theory & methodology

theory & methodology

Postby Eckart Stolle on 29 Jun 2008, 15:52

check this list here (some PDF open access):
http://www.mapress.com/zootaxa/collections/general.html
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Zootaxa 1761: 37-48 (2 May 2008)
New species and subspecies descriptions do not and should not always require a dead type specimen
THOMAS M. DONEGAN (UK)
Abstract
Dubois & Nemésio (2007) recently considered that the present International Code for Zoological Nomenclature
(“Code”) could reasonably be interpreted as requiring the deposition of dead vouchers for new species and subspecies
descriptions. They considered that, to the extent that there is lack of clarity, the Code should be amended so as to require
the deposition of a dead voucher. They doubted the utility of photographs and other materials for descriptions and sug-
gested that ethical or moral concerns about the taking of dead type specimens were poorly supported. Dubois & Nemésio
(2007)’s preferred interpretations of the current Code are not supported by members of the Commission. Possible reasons
why the collection of a dead type specimen might not be necessary or recommended include the setting of a good exam-
ple to communities in whose hands conservation action lies, government permit issues and the description of new taxa on
the brink of extinction where collecting may impact populations. The Code should be liberal in relation to the nature of
type specimens to enable taxonomists, who are the persons best placed to take decisions, to make appropriate judgments
for particular descriptions.
Key words: Nomenclatural availability, vouchers, collections, type specimen, illustrations, samples, ethics, DNA
sequences, Code, Commission

http://www.mapress.com/zootaxa/2008/f/zt01761p048.pdf
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Re: theory & methodology

Postby Eckart Stolle on 29 Jun 2008, 16:03

Zootaxa 1668: 10-18 (21 Dec. 2007) 44 references
Invertebrate systematics or spineless taxonomy?
QUENTIN D. WHEELER (USA)
Table of contents
Unapologetic Character Analysis
Take No Hostage Taxonomy
A New Solution to the Old Species Problem
Leadership
Back to Basics
Univocal Urgings
Conclusions
References

http://www.mapress.com/zootaxa/2007f/zt01668p018.pdf
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Re: theory & methodology

Postby Eckart Stolle on 29 Jun 2008, 16:04

Zootaxa 1668: 19-40 (21 Dec. 2007) 8 plates; 78 references
The Tree of Life Web Project
DAVID R. MADDISON (USA), KATJA-SABINE SCHULZ (USA) & WAYNE P. MADDISON (Canada)
http://www.mapress.com/zootaxa/2007f/zt01668p040.pdf
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Re: theory & methodology

Postby Eckart Stolle on 29 Jun 2008, 16:06

Zootaxa 1668: 47-54 (21 Dec. 2007) 2 plates; 27 references
Archives of a small planet: The significance of museum collections and museum-based research in invertebrate taxonomy
JUDITH E. WINSTON (USA)
Abstract
Museum natural science collections are valuable, in many cases irreplaceable, and vital to research in many disciplines
including taxonomy. Since 96% of known multicellular animals belong to one or another of the 34 invertebrate phyla,
the value of those collections for invertebrate taxonomy (of both living and fossil taxa) is even higher. Systematic work
that does not rely on museum specimens to verify or falsify the identities of the taxa studied is not science. Whether the
techniques used are molecular or morphological, high tech analysis, or careful observation, systematics is the primary
and most essential use of museum invertebrate collections. Their value and the case for their support for this primary and
many other compelling reasons has been argued eloquently time after time, yet support still lags far behind needs.
Key words: value of natural history collections, systematics funding
http://www.mapress.com/zootaxa/2007f/zt01668p054.pdf
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Re: theory & methodology

Postby Eckart Stolle on 29 Jun 2008, 16:09

Zootaxa 1586: 67-68 (17 Sep. 2007) 0 plates; 15 references Accepted: 31 Aug. 2007
Integrative taxonomists should use and produce DNA barcodes
JOSE M. PADIAL & IGNACIO DE LA RIVA (Spain)
http://www.mapress.com/zootaxa/2007f/zt01586p068.pdf
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Re: theory & methodology

Postby Eckart Stolle on 29 Jun 2008, 16:12

Zootaxa 1519: 27-68 (2 Jul. 2007) 2 plates; 133 references
Phylogeny, taxonomy and nomenclature: the problem of taxonomic categories and of nomenclatural ranks
ALAIN DUBOIS (France)
Abstract
The use of ranks and nominal-series in zoological nomenclature has recently been challenged by some authors who sup-
port unranked systems of nomenclature. It is here shown that this criticism is based on a double misunderstanding: (1)
the confusion between nomenclatural ranks and taxonomic categories; (2) the request for a monosemic nomenclatural
system, not for scientific reasons, but to please non-taxonomists, especially customers of the web. It is here argued that
nomenclatural ranks and taxonomic categories should be clearly distinguished and designated by different terms, and that
the Code should be modified in order to make this distinction clear. Whereas taxonomic categories have biological defi-
nitions, nomenclatural ranks do not, as they express only a position in a taxonomic hierarchy. If used consistently (which
is not always the case), the system of nomenclatural ranks is very useful for the storage and retrieval of taxonomic and
phylogenetic information. Taxa referred to a given rank in different groups cannot therefore be considered equivalent by
any criterion, so that using ranks for comparisons between taxa (e.g., for biodiversity richness assessment) is irrelevant
and misleading. Although the current Code needs to be improved in several respects, the superiority of this nomencla-
tural system, which is theory-free regarding taxonomy as it relies on ostensional allocation of nomina to taxa rather than...
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new important systematic/ phylogeny/ classification papersB

