2,434 research outputs found
Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case
abstract: Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.The article is published at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.011824
On Computing the Maximum Parsimony Score of a Phylogenetic Network
Phylogenetic networks are used to display the relationship of different
species whose evolution is not treelike, which is the case, for instance, in
the presence of hybridization events or horizontal gene transfers. Tree
inference methods such as Maximum Parsimony need to be modified in order to be
applicable to networks. In this paper, we discuss two different definitions of
Maximum Parsimony on networks, "hardwired" and "softwired", and examine the
complexity of computing them given a network topology and a character. By
exploiting a link with the problem Multicut, we show that computing the
hardwired parsimony score for 2-state characters is polynomial-time solvable,
while for characters with more states this problem becomes NP-hard but is still
approximable and fixed parameter tractable in the parsimony score. On the other
hand we show that, for the softwired definition, obtaining even weak
approximation guarantees is already difficult for binary characters and
restricted network topologies, and fixed-parameter tractable algorithms in the
parsimony score are unlikely. On the positive side we show that computing the
softwired parsimony score is fixed-parameter tractable in the level of the
network, a natural parameter describing how tangled reticulate activity is in
the network. Finally, we show that both the hardwired and softwired parsimony
score can be computed efficiently using Integer Linear Programming. The
software has been made freely available
Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case
Classifications and phylogenetic inferences of organismal groups change in
light of new insights. Over time these changes can result in an imperfect
tracking of taxonomic perspectives through the re-/use of Code-compliant or
informal names. To mitigate these limitations, we introduce a novel approach
for aligning taxonomies through the interaction of human experts and logic
reasoners. We explore the performance of this approach with the Perelleschus
use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies
published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of
names individuated according to their respective source publications), and 75
expert-asserted Region Connection Calculus articulations (e.g., congruence,
proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is
used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous
constraints and interpretations. The reasoning workflow optimizes the logical
consistency and expressiveness of the input and infers the set of maximally
informative relations among the entailed taxonomic concepts. The latter are
then used to produce merge visualizations that represent all congruent and
non-congruent taxonomic elements among the aligned input trees. In this small
use case with 6-53 input concepts per alignment, the information gained through
the reasoning process is on average one order of magnitude greater than in the
input. The approach offers scalable solutions for tracking provenance among
succeeding taxonomic perspectives that may have differential biases in naming
conventions, phylogenetic resolution, ingroup and outgroup sampling, or
ostensive (member-referencing) versus intensional (property-referencing)
concepts and articulations.Comment: 30 pages, 16 figure
Simple identification tools in FishBase
Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further
development. It explores the possibility of a holistic and integrated computeraided strategy
- …