From g.read from niwa.co.nz Wed Jun 4 16:02:10 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Wed Jun 4 16:05:05 2008 Subject: [Annelida] Caution - Error propagation Message-ID: <4847AB91.8045.00D5.0@niwa.co.nz> Hi Folks, Maybe the productive writings of Ann Arbor are more familiar to our North American members. A comment in this week's Nature notes that Professor Arbor has an h-index of 1 from the Web of Science database provided by Thomson Scientific's ISI Web of Knowledge. This is based on her five citations for the year 2007: two articles, two letters and one abstract. (Nature 453, 719 (5 June 2008) | doi:10.1038/453719c) In her other life Ann Arbor is a city in Michigan, and significantly a university town. A previous note observed that: "The career of the non-existent author Ann Arbor is well-known to connoisseurs of computerized databases and citation indexes. Usually listed as the last author, she is sometimes credited with the academic degree "MI". Ann is not actually a person, but the city of Ann Arbor, Michigan, home of the University of Michigan. Her 'degree' is a misinterpretation of the abbreviation for Michigan: MI. She pre-dates online computerized databases, and was often listed in the paper edition of Index Medicus. "Ms Arbor now has a UK rival in the team of Walton Hall and Milton Keynes. Like her, they are usually listed as last authors. The online database Google Scholar lists them as co-authors of 46 publications, in addition to their solo work (see http://tinyurl.com/386wuo). Walton Hall is actually a building on the campus of the Open University in Milton Keynes. These 'authors' have a useful role to play: they can be used to check the accuracy of the databases and indexes. (from: http://dx.doi.org/10.1038/452282b Nature 452, 282 (2008) | doi:10.1038/452282b.) In an age when 'information' is increasingly harvested for us by brute-force computer bots, as well as still data-entered by the uncomprehending, it pays to check back with the original - also now easier because of digitisation - to avoid adding to the bubbling stew of misinformation out there. Geoff -- Geoff Read http://www.annelida.net/ http://www.niwascience.co.nz/ncabb/ From smithack07 from gmail.com Mon Jun 9 01:32:16 2008 From: smithack07 from gmail.com (smitha ck) Date: Mon Jun 9 01:38:54 2008 Subject: [Annelida] request Message-ID: Hi all, May I know about Typhloscolecidae? I got a specimen,*Travisiopsis* sp. from 100m depth,Indian shelf. Expecting your valuable responses. -- regards Smitha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080608/ff4aa553/attachment.html From g.read from niwa.co.nz Mon Jun 9 02:26:22 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Mon Jun 9 02:36:26 2008 Subject: Typhloscolecidae Re: [Annelida] request In-Reply-To: References: Message-ID: <484D83DC.8045.00D5.0@niwa.co.nz> >>> On 9/06/2008 at 6:32 p.m., "smitha ck" wrote: > Hi all, > May I know about Typhloscolecidae? I got a specimen,*Travisiopsis* sp. from > 100m depth,Indian shelf. > Expecting your valuable responses. > -- > regards > Smitha The below citation might be relevant. ?resland, V. ; Bray, R. 2005: Parasites and headless chaetognaths in the Indian Ocean. Marine Biology 147(3): 725 - 734. abstract in part: "Typhloscolecid polychaetes, assigned to the genera Typhloscolex (Typhloscolex muelleri) and Travisiopsis (Travisiopsis dubia), feeding on chaetognaths are reported for the first time from the Indian Ocean. These parasitic/predatory polychaetes cause decapitation in the chaetognath Flacisagitta enflata, either by eating the head or by causing injuries to the neck or body. Data from eastern Africa to western India showed a peak of polychaete infestation and decapitation of F. enflata in the Seychelles. A 5% peak occurrence (turnover rate is unknown) of decapitated individuals indicates that this parasitism/predation may have an important impact on local F. enflata populations. [...] There seem to be several more possible sources of information if one simply googles "Travisiopsis indian ocean" Also useful: Dales, R. P. ; Peter, G. 1972: A synopsis of the pelagic polychaeta. Journal of Natural History. 6: 55-92. And a species list for the genus: http://www.marinespecies.org/aphia.php?p=taxdetails&id=129721 Cheers, Geoff -- Geoff Read http://www.annelida.net/ http://www.niwascience.co.nz/ncabb/ From yckingf from gmail.com Mon Jun 9 10:27:24 2008 From: yckingf from gmail.com (Francis King) Date: Mon Jun 9 14:46:48 2008 Subject: [Annelida] Morphology detailing required comment for hirudinae leeches Message-ID: <2f7c12960806090827y51c8da9eh4562b376d7cd2f04@mail.gmail.com> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: Full green sex organs 1 close up 2.JPG Type: image/jpeg Size: 37918 bytes Desc: not available Url : http://www.bio.net/bionet/mm/annelida/attachments/20080609/2ee6de45/Fullgreensexorgans1closeup2.jpeg -------------- next part -------------- A non-text attachment was scrubbed... 