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

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| remanei || d ||  || F/M || - || - || - || - || 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  
 
| remanei || d ||  || F/M || - || - || - || - || 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  
 
|-
 
|-
| drosophilae || f || DF5077 || F/M || - || - || - || - || Drosophilae ||  || rotting saguaro cactus in Arizona, a few isolates || DF5112 || IN SEQUENCING Blaxter || - || - || -  
+
| 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 || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
| plicata || g || SB355 || F/M || - || - || - || - || base ||  || - || - || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
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| monodelphis  || 1 || SB341 || F/M || J. Raschka || Berlin, Germany || 2001 || W. Sudhaus || base ||  || 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] || -  
 
| monodelphis  || 1 || SB341 || F/M || J. Raschka || Berlin, Germany || 2001 || W. Sudhaus || base ||  || 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] || -  
 
|-
 
|-
| sp. 2 || 2 || DF5070 || F/M || S. Wirth || Corsica, France || Oct 2001 || W. Sudhaus || Drosophilae || (sister of drosophilae) || 1 single isolate || - || IN SEQUENCING Blaxter || - || - || -  
+
| 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 || - || Drosophilae || Angaria || 3 isolates from Florida USA || - || SEQUENCED CalTech || [http://wormbase.org WORMBASE] || [https://doi.org/10.1101/gr.111021.110 Mortazavi et al.] || -  
 
| angaria || 3 || PS1010 || F/M || - || - || 1990 || - || Drosophilae || 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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| sinica || 5 ||  || F/M || M.-A. Félix || Chengyang, Guangxi, China || 6 May 2005 || M.-A. Félix || Elegans || Briggase || Isolates from China, Vietnam (Cutter, Ailion, Félix) || JU800 || SEQUENCED Cutter Blaxter || [http://wormbase.org WORMBASE] || - || -  
 
| sinica || 5 ||  || F/M || M.-A. Félix || Chengyang, Guangxi, China || 6 May 2005 || M.-A. Félix || Elegans || Briggase || Isolates from China, Vietnam (Cutter, Ailion, Félix) || JU800 || SEQUENCED Cutter Blaxter || [http://wormbase.org WORMBASE] || - || -  
 
|-
 
|-
| 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 || Sequencing_planned Blaxter || - || - || -  
+
| 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 || Sequenced Blaxter || - || - || -  
 
|-
 
|-
 
| afra || 7 || JU1199 || F/M || M. Herrmann || Begoro, Ghana || Jun 2007 || M.-A. Félix || Japonica group || Japonica || 2 isolates from West Africa (Félix) || JU1286 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
| afra || 7 || JU1199 || F/M || M. Herrmann || Begoro, Ghana || Jun 2007 || M.-A. Félix || Japonica group || Japonica || 2 isolates from West Africa (Félix) || JU1286 || SEQUENCED Blaxter || [http://caenorhabditis.org 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 group || Angaria || Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) || JU3312 || IN SEQUENCING Blaxter || - || - || -  
+
| sp. 8 || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 || M. Rockman || Angaria group || Angaria || 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 || Briggsae subgroup, sister of briggsae || 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] || - || -  
 
| nigoni || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India || 21 Dec 2007 || M.-A. Félix || Briggsae subgroup, sister of briggsae || 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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| doughertyi || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India || 27 Dec 2007 || M.-A. Félix || Brenneri subgroup || Brenneri || 6 isolates from South India || JU1771 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || RNA seq for JU1328 & JU1333  
 
| doughertyi || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India || 27 Dec 2007 || M.-A. Félix || Brenneri subgroup || Brenneri || 6 isolates from South India || JU1771 || SEQUENCED Blaxter || [http://caenorhabditis.org 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 || Brenneri subgroup || Brenneri || Common in tropical regions (not so far on the African continent, one in Asia) || - || SEQUENCED WashU || [http://wormbase.org WORMBASE] || - || -  
+
| tropicalis || 11 || JU1373 || H/M || V. Robert, L. Sablé || Saint-Benoît, La Réunion || Jan 2008 || M.-A. Félix || Brenneri subgroup || Brenneri || Common in tropical regions (not so far on the African continent, one in Asia) || - || SEQUENCED WashU, etc || [http://wormbase.org WORMBASE] || - || -  
 
