Parsimony analysis using implied weighting on an asian salamander family (amphibia, caudata)

Introduction

Caudata is a group that contains 578 species grouped into 67 genus, that forms part of the Lissamphibia together with modern Anura and extant Gymnophiona[1,2]. These species are contained within 10 families: Cryptobranchidae, Hynobiidae, Proteidae, Sirenidae, Dicamptodonidae, Ambystomatidae, Salamandridae, Plethodontidae, Amphiumidae and Rhyacotritonidae [2]. Since some genera of salamanders have been used as a study model [3–6], phylogenetic analyses with more robust resolution at the family level are necessary [3]. These investigations search for evolutionary patterns from comparatives studies, such as the mechanisms of tissue regeneration, and they can identify unique and derived characters and identify present homoplasy as long as they contain phylogenies with adequate resolutions [7]. This homoplasy is frequently found within the clade of caudata [8,9]. Many of the characters present in caudata have not developed due to synapomorphy, which may lead to the belief that this tendency may be reflected at the molecular level [10]. In this sense, using a phylogeny it’s possible to find answers about the behaviour, origin or development of certain characters, however, arguments explaining characteristics in plethodontids may not work for hynnobiids [10]. To search for these arguments, parsimony inference has been used for the phylogenies [3,8,9,11–13]. Even taking into account the aforementioned abundance of homoplasy throughout caudata, parsimony analyses have been using equal weights. The relationship between character weighing and parsimony was previously discussed and it was stated that "the most parsimonious cladogram is the hypothesis with the most explanatory power, given the weight that each character deserves", concluding that if the data is weighed appropriately, that data should always be preferred [14]. Furthermore, reducing the weight of characters with greater homoplasy is an issue that has been treated favourably on several occasions [15]. Implicit character weighing, as this method of weighing against homoplasy is known, improves analysis results even on large molecular data sets [16]. In other words, If the results of a given implied weighing outcome are not satisfactory “the results can only be criticized on the grounds that the weights have not been assigned in the best way” [15]. Said weighing can be done through a concavity function used in implied weighting, which is a decreasing function that weighs characters according to their homoplasy so that, when the fit of trees are compared, the influence of that homoplasy will be properly rescaled [17]. The influence of the homoplasy in the characters is altered with a constant, which is K, however, the use of a certain optimal value can be misleading because a group can appear only under this value, and the monophyly of this group cannot be considered as firmly established just because it occurs close or on that value [18].

Methodology

For this analysis, data was obtained from Weisrock [12]. With a total of 14 terminals used within the hynobiidae family with 1 mitochondrial gene and 1 nuclear gene (12S-16S and ND2-COI). For this, the sequences were aligned via MUSCLE [19] using Andrias japonicus as an outgroup and the present gaps were taken as missing information. The analysis was made using maximum parsimony and TNT v.1.5 [20], establishing parameters for the K value following previous guidelines [21], however in this work 5 values among said guidelines will be evaluated (20, 21, 23, 26, 30). Subsequently, a heuristic search was performed with the "mult" command using 100 replications, with the TBR method, 10 drifting iterations and using a random adittion sequence. The tree support was built by means of the "resample" command using 500 iterations of bootstrap. Saving each tree with its support values.

Results and discussions

Throughout the procedure, each value of K resulted in a tree on which bootstrap was applied, the topology of the trees conserves the same phylogenetic relationships among themselves except between Hynobiidae amjieensis and H. leechi, which presents a polytomy with the values of K = 26 and K = 30. In figure 1 you can see the tree with the best support obtained with the different values of K.

Fig. 1 Phylogeny of clade hynobiidae evaluated using value k = 23, includes the outgroup A. japonicus and bootstrap values

Fig. 2 Phylogeny of clade hynobiidae evaluated using value k = 30, includes the outgroup A. japonicus and bootstrap values

The relationships that are presented are mostly similar, however, the differences found between the topologies given by the values of K = 26 and K = 30 lead to support the topology shown in figure 2. Compared with the tree obtained by maximum parsimony from the original work, the bootstrap supports are higher, while the bootstrap values obtained by TNT during this analysis are not as well supported as those mentioned from Weisrock et al. work. This may be due to the genres taken for the present analysis. On the other hand, the phylogenetic relationships obtained here do not differ much from those obtained by Weisrock [12], a result that can also be associated with the number of species taken.

Conclusions

Implicit weighing was used during the parsimony analysis, and larger differences were expected in phylogenetic relationships that could reflect the impact of an assessment of the weight of traits based on their homoplasy. However, the results do not show such an impact, so it is thought that an evaluation with more data and more terminals in the data matrix to be used could show if there is a significant difference. However, and taking into account the results obtained here, it is possible that it will not have a marked difference regarding the use of equal weights of the characters to be used in maximum parsimony for clades where homoplasy is very marked throughout the characters.

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