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Name: Full green belly on glass plate 2008a bottom view.jpg Type: image/jpeg Size: 60238 bytes Desc: not available Url : http://www.bio.net/bionet/mm/annelida/attachments/20080609/2ee6de45/Fullgreenbellyonglassplate2008abottomview.jpg From gerard.bellan from univmed.fr Mon Jun 16 03:47:44 2008 From: gerard.bellan from univmed.fr (=?ISO-8859-1?Q?G=E9rard_BELLAN?=) Date: Mon Jun 16 14:42:07 2008 Subject: [Annelida] Lucien Laubier Message-ID: Dear Annelidian, I received this morning the following internal (Centre d'Oc?anologie de Marseille) message : Bonjour a tous, C'est avec beaucoup d'?motion que nous venons d'apprendre le deces de Monsieur Laubier dimanche matin a l'Institut Paoli Calmettes a Marseille. Nous n'avons pas encore d'informations au sujet de ses obs?ques mais nous ne manquerons pas de vous informer a ce sujet. Pour la Direction du COM, Katherine Walch Lucien Laubier passed away yesterday morning in a Marseilles (Cancer) Hospital. Lucien was ill for some years. He came at Station Marine d'Endoume time to time and both Denise (Bellan-Santini) and myself talked with him few weeks ago. I've no more details. I'll send you new message as soon as possible. So long, Lucien G?rard G?rard BELLAN gerard.bellan@univmed.fr Directeur de recherche Em?rite au CNRS Centre d'Oc?anologie de Marseille UMR DIMAR, Station marine d'Endoume, Rue Batterie des Lions 13007 Marseille, France Tel.: (33) 491 04 16 12 Fax : (33) 491 04 16 35 Mail : gerard.bellan@univmed.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080616/19e5217e/attachment.html From gerard.bellan from univmed.fr Mon Jun 16 03:50:57 2008 From: gerard.bellan from univmed.fr (=?ISO-8859-1?Q?G=E9rard_BELLAN?=) Date: Mon Jun 16 14:42:41 2008 Subject: [Annelida] Lucien Laubier death Message-ID: Last new about Lucien Laubier G?rard > De : Katherine WALCH > Date : 16 juin 2008 10:30:44 HAEC > ? : destinataires inconnus:; > Objet : Obseques L. Laubier > > Bonjour, > > > Les obseques du Professeur Lucien Laubier, decede dimanche matin > auront lieu mercredi 18 juin a 10h30 au Funerarium St Pierre 13005 > Marseille. Elles seront suivies de l'incineration. > > Bien cordialement > K. Walch G?rard BELLAN gerard.bellan@univmed.fr Directeur de recherche Em?rite au CNRS Centre d'Oc?anologie de Marseille UMR DIMAR, Station marine d'Endoume, Rue Batterie des Lions 13007 Marseille, France Tel.: (33) 491 04 16 12 Fax : (33) 491 04 16 35 Mail : gerard.bellan@univmed.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080616/7f12a55d/attachment.html From salvador.herrando-perez from adelaide.edu.au Tue Jun 17 02:58:02 2008 From: salvador.herrando-perez from adelaide.edu.au (Salvador Herrando-Perez) Date: Tue Jun 17 14:45:59 2008 Subject: [Annelida] polychaete and statistics: papers missing Message-ID: Dear colleagues, I am undertaking a literature review considering both polychaetes and statistical procedures addressing community patterns. The papers below I have been unable to get them from the authors or the on-line resources at my university. I would appreciate a pdf if available. Kind regards Salva Salvador Herrando-P?rez School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia Office phone: +61 8 8303 5254 / Office fax: +61 8 8303 4347 / Mobile phone: +61 406049010 https://www.adelaide.edu.au/directory/salvador.herrando-perez Munari, C; Mistri, M 2007 INDIAN JOURNAL OF MARINE SCIENCES Structure and secondary production of the macrobenthic community in an aquatic transition environment of the Gulf of Olbia, Mediterranean Sea Garraffoni, ARS; Camargo, MD 2007 CAHIERS DE BIOLOGIE MARINE A new application of morphometrics in a study of the variation in uncinal shape present within the Terebellidae (Polychaeta): a reevaluation from digital images Thomas, JV; Sreedevi, C; Kurup, BM 2006 INDIAN JOURNAL OF MARINE SCIENCES Variations on the infaunal polychaetes due to bottom trawling along the inshore waters of Kerala (south-west coast of India) Uysal, Z; Murina, GVV 2005 ISRAEL JOURNAL OF ZOOLOGY Monthly changes in the composition and abundance of meroplankton and pelagic polychaetes of the Cilician basin shelf waters (eastern Mediterranean) Antoniadou, C; Krestenitis, Y; Chintiroglou, C 2004 FRESENIUS ENVIRONMENTAL BULLETIN Structure of the "Amphioxus sand" community in Thermaikos bay (Eastern Mediterranean) dos Santos Brasil, AC; da Silva, SHG 2000 BULLETIN OF MARINE SCIENCE Spatial distribution of polychaeta in a soft-bottom community at Saco Do Ceu, Ilha Grande, Rio de Janeiro, Brazil Rodriguez-Villanueva, V; Martinez-Lara, R; Diaz-Castaneda, V 2000 BULLETIN OF MARINE SCIENCE Structure and composition of the benthic polychaete families in Bahia