Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"

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See [https://wormtails.bio.nyu.edu/fmi/webd/RhabditinaDB?homeurl=http://wormtails.bio.nyu.edu/Databases.html RhabditinaDB] for a comprehensive morphological and taxonomic database of Rhabditina, including ''Caenorhabditis''
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'''4 Nov 2014: Great news: Mark Blaxter has obtained funding including direct support from [http://genomics.ed.ac.uk Edinburgh Genomics] to sequence 15-20 further species and launched the ''Caenorhabditis Genomes Project'', see http://caenorhabditis.bio.ed.ac.uk/'''
 
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There is a BLAST server for the new genome data at [http://bang.bio.ed.ac.uk:4567/] and the new raw and preliminary assemblies can be downloaded from [ftp://bang.bio.ed.ac.uk/caenorhabditis/ the Blaxter lab FTP site].
 
 
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! Species name !! species number !! Reference strain !! Reproduction !! Collector !! Location !! Date !! Isolated by !! Phylogenetic affiliation !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome project see the Blaxter lab project page http://nematodes.org/genomes/index_caenorhabditis.html
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! Species !! number !! Reference strain !! Repro- duction !! Collector !! Location !! Date !! Isolated by !! Supergroup (annotation incomplete) !! Group (annotation incomplete) !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome !! Data ([http://wormbase.org WORMBASE] or other) !! Publications (incomplete) !! Other strains sequenced & other sequence data
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| elegans || a || N2 || H/M || - || - || - || - || Elegans || Elegans || world-wide (mostly temperate) distribution, 100s of isolates || N.A. || SEQUENCED Sanger WashU || [http://wormbase.org WORMBASE] || C. elegans Sequencing Consortium 1998 Science || >400 wild isolates sequenced, see [https://www.elegansvariation.org/ CeNDR]
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| briggsae || b || AF16 || H/M || - || - || - || - || Elegans || Elegans || world-wide distribution, 100s of isolates || N.A. || SEQUENCED WashU || [http://wormbase.org WORMBASE] || [https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0000045 Stein et al. 2003] || 37 wild isolates sequenced 30x (Cutter lab) ; All wild isolates sequenced, forthcoming in CaeNDR
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|-
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| japonica || c ||  || F/M || - || - || - || - || Elegans || Japonica || isolates from Japan (Yoshiga/Cutter) || DF5080 || SEQUENCED WashU || [http://wormbase.org WORMBASE] || - || -
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|-
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| remanei || d ||  || F/M || - || - || - || - || Elegans || Elegans || USA/Canada, Europe, Japan, Taiwan, 100s of isolates || PB4641, PX356, PX349 || SEQUENCED WashU, Phillips || [http://wormbase.org WORMBASE] || [https://doi.org/10.1371/journal.pgen.1005323 Fierst et al. 2015] || approx 35 wild isolates sequenced
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| drosophilae || f || DF5077 || F/M || - || - || - || - || Drosophilae ||  || rotting saguaro cactus in Arizona, a few isolates || DF5112 || SEQUENCED Blaxter || - || - || -
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| plicata || g || SB355 || F/M || - || - || - || - || base ||  || - || - || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
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| auriculariae ||  || NKZ352 || F/M || - || - || - || - || Auriculariae || sister to monodelphis || Platydema beetles in Japan; one strain at CGC || - || SEQUENCED Kikuchi || [https://www.nature.com/articles/s41598-021-85967-z Dayi et al. 2021] || - || -
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|-
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| monodelphis  || 1 || SB341 || F/M || J. Raschka || Berlin, Germany || 2001 || W. Sudhaus || Auriculariae ||  || A second isolate from Norway (Félix) || JU1667 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2 Slos et al. BMC Zool. 2017] || -
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|-
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| sp. 2 || 2 || DF5070 || F/M || S. Wirth || Corsica, France || Oct 2001 || W. Sudhaus || Drosophilae || (sister of drosophilae) || 1 single isolate || - || SEQUENCED Blaxter || - || - || -
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|-
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| angaria || 3 || PS1010 || F/M || - || - || 1990 || - || Angaria  || || 3 isolates from Florida USA || - || SEQUENCED CalTech || [http://wormbase.org WORMBASE] || [https://doi.org/10.1101/gr.111021.110 Mortazavi et al.] || -
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|-
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| brenneri || 4 ||  || F/M || - || - || - || - || Elegans || Elegans || tropical, ~30 isolates (Felix, Cutter, Braendle) || PB2801, VX223-225, VX227 || SEQUENCED WashU || [http://wormbase.org WORMBASE] || - || VX strains sequenced but not yet assembled (Cutter lab); RNA seq for 10 isolates http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis
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|-
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| sinica || 5 ||  || F/M || M.-A. Félix || Chengyang, Guangxi, China || 6 May 2005 || M.-A. Félix || Elegans || Elegans || Isolates from China, Vietnam (Cutter, Ailion, Félix) || JU800 || SEQUENCED Cutter Blaxter || [http://wormbase.org WORMBASE] || - || -
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|-
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| portoensis || 6 || EG4788 || F/M || M. Ailion, A.-J.  Rodrigues || Amares, Portugal || 28 Mar 2007 || M. Ailion || ||  || Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) || EG5626 || Sequenced Blaxter || - || - || -
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| afra || 7 || JU1199 || F/M || M. Herrmann || Begoro, Ghana || Jun 2007 || M.-A. Félix || Elegans || Japonica || 2 isolates from West Africa (Félix) || JU1286 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
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|-
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| sp. 8 || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 || M. Rockman || Angaria || close to sp. 24 and 56|| Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) || JU3312 || SEQUENCED Blaxter || - || - || -
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| nigoni || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India || 21 Dec 2007 || M.-A. Félix || Elegans || Elegans, sister of briggsae || Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) || JU1422 || SEQUENCED Schwarz || [https://doi.org/10.17605/osf.io/dkbwt OPEN SCIENCE FRAMEWORK] || - || -
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|-
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| doughertyi || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India || 27 Dec 2007 || M.-A. Félix || Elegans || Elegans|| 6 isolates from South India || JU1771 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || RNA seq for JU1328 & JU1333
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|-
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| tropicalis || 11 || JU1373 || H/M || V. Robert, L. Sablé || Saint-Benoît, La Réunion || Jan 2008 || M.-A. Félix || Elegans || Elegans|| Common in tropical regions (not so far on the African continent, one in Asia) || - || SEQUENCED WashU, etc || [http://wormbase.org WORMBASE] || - || All wild isolates sequenced, forthcoming in CaeNDR
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| castelli || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || Angaria || || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
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| virilis  || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008 || M.-A. Félix || Drosophilae  ||  || Several isolates from two locations in France || JU1968 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
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| imperialis || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia || 24 Jul 2009 || M. Ailion || Elegans || Japonica  || also Polynesia, Guadeloupe (Félix, Braendle) || EG5942-EG5947 || SEQUENCED Blaxter || - || - || -
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| kamaaina || 15 || QG122 || F/M || M. Rockman || Near Hanalei Bay, Kauai, Hawaii, USA || 2 Aug 2009 || M. Rockman || Elegans || Elegans || Kauai and Maui, 2 isolates || QG2076, QG2077 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || - || 
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|-
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| wallacei  || 16 || JU1873 || F/M || J.-B. Pénigault || Sanda Center, Bali, Indonesia || 11 Nov 2009 || J.-B. Pénigault || Elegans || Elegans  || 2 isolates from Indonesia (Félix) || JU1898 || in assembly Schwarz ||  || - || 
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| nouraguensis  || 17 || JU1825 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 21 Nov 2009 || C. Braendle, M.-A. Félix || Elegans || Japonica || Many isolates from French Guiana || JU2079 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || additional strains sequenced
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| macrosperma  || 18 || JU1857 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 23 Nov 2009 || C. Braendle, M.-A. Félix || Elegans || Japonica || A few isolates from Nouragues, French Guiana || JU2083 || SEQUENCED Cutter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
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| yunquensis  || 19 || EG6142 || F/M || S. Dalton || El Yunque, Puerto Rico || 28 Mar 2010 || S. Dalton, M. Ailion || Elegans || Japonica || Puerto Rico || XZ1517-XZ1520 || SEQUENCED Blaxter || - || - || -
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| guadeloupensis  || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010 || C. Braendle || Guadeloupensis ||  || Guadeloupe ||  || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || resequencing required
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| parvicauda || 21 || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base ||  || Also Polynesia, Thailand and Caribbean (Félix) || NIC534 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
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| latens || 23 || VX88 || F/M || G.-X. Wang || Jiufeng Village, Wuhan City, Hubei Province, China || 27 Oct 2009 || G.-X. Wang || Elegans || Elegans, sister of C. remanei || Several isolates from China (Cutter) || PX534, PX573, PX574, PX580 || SEQUENCED Phillips || [http://caenorhabditis.org Caenorhabditis DB] || - || -
 