|-
 
|-
 
| castelli || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || Angaria group || Angaria || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
| castelli || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || Angaria group || 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 super group ||  || Several isolates from two locations in France || JU1968 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
| virilis  || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008 || M.-A. Félix || Drosophilae super group ||  || Several isolates from two locations in France || JU1968 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
|-
 
|-
| imperialis || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia || 24 Jul 2009 || M. Ailion || Japonica group ||  || also Polynesia, Guadeloupe (Félix, Braendle) || EG5942-EG5947 || IN SEQUENCING Blaxter || - || - || -  
+
| imperialis || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia || 24 Jul 2009 || M. Ailion || Japonica group ||  || 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 super group ||  || Kauai and Maui, 2 isolates || QG2076, QG2077 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || - ||   
 
| 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 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || - ||   
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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 || Japonica group ||  || A few isolates from Nouragues, French Guiana || JU2083 || SEQUENCED Cutter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
| macrosperma  || 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 || SEQUENCED Cutter || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
|-
 
|-
| yunquensis  || 19 || EG6142 || F/M || S. Dalton || El Yunque, Puerto Rico || 28 Mar 2010 || S. Dalton, M. Ailion || Japonica group ||  || Puerto Rico || XZ1517-XZ1520 || IN SEQUENCING 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 || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
| guadeloupensis  || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010 || C. Braendle || Drosophilae supergroup ||  || Guadeloupe ||  || SEQUENCED_draft Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || resequencing required  
+
| guadeloupensis  || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010 || C. Braendle || Drosophilae supergroup ||  || Guadeloupe ||  || SEQUENCED Blaxter || [http://caenorhabditis.org 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 || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
| 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://doi.org/10.1101/398446, BIORXIV] || -  
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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 || Briggsae subgroup, sister of C. remanei ||  || Several isolates from China (Cutter) || PX534, PX573, PX574, PX580 || SEQUENCED Phillips || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
| 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 || SEQUENCED Phillips || [http://caenorhabditis.org Caenorhabditis DB] || - || -  
 
|-
 
|-
| sp. 24 || 24 || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || Angaria group, sister of sp. 8 || Angaria || Isolates from California, Panama, Mexico (Rockman, Félix) ||  || IN SEQUENCING Blaxter || - || - || -  
+
| sp. 24 || 24 || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || Angaria group, sister of sp. 8 || Angaria || 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 || Japonica group || Japonica || 2 isolates from Singapore || ZF1457 || IN SEQUENCING Blaxter || - || - || -  
+
| sp. 25 || 25 || ZF1222 || F/M || A. Seah, T. Inoue || Singapore || 3 Sep 2011 || T. Inoue || Japonica group || Japonica || 2 isolates from Singapore || ZF1457 || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
 
| zanzibari || 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 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
| zanzibari || 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 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
|-
 
|-
| sp. 27 || 27 || QX2263 || F/M || - || Buenos Aires, Argentina || 2 Mar 2012 || E. Andersen || Drosophilae supergroup, sister of portoensis ||  || Argentina ||  || IN SEQUENCING Blaxter || - || - || -  
+
| sp. 27 || 27 || QX2263 || F/M || - || Buenos Aires, Argentina || 2 Mar 2012 || E. Andersen || Drosophilae supergroup, sister of portoensis ||  || Argentina ||  || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
 
| panamensis || 28 || QG702 || F/M || M. Rockman || Barro Colorado Island, Panama || 23 Apr 2012 || M. Rockman || Japonica group || Japonica || several isofemale lines from Panama || QG2080, QG2081 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
| panamensis || 28 || QG702 || F/M || M. Rockman || Barro Colorado Island, Panama || 23 Apr 2012 || M. Rockman || Japonica group || Japonica || several isofemale lines from Panama || QG2080, QG2081 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
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| becei || 29 || QG704 || F/M || M. Rockman || Barro Colorado Island, Panama || 25 Apr 2012 || M. Rockman || Japonica group, sister of nouraguensis || Japonica || many isofemale lines from Panama || QG2082, QG2083 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
| becei || 29 || QG704 || F/M || M. Rockman || Barro Colorado Island, Panama || 25 Apr 2012 || M. Rockman || Japonica group, sister of nouraguensis || Japonica || many isofemale lines from Panama || QG2082, QG2083 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
|-
 