de Todos Santos, Baja California, Mexico Lopez, E; Vieitez, JM 1999 CAHIERS DE BIOLOGIE MARINE Polychaete assemblages on non-encrusting infralittoral algae from the Chafarinas Islands (SW Mediterranean) Mendez, N; Ruiz, MG 1998 REVISTA DE BIOLOGIA TROPICAL Superficial sediments and their relation to polychaete families in a subtropical embayment, Mexico Mendez, N; Flos, J; Romero, J 1998 BULLETIN OF MARINE SCIENCE Littoral soft-bottom polychaete communities in a pollution gradient in front of Barcelona (Western Mediterranean, Spain) Carrasco, FD 1997 BULLETIN OF MARINE SCIENCE Sublittoral macrobenthic fauna off Punta Coloso, Antofagasta, Northern Chile: High persistence of the polychaete assemblage Fromentin, JM; Dauvin, JC; Ibanez, F; Dewarumez, JM; Elkaim, B 1997 OCEANOLOGICA ACTA Long-term variations of four macrobenthic community structures PARDAL, MA; MARQUES, JC; BELLAN, G 1993 CAHIERS DE BIOLOGIE MARINE SPATIAL-DISTRIBUTION AND SEASONAL-VARIATION OF SUBTIDAL POLYCHAETE POPULATIONS IN THE MONDEGO ESTUARY (WESTERN PORTUGAL) OZOLINYSH, AV 1992 SOVIET JOURNAL OF ECOLOGY SEASONAL-CHANGES IN POLYCHAETA TAXOCENES OF THE SUBLITORAL IN THE FAR-EASTERN MARINE RESERVE CAPACCIONIAZZATI, R; VILLORAMORENO, S; GARCIACARRASCOSA, AM; TORRESGAVILA, FJ 1991 BULLETIN OF MARINE SCIENCE DISTRIBUTIONAL PATTERNS OF POLYCHAETA IN THE ALFAQUES INLET (EBRO RIVER DELTA - WESTERN MEDITERRANEAN) - FAUNISTIC AND COENOTIC ANALYSIS OF AN ESTUARINE SYSTEM VILLORAMORENO, S; CAPACCIONIAZZATI, R; GARCIACARRASCOSA, AM 1991 BULLETIN OF MARINE SCIENCE MEIOBENTHOS OF SANDY BEACHES FROM THE GULF-OF-VALENCIA (WESTERN MEDITERRANEAN) - ECOLOGY OF INTERSTITIAL POLYCHAETES -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080617/626e44fb/attachment.html From salvador.herrando-perez from adelaide.edu.au Tue Jun 17 03:00:00 2008 From: salvador.herrando-perez from adelaide.edu.au (Salvador Herrando-Perez) Date: Tue Jun 17 14:46:19 2008 Subject: [Annelida] polychaete-statistics: missed one! Message-ID: <26A16F3627FF402DA86D12D71E868C6C@ad.adelaide.edu.au> Diaz-Castaneda, V 2000 BULLETIN OF MARINE SCIENCE The early establishment and development of a polychaete community settled on artificial substrata at Todos Santos Bay, Baja California, Mexico -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080617/57a50905/attachment.html From g.read from niwa.co.nz Wed Jun 18 15:55:40 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Wed Jun 18 15:57:40 2008 Subject: [Annelida] Worm architecture & Fibonacci Message-ID: <485A1F0B.8045.00D5.0@niwa.co.nz> Greetings all & FYI, Fun with numbers and segment sequences and siblings. Glasby, C. J.; Glasby, S. P. ; Pleijel, F. 2008: Worms by number. Proceedings of the Royal Society B: Biological Sciences [efirst status] http://journals.royalsociety.org/content/m1411840133k2q32/ or DOI http://dx.doi.org/10.1098/rspb.2008.0418 Background: http://www.abc.net.au/science/articles/2008/06/18/2278459.htm?site=scien Abstract: This paper investigates alternation patterns in length, shape and orientation of dorsal cirri (fleshy segmental appendages) of phyllodocidans, a large group of polychaete worms (Annelida). We document the alternation patterns in several families of Phyllodocida (Syllidae, Hesionidae, Sigalionidae, Polynoidae, Aphroditidae and Acoetidae) and identify the simple mathematical rule bases that describe the progression of these sequences. Two fundamentally different binary alternation patterns were found on the first four segments: 1011 for nereidiform families and 1010 for aphroditiform families. The alternation pattern in all aphroditiform families matches a simple one-dimensional cellular automaton and that for Syllidae (nereidiform) matches the Fibonacci string sequence. Hesionidae (nereidiform) showed the greatest variation in alternation patterns, but all corresponded to various known substitution rules. Comparison of binary patterns of the first 22 segments using a distance measure supports the current ideas on phylogeny within Phyllodocida. These results suggest that gene(s) involved in post-larval segmental growth employ a switching sequence that corresponds to simple mathematical substitution rules. -- Geoff Read http://www.annelida.net/ http://www.niwascience.co.nz/ncabb/ From g.read from niwa.co.nz Thu Jun 19 17:05:49 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Thu Jun 19 17:12:58 2008 Subject: [Annelida] Dem bones, dem bones, dem cow bones Message-ID: <485B80FC.8045.00D5.0@niwa.co.nz> Greetings all and FYI, Dem bones, dem bones gonna walk around ... Another couple of efirsts in Proc Roy Soc Uk http://journals.royalsociety.org/content/102024/ Commentary: Glover, A. G.; Kemp, K. M.; Smith, C. R. ; Dahlgren, T. G. 2008: On the role of bone-eating worms in the degradation of marine vertebrate remains. Proceedings of the Royal Society B: