[Taxacom] Sorry, but you are out-of-line
Donat Agosti
agosti at amnh.org
Sun Nov 14 22:40:17 CST 2010
"I see Genbank as the equivalent of a library catalogue. It tells you
what is available and useful things about it. I don't care that a
library catalogue came from a card index and the cards have been
pulped. The books and articles are 'the stuff' and they can be
updated, recatalogued if necessary and converted to different forms.
And I hopewe can all agree that 'the stuff' is technology independent
and with a bit of care will be around for millenia. There is no faith
involved with this - it has happened."
It seems to me though that Genbank is MORE than a library catalogue, a collection of metadata and that is what I like about it:
At the bottom there is actually the gensequence, the real data.
If we would replace the gene sequence with the descriptioin, then you have all the basic information of a description. If it is written in XML then we do not have the problem of storing descriptions in multiple more or less propietory file formats.
And we are even much closer to a place where machines could do the job of reading it.
Here an example.
LOCUS EU155463 415 bp DNA linear INV 08-JUL-2008
DEFINITION Anochetus princeps wingless (Wg) gene, partial cds.
ACCESSION EU155463
VERSION EU155463.1 GI:163311286
KEYWORDS .
SOURCE Anochetus princeps
ORGANISM Anochetus princeps
Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata;
Vespoidea; Formicidae; Ponerinae; Ponerini; Anochetus.
REFERENCE 1 (bases 1 to 415)
AUTHORS Spagna,J.C., Vakis,A.I., Schmidt,C.A., Patek,S.N., Zhang,X.,
Tsutsui,N.D. and Suarez,A.V.
TITLE Phylogeny, scaling, and the generation of extreme forces in
trap-jaw ants
JOURNAL J. Exp. Biol. 211 (PT 14), 2358-2368 (2008)
PUBMED 18587130
REFERENCE 2 (bases 1 to 415)
AUTHORS Schmidt,C.A.
TITLE Direct Submission
JOURNAL Submitted (14-SEP-2007) Graduate Interdisciplinary Program in
Insect Science, University of Arizona, 225 Life Sciences South,
Tucson, AZ 85721, USA
FEATURES Location/Qualifiers
source 1..415
/organism="Anochetus princeps"
/mol_type="genomic DNA"
/specimen_voucher="CSC DNA 0096"
/db_xref="taxon:486637"
/country="Indonesia"
/identified_by="Chris Schmidt"
/note="authority: Anochetus princeps Emery, 1884"
gene <1..>415
/gene="Wg"
mRNA <1..>415
/gene="Wg"
/product="wingless"
CDS <1..>415
/gene="Wg"
/codon_start=2
/product="wingless"
/protein_id="ABY26635.1"
/db_xref="GI:163311287"
/translation="LPNFRVVGDNLKDRFDGASRVMVSNSDRTRGNGNGNTIISNSAS
NSVHGHREGPPRRHRYDFQLKPYNPEHKPPGLKDLVYLEPSPPFCEKNPKLGILGTHG
RACNDTSIGVDGCDLMCCGRGYKTQELMAYERCACT"
ORIGIN
1 gctgcccaac ttccgcgtgg tcggcgacaa cctgaaggac cgcttcgacg gcgcctcccg
61 ggtcatggtc agcaactcgg accgcacgcg cggtaacggc aacggcaaca ccatcatcag
121 caactccgcc agcaactcgg tgcacggcca tcgcgagggt ccgccgcgcc ggcaccgcta
181 cgacttccag ctcaagccgt acaacccgga gcacaagccg cccgggctga aggacctggt
241 ctacctggag ccgtcgccgc cgttctgcga gaagaacccg aagctcggca tcctgggcac
301 ccacggccgg gcctgcaacg acaccagcat cggcgtggac ggctgcgacc tcatgtgctg
361 cggcaggggc tacaagacgc aggagctgat ggcgtatgag aggtgcgcct gcacc
//
Just replace this last bit with this
tax:taxonx xsi:schemaLocation="http://www.taxonx.org/schema/v1 http://www.taxonx.org/schema/v1/taxonx1.xsd http://www.loc.gov/mods/v3 http://www.loc.gov/mods/v3/mods-3-1.xsd http://digir.net/schema/conceptual/darwin/2003/1.0 http://digir.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd">
−
<tax:taxonxHeader>
−
<mods:mods>
−
<mods:titleInfo>
−
<mods:title>
A revision of Malagasy species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae).
