Taxonomy: Review names with 3 parts

[dfalster]

Should these contain subsp?

e.g. Dodonaea viscosa cuneata should be Dodonaea viscosa subsp. cuneata

[SamCAndrew]

Yes I think they should it will make them more informative and consistent with APC names

[dfalster]

Revisiting this to see if it is still relevant. some of the original cases have been fixed with the above commit. But there are many more:

Of the names in the species list that are not currently recognised in TPL, currently there are 63 names with 2 spaces:

>  austraits$traits %>% left_join(austraits$taxonomy, by = "species_name") %>% filter(is.na(status) & species_name %>% stringr::str_count(" ") == 2) %>% pull(species_name) %>% unique() %>% paste(collapse=", ")

"Hibbertia sp. 1, Isopogon sp. A, Avena sativa cf, Eucalyptus sp. Kalbarri, Eucalyptus sp. Undulans, Wurmbea spPaynes Find, Unknown No. 1, Derris sp. Daintree, Desmodium rhytidophyllumsubsp. acutifoliolum, Phebalium sp. nov, Planchonella Mt Lewis, Vittadinia triloba/cuneata complex, Pultenaea sp. Maryborough, Craspedia sp. B, Clematis glycinoidesvar. glycinoides, Clematis glycinoidesvar. submutica, Trichosanthes sp. Kakadu, Desmodium Melville Is., Flemingia Rum Jungle, Tephrosia Hayes Ck, Tephrosia Katherine Gorge, Zornia Darwin Lawns, Stenocarpus top end', Astroloma sp. unknown, Caladenia sp. unknown, Conostylis sp. unknown, Stylidium sp. unknown, Thelymitra sp. unknown, Thomasia heterophylla ms, Cenchrus species A, Cyperus species A, Leucopogon species B, Westringia species A, Celmisia pugioniformis b.h., Poa nothamensis (Nelse), Actinotus sp. Walpole, Hydrocotyle hamelinensis ms, Andersonia sp. Frankland, Andersonia amabile ms, Andersonia virolens ms, Astroloma sp. Nannup, Leucopogon sp. Darradup, Astartea sp. Gingalup, Chamelaucium erythrochlorum ms, Chamelaucium floriferum ms, Chamelaucium roycei ms, Nemcia cordata ms, Tripterococcus brachylobus ms, Tripterococcus paniculatus ms, Caustis sp. Boyanup, Schoenus sp. Jindong, Paracaleana lineraifolia ms, Pterostylis brevisepala ms, Leptocarpus elegans ms, Lepyrodia porterae ms, Meeboldina tephrina ms, Meeboldina crebriculmis ms, Meeboldina kraussii ms, Meeboldina roycei ms, Meeboldina sp. White, Meeboldina thysanantha ms, Sporadanthus rivularis ms"

And with more than 2 spaces there are more than 162 names

> austraits$traits %>% left_join(austraits$taxonomy, by = "species_name") %>% filter(is.na(status) & species_name %>% stringr::str_count(" ") > 2) %>% pull(species_name) %>% unique() %>% paste(collapse=", ")