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| '''''angaria''''' || 3 || PS1010 || F/M || || ||1990 || || ''Drosophilae'' super-group, ''Angaria'' group || 3 isolates from Florida USA || - || Mortazavi et al. 2010 Genome Research, '''@Wormbase'''
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| agridulce || 24 || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || Angaria || close to sp. 8 and 56|| Isolates from California, Panama, Mexico (Rockman, Félix) ||  || SEQUENCED Blaxter || - || - || -
 
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| '''''brenneri''''' || 4 || || F/M || || || || || ''Elegans'' group ||tropical, ~30 isolates (Felix, Cutter, Braendle) || PB2801, VX223-225, VX227 || Wash U, '''@Wormbase'''; VX strains sequenced but not yet assembled (Cutter lab); RNA seq for 10 isolates http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis
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| sp. 25 || 25 || ZF1222 || F/M || A. Seah, T. Inoue || Singapore || 3 Sep 2011 || T. Inoue || Elegans || Japonica || 2 isolates from Singapore || ZF1457 || SEQUENCED Blaxter || - || - || -
 
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| '''''briggsae''''' || # || AF16 || '''H/M''' || || || || || ''Elegans'' group || world-wide distribution, 100s of isolates || N.A. || Stein et al. 2003 PLoS Biology, '''@Wormbase'''; 37 wild isolates sequenced 30x (Cutter lab)
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| zanzibari || 26 || JU2161 || F/M || M.-A. Félix || Zanzibar, Tanzania || 9 Mar 2012 || M.-A. Félix || Elegans || Elegans || 5 isolates from Zanzibar || JU2190 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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| '''''drosophilae''''' || # || DF5077 ||F/M || ||  ||  || || ''Drosophilae'' group || rotting saguaro cactus in Arizona, a few isolates || DF5112 ||  
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| sp. 27 || 27 || QX2263 || F/M || - || Buenos Aires, Argentina || 2 Mar 2012 || E. Andersen || || Portoensis || Argentina ||  || SEQUENCED Blaxter || - || - || -  
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|-'''
 
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| '''''elegans''''' || # || N2 || '''H/M''' ||  || || || || ''Elegans'' group || world-wide (mostly temperate) distribution, 100s of isolates || N.A. || ''C. elegans'' Sequencing Consortium 1998 Science, '''@Wormbase'''
 
 
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| '''''japonica''''' || # || || F/M|| || || || || ''Elegans'' super-group, ''Japonica'' group|| isolates from Japan (Yoshiga/Cutter) || DF5080 || Wash U, '''@Wormbase'''
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| panamensis || 28 || QG702 || F/M || M. Rockman || Barro Colorado Island, Panama || 23 Apr 2012 || M. Rockman || Elegans|| Japonica || several isofemale lines from Panama || QG2080, QG2081 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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| '''''plicata''''' || # || SB355 || F/M || || || || || ||  || || Blaxter, preliminary assembly available. High proportion of bacterial DNA. To be reprepared in Felix lab.
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| becei || 29 || QG704 || F/M || M. Rockman || Barro Colorado Island, Panama || 25 Apr 2012 || M. Rockman || Elegans || Japonica, sister of nouraguensis || many isofemale lines from Panama || QG2082, QG2083 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || >400 RIAILs, Rockman lab  
 
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| '''''remanei''''' || # || || F/M || || || || || ''Elegans'' group|| USA/Canada, Europe, Japan, Taiwan, 100s of isolates || PB4641, PX356, PX349 || Wash U, '''@Wormbase'''; PX strains sequenced and assembled (ms in review, Phillips/Cutter labs); approx 35 wild isolates sequenced
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| sp. 30 || 30 || DF5152 || F/M || - || Gallon Jug, Belize || 15 Nov 2012 || K. Kiontke || Drosophilae || || 4 isofemale lines from Belize || ongoing (K. Kiontke) || SEQUENCED Blaxter || - || - || -
 
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| '''sp. 1''' || 1 || SB341 || F/M || S. Wirth  || Berlin, Germany  || 2000?  || W. Sudhaus  || base of ''Caenorhabditis'' || 1 single isolate || JU1667  || Blaxter preliminary assembly http://nematodes.org/genomes/caenorhabditis_sp1/ ||  
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| uteleia || 31 || JU2469 || F/M || - || Madre de Dios, Peru || Jan 2013 || L. Frézal || Guadeloupensis ||  || 2 isolates from Peru || JU2585 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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| '''sp. 2''' || 2 || DF5070 || F/M || S. Wirth  || Corsica, France || Oct 2001 || W. Sudhaus || ''Drosophilae'' group, sister of ''C. drosophilae''  || 1 single isolate || ||  
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| sulstoni || 32 || SB454 || F/M || - || East Africa? || Feb 2013 || W. Sudhaus || Elegans || Japonica, sister of afra || 1 isolate, from the gut of the millipede Archispirostreptus gigas || JU2788 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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| '''''sinica''''' || 5 || || F/M || M.-A. Félix  || Chengyang, Guangxi, China  || 6 May 2005  || M.-A. Félix  || ''Briggsae'' subgroup  || Isolates from China, Vietnam (Cutter, Ailion, Félix) || JU800 ||   Cutter/Blaxter, '''@Wormbase'''
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| sp. 33 || 33 || BRC20065 || F/M || J. Wang || Taiwan || 24 May 2012 || J. Wang || Elegans || Elegans || 1 isolate from Taiwan || BRC20066 || IN SEQUENCING Wang Tsai || - || - || -
 
