User:Jts1882/Phylogeny and taxonomy resources

This page is a set of links to useful phylogeny and taxonomy resources. These will include specialist sites on perticular groups of organisms, checklists, databases, and important scientific papers.

General edit

Viruses edit

Bacteria and Archaea edit

  • GTDB release 07-RS207 (8th April 2022).
    • "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
    • "bac120_r207.sp_label". Genome Taxonomy Database. Retrieved 20 June 2022.
    • "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.</ref>
  • Bergey's Manual of Systematic Bacteriology https://www.bergeys.org/publications/
  • LPSN - List of Prokaryotic names with Standing in Nomenclature: home | classification | old version

Eukaryotes edit

  • Ruggiero scheme:
    • Ruggiero et al (2015) A Higher Level Classification of All Living Organisms.[1]


References

  1. ^ Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M. (2015). "A Higher Level Classification of All Living Organisms". PLOS ONE. 10 (4): e0119248. doi:10.1371/journal.pone.0119248. ISSN 1932-6203.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  2. ^ Adl, Sina M.; Bass, David; Lane, Christopher E.; Lukeš, Julius; Schoch, Conrad L.; Smirnov, Alexey; Agatha, Sabine; Berney, Cedric; Brown, Matthew W.; Burki, Fabien; Cárdenas, Paco; Čepička, Ivan; Chistyakova, Ludmila; del Campo, Javier; Dunthorn, Micah; Edvardsen, Bente; Eglit, Yana; Guillou, Laure; Hampl, Vladimír; Heiss, Aaron A.; Hoppenrath, Mona; James, Timothy Y.; Karpov, Sergey; Kim, Eunsoo; Kolisko, Martin; Kudryavtsev, Alexander; Lahr, Daniel J. G.; Lara, Enrique; Le Gall, Line; Lynn, Denis H.; Mann, David G.; Massana i Molera, Ramon; Mitchell, Edward A. D.; Morrow, Christine; Park, Jong Soo; Pawlowski, Jan W.; Powell, Martha J.; Richter, Daniel J.; Rueckert, Sonja; Shadwick, Lora; Shimano, Satoshi; Spiegel, Frederick W.; Torruella i Cortes, Guifré; Youssef, Noha; Zlatogursky, Vasily; Zhang, Qianqian (2018). "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes". Journal of Eukaryotic Microbiology. doi:10.1111/jeu.12691. ISSN 1066-5234.
  3. ^ Adl, Sina M.; Simpson, Alastair G. B.; Lane, Christopher E.; Lukeš, Julius; Bass, David; Bowser, Samuel S.; Brown, Matthew W.; Burki, Fabien; Dunthorn, Micah; Hampl, Vladimir; Heiss, Aaron; Hoppenrath, Mona; Lara, Enrique; le Gall, Line; Lynn, Denis H.; McManus, Hilary; Mitchell, Edward A. D.; Mozley-Stanridge, Sharon E.; Parfrey, Laura W.; Pawlowski, Jan; Rueckert, Sonja; Shadwick, Laura; Schoch, Conrad L.; Smirnov, Alexey; Spiegel, Frederick W. (2012). "The Revised Classification of Eukaryotes". Journal of Eukaryotic Microbiology. 59 (5): 429–514. doi:10.1111/j.1550-7408.2012.00644.x. ISSN 1066-5234.
  4. ^ Adl, Sina M.; Simpson, Alastair G. B.; Farmer, Mark A.; Andersen, Robert A.; Anderson, O. Roger; Barta, John R.; Bowser, Samuel S.; Brugerolle, Guy; Fensome, Robert A.; Fredericq, Suzanne; James, Timothy Y.; Karpov, Sergei; Kugrens, Paul; Krug, John; Lane, Christopher E.; Lewis, Louise A.; Lodge, Jean; Lynn, Denis H.; Mann, David G.; Mccourt, Richard M.; Mendoza, Leonel; Moestrup, Ojvind; Mozley-Standridge, Sharon E.; Nerad, Thomas A.; Shearer, Carol A.; Smirnov, Alexey V.; Spiegel, Frederick W.; Taylor, Max F. J. R. (2005). "The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists". The Journal of Eukaryotic Microbiology. 52 (5): 399–451. doi:10.1111/j.1550-7408.2005.00053.x. ISSN 1066-5234.
  5. ^ Adl, Sina M.; Leander, Brian S.; Simpson, Alastair G. B.; Archibald, John M.; Anderson, O. Roger.; Bass, David; Bowser, Samuel S.; Brugerolle, Guy; Farmer, Mark A.; Karpov, Sergey; Kolisko, Martin; Lane, Christopher E.; Lodge, Deborah J.; Mann, David G.; Meisterfeld, Ralf; Mendoza, Leonel; Moestrup, Øjvind; Mozley-Standridge, Sharon E.; Smirnov, Alexey V.; Spiegel, Frederick; Collins, Tim; Sullivan, Jack (2007). "Diversity, Nomenclature, and Taxonomy of Protists". Systematic Biology. 56 (4): 684–689. doi:10.1080/10635150701494127. ISSN 1076-836X.
  6. ^ Silar, Philippe (2016). Protistes Eucaryotes: Origine, Evolution et Biologie des Microbes Eucaryotes. pp. 1–462. ISBN 978-2-9555841-0-1.
  7. ^ Archibald, John M.; Simpson, Alastair G.B.; Slamovits, Claudio H., eds. (2017). Handbook of the Protists (2nd ed.). p. 1662. ISBN 331928147X.