"Acacia sp. Graveside Gorge (V.J.Levitzke 806), Arthropodium sp. South-east Highlands (N.G.Walsh 811), Brachychiton sp. Ormeau (L.H.Bird AQ435851), Isopogon sp. Watheroo (D.Foreman 477), Juncus sp. MacDonnell Ranges (B.G.Thomson 3412), Microseris sp. Snowfields (D.E.Albrecht 123), Pelargonium sp. Striatellum (G.W.Carr 10345), Synaphea spinulosa subsp. borealis, Tephrosia sp. Northern (K.F.Kenneally 11950), Panicum distachyum var. trichophorum, Grevillea synapheae subsp. a, Syzygium eucalyptoides subsp. eucalyptoides, Austrodanthonia sp2 var. a, Austrodanthonia sp2 var. b, Austrodanthonia sp3 var. b, Oplismenus sp1 cf (O. aemulus), Eucalyptus sp. Flinders Ranges, Psychotria sp. Utchee Creek, Haplostichanthus sp. Coop. Ck, Dillwynia sericea subsp. b, Jasminum didymum subsp. lineare, Rubus molluccanus var. trilobus, Capparis sp. (Forty Mile Scrub BH 3883RFK), Sida sp. (Small Flower BG 5657), Breynia sp. (Black Mountain BH 25658RFK), Taraxacum sp. aff. brakelii, Acacia nilotica subsp. indica, Acacia pennata subsp. kerrii, Leucopogon sp. (Burrum Heads A.R.Bean 7802), Thelymitra sp. aff. pauciflora, Gomphrena diffusa subsp. diffusa, Cochlospermum sp. Arnhem Land, Barringtonia acutangula subsp. acutangula, Muehlenbeckia Mt Brockman (L.A. Craven 2357), Dendrolobium 'Green Ant Ck', Indigofera trita subsp. trita, Zornia muelleriana subsp. mulleriana, Croton sp. aff. dockr illii Airy Shaw, Grevillea goodii subsp. goodii, Grevillea goodii subsp. pluricaulis, Chamaecrista sp. Cassia harneyi, Leptospermum madidum subsp. sativum, Orchid sp. unknown 1, Orchid sp. unknown 2, Orchid sp. unknown 3, Orchid sp. unknown 4, Acaena sp. A sensu Harden (1990), Acianthus sp. A sensu Harden (1993), Agrostis sp. B sensu Jacobs & Hastings (1993), Alternanthera sp. A sensu Harden (1990), Arabidella sp. A sensu Harden (1990), Arthropodium sp. A sensu Harden (1993), Arthropodium sp. B sensu Harden (1993), Astrotricha sp. B sensu Harden (1992), Atriplex sp. B sensu Jacobs (1990), Brachyscome sp.1 sensu PS Short 1999, Caladenia sp. A sensu Harden (1993), Caladenia sp. B sensu Harden (1993), Caladenia sp. C sensu Harden (1993), Calandrinia sp. A sensu Harden (1990), Chamaesyce sp. A sensu James & Harden (1990), Choretrum sp. A sensu Harden (1992), Corybas sp. A sensu Harden (1993), Cryptandra sp. A sensu Harden (1990), Daphnandra sp. 'Illawarra' (Schodde 3475), Dichondra sp. A sensu Harden (1992), Dichopogon sp. A sensu Harden (1993), Frankenia sp. A sensu Harden (1990), Gnaphalium sp. E sensu Everett (1992), Hibbertia sp. B sensu Harden (1990), Kunzea sp. 'Braidwood' (Powell 371), Kunzea sp. 'Middle Brother Mtn' (Wilson 505), Kunzea sp. 'Mt Cookem' (Benson 4470), Kunzea sp. 'Mt Kaputar' (Jackson 2246), Kunzea sp. 'Wadbilliga' (Rodd 6168), Leionema sp. 'Hungryway Creek' (Lemberg, NSW69237), Lepidium sp. B sensu Harden (1990), Lepyrodia sp. A sensu Harden (1993), Melichrus hirsutus J.B.Williams ms., Melichrus sp. Gibberagee (A.S.Benwell & J.B.Williams 97239), Notelaea sp. A sensu Harden (1992), Prasophyllum sp. A sensu Harden (1993), Pratia sp. A sensu Harden (1992), Prostanthera sp. C sensu Conn (1992), Prostanthera sp. E sensu Conn (1992), Pterostylis sp. 