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| '''''portoensis''''' || 6 || EG4788 || F/M || M. Ailion, A.-J. Rodrigues || Amares, Portugal || 28 Mar 2007  || M. Ailion  || ''Drosophilae'' super group  || Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) || EG5626  || sent to Blaxter
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| inopinata || 34 || NK74SC || F/M || N. Kanzaki || Shigaki Island, Japan || May 2013 || N. Kanzaki || Elegans || Elegans, with C. sp. 35 sister of C. elegans || 1 isolate from Japan. Associated with fig wasps and Ficus septica || - || SEQUENCED Kanzaki, Kikuchi || [http://caenorhabditis.org Caenorhabditis DB] || [https://www.nature.com/articles/s41467-018-05712-5 Kanzaki et al. Nat Comm 2019] || -
 
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| '''''afra''''' || 7 || JU1199 || F/M || M. Herrmann  || Begoro, Ghana  || Jun 2007  || M.-A. Félix || ''Japonica'' group  || 2 isolates from West Africa (Félix) || JU1286  || Wash U CONTAMINATED WITH SP. 9 www.nematodes.org/nematodegenomes/index.php/959_Nematode_Genomes
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| sp. 35 || 35 || DF5171 || F/M || - || Banda Ache, Indonesia || Aug 2013 || N. Kanzaki || Elegans || Elegans, with C. sp. 34 sister of C. elegans || 2 Isolates from Indonesia, associated with Ficus hispida || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || -
 
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| '''sp. 8''' || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 || M. Rockman || ''Angaria'' group|| Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman)  || ongoing using TGM13 (K. Kiontke)  ||  
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| niphades || 36 || NK02NV || F/M || N. Kanzaki || Tokyo, Japan || Apr 2013 || N. Kanzaki || Elegans || Japonica || 1 isolate from Japan. Associated with the weevil Niphades variegatus || - || SEQUENCED Kanzaki, Kikuchi || - || [https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-09011-8 Sun et al. BMC Genomics 2022] || -
 
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|'''''nigoni''''' || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India  || 21 Dec 2007 || M.-A. Félix  || ''Briggsae'' subgroup, sister of ''briggsae''  || Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue)  || JU1422 || (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer
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| dolens || 37 || NIC394 || F/M || C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn || Nouragues National Reserve, French Guiana || 18 Apr 2013 || C. Braendle || Angaria group || Angaria || 1 isolate from French Guiana || - || SEQUENCED Blaxter || - || - || -
 
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|'''''doughertyi''''' || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India  || 27 Dec 2007  || M.-A. Félix  || ''Brenneri'' subgroup || 6 isolates from South India || JU1771  || Blaxter, sequenced, preliminary assembly available;  RNA seq for JU1328 & JU1333 http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis
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| quiockensis || 38 || JU2745 || F/M || F. Besnard || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || Angaria|| || 1 isolate from Guadeloupe || JU2809 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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| '''''tropicalis''''' || 11 || JU1373 || '''H/M''' || V. Robert, L. Sablé || Saint-Benoît, La Réunion || Jan 2008 || M.-A. Félix || ''Brenneri'' subgroup || Common in tropical regions (not so far on the African continent, one in Asia) || N.A. || Wash U, '''@Wormbase'''
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| waitukubuli || 39 || NIC564 || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle || Elegans || Japonica || 1 isolate from Dominique || - || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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|-
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| '''''castelli''''' || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || ''Angaria'' group || 2 isolates from French Guiana  || JU1956  || Blaxter, sequenced
+
| tribulationis || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014 || L. Frézal || Elegans|| Elegans || 5 isolates from Australia, in fresh or rotting figs || JU2818 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
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|-
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| '''''virilis ''''' || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008  || M.-A. Félix || ''Drosophilae'' super group || A few isolates, all from Orsay, France || JU1968 || Blaxter, preliminary assembly available
+
| sp. 41 || 41 || BRC20276 || F/M || - || Solomon Islands || October 2014 || J. Wang || Elegans || Elegans || 2 isolates from Solomon Islands || - || IN SEQUENCING Wang Tsai || - || - || -
 
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| '''''imperialis''''' || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia  || 24 Jul 2009  || M. Ailion || ''Japonica'' group || also Polynesia, Guadeloupe (Félix, Braendle)  || EG5942-EG5947 || sent to Blaxter
+
| astrocarya || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || base || || one isolate from French Guiana || - || SEQUENCED Blaxter || - || - || -
 
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|-
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| '''''kamaaina''''' ||15 || QG122 || F/M || M. Rockman  || Near Hanalei Bay, Kauai, Hawaii, USA || 2 Aug 2009 ||  M. Rockman || ''Elegans'' super group || Kauai and Maui, 2 isolates || QG2076, QG2077 || under assembly, Rockman
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| vivipara || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle ||  || Portoensis || 2 isolates from Mexico; in orange berries || NIC1581, NIC2055 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || resequenced (PACBIO) Braendle
 
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|-
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| '''''wallacei ''''' || 16 || JU1873 || F/M || J.-B. Pénigault || Sanda Center, Bali, Indonesia || 11 Nov 2009 || J.-B. Pénigault || ''Brenneri'' subgroup  || 2 isolates from Indonesia (Félix) || JU1898 || Blaxter preliminary assembly available
+
| sp. 44 || 44 || BRC20300 || F/M || J. Wang || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || Elegans || Elegans || one isolate from Taiwan; in flowers || - || IN SEQUENCING Wang Tsai || - || - || -
 
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|-
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| '''''nouraguensis ''''' || 17 || JU1825 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 21 Nov 2009 || C. Braendle, M.-A. Félix || ''Japonica'' group ||  Many isolates from French Guiana || JU2079 || Blaxter, preliminary assembly available; additional strains sequenced also
+
| sp. 45 || 45 || NIC759 || F/M || C. Braendle || Sylvania, Dominica || 16 May 2014 || C. Braendle || Guadeloupensis || sister species of C. guadeloupensis || one isolate from Dominica; in Cecropia fruit || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''''macrosperma ''''' (ex-sp. 18) || 18 || JU1857 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 23 Nov 2009 || C. Braendle, M.-A. Félix || ''Japonica'' group  || A few isolates from Nouragues, French Guiana  || JU2083  || Blaxter, preliminary assembly available
+
| sp. 46 || 46 || NIC1120 || F/M || C. Braendle || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015 || C. Braendle || Elegans|| Japonica || one isolate from Peru || - || SEQUENCED Blaxter|| - || - || -
 