Fungi edit

Plants edit

References

  1. ^ PPG I (2016). "A community-derived classification for extant lycophytes and ferns". Journal of Systematics and Evolution. 54 (6): 563–603. doi:10.1111/jse.12229. ISSN 1674-4918.

Animals edit

References

  1. ^ Giribet, G.; Edgecombe, G.D. (2020). The Invertebrate Tree of Life. Princeton University Press. p. 21. ISBN 978-0-6911-7025-1. Retrieved 27 May 2023.

Invertebrates edit

  • General
    • World Register of Marine Species (WoRMS): Advanced search | databases | Taxon tree (very good for some marine groups, but limited for terrestrial groups)
    • Bugguide (many arthropod groups, but US and Canada only)

Arthropods edit

Insects edit

Holometabola edit


Species Files and FLOW databases (Polyneoptera and Paraneoptera) edit


Species Files databases with Wikidata and CoL links
Database old website new website taxa checklistbank (CoL) wd item wd identifier note
Arthropoda Species File: home n/a taxa Arthropoda Species File (Q115666025) n/a limited content
Polyneoptera Species File: home n/a taxa Polyneoptera Species File (Q115666028) n/a limited content
Zoraptera Species File
archive home taxa checklistbank Zoraptera Species File (Q115665927) identifier required updated
Dermaptera Species File
archive home taxa checklistbank Dermaptera Species File (Q115665911) identifier required updated
Plecoptera Species File
archive home taxa checklistbank Plecoptera Species File (Q115665917) identifier required updated
Orthoptera Species File
archive home taxa checklistbank Orthoptera Species File (Q57673331) Orthoptera Species File ID (P6050) updated
(new ids)
Grylloblattodea Species File
archive home taxa checklistbank Grylloblattodea Species File (Q122839961) identifier required updated
Mantophasmatodea Species File
archive home taxa checklistbank Mantophasmatodea Species File (Q115665941) identifier required updated
Embioptera Species File
archive home taxa checklistbank Embioptera Species File Online (Q115665913) identifier required updated
Phasmida Species File
archive home taxa checklistbank Phasmida Species File (Q49417701) Phasmida Species File ID (P4855) updated
(new ids)
Mantodea Species File
home preview taxa checklistbank Mantodea Species File (Q57714294) Mantodea Species File ID (P6055) pending
Cockroach Species File (Blattodea)
archive home taxa checklistbank Cockroach Species File (Q57715163) Cockroach Species File ID (P6052) updated
(new ids)
Isoptera Species File (Blattodea)
n/a home taxa checklistbank Isoptera Species File (Q122839980) identifier required resurrected
Paraneoptera Species File home n/a taxa Paraneoptera Species File Online (Q115665926) n/a limited content
Psocodea Species File
archive home taxa checklistbank Psocodea Species File (Q89384967) Psocodea Species File ID (P8145) updated
(new ids)
Thysanoptera
no species file
Hemiptera: in parts (incomplete)
see also FLOW
Aphid Species File
(Aphidomorpha<Sternorrhyncha)
archive home taxa checklistbank Aphid Species File (Q115665963) identifier required pending
Coleorrhyncha Species File
archive home taxa checklistbank Coleorrhyncha Species File (Q115666044) identifier required updated
Coreoidea Species File
(Pentatomomorpha<Heteroptera)
home preview taxa checklistbank Coreoidea Species File (Q57714687) Coreoidea Species File ID (P6053) pending
Lygaeoidea Species File
(Pentatomomorpha<Heteroptera)
archive home taxa checklistbank Lygaeoidea Species File (Q115641818) Lygaeoidea Species File ID (P11311)) updated
(new IDs)
3i World Auchenorrhyncha Database
old 3i website home taxa checklistbank World Auchenorrhyncha Database (Q107302695) World Auchenorrhyncha Database ID (P12057) updated

Fish edit

References

  1. ^ Stein, R. William; Mull, Christopher G.; Kuhn, Tyler S.; Aschliman,, Neil C.; Davidson,, Lindsay N. K.; Joy,, Jeffrey B.; Smith, Gordon J.; Dulvy, Nicholas K.; Mooers, Arne O. (2018). "Global priorities for conserving the evolutionary history of sharks, rays and chimaeras". Nature Ecology & Evolution (2): 288–298.{{cite journal}}: CS1 maint: extra punctuation (link)

Amphibia edit

Reptiles edit

Birds edit

Mammals edit

Archives of MSW3 at the Smithsonian edit

Archive of taxonomic browser on Smithsonian version of MSW3: Mammalia (captured 20110526)[1]

References

  1. ^ Wilson, Don E.; Reeder, DeeAnn M. "Mammal Species of the World". Smithsonian: National Museum of Natural History. Archived from the original on 26 May 2011.