'Botany Bay; (Bishop J2211-13), Pterostylis sp. B sensu Harden (1993), Pterostylis sp. C sensu Harden (1993), Pterostylis sp. D sensu Harden (1993), Pterostylis sp. E sensu Harden (1993), Pterostylis sp. F sensu Harden (1993), Pultenaea sp. 'Liverpool Range' (Johnson 963), Pultenaea sp. 'New England' (Coveny 16631), Pultenaea sp. 'Olinda' (Coveny 6616), Quassia sp. 'Moonee Creek' (King s.n., Nov 1949), Quassia sp. 'Mt. Nardi' (Floyd 1198), Senna form taxon 'artemisioides', Senna form taxon 'pruinosa', Sida sp. B sensu Harden (1990), Sida sp. C sensu Harden (1990), Sisyrinchium sp. A sensu James & Brown (1993), Stellaria sp. B sensu Doust (1990), Styphelia sp. A sensu Harden (1992), Styphelia sp. B sensu Harden (1992), Suaeda sp. A sensu Harden (1990), Teucrium sp. A sensu Conn (1992), Teucrium sp. D sensu Conn (1992), Eucalyptus umbra subsp. umbra, Melastoma malabathricum subsp. malabathricum, Tetratheca sp. Freycinet Pen. (A.C.Rozefelds 323), Eucryphia milliganii subsp. milliganii, Eucryphia milliganii subsp. pubsecens, Montia fontana subsp. fontana, Nematolepis squamea subsp. squamea, Boronia citriodora subsp. paulwilsonii, Hibbertia empetrifolia subsp. empetrifolia, Boronia pilosa subsp. pilosa, Nematolepis squamea subsp. retusa, Boronia pilosa subsp. tasmanensis, Zieria arborescens subsp. arborescens, Convolvulus angustissimus subsp. angustissimus, Sarcocornia quinqueflora subsp. quinqueflora, Sarcocornia quinqueflora subsp. tasmanica, Tetratheca sp. Flinders Island, Leionema bilobum subsp. truncatum, Australina pusilla subsp. pusila, Viola hederacea subsp. hederacea, Zieria veronicea subsp. veronicea, Australina pusilla subsp. muelleri, Tetratheca pilosa subsp. pilosa, Tetratheca pilosa subsp. latifolia, Melicytus sp. (Hymenanthera auct.), Brachysome spatulatha subsp. spathulata, Brachyscome spathulata (mt Nelse), Brachysome nivalis (mt Nelse), Celmisia snowpatch (mt Nelse), Celmisia snowpatch (mt Nelse)?, Danthonia alpicola (nelse. rock lover) Not flattened, Empodisma minus (green parts), Juncus articulatus (leaf and sheath), Juncus articulatus (leaf, sheath and stem), Ozothamnus hookeri (whole twigg reduced scale like leaves), Pea species 1 (Flowering no fruit), Poa phillipsiana (curled. Basalt hill. Shute.)?, Poa sp1. (Tightly inrolled, not bluegreen, not red sheath, mod spikey), Poa sp2 (red sheaths not rolled plants), Senecio linearifolius (subalp basalt), Stackhousia pulvinaris (yellow in bogs), Leucopogon sp. Whicher range, Sphenotoma sp. Stirling range, Anthotium sp. Peaceful Bay, Astartea sp. Big bracteoles, Astartea sp. Scott River, Hypocalymma sp. Scott River, Aotus sp. Scott River, Grevillea sp. Scott River, Thomasia sp. Big Brook, Patersonia sp. Swamp form, Calochilus sp. Southwest swamps, Pterostylis sp. Slender smail orchid, Thelymitra sp. Plain sun orchid, Thelymitra sp. Slender sun orchid"