|-
| sp. 30 || 30 || DF5152 || F/M || - || Gallon Jug, Belize || 15 Nov 2012 || K. Kiontke || Drosophilae subgroup ||  || 4 isofemale lines from Belize || ongoing (K. Kiontke) || IN SEQUENCING Blaxter || - || - || -  
+
| sp. 30 || 30 || DF5152 || F/M || - || Gallon Jug, Belize || 15 Nov 2012 || K. Kiontke || Drosophilae subgroup ||  || 4 isofemale lines from Belize || ongoing (K. Kiontke) || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
 
| uteleia || 31 || JU2469 || F/M || - || Madre de Dios, Peru || Jan 2013 || L. Frézal || May branch basally within the Elegans supergroup, see Slos et al. ||  || 2 isolates from Peru || JU2585 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
| uteleia || 31 || JU2469 || F/M || - || Madre de Dios, Peru || Jan 2013 || L. Frézal || May branch basally within the Elegans supergroup, see Slos et al. ||  || 2 isolates from Peru || JU2585 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
Line 88: Line 88:
 
| sp. 36 || 36 || NK02NV || F/M || N. Kanzaki || Tokyo, Japan || Apr 2013 || N. Kanzaki || Japonica group || Japonica || 1 isolate from Japan. Associated with the weevil Niphades variegatus || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || -  
 
| sp. 36 || 36 || NK02NV || F/M || N. Kanzaki || Tokyo, Japan || Apr 2013 || N. Kanzaki || Japonica group || Japonica || 1 isolate from Japan. Associated with the weevil Niphades variegatus || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || -  
 
|-
 
|-
| 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 || Angaria || 1 isolate from French Guiana || - || IN SEQUENCING Blaxter || - || - || -  
+
| 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 group || Angaria || 1 isolate from Guadeloupe || JU2809 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
 
| quiockensis || 38 || JU2745 || F/M || F. Besnard || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || Angaria group || Angaria || 1 isolate from Guadeloupe || JU2809 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || -  
Line 98: Line 98:
 
| sp. 41 || 41 || BRC20276 || F/M || - || Solomon Islands || October 2014 || J. Wang || Briggsae subgroup, sister species of C. sp. 40 || Briggsae || 2 isolates from Solomon Islands || - || IN SEQUENCING Wang Tsai || - || - || -  
 
| sp. 41 || 41 || BRC20276 || F/M || - || Solomon Islands || October 2014 || J. Wang || Briggsae subgroup, sister species of C. sp. 40 || Briggsae || 2 isolates from Solomon Islands || - || IN SEQUENCING Wang Tsai || - || - || -  
 
|-
 
|-
| sp. 42 || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || Drosophilae super group || Drosophilae || one isolate from French Guiana || - || IN SEQUENCING Blaxter || - || - || -  
+
| astrocarya || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || Drosophilae super group || Drosophilae || one isolate from French Guiana || - || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
| vivipara || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle || Drosophilae super group || Drsophilae || 2 isolates from Mexico; in orange berries || NIC1581 || SEQUENCED_draft Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || resequencing required  
+
| vivipara || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle || Drosophilae super group || Drsophilae || 2 isolates from Mexico; in orange berries || NIC1581 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || resequencing required  
 
|-
 
|-
 
| sp. 44 || 44 || BRC20300 || F/M || J. Wang || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || sister species of C. brenneri ||  || one isolate from Taiwan; in flowers || - || IN SEQUENCING Wang Tsai || - || - || -  
 
