specimens,Common alder 14288,,,,,Thaspium trifoliatum variety,,45,Specimens, 14295,,,,,Aralia racemosa,,33,Specimens,wild spikenard 14297,,,,,Aralia spinosa,,53,Specimens,Devil’s walking stick 14298,,,,,Hedera helix,,402,Specimens,English Ivy 14299,,,,,Panax quinquefolius,,88,Specimens,Ginseng 14307,,,,,Hexastylis arifolia v. arifolia,,70,Specimens,Little brown jugs 14314,,,,,Ageratina altissima v. altissima,,119,Specimens,white snakeroot 14315,,,,,Ageratina altissima v. roanensis,,69,Specimens, 14321,,,,,Antennaria plantaginifolia,,46,Specimens,Plantain-leaved pussy toes 14335,,,,,Aster cordifolius,,44,Specimens, 14353,,,,,Aster species,,45,Specimens, 14359,,,,,Asteraceae_genus species,,137,Specimens,Aster family species 14366,,,,,Cacalia atriplicifolia,,33,Specimens, 14374,,,,,Chrysopsis mariana,,36,Specimens,Maryland golden aster 14387,,,,,Coreopsis major variety,,129,Specimens,wood Tickseed 14403,,,,,Erigeron pulchellus v. pulchellus,,33,Specimens,Robin’s-plantain 14406,,,,,Eupatorium album,,59,Specimens,white eupatorium 14409,,,,,Eupatorium fistulosum,,33,Specimens,Joe-Pye-weed 14411,,,,,Eupatorium maculatum,,32,Specimens,Joe-Pye-weed 14414,,,,,Eupatorium rotundifolium,,41,Specimens,Round-leaved snake-root 14418,,,,,Eupatorium species,,60,Specimens, 14424,,,,,Eurybia surculosa,,33,Specimens,Recurved aster 14426,,,,,Eutrochium purpureum v. pupureum,,42,Specimens, 14430,,,,,Gamochaeta purpureum,,33,Specimens,Purple Cudweed 14459,,,,,Iva annua,,153,Specimens,Iva 14469,,,,,Lactuca species,,32,Specimens, 14486,,,,,Polymnia laevigata,,2000,Specimens,Tennessee Leafcup 14492,,,,,Prenanthes species,,236,Specimens, 14493,,,,,Prenanthes trifoliolata,,36,Specimens,Lion’s foot 14506,,,,,Rugelia nudicaulis,,165,Specimens, 14508,,,,,Senecio anonymus,,43,Specimens,Yellow ragwort 14521,,,,,Solidago altissima v. altissima,,44,Specimens, 14523,,,,,Solidago arguta variety,,36,Specimens,Sharp-leaved goldenrod 14525,,,,,Solidago caesia,,42,Specimens,Curtis goldenrod 14546,,,,,Solidago species,,276,Specimens, 14547,,,,,Solidago speciosa v. rigidiuscula,,53,Specimens, 14552,,,,,Symphyotrichum concolor,,53,Specimens, 14570,,,,,Verbesina alternifolia,,57,Specimens,wingstem 14571,,,,,Verbesina occidentalis,,41,Specimens,wingstem 14582,,,,,Campanulastrum americanum,,33,Specimens, 14583,,,,,Lobelia cardinalis,,34,Specimens,Cardinal Flower 14584,,,,,Lobelia inflata,,68,Specimens,Indian tabacco 14595,,,Fagales,Fagaceae,Quercus montana,,408,Specimens,chestnut oak 14596,,,,,Quercus muehlenbergii,,31,Specimens,Yellow oak 14600,,,,,Quercus species,,72,Specimens, 14601,,,,,Quercus stellata,,39,Specimens,Post oak 14634,,,Geraniales,Balsaminaceae,Impatiens capensis,,71,Specimens,”Orange jewelweed, touch-me-not” 14636,,,,,Impatiens species,,44,Specimens, 14641,,,,,Geranium maculatum,,86,Specimens,wild geranium 14649,,,,,Oxalis stricta,,31,Specimens,Yellow wood-sorrel 14679,,,,,Silene virginica,,59,Specimens,Fire Pink 14682,,,,,Stellaria corei,,30,Specimens,Core’s chickweed 14700,,,Celastrales,Aquifoliaceae,Ilex ambigua,,36,Specimens, 14704,,,,,Ilex opaca v. opaca,,455,Specimens,American holly 14711,,,,,Euonymus americanus,,252,Specimens,American strawberry-bush 14718,,,,,Cornus amomum,,50,Specimens,Silky Dogwood 14721,,,,,Cornus species,,58,Specimens, 14724,,,,,Galax urceolata,,307,Specimens, 14726,,,,,Diervilla sessilifolia,,33,Specimens,Sessile-leaved bush-honey-suck 14731,,,,,Lonicera japonica,,45,Specimens,Japanese Honeysuckle 14744,,,,,Sambucus racemosa v. racemosa,,49,Specimens, 14755,,,,,Viburnum nudum