Postby proctos on 20 Jul 2008, 04:13

A. P. Rasnitsyn "Ontology of Evolution and Methodology of Taxonomy", Paleontological Journal, Vol. 40, Suppl. 6, 2006, p. 679-737
Abstract
—The theoretical basis of evolutionary biology is presented and discussed to introduce the reader to
problems of evolutionary theory and particularly to the problem of paradigm selection. Advantages of the epigenetic
hypothesis over the synthetic one are demonstrated, and a wide array of inferences is analyzed including
the hypothesis of adaptive trade-off, which considers the organism as a finely tuned comprehensive whole that
is restricted in modification unless under more or less serious destabilization. The basic premises of phylogenetics,
taxonomy, and taxonomic nomenclature are also analyzed; this results in the inference that the phyletic
(refined traditional, Linnean) methodology has advantages over the cladistic one. The nature of the biological
taxon and the problems of taxonomy of taxonomically imperfect material (paleontological, parasitological,
etc.) are discussed.
http://www.divshare.com/download/4981510-dea
Victor Kolyada
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Re: theory & methodology

Postby Eckart Stolle on 27 Aug 2008, 15:30

http://www.pnas.org/content/105/34/12359.abstract?etoc (Open Access Articel)

Smith et al 2008 ( Published online before print August 20, 2008, doi: 10.1073/pnas.0805319105 PNAS August 26, 2008 vol. 105 no. 34 12359-12364):
Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections.

Abstract:
We DNA barcoded 2,597 parasitoid wasps belonging to 6 microgastrine braconid genera reared from parapatric tropical dry forest, cloud forest, and rain forest in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica and combined these data with records of caterpillar hosts and morphological analyses. We asked whether barcoding and morphology discover the same provisional species and whether the biological entities revealed by our analysis are congruent with wasp host specificity. Morphological analysis revealed 171 provisional species, but barcoding exposed an additional 142 provisional species; 95% of the total is likely to be undescribed. These 313 provisional species are extraordinarily host specific; more than 90% attack only 1 or 2 species of caterpillars out of more than 3,500 species sampled. The most extreme case of overlooked diversity is the morphospecies Apanteles leucostigmus. This minute black wasp with a distinctive white wing stigma was thought to parasitize 32 species of ACG hesperiid caterpillars, but barcoding revealed 36 provisional species, each attacking one or a very few closely related species of caterpillars. When host records and/or within-ACG distributions suggested that DNA barcoding had missed a species-pair, or when provisional species were separated only by slight differences in their barcodes, we examined nuclear sequences to test hypotheses of presumptive species boundaries and to further probe host specificity. Our iterative process of combining morphological analysis, ecology, and DNA barcoding and reiteratively using specimens maintained in permanent collections has resulted in a much more fine-scaled understanding of parasitoid diversity and host specificity than any one of these elements could have produced on its own.

------------------
A very interesting paper with a huge dataset, showing the limitations of morphology for IDing parasitic wasps. Although it can be argued that the provisional species (revealed by barcoding), which attack only specific hosts, are still the same species, these are distinct populations with distinct biology. They cant be separated as "morphospecies" but obviously they are separate "biospecies"...
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Re: theory & methodology

Postby Eckart Stolle on 10 Sep 2008, 23:35

http://www.pfeil-verlag.de/04biol/pdf/spix31_1_01.pdf
Spixiana 31 (1) 2008
Melzer & Schmidt 2008: Editorial – From character observation to species delimitation – Taxonomy as empirical science
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Re: theory & methodology

Postby Eckart Stolle on 08 Dec 2008, 14:10

Godfray et al. 2008: Pragmatism and Rigour can Coexist in Taxonomy.
Evol Biol (2008) 35:309–311
http://www.springerlink.com/content/r7v4629tp3g16655/

also see the references of this article...
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Re: theory & methodology

Postby Eckart Stolle on 26 Jan 2009, 11:17

http://www.sciencedirect.com/science?_o ... y%23Volume)&_cdi=6081&_sort=d&_docanchor=&_ct=15&_acct=C000053953&_version=1&_urlVersion=0&_userid=1606366&md5=d34f7eebae25a402d3a878b2cf4a7dab

Alice Valentini, Francois Pompanon and Pierre Taberlet (2009):
DNA barcoding for ecologists
Trends in Ecology & Evolution, Volume 24, Issue 2, February 2009, Pages 110-117

Abstract
DNA barcoding – taxon identification using a standardized DNA region – has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism’s remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.
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Re: theory & methodology

Postby Eckart Stolle on 26 Jan 2009, 12:12

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http://www.lyx.org/

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