Biological Sciences [efirst] http://dx.doi.org/10.1098/rspb.2008.0177 Reply: Vrijenhoek, R. C.; Collins, P. ; Van Dover, C. L. 2008: Bone-eating marine worms: habitat specialists or generalists? Proceedings of the Royal Society B: Biological Sciences [efirst] http://dx.doi.org/10.1098/rspb.2008.0350 Original article: Jones, W. J.; Johnson, S. B.; Rouse, G. W. ; Vrijenhoek, R. C. 2008: Marine worms (genus Osedax) colonize cow bones. Proceedings of the Royal Society B-Biological Sciences 275(1633): 387-391. Cheers, Geoff -- Geoff Read http://www.annelida.net/ http://www.niwascience.co.nz/ncabb/ From g.read from niwa.co.nz Sat Jun 21 03:54:27 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Sat Jun 21 03:57:58 2008 Subject: [Annelida] Vouchers again Message-ID: <485D6A81.8045.00D5.0@niwa.co.nz> Dear all, Noticed this from Fred and others in the latest issue of Molecular Phylogenetics and Evolution: http://www.sciencedirect.com/science/journal/10557903 Pleijel, F.; Jondelius, U.; Norlinder, E.; Nygren, A.; Oxelman, B.; Schander, C.; Sundberg, P. ; Thollesson, M. 2008: Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Molecular Phylogenetics and Evolution 48(1): 369-371. http://dx.doi.org/10.1016/j.ympev.2008.03.024 Quote for flavour: "Today there is a large number of sequences deposited at GenBank that are incorrectly labeled and, unless remedied, these will continuously be associated with the wrong taxa. Vouchers constitute an essential link between data and taxa, and provide a means to verify the taxonomic identity of the specimens sequenced. However, only a minority of journals require that vouchers connected to the genetic information be deposited in museums or other institutions. Furthermore, at GenBank there is currently no dedicated field for specification of vouchers." I know of instances where new molecular studies has found the misidentification in the old work, but are there cases where an actual taxonomist has re-examined the voucher and found the misidentification simply by eyeballing it? Precise (gps) geographic information is also very useful to include with molecular data, and, lacking a voucher, will be helpful if a species is not one of those that roam the seas via shipping, or doesn't appear to have a wide natural range. Misidentification goes on all the time in ecological papers with few consequences, and in taxonomic papers too (one hopes with a lesser frequency, but perfection is a distant goal for all of us). At least the GenBank ones will eventually be detected, vouchered or not, maybe in a highly embarrassing fashion for the original authors. You have been warned! Here is an interesting complex case in freshwater limpets involving a misidentified GenBank sequence: Walther, A. C.; Lee, T.; Burch, J. B. ; Foighil, D. O. 2006: Acroloxus lacustris is not an ancylid: A case of misidentification involving the cryptic invader Ferrissia fragilis (Mollusca: Pulmonata: Hygrophila). Molecular Phylogenetics and Evolution 39(1): 271-275. http://dx.doi.org/10.1016/j.ympev.2005.08.014 Even more interesting is that the misidentified entry (AY577462) as A lacustris is still seemingly uncorrected in GenBank. Why is this? Have I got this right? It seems very strange. See http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?46451261:NCBI:6982153 Geoff -- Geoff Read http://www.annelida.net/ http://www.niwascience.co.nz/ncabb/ From g.read from niwa.co.nz Sun Jun 22 15:29:13 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Sun Jun 22 15:31:34 2008 Subject: Fwd: RE: [Annelida] Vouchers again References: <485D6A81.8045.00D5.0@niwa.co.nz> Message-ID: <485F5ED8.8045.00D5.0@niwa.co.nz> Response of Sergio Salazar. Intended for the list. >>> On 22/06/2008 at 2:58 a.m., Sergio Salazar wrote: Dear friends, If the molecular studies have such a sad panorama, just think about the traditional ecological studies. Almost no journal request detailing identification manuals or procedures, nor the deposit of a reference collection. In a couple of papers on science and taxonomy policy (in Spanish, sorry), we have argued, among other things, that there is at least a 5:1 abundance of ecologists:taxonomists. If ecologists, despite the fact of being the main users of taxonomic publications, do not support taxonomy by citing key publications and by vouchering specimens, then who would back up our requests for more and better funding? Of course, if ecologists suddenly want to deposit their materials, we will face a very serious demand for space and expertise, making worse the current taxonomy crisis. Nevertheless, once our natural partners (ecologists) become our political allies, we might get better funding programs and help solve the staff and space issues in a not so far future. We have also stated that solving the taxonomy crisis is a national issue. National and state