v. cassinoides,,41,Specimens,wild raisin 14783,,,,,Lyonia ligustrina v. ligustrina,,73,Specimens,Maleberry 14788,,,,,Rhododendron calendulaceum,,335,Specimens,Flame Azalea 14793,,,,,Rhododendron minus,,1134,Specimens,small-leaved rhododendron 14798,,,,,Rhododendron species,,2610,Specimens, 14801,,,,,Vaccinium arboreum,,54,Specimens,Sparkleberry 14809,,,,,Vaccinium simulatum,,58,Specimens, 14810,,,,,Vaccinium species,,63,Specimens, 14817,,,,,Monotropa uniflora,,99,Specimens,Indian pipe 14848,,,,,Cercis canadensis v. canadensis,,242,Specimens,redbud 14851,,,,,Cladrastis kentukea,,202,Specimens,Yellowwood 14869,,,,,Desmodium species,,45,Specimens, 14874,,,,,Gleditsia triacanthos,,58,Specimens,Honeylocust 14883,,,,,Lespedeza cuneata,,160,Specimens,Cuneate bush-clover 14884,,,,,Lespedeza hirta,,37,Specimens,hairy Bush-clover 14888,,,,,Lespedeza species,,60,Specimens, 14906,,,Fagales,Betulaceae,Betula alleghaniensis v. alleghaniensis,,65,Specimens, 14909,,,,,Betula lutea,,32,Specimens,Yellow Birch 14910,,,,,Betula nigra,,44,Specimens,River Birch 14912,,,,,Betula species,,231,Specimens, 14918,,,,,Vitis species,,126,Specimens, 14937,,,,,Hydrangea radiata,,96,Specimens,white-leaf hydrangea 14940,,,,,Philadelphus hirsutus,,118,Specimens,small-flowered hairy mock-orange 14952,,,,,Amelanchier species,,116,Specimens, 14953,,,,,Amelanchier stolonifera,,36,Specimens,Running serviceberry 14958,,,,,Aruncus dioicus,,39,Specimens,Goats beard 14971,,,,,Crataegus species,,56,Specimens, 14980,,,,,Phacelia dubia v. dubia,,203,Specimens,small-flowered phacelia 14998,,,,Fagaceae,Castanea dentata,,868,Specimens,American chestnut 15006,,,,,Quercus imbricaria,,92,Specimens,shingle oak 15021,,,,,Carya ovata,,41,Specimens,Shagbark hickory 15023,,,,,Carya species,,184,Specimens, 15025,,,,,Juglans cinerea,,313,Specimens,butternut 15028,,,Lamiales,Boraginaceae,Cynoglossum virginianum v. virginianum,,45,Specimens,wild comfrey 15057,,,,,Lycopus virginicus,,31,Specimens,Virginia water-horehound 15079,,,,,Pycnanthemum species,,49,Specimens, 15081,,,,,Salvia lyrata,,31,Specimens,Lyre-leaved sage 15093,,,,,Stachys nuttallii,,61,Specimens, 15111,,,,,Calycanthus floridus v. glaucus,,67,Specimens, 15112,,,,,Calycanthus floridus variety,,195,Specimens,Sweetshrub 15114,,,,Lauraceae,Lindera.Plantae benzoin,,209,Specimens,Spicebush 15118,,,Magnoliales,Annonaceae,Asimina triloba,,82,Specimens,Paw-paw 15131,,,,Tiliaceae,Tilia americana v. americana,,118,Specimens,American basswood 15132,,,,,Tilia americana v. heterophylla,,789,Specimens,white Basswood 15133,,,,,Tilia americana variety,,178,Specimens, 15134,,,,,Tilia species,,94,Specimens,Basswood species 15143,,,,Onagraceae,Circaea alpina alpina,,47,Specimens, 15163,,,,Thymelaceae,Dirca palustris,,105,Specimens, 15174,,,,Papaveraceae,Sanguinaria canadensis,,91,Specimens,Bloodroot 15177,,,,,Plantago major,,86,Specimens,Plantain 15211,,,,,Polygonum sagittatum,,33,Specimens,tearthumb 15235,,,,,Caulophyllum thalictroides,,129,Specimens,Blue cohosh 15239,,,,,Podophyllum peltatum,,48,Specimens,May-apple 15246,,,,,Actaea podocarpa,,40,Specimens, 15248,,,,,Actaea racemosa v. racemosa,,117,Specimens, 15255,,,,,Cimicifuga racemosa,,31,Specimens, 15265,,,,,Hepatica nobilis v. acuta,,46,Specimens,Round-lobed hepatica 15275,,,,,Ranunculus hispidus,,34,Specimens,Carolina buttercup 15282,,,,,Thalictrum clavatum,,37,Specimens,Brook meadowrue 15290,,,,,Thalictrum species,,31,Specimens, 15309,,,Theales,Theaceae,Stewartia ovata,,32,Specimens,Mountain stewartia 15314,,,,,Morus rubra,,107,Specimens,red