|-
 
|-
−
| '''''yunquensis ''''' || 19 || EG6142 ||F/M || S. Dalton  || El Yunque, Puerto Rico || 28 Mar 2010  || S. Dalton, M. Ailion || ''Japonica'' group || Puerto Rico || XZ1517-XZ1520 || sent to Blaxter
+
| sp. 47 || 47 || NIC1127 || F/M || C. Braendle || Tambopata region, Amazon, Peru || 7 April 2015 || C. Braendle || Angaria ||  || one isolate from Peru || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''''guadeloupensis ''''' || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010  || C. Braendle || ''Drosophilae'' supergroup || Guadeloupe || ||   Blaxter, preliminary assembly available
+
| sp. 48 || 48 || BRC20359 || F/M || J. Wang || Khao Yai National park, Thailand || 4 May 2015 || J. Wang || Elegans || Elegans || one isolate from Thailand || - || SSEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''sp. 21''' || 21 || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base of ''Caenorhabditis'' || Also Polynesia, Thailand and Caribbean (Félix) || NIC534 || Blaxter, preliminary assembly available
+
| sp. 49 || 49 || BRC20376 || F/M || J. Wang || Solomon Islands || - || J. Wang || Elegans || Japonica || one isolate Solomon Islands || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''''latens ''''' || 23 || VX88 || F/M || G.-X. Wang  || Jiufeng Village, Wuhan City, Hubei Province, China || 27 Oct 2009 || G.-X. Wang || ''Briggsae'' subgroup, sister of ''C. remanei'' || Several isolates from China (Cutter) || PX534, PX573, PX574, PX580 || under assembly, Cutter/Phillips
+
| sp. 50 || 50 || BRC20387 || F/M || Dai || near Taipei City, Taiwan || 18 October 2015  ||J. Wang || Elegans || Japonica || two isolates from Taiwan || - || Sequencing_planned Blaxter || - || - || -
 
|-
 
|-
−
| '''sp. 24''' || 24 || QG555 || F/M || A. Paaby  || Santa Barbara, USA || July 2011 || A. Paaby || ''Angaria'' group, sister of sp. 8  || 1 isolate from California, 3 from Panama (Rockman), 1 from Mexico (Felix)  ||   ||
+
| sp. 51 || 51 || QG2915 || F/M || M. Rockman || Australia || 2017 || M Rockman || Elegans || Elegans || two isolates from Australia || QG2939 || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''sp. 25''' || 25 || ZF1222 || F/M || A. Seah, T. Inoue  || Singapore || 3 Sep 2011  || T. Inoue || ''Japonica'' group || 2 isolates from Singapore || ongoing (Inoue)  ||
+
| sp. 52 || 52 || QG2933 || F/M || M. Rockman || Australia || 2017 || M Rockman || ||  || one isolate from Australia || QG2935 || Sequencing_planned Blaxter || - || - || -
 
|-
 
|-
−
| '''sp. 26''' || 26 || JU2161 || F/M || M.-A. Félix || Zanzibar, Tanzania || 9 Mar 2012  || M.-A. Félix || ''Briggsae'' subgroup, close relative of ''C. sinica'' || 5 isolates from Zanzibar || JU2190 || Blaxter, preliminary assembly available
+
| oiwi || 53 || ECA821 || F/M || E. Andersen || Oahu, Hawaii || 2017 || T Crombie || Elegans || Elegans, sister of C. kamaaina || several isolates from Oahu and Kauai || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''sp. 27''' || 27 || QX2263 || F/M || || Buenos Aires, Argentina  || 2 Mar 2012 || E. Andersen  || ''Drosophilae'' supergroup, sister of ''portoensis''  || Argentina ||   ||
+
| sp. 54 || 54 || BRC20468 || F/M || Hsueh, Yen-Ping || Miaoli County?, Taiwan || 18 August 2016 || J Wang || Elegans || Elegans ||  || - || SEQUENCED Blaxter|| - || - || -
 
|-
 
|-
−
| '''sp. 28''' || 28 || QG702 || F/M || M. Rockman || Barro Colorado Island, Panama  || 23 Apr 2012 || M. Rockman  || ''Japonica'' group  || several isofemale lines from Panama  || QG2080, QG2081 || under assembly, Rockman
+
| sp. 55 || 55 || JU3317 || F/M || M.-A. Félix || Pugao Laozhai, Yuanyang, Yunnan, China || 5 March 2018 || M.-A. Félix || Elegans || Elegans || one isolate from Yunnan, China || JU3404 ||SEQUENCED Blaxter || - || - || -
 
|-
 
|-
−
| '''sp. 29''' || 29 ||QG704 || F/M || M. Rockman || Barro Colorado Island, Panama || 25 Apr 2012  || M. Rockman || ''Japonica'' group, sister of ''nouraguensis''  || many isofemale lines from Panama  || QG2082, QG2083 || under assembly, Rockman
+
| sp. 56 || 56 || JU2215 || F/M || M. Joron || Tarapoto, Peru || October 2012 || L. Frézal || Angaria || close to sp. 8 and 24|| one isolate from Peru || (JU3313 8x inbred and very sick) || SEQUENCED Blaxter || - || - ||
 +
|-
 +
| krikudae || 57 || QG3050 || F/M || M. Rockman || Barro Colorado Island, Panama || August 2018 || M. Rockman || Auriculariae || sister to monodelphis + auricularia || two isolates from Panama || QG3077 || || - || - || -
 
|-
 
|-
−
| '''sp. 30''' || 30 || DF5152  || F/M ||   ||  Gallon Jug, Belize  || 15 Nov 2012 || K. Kiontke || ''Drosophilae'' subgroup  || 4 isofemale lines from Belize  || ongoing (K. Kiontke)  ||
+
| sp. 58 || 58 || RS6130 || F/M || M. Herrmann || Bolivia || 2019 ||  M. Herrmann || || close to C. astrocarya || || JU3779 or JU3880 || sent to Blaxter || - || - || -
 
|-
 
|-
−
|| '''sp. 31''' || 31 || JU2469 || F/M  ||  || Madre de Dios, Peru || Jan 2013  || L. Frézal || ''Drosophilae'' super group ||  2 isolates from Peru  || JU2585 || Blaxter, preliminary assembly available  ||
+
| sp. 59 || 59 || RS6131 || F/M || M. Herrmann || Bolivia || 2019 || M. Herrmann || Elegans || Japonica, close to C. becei || || JU3778 || sent to Blaxter || - || - || -
 +
|-
 +
| sp. 60 || 60 || QG3550 || F/M || M. Rockman || Costa Rica || 2019 || M. Rockman || Elegans || Japonica || one isolate || QG4242 || SEQUENCED Rockman || - || - || -
 
|-
 
|-
−
| '''sp. 32''' || 32 || SB454 || F/M || || East Africa? || Feb 2013  || W. Sudhaus || ''Japonica'' group, sister of ''afra'' ||  1 isolate, from the gut of the millipede ''Archispirostreptus gigas'' || JU2788 ||  Blaxter, preliminary assembly available
+
| sp. 61 || 61 || JU4045 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 || M.-A. Félix || Elegans || Elegans || one isolate || JU4110 ||  || - || - || -
 