governments must provide funding to improve the current situation. The needs might be solved with a modest amount of money. The political will is more difficult to obtain, indeed. Support your nearest taxonomist, Sergio > Date: Sat, 21 Jun 2008 20:54:27 +1200> From: g.read@niwa.co.nz> To: annelida@magpie.bio.indiana.edu> CC: > Subject: [Annelida] Vouchers again> > Dear all,> > Noticed this from Fred and others in the latest issue of Molecular Phylogenetics and Evolution: > http://www.sciencedirect.com/science/journal/10557903 > > Pleijel, F.; Jondelius, U.; Norlinder, E.; Nygren, A.; Oxelman, B.; Schander, C.; Sundberg, P. ; Thollesson, M. 2008: Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Molecular Phylogenetics and Evolution 48(1): 369-371. -------------- next part -------------- A non-text attachment was scrubbed... Name: Header Type: application/octet-stream Size: 1286 bytes Desc: not available Url : http://www.bio.net/bionet/mm/annelida/attachments/20080623/eb1a57bc/Header.exe From Pat.Hutchings from austmus.gov.au Mon Jun 23 21:47:38 2008 From: Pat.Hutchings from austmus.gov.au (Pat Hutchings) Date: Mon Jun 23 21:49:27 2008 Subject: [Annelida] a new publication on position of polychaetes Message-ID: Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/bmp Size: 13854 bytes Desc: Picture (Device Independent Bitmap) Url : http://www.bio.net/bionet/mm/annelida/attachments/20080624/c9321d86/attachment.bin From kfitzhugh from nhm.org Tue Jun 24 00:47:14 2008 From: kfitzhugh from nhm.org (Kirk Fitzhugh) Date: Tue Jun 24 00:55:25 2008 Subject: [Annelida] a new publication on position of polychaetes References: Message-ID: Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: ole0.bmp Type: image/bmp Size: 13854 bytes Desc: Picture (Device Independent Bitmap) Url : http://www.bio.net/bionet/mm/annelida/attachments/20080623/f125f4a7/ole0.bin From polychaete1 from gmail.com Tue Jun 24 03:49:07 2008 From: polychaete1 from gmail.com (Mary Petersen) Date: Tue Jun 24 05:56:23 2008 Subject: [Annelida] Re: Pleijel et al.: Voucher specimens for molecular phylogenetic studies Message-ID: Hi Fred and colleagues, and others interested in good science, Thanks for your much needed protest! We don't seem to have access to the paper here - a pdf file would be greatly appreciated. It comforts me to see that I am not the only one who has complained about this. I earlier (before my return to USA in mid-December 2004) had repeatedly asked GenBank why they did not request that data be tied to extant specimens or that at least localities for the sequenced material be given, and was told that they could not request such information! My reply was "how could they consider it responsible NOT to request it?". Most of us are aware that especially "well-known" species are often misidentified and that locality- and habitat would at least narrow the field of possibilities. The demise of the "cosmopolitan" status of far too many species ought to prove that a bar code alone is not enough - we also need to be able to examine the specimens (or ones collected at the same time and place) if necessary. I also agree that also in ecological papers, literature used to identify the species should be specirfied. One can always use the most cited publication as default and list others as necessary. While revealing the exact locality of animals sought as trophies might cause problems, such concerns should not provide an excuse for ignoring these data for ALL species. Re keeping part of the sequenced specimen(s), in cases where the small size (e.g., meiofauna) means destruction of the entire animal, it is usually possible to get more than one specimen from an area. I sincerely hope your joint plea will make a difference and encourage GenBank to reconsider their policy and make your requests requirements. Thanks again for your efforts. Best wishes, Mary Dr. Mary E. Petersen Scholar in Residence, Polychaeta Darling Marine Center, University of Maine 193 Clark's Cove Road Walpole, ME 04573-3307, USA Tel.: +1 (207) 563-3146 ext. 222 polychaete1@gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080624/96fe656f/attachment.html From lena.kupriyanova from gmail.com Wed Jun 25 20:54:39 2008 From: lena.kupriyanova from gmail.com (Elena Kupriyanova) Date: Wed Jun 25 21:41:22 2008 Subject: [Annelida] Vouchers again Message-ID: <4862F6DF.3050305@gmail.com> Dear friends and colleagues, I have no doubts in my mind that vouchers are crucially important in molecular phylogenetic studies. And I cannot help noticing that the current situation is not as bad as Geoff's and Mary's messages might suggest. Although Mary mentions that in 2004GenBank did not request that data be tied to extant specimens, they certainly do now. Below is a copy of a message sent to me in Oct. 2007. *************************************************************************************************** Dear