The question is what to do from here. In the above list I actually can;'t see many species names of the form we were originally concerned about, e.g. Dodonaea viscosa cuneate

[rachaelgallagher]

Thanks Daniel. I am not sure its appropriate to simply add subsp. and var. to names even if the look like that is what they should have in them. The majority of name sin the latter list above are manuscript names (names that are not yet recognised). There is nothing we can do to reconcile these programatically as we would need to make a check on their progress in being written-up. One option is to indicate that these are not stable names taxonomically and place them in the excluded output?

[dfalster]

Thanks @rachaelgallagher Yes, uncertainty around names is indicated already via lack of suitable alignment with TPL or APC lists, AND/OR the TPLI_ID having status "unresolved".

Based on your common I'll shelve the idea of adding in subsp. or var. programmatically.

Before seeing your comment, I implemented the above commit, which routinely removes suffix " ms" from names. Nearly all of those came from single study (Wheeler_2002). IMO the uncertainty implied here would be similar for many papers. So the change means

e.g. Andersonia amabile ms becomes Andersonia amabile

Many of these have valid taxonomic alignments in the TPL. And the suffix " ms" is still present in the original name column.

Are you happy to keep that change?

The second change above standardises made some changes to master taxonomy list which should have already happened but were some how missed.

Rerunnning the code from above, the two changes above reduce the number of names with 2 or more spaces

Now only 43 names with 2 spaces:

>   austraits$traits %>% left_join(austraits$taxonomy, by = "species_name") %>% filter(is.na(status) & species_name %>% stringr::str_count(" ") == 2) %>% pull(species_name) %>% unique() %>% paste(collapse=", ")

"Hibbertia sp. 1, Isopogon sp. A, Avena sativa cf, Eucalyptus sp. Kalbarri, Eucalyptus sp. Undulans, Wurmbea spPaynes Find, Unknown No. 1, Derris sp. Daintree, Desmodium rhytidophyllumsubsp. acutifoliolum, Phebalium sp. nov, Planchonella Mt Lewis, Vittadinia triloba/cuneata complex, Pultenaea sp. Maryborough, Craspedia sp. B, Clematis glycinoidesvar. glycinoides, Clematis glycinoidesvar. submutica, Trichosanthes sp. Kakadu, Desmodium Melville Is., Flemingia Rum Jungle, Tephrosia Hayes Ck, Tephrosia Katherine Gorge, Zornia Darwin Lawns, Stenocarpus top end', Astroloma sp. unknown, Caladenia sp. unknown, Conostylis sp. unknown, Stylidium sp. unknown, Thelymitra sp. unknown, Cenchrus species A, Cyperus species A, Leucopogon species B, Melichrus hirsutus J.B.Williams., Westringia species A, Celmisia pugioniformis b.h., Poa nothamensis (Nelse), Actinotus sp. Walpole, Andersonia sp. Frankland, Astroloma sp. Nannup, Leucopogon sp. Darradup, Astartea sp. Gingalup, Caustis sp. Boyanup, Schoenus sp. Jindong, Meeboldina sp. White"

And 126 with more than 2 spaces:

>   austraits$traits %>% left_join(austraits$taxonomy, by = "species_name") %>% filter(is.na(status) & species_name %>% stringr::str_count(" ") > 2) %>% pull(species_name) %>% unique() %>% paste(collapse=", ")

