Phylogenomics with incomplete taxon coverage: the limits to inference

<p>Abstract</p> <p>Background</p> <p>Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, <it>decisiveness</it>, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa.</p> <p>Results</p> <p>We establish theoretical bounds on the impact of missing data on decisiveness. Results are derived for two contexts: a fixed taxon coverage pattern, such as that observed from an already assembled data set, and a randomly generated pattern derived from a process of sampling new data, such as might be observed in an ongoing comparative genomics sequencing project. Lower bounds on how many loci are needed for decisiveness are derived for the former case, and both lower and upper bounds for the latter. When data are not decisive for all trees, we estimate the probability of decisiveness and the chances that a given edge in the tree will be distinguishable. Theoretical results are illustrated using several empirical examples constructed by mining sequence databases, genomic libraries such as ESTs and BACs, and complete genome sequences.</p> <p>Conclusion</p> <p>Partial taxon coverage among loci can limit phylogenomic inference by making it impossible to distinguish among multiple alternative trees. However, even though lack of decisiveness is typical of many sparse phylogenomic data sets, it is often still possible to distinguish a large fraction of edges in the tree.</p

On the deduction of species relationships: a prÉcis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72495/1/j.1096-0031.2003.tb00366.x.pd

On the deduction of species relationships: a précis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72495/1/j.1096-0031.2003.tb00366.x.pd

Foundations of Digital Arch{\ae}oludology

Digital Archaeoludology (DAL) is a new field of study involving the analysis and reconstruction of ancient games from incomplete descriptions and archaeological evidence using modern computational techniques. The aim is to provide digital tools and methods to help game historians and other researchers better understand traditional games, their development throughout recorded human history, and their relationship to the development of human culture and mathematical knowledge. This work is being explored in the ERC-funded Digital Ludeme Project. The aim of this inaugural international research meeting on DAL is to gather together leading experts in relevant disciplines - computer science, artificial intelligence, machine learning, computational phylogenetics, mathematics, history, archaeology, anthropology, etc. - to discuss the key themes and establish the foundations for this new field of research, so that it may continue beyond the lifetime of its initiating project.Comment: Report on Dagstuhl Research Meeting. Authored/edited by all participants. Appendices by Thierry Depauli

Winthrop University Undergraduate Scholarship 2015 Book of Abstracts

University College proudly presents the fourth annual Winthrop University Undergraduate Scholarship Book of Abstracts. This year’s book chronicles the accomplishments of students and faculty mentors from 23 academic departments and programs, spanning all five colleges of the university: College of Arts and Sciences (CAS), College of Business Administration (CBA), College of Education (COE), College of Visual and Performing Arts (CVPA) and University College (UC).https://digitalcommons.winthrop.edu/undergradresearch_abstractbooks/1012/thumbnail.jp