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Reconstructing phylogeny from patchy data of rodents
Martínková, Natália ; Moravec, J.
To reveal phylogeny of sparsely sequenced taxa, standard methods could not be successfully used due to patchy character of data and new methods had to be developed. We summarize such methods and present their funcionality on phylogeny of Arvicolini voles. Analyzing tree space with terraces, we have found that supermatrix approach is superior to supertree approach in extracting signal from data and determining a resolved and well-supported phylogeny. The most widely used program from Bayesian phylogeny inference fails to determine the correct lengths of branches in a large supermatrix with a lot of missing data, it still successfully determines the true tree topology.
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Multilocus phylogeny of Sciurini tree squirrels
Pečnerová, P. ; Martínková, Natália
Phylogenetic relationships inside the tribe Sciurini produce conflict between older morphological research and modern molecular studies. We provided a detailed phylogenetic analysis by incorporating eight loci and various methods of data processing. We used prevailing and user-friendly software packages (Geneious, BioEdit, MrBayes, ModelTest). Evolutionary history of Sciurini squirrels was examined by means of Bayesian inference of concatenated data set and six supertree construction methods. The concatenated data and supertrees generated by SuperTriplets, modified MinCut, standard MRP and veto supertree (without source tree correction) yielded similar results with taxa grouped according to their zoogeographic distribution. The genus Tamiasciurus formed a separate evolutionary lineage at the base of our trees and the other taxa gradually diverged into Palaearctic/Indomalayan, Nearctic and Neotropical groups. The other used methods, MinCut, Purvis-MRP and veto (with source tree correction) showed deviations from this pattern.
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Tree of life in a gappy genomic era
Martínková, Natália
Increasing volume of publicly available DNA sequence data enables comprehensive studies that address integrative questions. For these projects, bioinformatic analysis requires advanced methods and computational infrestructure. I present the character of DNA sequence matrices for multilocus datasets, which contain large portions of missing data. A condition critical for analysis of multilocus data is that datasets for all loci or genes need to have partially overlapping taxon sets. The work-flow for analysing such data differs between supermatrix and supertree estimation of species trees. In the supermatrix approach, aligned sequences for all genes are concatenated and the species tree is estimated directly from a partitioned matrix. In the supertree approach, gene sequence alignments are used for inference of gene trees. Those are then combined into a species supertree. Smaller projects could benefit from utilising all available information in the supermatrix. Larger projects should rely on supertree methods for computational optimisation.
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Evolution of human socio-cultural and ecological traits: a phylogenetic (supertree) approach
DUDA, Pavel
Human species display complex intraspecies population structure and unparalleled behavioral and cultural diversity. In order to elucidate human population history and pattern of evolutionary change of socio-cultural and ecological traits, the first composite phylogenetic tree of 574 human populations (ethno-linguistic groups) was created on the basis of 129 recently published phylogenetic hypotheses based on genomic, genetic and linguistic data, utilizing supertree method matrix representation with parsimony. Subsequently, 56 selected socio-cultural and ecological characters based on ethnographic cross-cultural data were optimized on topology of obtained supertrees in order to reconstruct patterns of evolutionary change and states present in ancestral populations. The results are discussed in the light of recent studies of human phylogeography and cultural phylogenetic studies.
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