| sp. 44 || 44 || BRC20300 || F/M || J. Wang || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || sister species of C. brenneri ||  || 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 || sister species of  C. guadeloupensis ||  || one isolate from Dominica; in Cecropia fruit || - || IN SEQUENCING Blaxter || - || - || -  
+
| 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 || - || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
| sp. 46 || 46 || NIC1120 || F/M || C. Braendle || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015 || C. Braendle || Japonica group || Japonica || one isolate from Peru || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 46 || 46 || NIC1120 || F/M || C. Braendle || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015 || C. Braendle || Japonica group || 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 group || Angaria || one isolate from Peru || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 47 || 47 || NIC1127 || F/M || C. Braendle || Tambopata region, Amazon, Peru || 7 April 2015 || C. Braendle || Angaria group || 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 || sister of C. brenneri || Brenneri || one isolate from Thailand || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 48 || 48 || BRC20359 || F/M || J. Wang || Khao Yai National park, Thailand || 4 May 2015 || J. Wang || sister of C. brenneri || Brenneri || one isolate from Thailand || - || SSEQUENCED Blaxter || - || - || -  
 
|-
 
|-
| sp. 49 || 49 || BRC20376 || F/M || J. Wang || Solomon Islands || - || J. Wang || Japonica group? || Japonica || one isolate Solomon Islands || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 49 || 49 || BRC20376 || F/M || J. Wang || Solomon Islands || - || J. Wang || Japonica group? || Japonica || one isolate Solomon Islands || - || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
 
| sp. 50 || 50 || BRC20387 || F/M || Dai || near Taipei City, Taiwan || 18 October 2015  ||J. Wang || Elegans || Elegans || two isolates from Taiwan || - || Sequencing_planned Blaxter || - || - || -  
 
| sp. 50 || 50 || BRC20387 || F/M || Dai || near Taipei City, Taiwan || 18 October 2015  ||J. Wang || Elegans || Elegans || two isolates from Taiwan || - || Sequencing_planned Blaxter || - || - || -  
 
|-
 
|-
| sp. 51 || 51 || QG2915 || F/M || M. Rockman || Australia || 2017 || M Rockman || Elegans || Elegans || one isolate from Australia || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 51 || 51 || QG2915 || F/M || M. Rockman || Australia || 2017 || M Rockman || Elegans || Elegans || one isolate from Australia || - || SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
 
| sp. 52 || 52 || QG2933 || F/M || M. Rockman || Australia || 2017 || M Rockman || Drosophilae ||  || one isolate from Australia || - || Sequencing_planned Blaxter || - || - || -  
 
| sp. 52 || 52 || QG2933 || F/M || M. Rockman || Australia || 2017 || M Rockman || Drosophilae ||  || one isolate from Australia || - || Sequencing_planned Blaxter || - || - || -  
 
|-
 
|-
| sp. 53 || 53 || ECA821 || F/M || E. Andersen || Oahu, Hawaii || 2017 || T Crombie || sister of C. kamaaina ||  || several isolates from Oahu and Kauai || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 53 || 53 || ECA821 || F/M || E. Andersen || Oahu, Hawaii || 2017 || T Crombie || 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 ||  ||  || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 54 || 54 || BRC20468 || F/M || Hsueh, Yen-Ping || Miaoli County?, Taiwan || 18 August 2016 || J Wang || Elegans ||  ||  || - || SEQUENCED Blaxter|| - || - || -  
 
|-
 
|-
| sp. 55 || 55 || JU3317 || F/M || M.-A. Félix || Pugao Laozhai, Yuanyang, Yunnan, China || 5 March 2018 || M.-A. Félix || Elegans ||  || one isolate from Yunnan, China || - || Sequencing_planned Blaxter || - || - || -  
+
| sp. 55 || 55 || JU3317 || F/M || M.-A. Félix || Pugao Laozhai, Yuanyang, Yunnan, China || 5 March 2018 || M.-A. Félix || Elegans ||  || one isolate from Yunnan, China || - ||SEQUENCED Blaxter || - || - || -  
 
|-
 
|-
| sp. 56 || 56 || JU2215 || F/M || M. Joron || Tarapoto, Peru || October 2012 || L. Frézal || Angaria group, close to spp. 8 and 24 || Angaria || one isolate from Peru || (JU3313 8x inbred and very sick) || Sequencing_planned Blaxter || - || - || -
+
| sp. 56 || 56 || JU2215 || F/M || M. Joron || Tarapoto, Peru || October 2012 || L. Frézal || Angaria group, close to spp. 8 and 24 || Angaria || one isolate from Peru || (JU3313 8x inbred and very sick) || SEQUENCED Blaxter || - || - || -
 