Dr. Kupriyanova, Please find your assigned Accession Number(s) in the letter below. Although you provided unique descriptions for each of your sequence submissions, we note you did not include specimen vouchers for the organisms. Specimen vouchers provide a means to verify the identity of a taxon and are a source for additional molecular analyses. The voucher specimen is given a unique number, clearly annotated as being the source of a genetic sequence, and is deposited in a repository (such as a museum collection or herbarium). Send this information to gb-admin@ncbi.nlm.nih.gov in the following tab-delimited table format: accession number specimen-voucher ---------------- ---------------- EUxxxxxx AMNH 000000 EUxxxxxx C.S. Shen 2459 (HMAS) EUxxxxxx LCCC 0203 Thank you and we look forward to hearing from you soon. Sincerely, The GenBank Submissions Staff Bethesda, Maryland USA ************************************************************************************************** I am also positive (since all sequences I submitted to GenBank are accompanied by voucher numbers) that currently at GenBank there is a dedicated field for specification of vouchers. Clearly, if "only a minority of journals require that vouchers connected to the genetic information be deposited in museums or other institutions", this is something that needs to be changed in near future. Also, I wonder if the time has come for all descriptions of new species and all traditional taxonomic revisions to include some genetic information? It looks like nowadays sequencing is less problematic than proper ids: ) would love to hear any ideas on the topic Wormly, Lena > Noticed this from Fred and others in the latest issue of Molecular Phylogenetics and Evolution: > http://www.sciencedirect.com/science/journal/10557903 > > Pleijel, F.; Jondelius, U.; Norlinder, E.; Nygren, A.; Oxelman, B.; Schander, C.; Sundberg, P. ; Thollesson, M. 2008: Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Molecular Phylogenetics and Evolution 48(1): 369-371. http://dx.doi.org/10.1016/j.ympev.2008.03.024 > > Quote for flavour: "Today there is a large number of sequences deposited at GenBank that are incorrectly labeled and, unless remedied, these will continuously be associated with the wrong taxa. Vouchers constitute an essential link between data and taxa, and provide a means to verify the taxonomic identity of the specimens sequenced. However, only a minority of journals require that vouchers connected to the genetic information be deposited in museums or other institutions. Furthermore, at GenBank there is currently no dedicated field for specification of vouchers." > > > From g.read from niwa.co.nz Wed Jun 25 21:37:14 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Wed Jun 25 21:42:32 2008 Subject: [Annelida] Vouchers again In-Reply-To: <485D6A81.8045.00D5.0@niwa.co.nz> References: <485D6A81.8045.00D5.0@niwa.co.nz> Message-ID: <4863A99A.8045.00D5.0@niwa.co.nz> >>> On 21/06/2008 at 8:54 p.m., "Geoff Read" wrote: > I know of instances where new molecular studies has found the > misidentification in the old work, but are there cases where an actual > taxonomist has re-examined the voucher and found the misidentification simply > by eyeballing it? None has been mentioned to me. So, strike one against the usefulness of vouchers? > Here is an interesting complex case in freshwater limpets involving a > misidentified GenBank sequence: > > Walther, A. C.; Lee, T.; Burch, J. B. ; Foighil, D. O. 2006: Acroloxus > lacustris is not an ancylid: A case of misidentification involving the > cryptic invader Ferrissia fragilis (Mollusca: Pulmonata: Hygrophila). > Molecular Phylogenetics and Evolution 39(1): 271-275. > http://dx.doi.org/10.1016/j.ympev.2005.08.014 > > Even more interesting is that the misidentified entry (AY577462) as A > lacustris is still seemingly uncorrected in GenBank. Why is this? Have I got > this right? It seems very strange. > See http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?46451261:NCBI:6982153 There does not seem to be a process for corrections or warning annotations to GenBank identifications by subsequent workers, and the very notion of original misidentification may be an alien concept to the working processes there. So one shows the voucher is misidentified but there no obvious path to get this recorded? Is this correct? Strike two against the usefulness of vouchers? "Revisions or updates to GenBank entries can be made by the submitters" Right, only by the submitters, but they don't do it. They just hold tight, take the heat, and pretend (in the GenBank record) they didn't stuff up. Strike three and out for usefulness of vouchers in practice? Ps - a case of switched identities between the sequences of 2 vastly different worm taxa