Assessing internal support with large phylogenetic DNA matrices.
Explore the source record for details and available documents.
Data Interpretation, Statistical↗
Biomedical subjects
Vincent Savolainen
Publications and source records attributed to Vincent Savolainen.
Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae).
Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well-documented amphidiploids are similar or identical to one of their two parents-usually, but not always, the maternal parent-and are not in any sense themselves 'hybrid'. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of unknown origin, and it is in this perspective that analysis of ITS sequences is highly informative.
DNA, Plant↗
Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils.
Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied because of gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia + Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are "molecular living fossils," consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.
Journal Article↗
Radiation in the Cape flora and the phylogeny of peacock irises Moraea (Iridaceae) based on four plastid DNA regions.
Phylogenetic analyses of four plastid DNA regions, the rbcL exon, trnL intron, trnL-trnF intergenic spacer, and rps16 intron from each of 73 species in the African genus Moraea (Iridaceae: Irideae) including accessions of all major species clusters in the genus, show Moraea to be paraphyletic when Barnardiella, Galaxia, Hexaglottis, Homeria (all southern African), and Gynandriris (Eurasian as well) were recognized as separate genera. There are several small, isolated species clusters at the basal nodes of the tree that are all restricted to the winter-rainfall zone of southern Africa (the Greater Cape floral kingdom) and a few, highly derived, large species groups that have radiated extensively within the winter-rainfall zone. Mapping of floral traits shows that an Iris-type flower is ancestral in Moraea. Floral changes are associated with shifts in pollination systems, either from passive pollen deposition on long-tongued bees foraging for nectar to active pollen collection by female bees foraging for pollen, fly, or hopliine scarab beetle pollination. Dating the nodes of the phylogenetic tree using non-parametric rate smoothing with a calibration point derived from broad dating of the angiosperms indicates that the divergence between Moraea and its sister genus Ferraria occurred about 25 mya in the early Miocene. The early radiation of Moraea took place against a background of aridification and the spread of open habitats, such as desert, shrubland, and fynbos.
Evolution, Molecular↗
Building supertrees: an empirical assessment using the grass family (Poaceae).
Large and comprehensive phylogenetic trees are desirable for studying macroevolutionary processes and for classification purposes. Such trees can be obtained in two different ways. Either the widest possible range of taxa can be sampled and used in a phylogenetic analysis to produce a "big tree," or preexisting topologies can be used to create a supertree. Although large multigene analyses are often favored, combinable data are not always available, and supertrees offer a suitable solution. The most commonly used method of supertree reconstruction, matrix representation with parsimony (MRP), is presented here. We used a combined data set for the Poaceae to (1) assess the differences between an approach that uses combined data and one that uses different MRP modifications based on the character partitions and (2) investigate the advantages and disadvantages of these modifications. Baum and Ragan and Purvis modifications gave similar results. Incorporating bootstrap support associated with pre-existing topologies improved Baum and Ragan modification and its similarity with a combined analysis. Finally, we used the supertree reconstruction approach on 55 published phylogenies to build one of most comprehensive phylogenetic trees published for the grass family including 403 taxa and discuss its strengths and weaknesses in relation to other published hypotheses.
Data Interpretation, Statistical↗
Phylogeny reconstruction and functional constraints in organellar genomes: plastid atpB and rbcL sequences versus animal mitochondrion.
Explore the source record for details and available documents.
Animals↗
Is cladogenesis heritable?
The heritability of speciation rates and extinction risks is a crucial parameter in models of macroevolution, but little direct evidence has been available to assess the occurrence, strength, or generality of this heritability. We tested for heritability using correlations between ancestral and descendent branch lengths in phylogenetic trees, an approach first applied to a bird phylogeny by Harvey et al. (1991, pages 123-137 in Genes in ecology [R. J. Berry et al., eds.], Blackwell Scientific, Oxford). We applied Harvey et al.'s test to some of the largest DNA sequence-based phylogenetic analyses published to date for plants, insects, fungi, and bacteria. If one of two parent lineages splits first and if this is the case for any heritable reason, then on average we expect its daughter lineages to also split first. We also used a randomization procedure to assess significance of branch length heritability. Using maximum parsimony and maximum likelihood branch lengths and trees made ultrametric after nonparametric rate smoothing or by enforcing a molecular clock, we found a pattern for most clades consistent with heritable net cladogenesis. Heritability of cladogenesis may be a general phenomenon, detectable across a large number of lineages and a broad range of taxa.
Animals↗