Mulberry 15319,,,,,Ulmus alata,,37,Specimens,winged elm 15320,,,,,Ulmus americana,,156,Specimens,American elm 15326,,,,,Pilea pumila,,35,Specimens,”Richweed, clearweed” 15336,,,,,Passiflora lutea,,44,Specimens,Yellow passion-flower 15338,,,,Violaceae,Hybanthus concolor,,62,Specimens,green violet 15342,,,,,Viola canadensis v. canadensis,,673,Specimens,Canadian violet 15344,,,,,Viola cucullata,,453,Specimens,Marsh blue violet 15346,,,,,Viola hirsutula,,238,Specimens,Southern wood violet 15348,,,,,Viola labradorica,,784,Specimens, 15349,,,,,Viola lanceolata,,200,Specimens,Lance-leaved violet 15352,,,,,Viola palmata,,85,Specimens,Three-lobed violet 15353,,,,,Viola pedata,,145,Specimens,Birds foot violet 15357,,,,,Geum canadense,,33,Specimens,white Avens 15373,,,,,Physocarpus opulifolius v. opulifolius,,30,Specimens,Ninebark 15382,,,,,Prunus americana,,42,Specimens,wild plum 15391,,,,,Prunus serotina v. serotina,,1257,Specimens,Black cherry 15413,,,,,Rubus flagellaris,,40,Specimens,Northern Dewberry 15419,,,,,Rubus phoenicolasius,,93,Specimens,wineberry 15420,,,,,Rubus species,,430,Specimens, 15430,,,,Saxifragaceae,Astilbe biternata,,38,Specimens,false goats beard 15433,,,,,Heuchera americana,,38,Specimens,Alumroot 15442,,,,,Mitella diphylla,,41,Specimens,Bishops cap 15443,,,,,Parnassia asarifolia,,108,Specimens,grass-of-Parnassus 15449,,,,,Tiarella cordifolia,,233,Specimens, 15459,,,,,Galium circaezans v. circaezans,,76,Specimens,wild Licorice 15465,,,,,Galium pilosum variety,,30,Specimens, 15466,,,,,Galium species,,75,Specimens, 15474,,,,,Houstonia purpurea v. purpurea,,65,Specimens,woodland bluets 15475,,,,,Houstonia purpurea variety,,97,Specimens, 15480,,,,,Mitchella repens,,359,Specimens,Partridgeberry 15493,,,,,Salix nigra,,52,Specimens,Black willow 15494,,,,,Salix sericea,,39,Specimens,Silky willow 15498,,,,,Phoradendron leucarpum,,55,Specimens, 15501,,,,,Acer negundo,,41,Specimens,Box-elder 15506,,,,,Acer rubrum v. rubrum,,92,Specimens,Trident maple 15508,,,,,Acer rubrum variety,,9526,Specimens, 15516,,,,,Rhus copallinum variety,,102,Specimens, 15517,,,,,Rhus glabra,,34,Specimens,Smooth Sumac 15521,,,,,Toxicodendron radicans radicans,,274,Specimens,Poison ivy 15529,,,,Simaroubaceae,Ailanthus altissima,,37,Specimens,tree-Of-Heaven

 

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About Tanner Jessel

I am a recent M.S. in Information Science graduate from the University of Tennessee School of Information Science. I was formerly a graduate research assistant funded by DataONE (Data Observation Network for Earth). Prior, I worked for four years as a content lead and biodiversity scientist with the U.S. Geological Survey's Biodiversity Informatics Program. Building on my work experience in biodiversity and environmental informatics, my work with DataONE focused on exploring the nature of scientific collaborations necessary for scientific inquiry. I also conducted research concerning user experience and usability, and assisted in development of member nodes with an emphasis on spatial data and infrastructure. I assisted with research designed to understand sociocultural issues within collaborative research communities. Through August 1, 2014, I was based at the Center for Information and Communication Studies at the University of Tennessee School of Information Science in Knoxville, Tennessee.

Posted on February 24, 2014, in Research, Scholarly Life and tagged , . Bookmark the permalink. Leave a comment.

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