The Ghost of Paley
Posts: 1703
Joined: Oct. 2005
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Martin wrote:
| Quote | | Secondly, the phrase ‘all three fish classes’ is simply Arnason et al.’s mistake re-stated. It assumes the correctness of the ‘fish typology’ as a natural group. However, there is ample evidence that tetrapods are descended from some ‘fish’ and that taxa of interest to us here belong along that branch. |
And maybe one day Arnason will find it. Let's review some complaints of the original Arnason study:
1) No tetrapods
2) Not enough lungfish/coelacanth species
3) Bad root, partly due to 1)
Let's take the last part first. Here's an unrooted tree from from an earlier study. As one can see, the lamprey creates trouble when used as an outgroup, because of the tendency of its mitochondrial DNA to cluster with tetrapods (I can cite other sources for this claim). On the other hand, its nuclear DNA behaves better under the evolutionary whip. So should this organism be used? Depends on the researcher's presuppositions.
To address the first two points, let's examine fresh studies. After making the very adjustments that Martin et al. demand, our dear Aranson finds that the results don't improve:
| Quote | (1) Morphological and molecular trees of gnathostome relationships commonly depict lungfishes and tetrapods as sister groups. However, in many cases, the placement of the rooting point of these trees has depended on arbitrary assumptions. Traditionally, these trees show Chondrichthyes (cartilaginous fishes) as the sister group of remaining gnathostomes, a position that is inconsistent with the palaeontological age of the Chondrichthyes, which is younger than that of bony fishes.
(2) Analyses of mt data sets do not identify the commonly accepted gnathostome tree. Instead, when the tree is rooted with a non-gnathostome outgroup it splits into one tetrapod and one piscine branch. Chondrichthyes fall among other lineages on the piscine branch. The mt tree is inconsistent with the common notion of evolution from cartilaginous fishes to ray-finned fishes and from here to lobe-finned fishes (lungfishes and coelacanths) and tetrapods
(3) Gnathostome mt distances are consistent with a basal split between tetrapods and all gnathostomous fishes. The distances do not suggest that the evolutionary rates of the chondrichthyan mt genomes are anomalous compared to other mt genomes.
(4) The mt tree suggests that lungs and air breathing are ‘‘primitive’’ conditions among extant gnathostomes. If so, tetrapods and basal lineages on the piscine branch have retained this condition, while the swim bladder and the absence of this organ in some piscine lineages, constitute derived conditions.
(5) Some nuclear data sets favour the mt tree, while others don’t. The correct tree of basal gnathostome relationships is not known, but the mt trees are reproduced by currently acknowledged phylogenetic approaches. The amount of data that can be extracted from mt genomes is finite. Therefore, by necessity, extended analyses of deep gnathostome relationships must be based on the establishment of larger nuclear data sets and a more comprehensive taxon sampling. |
By the way, Bichirs and ropefish were the basal piscines, leading to the oddly creationist mantra: "a tetrapod is a tetrapod, and a fish, a fish".
Hey guys, take a look at Table One: I think you'll find enough Dipnoids and 4pods to keep you occupied. And finally, another side of Brinkmann.
| Quote | | The gene order of the mitochondrial genomes of the South American and Australian lungfish conforms to the consensus gene order among gnathostome vertebrates. The phylogenetic analyses of the complete set of mitochondrial proteins (without ND6) suggest that the lungfish are the closest relatives of the tetrapods, although the support in favor of this scenario is not statistically significant. The two other smaller data sets (tRNA and rRNA genes) give inconsistent results depending on the different reconstruction methods applied and cannot significantly rule out any of the three alternative hypotheses. Nuclear protein-coding genes, which might be better phylogenetic markers for this question, support the lungfish–tetrapod sister-group relationship (Brinkmann et al. 2004). [Paley's emphasis] |
While Arnason may be sliding over to the dark side, ya'll still have Brinkmann, at least. Heat therapy, anyone?
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Dey can't 'andle my riddim.
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