|-  
 
|-  
 
| sp. 57 || 57 || QG3050 || F/M || M. Rockman || Barro Colorado Island, Panama || August 2018 || M. Rockman || near monodelphis and sonorae? ||  || two isolates from Panama || in inbreeding ||  || - || - || -  
 
| sp. 57 || 57 || QG3050 || F/M || M. Rockman || Barro Colorado Island, Panama || August 2018 || M. Rockman || near monodelphis and sonorae? ||  || two isolates from Panama || in inbreeding ||  || - || - || -  

Revision as of 16:57, 1 July 2019

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 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 world-wide distribution, 100s of isolates N.A. SEQUENCED WashU WORMBASE Stein et al. 2003 37 wild isolates sequenced 30x (Cutter lab)
japonica c F/M - - - - Elegans Japonica isolates from Japan (Yoshiga/Cutter) DF5080 SEQUENCED WashU WORMBASE - -
remanei d F/M - - - - 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 - -
monodelphis 1 SB341 F/M J. Raschka Berlin, Germany 2001 W. Sudhaus base 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 - Drosophilae 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 Briggase 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 Drosophilae super group Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) EG5626 Sequenced Blaxter - - -
afra 7 JU1199 F/M M. Herrmann Begoro, Ghana Jun 2007 M.-A. Félix Japonica group 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 group Angaria 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 Briggsae subgroup, sister of briggsae 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 Brenneri subgroup Brenneri 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 Brenneri subgroup Brenneri Common in tropical regions (not so far on the African continent, one in Asia) - SEQUENCED WashU, etc WORMBASE - -
castelli 12 JU1426 F/M P. Châtelet Nouragues Forest, French Guiana May 2008 M.-A. Félix Angaria group 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 super group 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 Japonica group 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 super group 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 Brenneri subgroup 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 Japonica group 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 Japonica group 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 Japonica group Puerto Rico XZ1517-XZ1520 SEQUENCED Blaxter - - -
guadeloupensis 20 NIC113 F/M C. Braendle Soufrière Forest trail, Guadeloupe Mar 2010 C. Braendle Drosophilae supergroup 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 BIORXIV -
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 SEQUENCED Phillips Caenorhabditis DB - -
sp. 24 24 QG555 F/M A. Paaby Santa Barbara, USA July 2011 A. Paaby Angaria group, sister of sp. 8 Angaria 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 Japonica group Japonica 2 isolates from Singapore ZF1457 SEQUENCED Blaxter - - -
zanzibari 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 SEQUENCED Blaxter Caenorhabditis DB BIORXIV -
sp. 27 27 QX2263 F/M - Buenos Aires, Argentina 2 Mar 2012 E. Andersen Drosophilae supergroup, sister of portoensis Argentina SEQUENCED Blaxter - - -
panamensis 28 QG702 F/M M. Rockman Barro Colorado Island, Panama 23 Apr 2012 M. Rockman Japonica group Japonica several isofemale lines from Panama QG2080, QG2081 SEQUENCED Rockman Caenorhabditis DB BIORXIV -
becei 29 QG704 F/M M. Rockman Barro Colorado Island, Panama 25 Apr 2012 M. Rockman Japonica group, sister of nouraguensis Japonica many isofemale lines from Panama QG2082, QG2083 SEQUENCED Rockman Caenorhabditis DB BIORXIV -
sp. 30 30 DF5152 F/M - Gallon Jug, Belize 15 Nov 2012 K. Kiontke Drosophilae subgroup 4 isofemale lines from Belize ongoing (K. Kiontke) SEQUENCED Blaxter - - -
