Biol460 Molecular Genetics Answers Assessment Answers

Answer:

Robinsonia genus plants are terrestrial and indigenous to the Juan Fernández Islands, comprising of 8 species. Phylogenetic studies have suggested them to be nested within the Senecio genus, though these two genus are morphologically distinct (Pelser et al. 2010). The current study attempts to understand the phylogenetic relations between Robinsonia genus and Senecio genus. Two plant species from the Robinsonia genus Robinsonia gracilis and Robinsonia berteroi, thirteen plant species from the Senecio genus, Senecio algens, Senecio arnicoides, Senecio calocephalus, Lasiocephalus campanulatus, Senecio chilensis, Senecio cremeiflorus, Senecio fistulosus, Senecio gayanus, Senecio lastarrianus, Senecio nemorensis, Senecio polygaloides, Senecio triodonvar.triodon and Senecio viscosus were selected for the study. The nucleotide substitution model was selected by JModeltest (Darriba et al. 2012; Guindon and Gascuel 2003), the likelihood scores were computed followed by AIC (Akaiki Information Criterion) calculations. The analysis suggested TIM2+G (transition model; Bayesian analysis performed with this model) model with likelihood score: -lnL = 2312.4932, nst=6, rate=gamma and the following nucleotide frequencies:

freqA = 0.2556  freqC = 0.2063  freqG = 0.2585  freqT = 0.2796

The phylogenetic tree was generated through Bayesian analysis (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003) and constructed using FigTree software. The nst, rate, and statefreqpr were varied to observe their effect on the phylogenetic tree. Considering nst=1 wherein the nucleotide substitution happens at the same frequency and rate as equal/gamma/propinv/invgamma and statefreqpr as fixed/ Dirichlet it was observed that Robinsonia berteroi clustered with Senecio arnicoides but not very closely with Robinsonia gracilis which forms an individual clade (Figure 1). The change in the rate to adgamma led to a different phylogenetic tree wherein Robinsonia gracilis clustered with Senecio algens and Lasiocephalus campanulatus and Robinsonia berteroi formed an individual clade (Figure 1). The results suggested Robinsonia as monophyletic as it clustered with other Senecio species, with these parameters the posterior probabilities were higher than 0.5 and mostly 1.

Considering nst=2, wherein nucleotide transition occurs at different frequency compared to transversions, rate as equal/gamma/propinv/invgamma and statefreqpr as fixed/ Dirichlet the observed phylograms were similar to phylograms generated while keeping nst=1. However, by changing the rate to adgamma the arrangement of the clades varied wherein Robinsonia gracilis clustered with nine Senecio species connected by a root and Robinsonia berteroi formed an individual clade (Figure 2). The results with nst=2 also suggested Robinsonia as monophyletic as it clustered with other Senecio species, with these parameters the posterior probabilities were higher than 0.5 and mostly 1 similar to those calculated with nst=1.

Considering nst=6, wherein substitutions occur at different frequency rate as equal/gamma/invgamma and statefreqpr as fixed/ Dirichlet the observed phylograms were similar to phylograms generated while keeping nst=1/2. However, by changing the rate to adgamma the arrangement of the clades varied wherein Robinsonia gracilis clustered closely with Lasiocephalus campanulatus and Senecio species connected by a root and Robinsonia berteroi formed an individual clade (Figure 3). With nst=6 slight variation in the arrangement of Senecio viscosus in the phylogram was observed when the rate is propinv, here a reduction in the posterior probabilities values from ~0.9 to ~0.5 was observed due to the formation of individual clade by Senecio viscosus. The results with nst=6 also suggested Robinsonia as monophyletic as it clustered with other Senecio species, with these parameters the posterior probabilities were higher than 0.5 and mostly 1 similar to those calculated with nst=1/2. The analysis also suggested no significant variation by changes in the statefreqpr parameter, the variation observed was vastly contributed by rate=adgamma.

Phylogram for Robinsonia and Senecio genus. Here nst=1, the five rate parameters are marked on the right of the respective phylogram rows and statefreqpr marked at the bottom of respective phylogram columns. Numbers on the branch represents posterior probabilities

Phylogram for Robinsonia and Senecio genus. Here nst=2, the five rate parameters are marked on the right of the respective phylogram rows and statefreqpr marked at the bottom of respective phylogram columns. Numbers on the branch represents posterior probabilities.

Phylogram for Robinsonia and Senecio genus. Here nst=6, the five rate parameters are marked on the right of the respective phylogram rows and statefreqpr marked at the bottom of respective phylogram columns. Numbers on the branch represents posterior probabilities.

Discussion

The plant genus Robinsonia (8 species) and Senecio  are native to South America (Pelser et al. 2007).  These genus have known to be monophyletic based on the phylogenetic analysis of DNA from plastids and ITS-ETS Internal Transcribed Spacer-External Transcribed Sequence (Pelser et al. 2010). The phylogenetic analysis conducted from the DNA sequences of the nuclear Internal Transcribed Spacer region of the 18S–5.8S–26S nuclear ribosomal cistron suggested them to be monophyletic, concurring with the published work. It was observed that Robinsonia species were homologous to Senecio but homoplasious to the species of their own genus. Variation in the three different parameters (nst, rate, and statefreqpr) of Bayesian analysis yielded similar results with slight modifications, however, all the phylograms suggested the genus Robinsonia is monophyletic.

Reference

Darriba D, Taboada GL, Doallo R, Posada D (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772.

Guindon S, Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood". Systematic Biology 52: 696-704.

Huelsenbeck JP, Ronquist F (2001). MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.                      

Pelser PB, Nordenstam B, Kadereit JW, Watson LE (2007). An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new delimitation of Senecio L. Taxon 56, 1077- 1104.

Pelser PB, Tepe EJ, Kennedy AH, Watson LE (2010). The fate of Robinsonia (Asteraceae): sunk in Senecio, but still monophyletic? Phytotaxa 5, 31-46.

Ronquist F, Huelsenbeck JP (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.