has been mentioned to me privately. One just happens to be a taxon I'm interested in. Nice to know - but it should be GenBank which told me. Geoff From lena.kupriyanova from gmail.com Wed Jun 25 22:49:00 2008 From: lena.kupriyanova from gmail.com (Elena Kupriyanova) Date: Wed Jun 25 23:09:36 2008 Subject: [Annelida] Vouchers again In-Reply-To: <4863A99A.8045.00D5.0@niwa.co.nz> References: <485D6A81.8045.00D5.0@niwa.co.nz> <4863A99A.8045.00D5.0@niwa.co.nz> Message-ID: <486311AC.7070106@gmail.com> Geoff Read wrote: >> I know of instances where new molecular studies has found the >> misidentification in the old work, but are there cases where an actual >> taxonomist has re-examined the voucher and found the misidentification simply >> by eyeballing it? >> > > None has been mentioned to me. So, strike one against the usefulness of vouchers? > I think it is too early for that to happen. After multiple sequences of (supposedly) same species accumulate on GenBank, examining vouchers will be important to decide whether a mis-indentification was the explanation of inferred genetic variation >> Here is an interesting complex case in freshwater limpets involving a >> misidentified GenBank sequence: >> >> Walther, A. C.; Lee, T.; Burch, J. B. ; Foighil, D. O. 2006: Acroloxus >> lacustris is not an ancylid: A case of misidentification involving the >> cryptic invader Ferrissia fragilis (Mollusca: Pulmonata: Hygrophila). >> Molecular Phylogenetics and Evolution 39(1): 271-275. >> http://dx.doi.org/10.1016/j.ympev.2005.08.014 >> >> Even more interesting is that the misidentified entry (AY577462) as A >> lacustris is still seemingly uncorrected in GenBank. Why is this? Have I got >> this right? It seems very strange. >> See http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?46451261:NCBI:6982153 >> > > There does not seem to be a process for corrections or warning annotations to GenBank identifications by subsequent workers, > and the very notion of original misidentification may be an alien concept to the working processes there. So one shows the voucher is misidentified but there no obvious path to get this recorded? Is this correct? Strike two against the usefulness of vouchers? > I am not sure, but an inquiry can be sent to GenBank. Again, GenBank's policies are not set in stone, they are evolving, and if we can show that such a path is needed, I am sure it will be created > "Revisions or updates to GenBank entries can be made by the submitters" Right, only by the submitters, but they don't do it. They just hold tight, take the heat, and pretend (in the GenBank record) they didn't stuff up. Strike three and out for usefulness of vouchers in practice? > Again, as I said above - with multiple diverse sequences attributable to one species such a stuff up will be really difficult to hide > Ps - a case of switched identities between the sequences of 2 vastly different worm taxa has been mentioned to me privately. One just happens to be a taxon I'm interested in. Nice to know - but it should be GenBank which told me. > What does BLAST tell in this case? And why to not to correct this mistake now, once it is known? Wormly, Lena From g.read from niwa.co.nz Wed Jun 25 23:33:33 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Wed Jun 25 23:37:01 2008 Subject: [Annelida] Vouchers again Message-ID: <4863C4DD.8045.00D5.0@niwa.co.nz> >>> On 26/06/2008 at 3:49 p.m., Elena Kupriyanova wrote GBR >> "Revisions or updates to GenBank entries can be made by the submitters" > Right, only by the submitters, but they don't do it. They just hold tight, > take the heat, and pretend (in the GenBank record) they didn't stuff up. > Strike three and out for usefulness of vouchers in practice? Lena > Again, as I said above - with multiple diverse sequences attributable to > one species such a stuff up will be really difficult to hide GBR >> Ps - a case of switched identities between the sequences of 2 vastly > different worm taxa has been mentioned to me privately. One just happens to > be a taxon I'm interested in. Nice to know - but it should be GenBank which > told me. Lena > What does BLAST tell in this case? And why to not to correct this > mistake now, once it is known? BLAST shows that it is definitely a crazy id :-) - as my informant suggested. I think this one is so obvious it will not trouble anyone. Lena, thanks for your perspective, as a very experienced user. Of course I really do think vouchers are most important. I'm not sure whether the 'no dedicated field' in Genbank claim in the Fred Pleijel et al paper under discussion really meant that there was no high level field (ie, would be a separate table in the database) with subfields to it. At the moment the voucher info seems to appear parked into a general comments area in the display. If so, that's unsatisfactory. The paper mentions