Manually check "new" and vulnerable species

[pieterprovoost]

Manually check "new" and vulnerable species, see list in pdf report.

[SSuominen1]

Neoparamoeba aestuarina - micro-organism (not in qc report?), I guess fine? Craterium leucocephalum - slime-mold, or beetle (vsearch), remove I think. Thalassodrilides gurwitschi - ok, caribbean species Bhawania goodei - ok Polydora webster - ok Timarete caribous - ok Siphonosoma cumanense - ok Rhopalosiphum padi - bird cherry oat aphid, major pest in cereal crops, possible, but not sure, and not our target so remove? Macrosteles quadrilineatus - leafhopper found in US, also a pest. Let's focus on marine species?, so remove Elasmopus nkjaf - 100% similarity, but only 2 references, japanese. Maybe a closely related local species that is not in the reference databases. new species described in 2019. will need expert opinion, so remove? Portunus sanguinolentus - west pacific and indian ocean blood-spotted swimming crab, however, good sequence backing. Portunus_sp._USNM_IZ_1450064 is the only 100% match, from a barcoding project in Florida. Could be that the locals would know what to name it, but I guess based on this info the name is wrong. Barcoding article: https://academic.oup.com/icesjms/article/78/9/3397/6277123

[SSuominen1]

Cladosporium herbarum - common worldwide fungus (focus on marine, remove?) Aspergillus versicolor - mold, remove Cylindrotheca closterium - ok Haslea crucigera - ok Navicula minima - freshwater diatom, remove? Phaeodactylum tricornutum - probably ok, documented distribution all around (also Mexico) https://www.algaebase.org/search/species/detail/?species_id=S7904772cad5d1cab Bugula rochae - south american. Probably a different local species rdp: 0.85. remove Amathia evelinae - south american, but good sequence matches, difficult to say, maybe the locals can think about this? Chlorarachnion reptans - unicellular algae, ok Dolichomastix tenuilepis - difficult to say, only found in Italy and Australia? expert opinion needed, remove? Ecteinascidia styeloides- ok https://www.sealifebase.ca/summary/Ecteinascidia-styeloides.html Botrylloides simodensis - remove, probably a different botrylloides Anas poecilorhyncha - remove, this is an indian species, and rdp 0.85 Ardea cinerea - grey heron, wrong, probably a local heron species instead. We could ask the locals? but for now remove? Falco sparverius - ok Hypanus rudis - An equal match to: Dasyatis americana on blast, so most likely it is that one instead!

[wardappeltans]

Ok to remove non marine app and doubtful identifications

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Cladosporium herbarum - common worldwide fungus (focus on marine, remove?) Aspergillus versicolor - mold, remove Cylindrotheca closterium - ok Haslea crucigera - ok Navicula minima - freshwater diatom, remove? Phaeodactylum tricornutum - probably ok, documented distribution all around (also Mexico) https://www.algaebase.org/search/species/detail/?species_id=S7904772cad5d1cab Bugula rochae - south american. Probably a different local species rdp: 0.85. remove Amathia evelinae - south american, but good sequence matches, difficult to say, maybe the locals can think about this? Chlorarachnion reptans - unicellular algae, ok Dolichomastix tenuilepis - difficult to say, only found in Italy and Australia? expert opinion needed, remove? Ecteinascidia styeloides- ok https://www.sealifebase.ca/summary/Ecteinascidia-styeloides.html Botrylloides simodensis - remove, probably a different botrylloides Anas poecilorhyncha - remove, this is an indian species, and rdp 0.85 Ardea cinerea - grey heron, wrong, probably a local heron species instead. We could ask the locals? but for now remove? Falco sparverius - ok Hypanus rudis - An equal match to: Dasyatis americana on blast, so most likely it is that one instead!

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[SSuominen1]

Mirounga leonina - cross-contamination from the other samples (french austral lands) - remove Neophocaena phocaenoides - remove, indian species. tax results mixed including a fungi, so likely a misidentification in the ref db. Albula glossodonta - change to: Albula vulpes (vsearch match) Myrophis vafer - change to: Myrophis punctatus (vsearch match) Sphyraena jello - change to: Sphyraena_barracuda (an equal vsearch match) Caranx ignobilis - many of the caranx species have a 100% similarity in 12Steleo (only marker where this was found), so not reliable - remove Brevoortia tyrannus - most likely Brevoortia patronus instead (better blast hit, distribution) Carassius auratus - goldfish, freshwater/brackish, 12Steleo match only not likely? or contamination or runoff? Lucania goodei - freshwater fish found throughout florida (runoff?) ok.

[pieterprovoost]

Thanks @SSuominen1, added a CSV here with AphiaIDs to delete or update: https://github.com/iobis/analysis-everglades/blob/master/species_lists/cleanup.csv

[SSuominen1]

Poecilia sphenops - freshwater/brackish, but close by, remove? Lutjanus argentimaculatus - change to Lutjanus griseus (vsearch match) Diplodus kotschyi - change to more likely diplodus holbrookii (12Steleo both 100% match) Gobiosoma ginsburgi- remove, as likely: Gobiosoma robustum Epinephelus lanceolatus - only 12Steleo, can just as likely be the itajara species, remove Syngnathus schlegeli - most likely syngnathus floridae - remove Stephanolepis cirrhifer- most likely Stephanolepis hispida - remove Sphoeroides_parvus - ok Boloceroides mcmurrichi - difficult, good matches, but top match is vsearch actinaria sp. expert needed? Diadumene leucolena - ok Edwardsia longicornis - possibly a different local species which is not in the database? (95% on blast, wrong distribution) Nanozoanthus harenaceus - genetically good evidence (but not known distribution?) ok. Zancleopsis dichotoma - ok Clytia hemisphaerica - ok Obelia bidentata - ok Vallicula multiformis - ok Thyonella gemmata - ok Gnathostomula mediterranea - prob fine? Ameritella mitchelli - ok Philinopsis pusa - ok Bulla arabica - good genetic evidence, but wrong distribution, confirm with locals? Learchis poica - ok Dondice occidentalis - not in qc list? prob fine Cyerce antillensis - ok Amphidinium massartii - ok Tetrastemma elegans - ok Tetrastemma_wilsoni - ok Tubulanus riceae - not sure, no distribution recorded Phoronis psammophila - ok

[SSuominen1]

Callyspongia (Cladochalina) aculeata - ok Callyspongia (Cladochalina) diffusa - remove Cladocroce burapha - not good enough evidence - remove Haliclona (Halichoclona) vansoesti - caribbean - possible? Gelliodes wilsoni - unlikely, remove Pachychalina tenera - genetically ok evidence, possible? Mycale (Carmia) fibrexilis - good genetic evidence possible? Amorphinopsis fenestrata - not sure, remove? Halichondria (Halichondria) melanadocia - ok Geodia neptuni - ok Poecillastra_laminaris - not enough evidence, remove Acanthosiphonia echinata - ok

[SSuominen1]

Limulus_polyphemus - high confidence Negaprion brevirostris - high confidence Sphyrna_tiburo - high confidence Hypanus americanus - high confidence Trichechus manatus - high confidence Megalops atlanticus - high confidence Epinephelus itajara - good confidence Caretta caretta - high confidence

[pieterprovoost]

Thanks @SSuominen1!