uteleia 31 JU2469 F/M - Madre de Dios, Peru Jan 2013 L. Frézal May branch basally within the Elegans supergroup, see Slos et al. 2 isolates from Peru JU2585 SEQUENCED Blaxter Caenorhabditis DB BIORXIV -
sulstoni 32 SB454 F/M - East Africa? Feb 2013 W. Sudhaus Japonica group, sister of afra Japonica 1 isolate, from the gut of the millipede Archispirostreptus gigas JU2788 SEQUENCED Blaxter Caenorhabditis DB BIORXIV -
sp. 33 33 BRC20065 F/M J. Wang Taiwan 24 May 2012 J. Wang Elegans Briggsae 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 supergroup, with C. sp. 35 sister of C. elegans 1 isolate from Japan. Associated with fig wasps and Ficus septica - SEQUENCED Kanzaki, Kikuchi Caenorhabditis DB - -
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 - IN SEQUENCING Kanzaki, Kikuchi - - -
sp. 36 36 NK02NV F/M N. Kanzaki Tokyo, Japan Apr 2013 N. Kanzaki Japonica group Japonica 1 isolate from Japan. Associated with the weevil Niphades variegatus - IN SEQUENCING Kanzaki, Kikuchi - - -
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 group Angaria 1 isolate from Guadeloupe JU2809 SEQUENCED Blaxter Caenorhabditis DB BIORXIV -
waitukubuli 39 NIC564 F/M C. Braendle Dominica 13 May 2014 C. Braendle Japonica group Japonica 1 isolate from Dominique - SEQUENCED Blaxter Caenorhabditis DB BIORXIV -
tribulationis 40 JU2774 F/M J.-B. Pénigault Danbulla, Australia 08 August 2014 L. Frézal Briggsae subgroup, close relative of C. sinica Briggsae 5 isolates from Australia, in fresh or rotting figs JU2818 SEQUENCED Blaxter Caenorhabditis DB BIORXIV -
sp. 41 41 BRC20276 F/M - Solomon Islands October 2014 J. Wang Briggsae subgroup, sister species of C. sp. 40 Briggsae 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 Drosophilae super group Drosophilae one isolate from French Guiana - SEQUENCED Blaxter - - -
vivipara 43 NIC1070 F/M C. Gosse Chichén Itzá, Yucatán, Mexico 17 October 2014 C. Braendle Drosophilae super group Drsophilae 2 isolates from Mexico; in orange berries NIC1581 SEQUENCED Blaxter Caenorhabditis DB BIORXIV resequencing required
sp. 44 44 BRC20300 F/M J. Wang Shihting mountain near Taipei City, Taiwan Dec 2014 J. Wang sister species of C. brenneri 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 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 Japonica group 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 group 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 sister of C. brenneri Brenneri one isolate from Thailand - SSEQUENCED Blaxter - - -
sp. 49 49 BRC20376 F/M J. Wang Solomon Islands - J. Wang Japonica group? Japonica one isolate Solomon Islands - SEQUENCED Blaxter - - -
sp. 50 50 BRC20387 F/M Dai near Taipei City, Taiwan 18 October 2015 J. Wang Elegans Elegans two isolates from Taiwan - Sequencing_planned Blaxter - - -
sp. 51 51 QG2915 F/M M. Rockman Australia 2017 M Rockman Elegans Elegans one isolate from Australia - SEQUENCED Blaxter - - -
sp. 52 52 QG2933 F/M M. Rockman Australia 2017 M Rockman Drosophilae one isolate from Australia - Sequencing_planned Blaxter - - -
sp. 53 53 ECA821 F/M E. Andersen Oahu, Hawaii 2017 T Crombie 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 - SEQUENCED Blaxter - - -
sp. 55 55 JU3317 F/M M.-A. Félix Pugao Laozhai, Yuanyang, Yunnan, China 5 March 2018 M.-A. Félix Elegans one isolate from Yunnan, China - SEQUENCED Blaxter - - -
sp. 56 56 JU2215 F/M M. Joron Tarapoto, Peru October 2012 L. Frézal Angaria group, close to spp. 8 and 24 Angaria one isolate from Peru (JU3313 8x inbred and very sick) SEQUENCED Blaxter - - -
sp. 57 57 QG3050 F/M M. Rockman Barro Colorado Island, Panama August 2018 M. Rockman near monodelphis and sonorae? two isolates from Panama in inbreeding - - -


Species numbers are assigned by Karin Kiontke, NYU.

Published phylogeny, up to sp. 21:

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

See Stevens et al. 2019 [1]

and the latest unpublished phylogeny [2]. Thank you Lewis!