that Barcoding of Life Database handles vouchers info better. Geoff From e.punzo from an.ismar.cnr.it Thu Jun 26 09:11:41 2008 From: e.punzo from an.ismar.cnr.it (elisa punzo) Date: Thu Jun 26 12:46:49 2008 Subject: [Annelida] Adriatic Polychaetes Message-ID: <7.0.1.0.1.20080626160844.025551f0@an.ismar.cnr.it> Hi, I'm an italian student and I would like to have some papers about Mediterranean polychaetes (in particular Adriatic Polychaetes) that live at 500-1000 m depth. I need also to have informations about dredging at these depths. Thank you very much in advance Elisa Punzo From g.read from niwa.co.nz Thu Jun 26 16:08:06 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Thu Jun 26 16:12:15 2008 Subject: [Annelida] Vouchers again In-Reply-To: <4863C4DD.8045.00D5.0@niwa.co.nz> References: <4863C4DD.8045.00D5.0@niwa.co.nz> Message-ID: <4864ADF5.8045.00D5.0@niwa.co.nz> >>> On 26/06/2008 at 4:33 p.m., "Geoff Read" wrote: > GBR >>> "Revisions or updates to GenBank entries can be made by the submitters" >> Right, only by the submitters, but they don't do it. However, I'm told that the 'only' above is not correct because others can submit comments. Quote: "There is a procedure for "third-party annotation" whereby corrections etc. may be submitted by people other than the original authors. I believe that any such contribution must be based on already-published material." And the GenBank help has: "If you have comments or updates to a record that does not belong to you, please email info@ncbi.nlm.nih.gov, the general NCBI Service Desk and be sure to provide the accession number of the record on which you are commenting." So that's the process to try if the submitter seems to be unresponsive. Posting of aquatic invert examples where third parties have help resolve a problem with a GenBank entry would be welcome. Geoff From csuzdi01 from gmail.com Fri Jun 27 06:57:46 2008 From: csuzdi01 from gmail.com (Csuzdi Csaba) Date: Fri Jun 27 17:03:44 2008 Subject: [Annelida] Vouchers again In-Reply-To: <4864ADF5.8045.00D5.0@niwa.co.nz> References: <4863C4DD.8045.00D5.0@niwa.co.nz> <4864ADF5.8045.00D5.0@niwa.co.nz> Message-ID: Dear All, I completely agree with the previous posts. But unfortunately not only incorrect identifications but sometimes completely nonsense entries remain for years uncorrected in the database. See the entries AY178854, AY187629 and so on which refer to an "earthworm" species *Lumbricus bimastus* that is a combination of a correct (*Lumbricus*) and an incorrect genus name (* Bimastus* instead of Bimastos). Regards, Cs. Csuzdi 2008/6/26 Geoff Read : > >>> On 26/06/2008 at 4:33 p.m., "Geoff Read" wrote: > > > GBR > >>> "Revisions or updates to GenBank entries can be made by the submitters" > >> Right, only by the submitters, but they don't do it. > > However, I'm told that the 'only' above is not correct because others can > submit comments. > > Quote: "There is a procedure for "third-party annotation" whereby > corrections etc. may be submitted by people other than the original authors. > I believe that any such contribution must be based on already-published > material." > > And the GenBank help has: "If you have comments or updates to a record that > does not belong to you, please email info@ncbi.nlm.nih.gov, the general > NCBI Service Desk and be sure to provide the accession number of the record > on which you are commenting." > > So that's the process to try if the submitter seems to be unresponsive. > Posting of aquatic invert examples where third parties have help resolve a > problem with a GenBank entry would be welcome. > > Geoff > > > > > _______________________________________________ > Annelida mailing list > Post: Annelida@net.bio.net > Help/archive: http://www.bio.net/biomail/listinfo/annelida > Resources: http://www.annelida.net > -- res. Prof. Dr. Csaba Csuzdi D. Sc. Systematic Zoology Research Group of HAS and Hungarian Natural History Museum H-1088 Budapest, Baross str. 13. www.pedozoologia.net -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/annelida/attachments/20080627/e9b8ecca/attachment.html From g.read from niwa.co.nz Sat Jun 28 01:05:36 2008 From: g.read from niwa.co.nz (Geoff Read) Date: Sat Jun 28 01:07:28 2008 Subject: [Annelida] a new publication on position of polychaetes In-Reply-To: References: Message-ID: <48667D6F.8045.00D5.0@niwa.co.nz> Hi Pat, Do you have a link yet for the supplementary electronic material (mentioned p341) please? I cannot see it at the journal site of http://zoolstud.sinica.edu.tw/ Cheers, Geoff >>> On 24/06/2008 at 2:47 p.m., "Pat Hutchings" wrote: > People may be interested in this newly released paper > > 1. Colgan, DJ., Hutchings, PA., & Beacham E. 2008. Multi-Gene > Analyses of the Phylogenetic Relationships among the Mollusca, Annelida, > and Arthropoda Zoological Studies 47(3): 338-351