Talk:Retrotransposon marker

Copied content / possible copyvio

This article contains several segments that are almost or exactly word-to-word identical with ones found in the previously published scientific articles [1] and [2]. I've contacted the original contributor (User:Fulmar) by e-mail to ask if they're one of the authors of these articles or otherwise have permission to use the content.

The latter (Kriegs et al. 2006) article at least is licensed under a free license (CC-BY) which would permit reuse on Wikipedia, but only if accompanied by explicit attribution, which the article currently lacks.

In fact, most of the original version seems to be derived from one of these sources or the other. For comparison, I've reproduced the content of the original version and the corresponding segments from the source articles side by side below:

Original Wikipedia version	Schmitz et al. 2005
The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data.	The analysis of SINEs – short interspersed elements – as molecular cladistic markers represents a particularly interesting complement to sequence data.
Original Wikipedia version	Schmitz et al. 2005
The reason for this is that Retrotransposons are assumed to represent powerful noise-free synapomorphies (Shedlock and Okada, 2000,). The target sites are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is negligible even over evolutionary time scales. Retrotransposon integrations are assumed to be irreversible events since no eminent biological mechanisms have yet been described for the precise re-excision of class I transposons, but also see van de Lagemaat et al., 2005. A clear differentiation between ancestral and derived character state at the respective locus thus becomes possible. In combination, the virtual lack of homoplasy together with a clear character polarity make Retrotransposon integration markers ideal tools for determining the common ancestry of taxa by a shared derived transpositional event (Hamdi et al., 1999; Shedlock and Okada, 2000).	The reason for this is that SINEs are assumed to represent powerful noise-free Hennigian synapomorphies as formulated by Shedlock and Okada (2000). Considering the relatively unspecified targets and the size of a typical primate nuclear genome, the chance of SINE sequence integrations independently involving the same targets is negligible even over evolutionary time scales. Moreover, SINE integrations are assumed to be irreversible events since no biological mechanisms have yet been described for the precise re-excision of class I transposons. A clear differentiation between ancestral and derived character state at the respective locus thus becomes possible. Both features – the virtual lack of homoplasies combined with a clear character polarity – render SINE integration markers ideal tools for determining the common ancestry of two taxa by a shared derived transpositional event (Hamdi et al., 1999; Shedlock and Okada, 2000).
Original Wikipedia version	Kriegs et al. 2006
The "presence" of a given Retrotransposon in related taxa implies their orthologues integration, a derived condition acquired via a common ancestry, while the "absence" of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of Retrotransposons that were actively integrating before the divergence of a particular species.	The "presence" of given retroposed elements in related taxa implies their orthologous integration, a derived condition acquired via a common ancestry, while the "absence" of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of retroposed elements that were actively integrating before the divergence of a particular species.
Original Wikipedia version	Kriegs et al. 2006
Examples for phylogenetic studies based on Retrotransposon presence/absence data are the definition of Whales as members of the order Cetartiodactyla with hippos being their closest living relatives (Nikaido et al., 1999), hominoid relationships (Salem et al. 2003), the Strepsirrhine tree (Roos et al., 2004) and the placental mammalian evolution (Kriegs et al., 2006).	For example, retropositions provided conclusive evidence for the position of whales (Cetacea) within Cetartiodactyla [26], the monophyly of Afrotheria [27], hominoid relationships [28], and the topology of the primate strepsirrhine tree [29].

The last paragraph isn't copied quite as verbatim as the others, but even that shows obvious similarity. The others contain significant verbatim sections, but also many changes in phrasing and structure.

Anyway, for now I'm going to wait and see if the original contributor responds — based on his contributions, it seems quite plausible to me that he might in fact be the original copyright holder to this content. The way I see it, the original articles are already freely available online, so there's no income loss and thus no need delete this in a hurry unless someone actually complains. But if we can't confirm that we have permission to use this content, it will have to go eventually. In any case, even with permission, we do need to attribute the content properly. —Ilmari Karonen (talk) 00:22, 16 August 2006 (UTC)

Alright. It seems that at the very least, the content from Schmitz et al. needs to be rewritten to avoid a possible copyvio. Oh, and the content from Kreigs et al. has to be explicitly attributed. In addition, I think the entire page could use some reworking. It's not quite structured like a "real" article -- no introductory paragraph, no sections other than "References". And does anyone else think that this page merits inclusion in Wikipedia:WikiProject_Molecular_and_Cellular_Biology? --Iknowyourider (talk) 05:49, 14 June 2007 (UTC)