|-
 
|-
−
| '''sp. 33''' || 33 || BRC20065 ||F/M || J. Wang || Taiwan || 24 May 2012 || J. Wang ||   ''Briggsae'' subgroup || 1 isolate from Taiwan || BRC20066 || planned by J. Wang
+
| sp. 62 || 62 || JU4050 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 || M.-A. Félix || Elegans  || Elegans || one isolate || JU4112 || || - || - || -
 
|-
 
|-
−
| '''sp. 34''' || 34 || NK74SC || F/M || N. Kanzaki  ||Ishigaki Island, Japan || May 2013  || N. Kanzaki ||  ''Elegans'' supergroup, with ''C.'' sp. 35 sister of ''C. elegans'' || 1 isolate from Japan. Associated with fig wasps and ''Ficus septica'' ||   || started by N. Kanzaki and collaborators
+
| sp. 63 || 63 || JU4056 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 || M.-A. Félix || Elegans || Elegans, close to sp. 33 || one isolate || JU4113 ||  || - || - || -
 
|-
 
|-
−
| '''sp. 35''' || 35 || DF5171 || F/M ||   || Banda Ache, Indonesia  || Aug 2013  || N. Kanzaki ||  ''Elegans'' supergroup, with ''C.'' sp. 34 sister of ''C. elegans'' ||  2 Isolates from Indonesia, associated with ''Ficus hispida'' ||   ||  
+
| sp. 64 || 64 || JU4061 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 || M.-A. Félix ||  || Portoensis || one isolate || JU4117 || SEQUENCED Braendle || - || - || -
 
|-
 
|-
−
| '''sp. 36''' || 36 || NK02NV || F/M || N. Kanzaki || Tokyo, Japan || Apr 2013  || N. Kanzaki || ''Japonica'' group || 1 isolate from Japan. Associated with the weevil ''Niphades variegatus''  ||  ||
+
| sp. 65 || 65 || JU4086 || F/M || M.-A. Félix || Dalat area, Vietnam || 2019 || M.-A. Félix || Elegans || Elegans || four isolates from Vietnam || JU4118 ||  || - || - || -
 
|-
 
|-
−
| '''sp. 37''' || 37 || NIC394  || F/M || C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn || Nouragues National Reserve, French Guiana ||  18 Apr 2013 || C. Braendle  || ''Angaria'' group || 1 isolate from French Guiana  ||   ||
+
| sp. 66 || 66 || JU4096 || F/M || M.-A. Félix || Dalat area, Vietnam || 2019 ||  M.-A. Félix || Elegans || Elegans, close to sp. 48 and brenneri || seven isolates from Vietnam || JU4121 ||  || - || - || -
 
|-
 
|-
−
| '''sp. 38''' || 38 || JU2745  || F/M || F. Besnard  ||  Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || ''Angaria'' group || 1 isolate from Guadeloupe  || JU2809 || Blaxter, preliminary assembly available
+
| sp. 67 || 67 || QG4215 || F/M || M. Rockman, E. Andersen || Paluma Range, Australia || 2020 ||  M. Rockman || Elegans || Japonica, near sp. 49 and 50 || one isolate || QG4243 || || - || - || -
 
|-
 
|-
−
| '''sp. 39''' || 39 || NIC564  || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle  || ''Japonica'' group || 1 isolate from Dominique  ||   || Blaxter, sequenced
+
| sp. 68 || 68 ||NIC2161 || F/M || C. Braendle, A. Cutter || Nouragues Natural Reserve, French Guiana || 2014 || C. Braendle || Drosophilae || near sp. 30 || one isolate || ongoing || || - || - || -
 
|-
 
|-
−
| '''sp. 40''' || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014 || L. Frézal || ''Briggsae'' subgroup, close relative of ''C. sinica'' || 5 isolates from Australia, in fresh or rotting figs || JU2818 || Blaxter, preliminary assembly available
+
| sp. 69 || 69 ||NIC2374 || F/M || C. Braendle || Nouragues Natural Reserve, French Guiana || 2021 ||  C. Braendle || Angaria || near dolens || one isolate || ongoing ||  || - || - || -
 
|-
 
|-
−
| '''sp. 41''' || 41 || BRC20276 || F/M || || Salomon Islands || October 2014  || J. Wang || ''Briggsae'' subgroup, sister species of C. sp. 40 || 2 isolates from Salomon Islands ||  ||
+
| sp. 70|| 70 ||TT3412 || F/M || S. Nagarajan, T. Pathak, K. Puraje, M.-A. Félix|| Neral, Marahashtra, India || 2022 || T. Pathak, M.-A. Félix, S. Koushika||  || closest to parvicauda || one isolate || JU4419-21 ||  || - || - || -
 
|-
 
|-
−
| '''sp. 42''' || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle ||  ''Drosophilae'' super group || one isolate from French Guiana || ||  
+
| sp. 71|| 71 ||BRC20593 || F/M || J. Wang|| Vietnam || 2023 || J. Wang|| ||  || 2 isolates  ||  || || - || - || -
 
|-
 
|-
−
| '''sp. 43''' || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle || ''Drosophilae'' super group || 2 isolates from Mexico; in orange berries ||  || Blaxter, preliminary assembly available
+
| sp. 72|| 72 ||QG4708 || F/M || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Pohnpei, Federated States of Micronesia || 2024 || T. Nguyen, M. Rockman, S. Tintori, H. Yomai||  || || 12 isolates || ||  || - || - || -
 
|-
 
|-
−
| '''sp. 44''' || 44 || BRC20300 || F/M || || Shihting mountain near Taipei City, Taiwan || Dec 2014  || J. Wang || sister species of ''C. brenneri'' || one isolate from Taiwan; in flowers ||  ||  
+
| sp. 73|| 73 ||QG4797 || F/M || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Pohnpei, Federated States of Micronesia || 2024 || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Japonica || near imperialis || 11 isolates || ||  || - || - || -
 
|-
 
|-
−
| '''sp. 45''' || 45 || NIC759 || F/M || C. Braendle  || Sylvania, Dominica || 16 May 2014 ||C. Braendle || sister species of ''C. guadeloupensis'' || one isolate from Dominica; in ''Cecropia'' fruit || ||  
+
| sp. 74|| 74 ||QG4644 || F/M || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Pohnpei, Federated States of Micronesia || 2024 || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Japonica || near imperialis || 22 isolates || ||  || - || - || -
 
|-
 
|-
−
| '''sp. 46''' || 46 || NIC1120 || F/M || C. Braendle  || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015  ||C. Braendle || ''Japonica'' group || one isolate from Peru ||  ||  
+
| sp. 75|| 75 ||QG4848 || F/M || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Pohnpei, Federated States of Micronesia || 2024 || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Japonica || near imperialis || 1 isolate ||  || || - || - || -
 
|-
 
|-
−
| '''sp. 47''' || 47 || NIC1127 || F/M || C. Braendle  || Tambopata region, Amazon, Peru ||  7 April 2015 ||C. Braendle || ''Angaria'' group || one isolate from Peru || ||  
+
| sp. 76|| 76 ||QG4628 || F/M || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| Pohnpei, Federated States of Micronesia || 2024 || T. Nguyen, M. Rockman, S. Tintori, H. Yomai|| ||  || 100s of isolates || || || - || - || -
−
 
 
 
|}
 
|}
  
  
−
''Species numbers are assigned by Karin Kiontke, NYU.'' 
 
