Cirripede Phylogeny Using a Novel Approach: Molecular Morphometrics

Abstract

We present a new method using nucleic acid secondary structure to assess phylogenetic relationships among species. In this method, which we term "molecular morphometrics," the measurable structural parameters of the molecules (geometrical features, bond energies, base composition, etc.) are used as specific characters to construct a phylogenetic tree. This method relies both on traditional morphological comparison and on molecular sequence comparison. Applied to the phylogenetic analysis of Cirripedia, molecular morphometrics supports the most recent morphological analyses arguing for the monophyly of Cirripedia sensu stricto (Thoracica + Rhizocephala + Acrothoracica). As a proof, a classical multiple alignment was also performed, either using or not using the structural information to realign the sequence segments considered in the molecular morphometrics analysis. These methods yielded the same tree topology as the direct use of structural characters as a phylogenetic signal. By taking into account the secondary structure of nucleic acids, the new method allows investigators to use the regions in which multiple alignments are barely reliable because of a large number of insertions and deletions. It thus appears to be complementary to classical primary sequence analysis in phylogenetic studies.

What Makes the Arc-Preserving Subsequence Problem Hard?

“…Thus, we conclude that for any 1 ≤ i ≤ q, T ci is obtained by deleting two of the three bases G of S ci . (2) By the above argument concerning the bases A appearing after S c1 [1] and T c1 [1], we know that if (T, Q) can be obtained from (S, P ), then T e xm [2] is matched to S e xm [3] for any 1 ≤ m ≤ n. Thus, for any 1 ≤ m ≤ n, T e xm is obtained from S e xm , and in particular T e xm [1] is matched to either S e xm [1] or S e xm [2]. (3) By definition, as there is no arc incident to bases of T , at least one base incident to every arc of P has to be deleted.…”

“…Therefore, every base A appearing after S c1 [1] and T c1 [1] must be matched. That is, for each 1 ≤ i ≤ q, T ci [3] is matched to S ci [5]. In particular, T cq [3] is matched to S cq [5].…”

“…That is, for each 1 ≤ i ≤ q, T ci [3] is matched to S ci [5]. In particular, T cq [3] is matched to S cq [5]. But since there are as many bases U between S c1 [1] and S cq [5] as there are between T c1 [1] and T cq [3], any base U in this interval in S must be matched to any base U in this interval in T ; that is, for any 1 ≤ i ≤ q, T ci [1] is matched to S ci [1].…”

“…-if x m = T rue then B contains each base of S [2], -if j i = 1 then B contains S ci [3] and S ci [4], -if j i = 2 then B contains S ci [2] and S ci [4], -if j i = 3 then B contains S ci [2] and S ci [3].…”

“…These structures suggest a significant common function for the studied RNA molecules [16,18,13,8], -RNA classification of various species (phylogeny) [4,3,21], -RNA folding prediction by considering a set of already known secondary structures [24,14], -identification of a consensus structure and consequently of a common role for molecules [22,5].…”