Home About us Contact
|
Home About us Contact | ||
|
|
||
Consensus Tree (consensus + tree)
Selected AbstractsAn investigation of the cranial evolution of Asian pitvipers (Serpentes: Crotalinae), with comments on the phylogenetic position of Peltopelor macrolepisACTA ZOOLOGICA, Issue 4 2010Peng Guo Abstract Guo, P., Jadin, R.C., Malhotra, A. and Li, C. 2009. An investigation of the cranial evolution of Asian pitvipers (Serpentes: Crotalinae), with comments on the phylogenetic position of Peltopelor macrolepis,Acta Zoologica (Stockholm) 91: 402,407. We investigated the evolution of 12 cranial characters of 31 species of Asian pitvipers by examining the character state changes on a consensus tree modified from broadly consistent molecular results. We found that these characters appear stable with only one intraspecific polymorphism. Nine of the 12 characters form useful synapomorphies, whereas three are ambiguous and evolutionarily plastic. Clades that are supported with numerous apomorphies are the Trimeresurus group [consisting of the recently defined genera Trimeresurus sensuMalhotra and Thorpe (2004), Parias, Popeia, Viridovipera, Himalayophis, and Cryptelytrops] and the genera Protobothrops, Parias, and Viridovipera. Two species previously considered as congeners but now known to be distantly related, Ovophis monticola and ,Ovophis'okinavensis, have nearly identical character states, demonstrating substantial convergence in cranial characters. Finally, we attempt to infer the phylogenetic position of Peltopelor macrolepis by comparing its cranial features with that of other pitvipers. [source] Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal,Vicariance Analysis and a case using Aesculus L. (Sapindaceae) including fossilsJOURNAL OF SYSTEMATICS EVOLUTION, Issue 5 2009A.J. HARRIS Abstract, We propose a simple statistical approach for using Dispersal,Vicariance Analysis (DIVA) software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as where Y is a node, and F(rY) is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage "x", where x may vary due to phylogenetic uncertainty (polytomies and nodes with posterior probability <100%). Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp*F(rY) on the Bayesian consensus tree when both variables are <100%, where pp is the posterior probability and F(rY) is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and of Aesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic ranges of the parental nodes of the lineages of Aesculus with moderate to high probabilities. The probabilities were greater than those estimated using the simple calculation of pp*F(ry) at a statistically significant level for two of the six lineages. We also found that adding fossil wildcard taxa in phylogenetic analysis generally increased P for ancestral ranges including the fossil's distribution area. The ,P was more dramatic for ranges that include the area of a wildcard fossil with a distribution area underrepresented among extant taxa. This indicates the importance of including fossils in biogeographic analysis. Exmination of range subdivision at the parental nodes revealed potential range evolution (extinction and dispersal events) along the stems of A. californica and sect. Parryana. [source] A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphologyBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2001OLE SEBERG FLS A cladistic analysis, primarily based on morphology, is presented from 40 diploid taxa representing the 24 monogenomic genera of the Triticeae. General problems related to the treatment of hybrids and supposedly allopolyploid heterogenomic taxa are highlighted. Special emphasis is given to taxa not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx. 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent. [source] Partitioned Bremer support and multiple treesCLADISTICS, Issue 4 2002Christine L. Lambkin Partitioned Bremer support (PBS) is a valuable means of assessing congruence in combined data sets, but some aspects require clarification. When more than one equally parsimonious tree is found during the constrained search for trees lacking the node of interest, averaging PBS for each data set across these trees can conceal conflict, and PBS should ideally be examined for each constrained tree. Similarly, when multiple most parsimonious trees (MPTs) are generated during analysis of the combined data, PBS is usually calculated on the consensus tree. However, extra information can be obtained if PBS is calculated on each of the MPTs or even suboptimal trees. [source] A Cladistic Analysis of the New World Species of Lotus L. (Fabaceae, Loteae)CLADISTICS, Issue 3 2000Ana M. Arambarri The genus Lotus L. is a monophyletic group diagnosed by the possession of a standard claw with thickened infolded margin, stamens diadelphous, and the style hardened from the base. It comprises approximately 200 species distributed throughout the world. A cladistic analysis of the New World species was performed using 39 morphological and anatomical characters (29 from seed morphology and anatomy, 1 from plant habit, 1 from leaf morphology, 6 from flower morphology, and 2 from fruit morphology). Dorycnium, Edentolotus, Krokeria, and Pedrosia, of the Old World, and 28 species of the New World were considered terminal taxa. Tetragonolobus Scop. was chosen to root the cladograms and Dorycnium Mill. to reroot them. With Tetragonolobus the analysis yielded 15 equally parsimonious trees, each with a length of 74 steps, a consistency index of 0.62, and a retention index of 0.89. The 15 initial trees and the strict consensus tree defined 12 monophyletic groups. All terminal taxa form a monophyletic group diagnosed by the presence of a radicular lobe discernible to conspicuous (character 10); rim aril thick (character 13); stipules absent (character 31); and style simple and nondilated (character 36). The New World species form a monophyletic group on the basis of the seed relationship of length to width in hilar view 1.5:1 to 2:1 (character 5); micropyle linear-deltoid to bifurcate (character 19); and keel erostrate (character 33). Identical monophyletic groups were obtained when Dorycnium was used as root. These results are discussed in the context of data on cytology and morphology. [source] Unstable taxa in cladistic analysis: identification and the assessment of relevant charactersCLADISTICS, Issue 5 2009Diego Pol A common problem in phylogenetic analysis is the presence of unstable taxa that are depicted in multiple positions in optimal topologies. These uncertainties are reflected in strict consensus trees with polytomies that hamper the interpretation of the phylogenetic results. We propose a protocol for detecting unstable branches (either terminal taxa or clades) and identifying particular characters related to their instability in cladistic analysis. This procedure is based on an iterative evaluation of the agreement of triplets among the optimal topologies (i.e. most-parsimonious trees, MPTs) and examination of character optimizations on these trees. Different types of characters underlying the unstable behaviour of taxa are detected: those with conflicting scorings that support alternative positions of problematic taxa and those with missing data in the unstable taxa that could reduce their instability if they are scored. The entire process is automated through a TNT script that provides a list of characters related to the instability of each unstable taxon. The outcome of this procedure can be used as a guide for further research efforts focused on the revision or addition of (morphological or molecular) phylogenetic data for elucidating the affinities of unstable taxa. ,© The Willi Hennig Society 2009. [source] | ||||||||||