  
 
'''Published phylogeny, up to sp. 21:'''
 
'''Published phylogeny, up to sp. 21:'''
Line 124: Line 183:
 
</gallery>
 
</gallery>
 
'''Updated phylogeny, up to sp. 32:'''
 
'''Updated phylogeny, up to sp. 32:'''
 +
 
http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png
 
http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png
 +
 +
 +
'''2017 phylogeny of a subset of species, based on their genome sequences by Slos et al.'''
 +
 +
https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2
 +
 +
'''Stevens et al. 2019, with genomic data from 32 species'''
 +
[https://onlinelibrary.wiley.com/doi/10.1002/evl3.110]
 +
 +
'''Stevens et al. 2020, adding <i>C. bovis</i>'''
 +
[https://www.sciencedirect.com/science/article/pii/S0960982220301184#fig3]
 +
 +
'''Sloat et al. 2022, with genomic data from 36 species'''
 +
[https://onlinelibrary.wiley.com/doi/10.1002/ece3.9124]
 +
 +
'''and the latest unpublished phylogeny'''
 +
[http://caenorhabditis.org/?page_id=151]. Thank you Lewis!

Latest revision as of 20:52, 22 March 2024

See RhabditinaDB for a comprehensive morphological and taxonomic database of Rhabditina, including Caenorhabditis

