122,484 research outputs found
Collaborative e-science architecture for Reaction Kinetics research community
This paper presents a novel collaborative e-science architecture (CeSA) to address two challenging issues in e-science that arise from the management of heterogeneous distributed environments: (i) how to provide individual scientists an integrated environment to collaborate with each other in distributed, loosely coupled research communities where each member might be using a disparate range of tools; and (ii) how to provide easy access to a range of computationally intensive resources from a desktop. The Reaction Kinetics research community was used to capture the requirements and in the evaluation of the proposed architecture. The result demonstrated the feasibility of the approach and the potential benefits of the CeSA
Making the most of clade selection
Clade selection is unpopular with philosophers who otherwise accept multilevel selection theory. Clades cannot reproduce, and reproduction is widely thought necessary for evolution by natural selection, especially of complex adaptations. Using microbial evolutionary processes as heuristics, I argue contrariwise, that (1) clade growth (proliferation of contained species) substitutes for clade reproduction in the evolution of complex adaptation, (2) clade-level properties favoring persistence â species richness, dispersal, divergence, and possibly intraclade cooperation â are not collapsible into species-level traits, (3) such properties can be maintained by selection on clades, and (4) clade selection extends the explanatory power of the theory of evolution
Economical genotyping of little blue penguin (Eudyptula minor) clades from feather-based DNA
Determination of clade membership is a crucial requirement for many research questions addressing phylogeography, population structure, mating patterns, speciation, and hybridisation. The little blue penguin (Eudyptula minor) can be separated into two deeply divergent clades. However, assigning clade membership in little blue penguins requires molecular methods. Genetic sequencing can be used to identify clade membership but is expensive. Here, we present an economical alternative to the use of sequencing to determine little blue penguin clade membership. We extracted DNA from feathers using a method that produced reasonable quantities of DNA. We then amplified the D-loop section of the mitochondrial control region from total genomic DNA extracts, using the primers 'C L-tRNAglu' and 'D H-Dbox' followed by digestion with the restriction enzyme AluI. When visualised on a gel, distinctive banding patterns clearly indicated clade membership. We sequenced a subset of our samples and verified the accuracy of this method. The methods we present should facilitate little blue penguin research through a cost-effective approach to clade analysis as well as a successful technique to extract DNA from feathers when blood or tissue samples are not available
Determining species tree topologies from clade probabilities under the coalescent
One approach to estimating a species tree from a collection of gene trees is
to first estimate probabilities of clades from the gene trees, and then to
construct the species tree from the estimated clade probabilities. While a
greedy consensus algorithm, which consecutively accepts the most probable
clades compatible with previously accepted clades, can be used for this second
stage, this method is known to be statistically inconsistent under the
multispecies coalescent model. This raises the question of whether it is
theoretically possible to reconstruct the species tree from known probabilities
of clades on gene trees. We investigate clade probabilities arising from the
multispecies coalescent model, with an eye toward identifying features of the
species tree. Clades on gene trees with probability greater than 1/3 are shown
to reflect clades on the species tree, while those with smaller probabilities
may not. Linear invariants of clade probabilities are studied both
computationally and theoretically, with certain linear invariants giving
insight into the clade structure of the species tree. For species trees with
generic edge lengths, these invariants can be used to identify the species tree
topology. These theoretical results both confirm that clade probabilities
contain full information on the species tree topology and suggest future
directions of study for developing statistically consistent inference methods
from clade frequencies on gene trees.Comment: 25 pages, 2 figure
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