</mods:title>
</mods:titleInfo>
−
<mods:name type="personal">
−
<mods:role>
<mods:roleTerm>Author</mods:roleTerm>
</mods:role>
<mods:namePart>Fisher, B. L.</mods:namePart>
</mods:name>
−
<mods:name type="personal">
−
<mods:role>
<mods:roleTerm>Author</mods:roleTerm>
</mods:role>
<mods:namePart>Smith, M. A.</mods:namePart>
</mods:name>
<mods:typeOfResource>text</mods:typeOfResource>
−
<mods:relatedItem type="host">
−
<mods:titleInfo>
<mods:title>PlosOne</mods:title>
</mods:titleInfo>
−
<mods:part>
−
<mods:detail type="volume">
<mods:number>3</mods:number>
</mods:detail>
−
<mods:extent unit="page">
<mods:start>1</mods:start>
<mods:end>23</mods:end>
</mods:extent>
<mods:date>2008</mods:date>
</mods:part>
</mods:relatedItem>
<mods:identifier type="HNS-PUB">21401</mods:identifier>
−
<mods:location>
<mods:url>http://hdl.handle.net/10199/15447</mods:url>
</mods:location>
</mods:mods>
</tax:taxonxHeader>
−
<tax:taxonxBody>
−
<tax:treatment>
−
<tax:nomenclature>
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
Anochetus boltoni Fisher
</tax:name>
sp. nov.
</tax:nomenclature>
−
<tax:div type="description">
−
<tax:p>
urn:lsid:zoobank.org:act:B6C072CF-1CA6-40C7-8396- 534E91EF7FBB Figures: worker 2a,b, 5a; male 2c,d, 8a; map 6a
</tax:p>
</tax:div>
−
<tax:nomenclature>
Type Material:
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>49.775</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.43667</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Andapa</dc:Locality>
<dc:YearCollected>12.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>03</dc:DayCollected>
<dc:Collector>B. L. Fisher</dc:Collector>
<dc:TypeStatus>Holotype</dc:TypeStatus>
</tax:xmldata>
Holotype worker, MADAGASCAR: Antsiranana, Parc National de Marojejy, Manantenina River, 28.0 km38° NE Andapa , 8.2 km 333° NNW Manantenina , 14°26'12"S , 049°46'30"E , 450 m, sifted litter, rainforest, 12-15 Nov 2003 (coll. B. L. Fisher et al.), comma collection code: BLF08985 pin code: CASENT0104542 ( CASC )
</tax:collection_event>
.
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>49.775</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.43667</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Andapa</dc:Locality>
<dc:YearCollected>12.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>03</dc:DayCollected>
<dc:Collector>B. L. Fisher</dc:Collector>
<dc:TypeStatus>Paratype</dc:TypeStatus>
</tax:xmldata>
Paratype . 8 workers with same data as holotype but pins coded, CASENT0487895
</tax:collection_event>
,
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>49.775</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.43667</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Andapa</dc:Locality>
<dc:YearCollected>12.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>03</dc:DayCollected>
<dc:Collector>B. L. Fisher</dc:Collector>
<dc:TypeStatus>Paratype</dc:TypeStatus>
</tax:xmldata>
CASENT0487896
</tax:collection_event>
,
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>49.775</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.43667</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Andapa</dc:Locality>
<dc:YearCollected>12.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>03</dc:DayCollected>
<dc:Collector>B. L. Fisher</dc:Collector>
<dc:TypeStatus>Paratype</dc:TypeStatus>
</tax:xmldata>
CASENT0487897
</tax:collection_event>
,
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>49.775</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.43667</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Andapa</dc:Locality>
<dc:YearCollected>12.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>03</dc:DayCollected>
<dc:Collector>B. L. Fisher</dc:Collector>
<dc:TypeStatus>Paratype</dc:TypeStatus>
</tax:xmldata>
CASENT0006943 . ( BMNH , MCZ , CAS )
</tax:collection_event>
;
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>49.775</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.43667</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Andapa</dc:Locality>
<dc:YearCollected>12.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>03</dc:DayCollected>
<dc:Collector>B. L. Fisher</dc:Collector>
<dc:TypeStatus>Paratype</dc:TypeStatus>
</tax:xmldata>
CO1 Barcode from paratype collection and coded CASENT0487895-D01
</tax:collection_event>
</tax:nomenclature>
−
<tax:div type="multiple">
−
<tax:figure>
−
<tax:p>
Figure 2.