Species number Reference strain Repro- duction Collector Location Date Isolated by Supergroup (annotation incomplete) Group (annotation incomplete) Geographic distribution and available isolates (lab) Inbred strain Genome Data (WORMBASE or other) Publications (incomplete) Other strains sequenced & other sequence data
elegans a N2 H/M - - - - Elegans Elegans world-wide (mostly temperate) distribution, 100s of isolates N.A. SEQUENCED Sanger WashU WORMBASE C. elegans Sequencing Consortium 1998 Science >400 wild isolates sequenced, see CeNDR
briggsae b AF16 H/M - - - - Elegans Elegans world-wide distribution, 100s of isolates N.A. SEQUENCED WashU WORMBASE Stein et al. 2003 37 wild isolates sequenced 30x (Cutter lab) ; All wild isolates sequenced, forthcoming in CaeNDR
japonica c F/M - - - - Elegans Japonica isolates from Japan (Yoshiga/Cutter) DF5080 SEQUENCED WashU WORMBASE - -
remanei d F/M - - - - Elegans Elegans USA/Canada, Europe, Japan, Taiwan, 100s of isolates PB4641, PX356, PX349 SEQUENCED WashU, Phillips WORMBASE Fierst et al. 2015 approx 35 wild isolates sequenced
drosophilae f DF5077 F/M - - - - Drosophilae rotting saguaro cactus in Arizona, a few isolates DF5112 SEQUENCED Blaxter - - -
plicata g SB355 F/M - - - - base - - SEQUENCED Blaxter Caenorhabditis DB - -
auriculariae NKZ352 F/M - - - - Auriculariae sister to monodelphis Platydema beetles in Japan; one strain at CGC - SEQUENCED Kikuchi Dayi et al. 2021 - -
monodelphis 1 SB341 F/M J. Raschka Berlin, Germany 2001 W. Sudhaus Auriculariae A second isolate from Norway (Félix) JU1667 SEQUENCED Blaxter Caenorhabditis DB Slos et al. BMC Zool. 2017 -
sp. 2 2 DF5070 F/M S. Wirth Corsica, France Oct 2001 W. Sudhaus Drosophilae (sister of drosophilae) 1 single isolate - SEQUENCED Blaxter - - -
angaria 3 PS1010 F/M - - 1990 - Angaria 3 isolates from Florida USA - SEQUENCED CalTech WORMBASE Mortazavi et al. -
brenneri 4 F/M - - - - Elegans Elegans tropical, ~30 isolates (Felix, Cutter, Braendle) PB2801, VX223-225, VX227 SEQUENCED WashU WORMBASE - VX strains sequenced but not yet assembled (Cutter lab); RNA seq for 10 isolates http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis
sinica 5 F/M M.-A. Félix Chengyang, Guangxi, China 6 May 2005 M.-A. Félix Elegans Elegans Isolates from China, Vietnam (Cutter, Ailion, Félix) JU800 SEQUENCED Cutter Blaxter WORMBASE - -
portoensis 6 EG4788 F/M M. Ailion, A.-J. Rodrigues Amares, Portugal 28 Mar 2007 M. Ailion Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) EG5626 Sequenced Blaxter - - -
afra 7 JU1199 F/M M. Herrmann Begoro, Ghana Jun 2007 M.-A. Félix Elegans Japonica 2 isolates from West Africa (Félix) JU1286 SEQUENCED Blaxter Caenorhabditis DB - -
sp. 8 8 QX1182 F/M M. Rockman Backyard of 93 Mercer St., Jersey City, NJ, USA 28 Jul 2007 M. Rockman Angaria close to sp. 24 and 56 Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) JU3312 SEQUENCED Blaxter - - -
nigoni 9 JU1325 F/M M.-A. Félix Trivandrum Zoo, Kerala, India 21 Dec 2007 M.-A. Félix Elegans Elegans, sister of briggsae Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) JU1422 SEQUENCED Schwarz OPEN SCIENCE FRAMEWORK - -
doughertyi 10 JU1333 F/M M.-A. Félix Angela Spice Garden, Kerala, India 27 Dec 2007 M.-A. Félix Elegans Elegans 6 isolates from South India JU1771 SEQUENCED Blaxter Caenorhabditis DB - RNA seq for JU1328 & JU1333
tropicalis 11 JU1373 H/M V. Robert, L. Sablé Saint-Benoît, La Réunion Jan 2008 M.-A. Félix Elegans Elegans Common in tropical regions (not so far on the African continent, one in Asia) - SEQUENCED WashU, etc WORMBASE - All wild isolates sequenced, forthcoming in CaeNDR
castelli 12 JU1426 F/M P. Châtelet Nouragues Forest, French Guiana May 2008 M.-A. Félix Angaria Several isolates from French Guiana (Félix, Braendle, Cutter) JU1956 SEQUENCED Blaxter Caenorhabditis DB - -
virilis 13 JU1528 F/M M.-A. Félix Orsay apple orchard 9 Sep 2008 M.-A. Félix Drosophilae Several isolates from two locations in France JU1968 SEQUENCED Blaxter Caenorhabditis DB - -
imperialis 14 EG5716 F/M D. Ailion Moorea, French Polynesia 24 Jul 2009 M. Ailion Elegans Japonica also Polynesia, Guadeloupe (Félix, Braendle) EG5942-EG5947 SEQUENCED Blaxter - - -
kamaaina 15 QG122 F/M M. Rockman Near Hanalei Bay, Kauai, Hawaii, USA 2 Aug 2009 M. Rockman Elegans Elegans Kauai and Maui, 2 isolates QG2076, QG2077 SEQUENCED Rockman Caenorhabditis DB -
wallacei 16 JU1873 F/M J.-B. Pénigault Sanda Center, Bali, Indonesia 11 Nov 2009 J.-B. Pénigault Elegans Elegans 2 isolates from Indonesia (Félix) JU1898 in assembly Schwarz -
nouraguensis 17 JU1825 F/M C. Braendle, M.-A. Félix Nouragues Forest, French Guiana 21 Nov 2009 C. Braendle, M.-A. Félix Elegans Japonica Many isolates from French Guiana JU2079 SEQUENCED Blaxter Caenorhabditis DB - additional strains sequenced
macrosperma 18 JU1857 F/M C. Braendle, M.-A. Félix Nouragues Forest, French Guiana 23 Nov 2009 C. Braendle, M.-A. Félix Elegans Japonica A few isolates from Nouragues, French Guiana JU2083 SEQUENCED Cutter Caenorhabditis DB - -
yunquensis 19 EG6142 F/M S. Dalton El Yunque, Puerto Rico 28 Mar 2010 S. Dalton, M. Ailion Elegans Japonica Puerto Rico XZ1517-XZ1520 SEQUENCED Blaxter - - -
guadeloupensis 20 NIC113 F/M C. Braendle Soufrière Forest trail, Guadeloupe Mar 2010 C. Braendle Guadeloupensis Guadeloupe SEQUENCED Blaxter Caenorhabditis DB - resequencing required
parvicauda 21 NIC134 F/M C. Gimond Island of Sainte Marie, Madagascar Dec 2010 C. Braendle base Also Polynesia, Thailand and Caribbean (Félix) NIC534 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
latens 23 VX88 F/M G.-X. Wang Jiufeng Village, Wuhan City, Hubei Province, China 27 Oct 2009 G.-X. Wang Elegans Elegans, sister of C. remanei Several isolates from China (Cutter) PX534, PX573, PX574, PX580 SEQUENCED Phillips Caenorhabditis DB - -
agridulce 24 QG555 F/M A. Paaby Santa Barbara, USA July 2011 A. Paaby Angaria close to sp. 8 and 56 Isolates from California, Panama, Mexico (Rockman, Félix) SEQUENCED Blaxter - - -
sp. 25 25 ZF1222 F/M A. Seah, T. Inoue Singapore 3 Sep 2011 T. Inoue Elegans Japonica 2 isolates from Singapore ZF1457 SEQUENCED Blaxter - - -
zanzibari 26 JU2161 F/M M.-A. Félix Zanzibar, Tanzania 9 Mar 2012 M.-A. Félix Elegans Elegans 5 isolates from Zanzibar JU2190 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 27 27 QX2263 F/M - Buenos Aires, Argentina 2 Mar 2012 E. Andersen Portoensis Argentina SEQUENCED Blaxter - - -
panamensis 28 QG702 F/M M. Rockman Barro Colorado Island, Panama 23 Apr 2012 M. Rockman Elegans Japonica several isofemale lines from Panama QG2080, QG2081 SEQUENCED Rockman Caenorhabditis DB Stevens et al. Evol Lett 2019 -
becei 29 QG704 F/M M. Rockman Barro Colorado Island, Panama 25 Apr 2012 M. Rockman Elegans Japonica, sister of nouraguensis many isofemale lines from Panama QG2082, QG2083 SEQUENCED Rockman Caenorhabditis DB Stevens et al. Evol Lett 2019 >400 RIAILs, Rockman lab
sp. 30 30 DF5152 F/M - Gallon Jug, Belize 15 Nov 2012 K. Kiontke Drosophilae 4 isofemale lines from Belize ongoing (K. Kiontke) SEQUENCED Blaxter - - -
uteleia 31 JU2469 F/M - Madre de Dios, Peru Jan 2013 L. Frézal Guadeloupensis 2 isolates from Peru JU2585 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sulstoni 32 SB454 F/M - East Africa? Feb 2013 W. Sudhaus Elegans Japonica, sister of afra 1 isolate, from the gut of the millipede Archispirostreptus gigas JU2788 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 33 33 BRC20065 F/M J. Wang Taiwan 24 May 2012 J. Wang Elegans Elegans 1 isolate from Taiwan BRC20066 IN SEQUENCING Wang Tsai - - -
