Very interesting article on polypteridae evolution (warning hard read)

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I think they were saying the opposite. They were always thought to be close (as in subspecies) because of their physical traits, but with this genetic evidence..."Taxonomic changes are clearly needed and we recognize P. e. congicus and P. e. endlicheri as distinct species, P. congicus and P. endlicheri". They found a similar situation with P. palmas.

When they say "Polypterus endlicheri is paraphyletic with respect to both P. bichir and P. ansorgii", that means that one of them is more related to P. bichir and the other is more related to P. ansorgii (as demonstrated in the second cladogram). However, I'm definitely hesitant to believe one study 100%. Especially since they only had ~2 specimens of each species.

what i meant was but didnt have time to go into detail because of work, is that all Lowers under the 2nd figure are all under the same 1.0 bracket while the Uppers are in several, in the 3rd figure they are all consecutive in their vertebrae analysis, and in the 4th figure they all lay in about the same area, with the single exception of the congicus i believe. I wasnt saying some are more distant then others, but I would when they were beginning to have lower jaw species they were probably quite similar, with slight variation in color and morphology as we see today.

like you yes i wont put all too much stock in one study, it seems to have been done well other then the specimen number. Im looking forward to more detailed analysis of these ancient fish. They are basically why i got into fish keeping, then i started finding other species i liked
 
They made a little mistake confusing P. mokelembembe to the P. retropinnis on this journal, here is the updated version of it.

http://www.biomedcentral.com/1471-2148/10/209

That was a little more than just a little mistake... Many after reading this paper thrashed the authors over it.. That was a major review mistake and sloppy. It has been clear for some time based on other papers that P.retropinnis is an outlier and that Mokie's belong to the Weeksi, Ornatipinnis clade. How they missed the proper ID even after reviewing Schliewen UK, Schäfer F. Polypterus mokelembembe, a new species of bichir from the central Congo River basin (Actinopterygii: Cladistia: Polypteridae) Zootaxa. 2006;1129:23–36. is a mystery... This mistake did not bode all that well for the authors.
 
what i meant was but didnt have time to go into detail because of work, is that all Lowers under the 2nd figure are all under the same 1.0 bracket while the Uppers are in several, in the 3rd figure they are all consecutive in their vertebrae analysis, and in the 4th figure they all lay in about the same area, with the single exception of the congicus i believe. I wasnt saying some are more distant then others, but I would when they were beginning to have lower jaw species they were probably quite similar, with slight variation in color and morphology as we see today.

Huh? I'm not sure I understand what you're saying. Each of those figures displays different data, and organisms grouped in the same bracket are believed to share a common ancestor. Craniofacial modeling doesn't have to match meristic characteristics such as vertebrae counts. And color variation usually means relatively little in terms of taxonomy. Again, maybe I just misinterpreted your post.
 
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