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:2346" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
</tax:xmldata>
Anochetus
</tax:name>
spp. full face and lateral view. A-B,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
boltoni
</tax:name>
worker CASENT0104542. C-D,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
boltoni
</tax:name>
male CASENT0063847. E-F,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235701" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>goodmani</dc:Species>
</tax:xmldata>
goodmani
</tax:name>
worker CASENT0104543. G-H,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235701" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>goodmani</dc:Species>
</tax:xmldata>
goodmani
</tax:name>
ergatoid queen CASENT0454531. doi:10.1371/journal.pone.0001787.g002
</tax:p>
</tax:figure>
−
<tax:figure>
−
<tax:p>
3.
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:25263" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>grandidieri</dc:Species>
</tax:xmldata>
Anochetus grandidieri
</tax:name>
full face and lateral view. A-B, large worker CASENT0497580. C-D, small worker CASENT0033463. E-F, large queen CASENT0041177. G-H, small queen CASENT0498467. I -J, male CASENT0049858. doi:10.1371/journal.pone.0001787.g003
</tax:p>
</tax:figure>
</tax:div>
−
<tax:div type="description">
−
<tax:p>
Worker measurements: maximum and minimum based on all specimens, n= 20, (holotype): HL 1.80-2.08 (1.95), HW 1.61- 1.89 (1.71), CI 87-98 (88), EL 0.33-0.41 (0.36), ML 1.15-1.25 (1.20), MI 59-66 (61), SL 1.83-1.96 (1.84) SI 101-115 (107), WL 2.63-2.89 (2.73), FL 1.97-2.13 (2.03), PW 0.95-1.06 (1.00).
</tax:p>
−
<tax:p>
Male measurements: maximum and minimum based on n = 2 from Madagascar: HL 0.89-0.91, HW 1.05-1.13, CI 118- 125, EL 0.56-0.62, SL 0.24, SI 21-23, WL 2.20-2.24, FL 1.75-1.80
</tax:p>
</tax:div>
−
<tax:div type="diagnosis">
−
<tax:p>
Worker Diagnosis: Blade of mandible with five teeth and denticles located along distal two thirds of blade's length. Propodeum with short teeth (Fig. 5a). Dorsolateral margin of petiole with long spine (Fig. 5a). In frontal view, petiolar margin deeply U-shaped. Pilosity, sculpture as in Figures 2a,b.
</tax:p>
</tax:div>
−
<tax:nomenclature>
Male caste: Dorsolateral margin of petiole with acute spine. The species is most similar to
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235701" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>goodmani</dc:Species>
</tax:xmldata>
A. goodmani
</tax:name>
, but can be easily distinguished by its petiole node with a pair of large apical spines.
</tax:nomenclature>
−
<tax:div type="distribution">
−
<tax:p>
Distribution and biology. The distribution is limited to collections made between 450 m and 750 m in rainforest in Parc National de Marojejy and 240 m from Ambanitaza near Antalaha (Fig. 4a). It has been collected three times in rotten logs and once in a leaf litter sample. Males have been collected in malaise samples on 20-25 Dec 2004 at 488 m in Parc National de Marojejy
</tax:p>
−
<tax:p>
CO1. The two populations where collections have been made to date are characterized by a deep divergence within the DNA barcode region (Maximum - 8%) (Fig. 15).
</tax:p>
</tax:div>
−
<tax:div type="diagnosis">
−
<tax:p>
Diagnostic barcoding loci.
