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A ray-fin fish tree of life

Started by Guest_TomNear_* , Aug 06 2012 04:29 PM

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10 replies to this topic

#1 Guest_TomNear_*

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Posted 06 August 2012 - 04:29 PM

Hello Nanfers,
This is a little abstract, but applicable to NA freshwater fishes. My lab group has just published a large-scale DNA-based phylogeny that samples all lineages of ray-finned fishes, or Actinopterygii. Of course, we used as many North American freshwater species as possible!

For the real fish phylogeny nerds, this is based entirely on nuclear gene sequence data. There is no mitochondrial DNA data in this analysis.

Also, Yale University press office wrote a release and I will paste a link to the story.

http://news.yale.edu...ray-finned-fish

Happy Fish Studying!
Tom Near

Attached Files

Near_et_al_InPress.pdf 2.31MB 83 downloads

#2 Guest_rjmtx_*

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Posted 06 August 2012 - 09:05 PM

Thanks for posting.

#3 Guest_FirstChAoS_*

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Posted 07 August 2012 - 02:39 AM

Thanks you answered one question I had. After reading a aquarium fish magazine that stated cichlids were related to wrasse, parrotfish, and surf perches and likely branches off between wrasse and parrotfish. I was wondering what other fish were closely related. When it came to perch and sunfish when you step back it sort of goes haywire and you get a list of all fish with a mix of spiny and soft dorsal rays, Now I can see sunfish are close to the temperate perch (also pygmy sunnies, but I knew that).

#4 Guest_TomNear_*

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Posted 07 August 2012 - 07:38 AM

Hello Chaos, Yes the cichlid result is from another paper that we have in press at the journal Systematic Biology. The paper is available online, but has not yet been typeset. I'll post a version of that when we get the corrected and typeset page proofs. We had a paper earlier this year that identified a lineage containing Centrachidae (plus Elassoma) and the temperate perches, along with the Sinipercidae (not sure about common names, but I call them Asian Basses). That paper was posted in the "Scientific Discussion."

Your observation that the phylogeny goes haywire in the meat of the spiny-finned fish lineage (I may use that description in talks) is right on. We are expanding this part of the phylogeny to include more than 500 sampled species of percomorphs and the phylogenies are exhibiting a number of important surprises. More on that in a few months...

#5 Guest_FirstChAoS_*

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Posted 07 August 2012 - 01:11 PM

That would be neat to see, especially if it forms a neat "story" like the cichlid case does. (which itself leads to lots of questions such as why did saltwater cichlids die out but their marine cousins remained, were their once generalist parrotfish before they became reef specialists, etc.)

I hope it doesn't become another annoying "common ancestor" thing. It seems nowadays no one wants to say Group A branched off from group B. Instead they say they both branch from a common ancestor. This makes sense if the ancestor is truely unknown. but all too often it is used almost as if it avoids the issue which annoys me. When I hear the "common ancestor" thing I want to ask What KIND of creature is this ancestor? what is it's family? genus? species? what annoys me is a common ancestor has none of those, it is a fish shaped place holder. This makes sense if it is unknown, but sometimes it just feels like a way to avoid things.

#6 Guest_fundulus_*

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Posted 07 August 2012 - 03:18 PM

There has been recent work on the origin of different groups within the wrasses, most especially the parrotfishes. See the open access article, "Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?" in BMC Evolutionary Biology 2009, 9:255 by Alfaro et al. The same core group of authors have other recent work along the same line.

#7 Guest_TomNear_*

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Posted 07 August 2012 - 04:30 PM

Chaos, Our other paper finds that Labroidei, the group which used to contain cichlids, wrasses, parrotfish (which are nested in wrasses, Labridae), surfperches, and pomacentrids, is not a natural group or clade. Instead, we describe a new lineage, called Ovalentaria, that contains Cichlidae, Pomacentridae, mullets, all atherinomorphs (guppies, mollies, topminnows, mosquitofish, halfbeaks, flyingfish, ricefish, etc), polycentrids (but not nandids), pseudochromids, blennies, gobiosocids, and several other disparate percomorph lineages. One trait shared by many of these lineages is dermersal adhesive eggs and larvae with filaments. One of the most exciting results is that within the new Ovalentaria Cichlidae and Pholidichthys (two species of Engineer Gobies) are most closely related.

Labridae (wrasses, parrotfishes, and whitings) is distantly related to this clade.

#8 Guest_fundulus_*

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Posted 07 August 2012 - 05:51 PM

That's certainly a re-do. I haven't had a chance to really read your paper yet.

#9 Guest_AussiePeter_*

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Posted 09 August 2012 - 09:33 AM

I hope it doesn't become another annoying "common ancestor" thing. It seems nowadays no one wants to say Group A branched off from group B. Instead they say they both branch from a common ancestor. This makes sense if the ancestor is truely unknown. but all too often it is used almost as if it avoids the issue which annoys me. When I hear the "common ancestor" thing I want to ask What KIND of creature is this ancestor? what is it's family? genus? species? what annoys me is a common ancestor has none of those, it is a fish shaped place holder. This makes sense if it is unknown, but sometimes it just feels like a way to avoid things.

The reason people say common ancestor is because that is what it is, it isn't that Group A branched from Group B (or visa versa). To say it the latter way is incorrect as groups A and B diverged from a common ancestor. Prior to that group A and B were the same thing, but probably not the same as either group A or B today. By examining the phylogeny you can get an idea of what the common ancestor was like, but it may not have been the same as what group A or B is today. The way that you wish to say it is that group A existed first, then at some point in time group B separated from it, which implies that group A is the same today as it was before group B separated from it. But that isn't necessarily true (although it could be fairly similar in some cases). The whole ancestry thing can all get a bit tricky to wrap one's brain around. The same issue applies to "ancestral" species. All extant (living) species today are the same age relative to their common ancestor. That's another aspect that people often get confused about.

Cheers
Peter

#10 Guest_redfire311_*

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Posted 01 September 2012 - 09:30 PM

Tom-- Thanks so much for posting! It's very difficult to find a tree as complete as that, let alone one that is new and I trust. The number of hours I've spent in MS Paint drawing lines....

I have to email my old professors now, who taught me ichthyozoology without using a tree (hence why I make my own!).

Dave Sanderson-Kilchenstein
SUNY Brockport

#11 Guest_gerald_*

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Posted 14 November 2012 - 11:29 AM

Been looking at Tom's paper again. Glad to see my old gut feelings corroborated ... that seahorses are close kin to tunas, flounders cluster with billfish, and anglerfish with puffers. How did we miss the obvious for so long? |:>)