martes, 22 de septiembre de 2015

¿Total evidence, nuclear genes or non-nuclear genes? Here is the dilemma.

Introduction.

Datation methods for evolutionary process studies are broad used in different groups like Chiroptera (Teeling et al. 2005) or Gimnosperms (Rydin & Petra. 2009). Even the non-nuclear DNA are the most widely reported by its own characteristics: high rate evolution, uniparental inheritance or absence of recombination (Zardoya & Meyer. 1996). The results on datation using nuclear partitions and non-nuclear partitions could be differentials (Vawter & Brown. 1986), but this subject had not been evaluated even though with the widely use of the technique. The main goal in this work is contrast the estimate datation times and the standard deviation using nuclear genes, non-nuclear genes and combination of both.

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Materials and Methods.

Data: 3 different partitions were created: Non-nuclear genes, nuclear genes and total evidence (Nuclear + Non-nuclear) for three taxas: Testudines, Picidae (Aves), Chiroptera (Mammalia) and Gimnospermas.

Phylogeny: A phylogenetic analysis under Maximum Likelihood with the Jukes Cantor nucleotide model with PhyML v. 3.0 (2012-12-08)(Guidon et al. 2010) was run for each partition. To avoid nucleotide model influence in the estimation, the same model were implemented in all partitions.

Datation: The Heuristic rate smoothing  algorithm (HSRA) implemented  in the BaseML packages from the software PALM (Yang. 2004) was used for the SD and datation time estimation. Two clock model were used: Strict Clock (SC) and Local Clock (LC). For each group  as minimum 3 fossils calibration points where implemented in the analysis (Magallon et al. 2013).

Analysis: The delta of standard deviation (ΔSD) and the datation time estimate were compared among each partition in a group. A Spearman correlation was made between  the ΔSD and the number of common nodes (Fig. 1) in each group.

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Results and Discussion.

On average, the topologies present a 40% of common nodes (range: 33 - 47%), and compare those nodes no differences in the datations generate under SC and LC where found in all groups. Chiroptera and Picidae present a trend in the SD where nuclear and total evidence partitions had the lowest values; While Gimnosperms and Testudines no present any trend in the SD (Fig. 2). Using the ΔSD, in general the nuclear and total evidence were the partition with the lowest values. Just Testudines present a different resutl, where the non-nuclear and nuclear partitions had the lowest values (Fig. 2).

The Spearman correlation shows inversely proportional relationship between the common node number and the ΔSD, despiting that it wasn't significant (p > 0.05) the relation is not descarted because the low number of taxonomic groups (< 5)(Fig.3) and it could be associate to the reduce number of terminals in the phylogeny.

Comparing with other previous works (Teeling et al. 2005; Rydin & Perea. 2009; Lourenco et al. 2012), the total evidence paritition present similar results in the datation times and SD. The partition combined are recomended in datation analysis, but also nuclear genes are a good choice too. Is necessary evaluate the effect of the number of of tips (terminals) in the phylogeny, and the use of different nucleotide evolution models.

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Figures. 
Figure 1. Two  comparable nodes between two differents topologies.

Figure 2. Standard deviation (SD) for all internal nodes of partitions from each group.
 
Figure 3. ΔSD values for each partition in each group and the Spearman regression with its respective rho value.


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Bibliography.
 
Catarina Rydin & Petra Korall. 2009: Evolutionary Relationships in Ephedra (Gnetales), with Implications for Seed Plant Phylogeny. Int. J. Plant. Sci. 170 (8):1031-1043.

Emma C. Teeling, Mark S. Springer, Ole Madsen, Paul Bates, Stephen J. O'Brien and William J. Murphy. 2005: A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record. Science Vol (307): 580-584.

Guidon S., Dufayard J. F., Lefort V., Anisimova M., Hordijk W., and Gascuel O. 2010: New algorithm and methods to estimate maximum likelihood phylogenies: assessing the perfomance of PhyML 3.0. Systematic Biology, 59 (3): 307-321.

Joao M. Lourenco, Julien Claude, Nicolas Galtier and Ylenia Chiari. 2012: Dating cryptodiran nodes: Origin and diversification of the turtle superfamily Testudinoidea. Molecular Phylogenetics and Evolution. 62: 496-507.

Lisa Vawter and wesley M. Brown. 1986: Nuclear and Mitochondrial DNA Comparisons Reveal Extreme Rate Variation in the Molecular Clock. Science Vol (234): 194-195.
Susana Magallon, Khidir W. Hilu and Dietmar Quandt. 2013: Land plant evolutionary timeline: Gene effect are scondary to fossil constraints in relaxed clock estimation of age and substitution rates. American Journal of Botany 100 (3): 000-018.

Rafael Zardoya & Axel Meyer. 1996: Phylogenetic perfomance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular Biology and Evolution 13 (7): 933-942.

Ziheng Yang. 2004: A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zoologica Sinica. 50(4): 645-656.
 
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Supplements.

1.
 
Genes: 


Picidae (Aves): COI, ND2, CYTB, Brahama Protein (BRM), Beta-Fibrogen (BFG), Aconitasa 1 (ACO1).

Chiroptera: 16s, COX, ND2, CYTB, RAG1, RAG2, ATP7a, BRCA1.

Gimnosperms: MATK, RBCL, ATPB, 18s, 26s, 5.8s.

Testudines: 12s, COX, CYTB, NAD4, RAG, Brain-derived Neurotrophic Factor (BNDF), Aryl Hydrocarbon Receptor 1 (AHR), Nerve Growth Factor (NGF).

2.

Fossils.

Picidae (Aves). Colaptes 1.8 Mya. Pliopicus spp. 13.6 Mya. Paleonerpes shorti. 11 Mya.

Chiroptera. (mayor información: E.C.Teeling et al., 2005 10.1126/science.1105113). Notonycteris spp. 30 Mya. Trachypteron franzeni (Emballonuridae) 37 Mya. Philisis spp. + Chamtwaria spp. + Chibanycteris spp. 37 Mya. Brachipposideros spp. + Pseudorhinolophus spp. 55 Mya.

Gimnospermas. Antarcticycas spp. 171 Mya. Rissikia spp. 245 Mya. Palaeognetaleana asupicia. 125 Mya.

Testudines. Chrysemys antiqua. 33.8 Mya. Cearachelys placidoi. 121 Mya. Proterochersis spp. 140 Mya. Hoplochelys spp 50 Mya.
 
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This work was presented at the V Simposio Colombiano de Biología Evolutiva, on poster presentation and is avaible here.