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
A. boltoni
</tax:name>
: ATCT-42-45 & RTTAR-66-70
</tax:p>
</tax:div>
−
<tax:div type="discussion">
−
<tax:div type="discussion">
−
<tax:p>
Discussion: Specimens from Ambanitaza differ notably in shape of propodeal spines and length of spines on petiole from those of the type locality. Though these localities are quite close (40 km apart), these character differences are noticeable, and correspond to significant differences in CO1 (34 base pairs) and ITS1. While specimens from each location were invariant within 18S , there is a 7 bp insertion within ITS1 that is characteristic of the Ambanitaza population which is missing from all specimens from Marojejy. Ultimately, more collections need to be made and evaluated in order to test the hypothesis that these populations represent separate species. One important factor to consider in the testing of that hypothesis is reproductive strategy, which is, to our knowledge, through fission. Though the queen caste is not known, based on overall similarity of workers with
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235701" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>goodmani</dc:Species>
</tax:xmldata>
A. goodmani
</tax:name>
, it is likely that the queen of
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
boltoni
</tax:name>
is wingless. Queens have never been collected during the 12 month malaise trap sampling even though males were collected. Species that reproduce by fission may show greater geographic differences in morphology and CO1.
</tax:p>
</tax:div>
</tax:div>
−
<tax:div type="multiple">
−
<tax:figure>
−
<tax:p>
Figure 4.
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:25279" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>madagascarensis</dc:Species>
</tax:xmldata>
Anochetus madagascarensis
</tax:name>
full face and lateral view. A-B, worker CASENT0104547. C-D, queen CASENT0498419. E-F, male CASENT0049282. doi:10.1371/journal.pone.0001787.g004
</tax:p>
</tax:figure>
−
<tax:figure>
−
<tax:p>
5.
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:2346" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
</tax:xmldata>
Anochetus
</tax:name>
workers, upper part of petiole from front view. A,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
boltoni
</tax:name>
CASENT0104542. B,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235701" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>goodmani</dc:Species>
</tax:xmldata>
goodmani
</tax:name>
CASENT0104543. C,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:25263" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>grandidieri</dc:Species>
</tax:xmldata>
grandidieri
</tax:name>
(large form) CASENT0497580. D,
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:25279" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>madagascarensis</dc:Species>
</tax:xmldata>
madagascarensis
</tax:name>
CASENT0498309. doi:10.1371/journal.pone.0001787.g005
</tax:p>
</tax:figure>
</tax:div>
−
<tax:div type="materials_examined">
−
<tax:p>
Additional material examined for
−
<tax:name>
<tax:xid identifier="urn:lsid:biosci.ohio-state.edu:osuc_concepts:235700" source="HNS"/>
−
<tax:xmldata>
<dc:Genus>Anochetus</dc:Genus>
<dc:Species>boltoni</dc:Species>
</tax:xmldata>
Anochetus boltoni
</tax:name>
: In addition to the type material, specimens from 4 additional collecting events from the following three localities were examined in this study.
−
<tax:collection_event>
−
<tax:xmldata>
<dc:Country>MADAGASCAR</dc:Country>
<dc:StateProvince>Province Antsiranana</dc:StateProvince>
<dc:Locality>Parc National de Marojejy</dc:Locality>
</tax:xmldata>
MADAGASCAR : Province Antsiranana : Parc National de Marojejy , Manantenina River, 27.6 km 35° NE Andapa
</tax:collection_event>
;
−
<tax:collection_event>
−
<tax:xmldata>
<dc:Country>MADAGASCAR</dc:Country>
<dc:Locality>Parc National de Marojejy</dc:Locality>
</tax:xmldata>
Parc National de Marojejy , Manantenina River, 28.0 km 38° NE Andapa
</tax:collection_event>
;
−
<tax:collection_event>
−
<tax:xmldata>
<dc:DecimalLongitude>50.18367</dc:DecimalLongitude>
<dc:DecimalLatitude>-14.67933</dc:DecimalLatitude>
<dc:Country>Madagascar</dc:Country>
<dc:Locality>Foret Ambanitaza</dc:Locality>
<dc:YearCollected>27.1</dc:YearCollected>
<dc:MonthCollected>.2</dc:MonthCollected>
<dc:DayCollected>04</dc:DayCollected>
<dc:Collector>B.L.Fisher</dc:Collector>
</tax:xmldata>
Foret Ambanitaza , 26.1 km 347° Antalaha
</tax:collection_event>
. This material shows greater variation in number of denticles along blade of mandible, ranging from 5-7, compared to the paratypic material.
</tax:p>
</tax:div>
</tax:treatment>
</tax:taxonxBody>
</tax:taxonx>
Donat
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