inopinata 34 NK74SC F/M N. Kanzaki Shigaki Island, Japan May 2013 N. Kanzaki Elegans Elegans, with C. sp. 35 sister of C. elegans 1 isolate from Japan. Associated with fig wasps and Ficus septica - SEQUENCED Kanzaki, Kikuchi Caenorhabditis DB Kanzaki et al. Nat Comm 2019 -
sp. 35 35 DF5171 F/M - Banda Ache, Indonesia Aug 2013 N. Kanzaki Elegans Elegans, with C. sp. 34 sister of C. elegans 2 Isolates from Indonesia, associated with Ficus hispida - IN SEQUENCING Kanzaki, Kikuchi - - -
niphades 36 NK02NV F/M N. Kanzaki Tokyo, Japan Apr 2013 N. Kanzaki Elegans Japonica 1 isolate from Japan. Associated with the weevil Niphades variegatus - SEQUENCED Kanzaki, Kikuchi - Sun et al. BMC Genomics 2022 -
dolens 37 NIC394 F/M C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn Nouragues National Reserve, French Guiana 18 Apr 2013 C. Braendle Angaria group Angaria 1 isolate from French Guiana - SEQUENCED Blaxter - - -
quiockensis 38 JU2745 F/M F. Besnard Guadeloupe (Basse Terre) 09 June 2014 F. Besnard Angaria 1 isolate from Guadeloupe JU2809 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
waitukubuli 39 NIC564 F/M C. Braendle Dominica 13 May 2014 C. Braendle Elegans Japonica 1 isolate from Dominique - SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
tribulationis 40 JU2774 F/M J.-B. Pénigault Danbulla, Australia 08 August 2014 L. Frézal Elegans Elegans 5 isolates from Australia, in fresh or rotting figs JU2818 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 41 41 BRC20276 F/M - Solomon Islands October 2014 J. Wang Elegans Elegans 2 isolates from Solomon Islands - IN SEQUENCING Wang Tsai - - -
astrocarya 42 NIC1040 F/M C. Braendle/A. Cutter Nouragues Forest, French Guiana August 2014 C. Braendle base one isolate from French Guiana - SEQUENCED Blaxter - - -
vivipara 43 NIC1070 F/M C. Gosse Chichén Itzá, Yucatán, Mexico 17 October 2014 C. Braendle Portoensis 2 isolates from Mexico; in orange berries NIC1581, NIC2055 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 resequenced (PACBIO) Braendle
sp. 44 44 BRC20300 F/M J. Wang Shihting mountain near Taipei City, Taiwan Dec 2014 J. Wang Elegans Elegans one isolate from Taiwan; in flowers - IN SEQUENCING Wang Tsai - - -
sp. 45 45 NIC759 F/M C. Braendle Sylvania, Dominica 16 May 2014 C. Braendle Guadeloupensis sister species of C. guadeloupensis one isolate from Dominica; in Cecropia fruit - SEQUENCED Blaxter - - -
sp. 46 46 NIC1120 F/M C. Braendle Macchu Picchu, Aguas Calientes, Peru 7 April 2015 C. Braendle Elegans Japonica one isolate from Peru - SEQUENCED Blaxter - - -
sp. 47 47 NIC1127 F/M C. Braendle Tambopata region, Amazon, Peru 7 April 2015 C. Braendle Angaria one isolate from Peru - SEQUENCED Blaxter - - -
sp. 48 48 BRC20359 F/M J. Wang Khao Yai National park, Thailand 4 May 2015 J. Wang Elegans Elegans one isolate from Thailand - SSEQUENCED Blaxter - - -
sp. 49 49 BRC20376 F/M J. Wang Solomon Islands - J. Wang Elegans Japonica one isolate Solomon Islands - SEQUENCED Blaxter - - -
sp. 50 50 BRC20387 F/M Dai near Taipei City, Taiwan 18 October 2015 J. Wang Elegans Japonica two isolates from Taiwan - Sequencing_planned Blaxter - - -
sp. 51 51 QG2915 F/M M. Rockman Australia 2017 M Rockman Elegans Elegans two isolates from Australia QG2939 SEQUENCED Blaxter - - -
sp. 52 52 QG2933 F/M M. Rockman Australia 2017 M Rockman one isolate from Australia QG2935 Sequencing_planned Blaxter - - -
oiwi 53 ECA821 F/M E. Andersen Oahu, Hawaii 2017 T Crombie Elegans Elegans, sister of C. kamaaina several isolates from Oahu and Kauai - SEQUENCED Blaxter - - -
sp. 54 54 BRC20468 F/M Hsueh, Yen-Ping Miaoli County?, Taiwan 18 August 2016 J Wang Elegans Elegans - SEQUENCED Blaxter - - -
sp. 55 55 JU3317 F/M M.-A. Félix Pugao Laozhai, Yuanyang, Yunnan, China 5 March 2018 M.-A. Félix Elegans Elegans one isolate from Yunnan, China JU3404 SEQUENCED Blaxter - - -
sp. 56 56 JU2215 F/M M. Joron Tarapoto, Peru October 2012 L. Frézal Angaria close to sp. 8 and 24 one isolate from Peru (JU3313 8x inbred and very sick) SEQUENCED Blaxter - -
krikudae 57 QG3050 F/M M. Rockman Barro Colorado Island, Panama August 2018 M. Rockman Auriculariae sister to monodelphis + auricularia two isolates from Panama QG3077 - - -
sp. 58 58 RS6130 F/M M. Herrmann Bolivia 2019 M. Herrmann close to C. astrocarya JU3779 or JU3880 sent to Blaxter - - -
sp. 59 59 RS6131 F/M M. Herrmann Bolivia 2019 M. Herrmann Elegans Japonica, close to C. becei JU3778 sent to Blaxter - - -
sp. 60 60 QG3550 F/M M. Rockman Costa Rica 2019 M. Rockman Elegans Japonica one isolate QG4242 SEQUENCED Rockman - - -
sp. 61 61 JU4045 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Elegans Elegans one isolate JU4110 - - -
sp. 62 62 JU4050 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Elegans Elegans one isolate JU4112 - - -
sp. 63 63 JU4056 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Elegans Elegans, close to sp. 33 one isolate JU4113 - - -
sp. 64 64 JU4061 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Portoensis one isolate JU4117 SEQUENCED Braendle - - -
sp. 65 65 JU4086 F/M M.-A. Félix Dalat area, Vietnam 2019 M.-A. Félix Elegans Elegans four isolates from Vietnam JU4118 - - -
sp. 66 66 JU4096 F/M M.-A. Félix Dalat area, Vietnam 2019 M.-A. Félix Elegans Elegans, close to sp. 48 and brenneri seven isolates from Vietnam JU4121 - - -
sp. 67 67 QG4215 F/M M. Rockman, E. Andersen Paluma Range, Australia 2020 M. Rockman Elegans Japonica, near sp. 49 and 50 one isolate QG4243 - - -
sp. 68 68 NIC2161 F/M C. Braendle, A. Cutter Nouragues Natural Reserve, French Guiana 2014 C. Braendle Drosophilae near sp. 30 one isolate ongoing - - -
sp. 69 69 NIC2374 F/M C. Braendle Nouragues Natural Reserve, French Guiana 2021 C. Braendle Angaria near dolens one isolate ongoing - - -
sp. 70 70 TT3412 F/M S. Nagarajan, T. Pathak, K. Puraje, M.-A. Félix Neral, Marahashtra, India 2022 T. Pathak, M.-A. Félix, S. Koushika closest to parvicauda one isolate JU4419-21 - - -
sp. 71 71 BRC20593 F/M J. Wang Vietnam 2023 J. Wang 2 isolates - - -
sp. 72 72 QG4708 F/M T. Nguyen, M. Rockman, S. Tintori, H. Yomai Pohnpei, Federated States of Micronesia 2024 T. Nguyen, M. Rockman, S. Tintori, H. Yomai 12 isolates - - -
sp. 73 73 QG4797 F/M T. Nguyen, M. Rockman, S. Tintori, H. Yomai Pohnpei, Federated States of Micronesia 2024 T. Nguyen, M. Rockman, S. Tintori, H. Yomai Japonica near imperialis 11 isolates - - -
sp. 74 74 QG4644 F/M T. Nguyen, M. Rockman, S. Tintori, H. Yomai Pohnpei, Federated States of Micronesia 2024 T. Nguyen, M. Rockman, S. Tintori, H. Yomai Japonica near imperialis 22 isolates - - -
sp. 75 75 QG4848 F/M T. Nguyen, M. Rockman, S. Tintori, H. Yomai Pohnpei, Federated States of Micronesia 2024 T. Nguyen, M. Rockman, S. Tintori, H. Yomai Japonica near imperialis 1 isolate - - -
sp. 76 76 QG4628 F/M T. Nguyen, M. Rockman, S. Tintori, H. Yomai Pohnpei, Federated States of Micronesia 2024 T. Nguyen, M. Rockman, S. Tintori, H. Yomai 100s of isolates - - -


Published phylogeny, up to sp. 21:

  • Kiontke et al. 2011 BMC Evolutionary Biology 11: 339.

Published phylogeny from Kiontke et al. 2011 with species names from Félix, Braendle & Cutter 2014

Updated phylogeny, up to sp. 32:

http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png


2017 phylogeny of a subset of species, based on their genome sequences by Slos et al.

https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2

Stevens et al. 2019, with genomic data from 32 species [1]

Stevens et al. 2020, adding C. bovis [2]

Sloat et al. 2022, with genomic data from 36 species [3]

and the latest unpublished phylogeny [4]. Thank you Lewis!

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