[1] "Acacia sp. Graveside Gorge (V.J.Levitzke 806), Arthropodium sp. South-east Highlands (N.G.Walsh 811), Brachychiton sp. Ormeau (L.H.Bird AQ435851), Isopogon sp. Watheroo (D.Foreman 477), Juncus sp. MacDonnell Ranges (B.G.Thomson 3412), Microseris sp. Snowfields (D.E.Albrecht 123), Pelargonium sp. Striatellum (G.W.Carr 10345), Synaphea spinulosa subsp. borealis, Tephrosia sp. Northern (K.F.Kenneally 11950), Panicum distachyum var. trichophorum, Austrodanthonia sp2 var. a, Austrodanthonia sp2 var. b, Austrodanthonia sp3 var. b, Oplismenus sp1 cf (O. aemulus), Eucalyptus sp. Flinders Ranges, Psychotria sp. Utchee Creek, Haplostichanthus sp. Coop. Ck, Rubus molluccanus var. trilobus, Capparis sp. (Forty Mile Scrub BH 3883RFK), Sida sp. (Small Flower BG 5657), Breynia sp. (Black Mountain BH 25658RFK), Taraxacum sp. aff. brakelii, Leucopogon sp. (Burrum Heads A.R.Bean 7802), Thelymitra sp. aff. pauciflora, Cochlospermum sp. Arnhem Land, Muehlenbeckia Mt Brockman (L.A. Craven 2357), Dendrolobium 'Green Ant Ck', Croton sp. aff. dockr illii Airy Shaw, Chamaecrista sp. Cassia harneyi, Orchid sp. unknown 1, Orchid sp. unknown 2, Orchid sp. unknown 3, Orchid sp. unknown 4, Acaena sp. A sensu Harden (1990), Acianthus sp. A sensu Harden (1993), Agrostis sp. B sensu Jacobs & Hastings (1993), Alternanthera sp. A sensu Harden (1990), Arabidella sp. A sensu Harden (1990), Arthropodium sp. A sensu Harden (1993), Arthropodium sp. B sensu Harden (1993), Astrotricha sp. B sensu Harden (1992), Atriplex sp. B sensu Jacobs (1990), Brachyscome sp.1 sensu PS Short 1999, Caladenia sp. A sensu Harden (1993), Caladenia sp. B sensu Harden (1993), Caladenia sp. C sensu Harden (1993), Calandrinia sp. A sensu Harden (1990), Chamaesyce sp. A sensu James & Harden (1990), Choretrum sp. A sensu Harden (1992), Corybas sp. A sensu Harden (1993), Cryptandra sp. A sensu Harden (1990), Daphnandra sp. 'Illawarra' (Schodde 3475), Dichondra sp. A sensu Harden (1992), Dichopogon sp. A sensu Harden (1993), Frankenia sp. A sensu Harden (1990), Gnaphalium sp. E sensu Everett (1992), Hibbertia sp. B sensu Harden (1990), Kunzea sp. 'Braidwood' (Powell 371), Kunzea sp. 'Middle Brother Mtn' (Wilson 505), Kunzea sp. 'Mt Cookem' (Benson 4470), Kunzea sp. 'Mt Kaputar' (Jackson 2246), Kunzea sp. 'Wadbilliga' (Rodd 6168), Leionema sp. 'Hungryway Creek' (Lemberg, NSW69237), Lepidium sp. B sensu Harden (1990), Lepyrodia sp. A sensu Harden (1993), Melichrus sp. Gibberagee (A.S.Benwell & J.B.Williams 97239), Notelaea sp. A sensu Harden (1992), Prasophyllum sp. A sensu Harden (1993), Pratia sp. A sensu Harden (1992), Prostanthera sp. C sensu Conn (1992), Prostanthera sp. E sensu Conn (1992), Pterostylis sp. 'Botany Bay; (Bishop J2211-13), Pterostylis sp. B sensu Harden (1993), Pterostylis sp. C sensu Harden (1993), Pterostylis sp. D sensu Harden (1993), Pterostylis sp. E sensu Harden (1993), Pterostylis sp. F sensu Harden (1993), Pultenaea sp. 'Liverpool Range' (Johnson 963), Pultenaea sp. 'New England' (Coveny 16631), Pultenaea sp. 'Olinda' (Coveny 6616), Quassia sp. 'Moonee Creek' (King s.n., Nov 1949), Quassia sp. 'Mt. Nardi' (Floyd 1198), Senna form taxon 'artemisioides', Senna form taxon 'pruinosa', Sida sp. B sensu Harden (1990), Sida sp. C sensu Harden (1990), Sisyrinchium sp. A sensu James & Brown (1993), Stellaria sp. B sensu Doust (1990), Styphelia sp. A sensu Harden (1992), Styphelia sp. B sensu Harden (1992), Suaeda sp. A sensu Harden (1990), Teucrium sp. A sensu Conn (1992), Teucrium sp. D sensu Conn (1992), Tetratheca sp. Freycinet Pen. (A.C.Rozefelds 323), Tetratheca sp. Flinders Island, Melicytus sp. (Hymenanthera auct.), Brachysome spatulatha subsp. spathulata, Brachyscome spathulata (mt Nelse), Brachysome nivalis (mt Nelse), Celmisia snowpatch (mt Nelse), Celmisia snowpatch (mt Nelse)?, Danthonia alpicola (nelse. rock lover) Not flattened, Empodisma minus (green parts), Juncus articulatus (leaf and sheath), Juncus articulatus (leaf, sheath and stem), Ozothamnus hookeri (whole twigg reduced scale like leaves), Pea species 1 (Flowering no fruit), Poa phillipsiana (curled. Basalt hill. Shute.)?, Poa sp1. (Tightly inrolled, not bluegreen, not red sheath, mod spikey), Poa sp2 (red sheaths not rolled plants), Senecio linearifolius (subalp basalt), Stackhousia pulvinaris (yellow in bogs), Leucopogon sp. Whicher range, Sphenotoma sp. Stirling range, Anthotium sp. Peaceful Bay, Astartea sp. Big bracteoles, Astartea sp. Scott River, Hypocalymma sp. Scott River, Aotus sp. Scott River, Grevillea sp. Scott River, Thomasia sp. Big Brook, Patersonia sp. Swamp form, Calochilus sp. Southwest swamps, Pterostylis sp. Slender smail orchid, Thelymitra sp. Plain sun orchid, Thelymitra sp. Slender sun orchid"

[dfalster]

I'm happy with this now so will close. But feel free to sing out @rachaelgallagher @SamCAndrew if you think more needs to be done