Thread:Jurassic Park Treasury/@comment-11047508-20130610075940/@comment-3213993-20130715080117

I am now calling the Cretaceous weevil sequence into question. You said that Martin and Gutierrez may be wrong because the sequence only shows 98% similarity to modern weevils. However, I read their paper, and they said this. From the GenBank database we retrieved 30 ho-mologous sequences belonging to coleoptera and otherrelated insect groups (table 1) and aligned them usingCLUSTAL W (Thompson, Higgins, and Gibson 1994).Maximum-likelihood pairwise distances (transition/transversion ratio52) were calculated with the programDNADIST (Felsenstein 1993). The outgroup was anodonate,Aeschna cyanea(X89481). Dipterans sequenc-es were discarded because of their high rate of nucleo-tide substitution (Friedrich and Tautz 1997). The dis-tance between the outgroup andLebanorhinuswas com-pared to the distances between the outgroup and otherinsects with a Wilcoxon nonparametric test. The differ-ence was nonsignificant (p50.389), suggesting that theLebanorhinussequence is not ancient. The distance be-tween the outgroup and the fossil weevil was 0.130 andthe mean distance between the former and the other in-sects was 0.127.One might think that such a test would not discrim-inate a 120–135 MYA old sequence from an extant one;to counter that, we have estimated how much divergencewould have been lost by a 18S rRNA that stoppedevolving 120–135 MYA. First, as an estimation of the18S rRNA substitution rate, we have used the estimatedmetazoan substitution rate given by Wray, Levinton, andShapiro (1996). For a period of 120 MYA, the expecteddivergence is 0.018. The mean distance between the out-group and extant sequences is 0.127; then, the distancebetween the outgroup and an 120-Myr-old sequenceshould be 0.109, the test now being significant (p,0.0001).We think that theLebanorhinussequence may bean extant beetle contamination. For instance, Waldenand Robertson (1997) recovered abeetlesequence whenthey were amplifying DNA from an amber-entombedbee specimen, but no coleoptera was studied before intheir laboratory. I don't understand much of that, but I think what they're saying is that the Lebanorhinus specimen may have been contaminated by a modern beetle because the 18s rRNA gene doesn't have the expected amount of divergence for a DNA sequence that old. Did you consider this?