Dataset Information

Best match graphs and reconciliation of gene trees with species trees.

ABSTRACT: A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.

SUBMITTER: Geiß M

PROVIDER: S-EPMC7052050 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Best match graphs and reconciliation of gene trees with species trees.

Geiß Manuela M Laffitte Marcos E González MEG Sánchez Alitzel López AL Valdivia Dulce I DI Hellmuth Marc M Rosales Maribel Hernández MH Stadler Peter F PF

Journal of mathematical biology 20200130 5

A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We fur ...[more]

PMID: 32002659

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Project description:Polyculture is a potentially interesting rearing practice for future aquaculture developments. Nevertheless, it may result in beneficial as well as detrimental consequences for fish production. One way to maximize the benefits of polyculture is to combine species with high levels of compatibility and complementarity. This requires the development of a ranking procedure, based on a multi-trait assessment, that highlights the most suitable species combinations for polyculture. Moreover, in order to ensure the relevance of such a procedure, it is important to integrate the socio-economic expectations by assigning relative weights to each trait according to the stakeholder priorities. Here, we proposed a ranking procedure of candidate fish polycultures (i.e., species combinations that could be potentially interesting for aquaculture) based on a multi-trait assessment approach and the stakeholder priorities. This procedure aims at successively (i) weighting evaluation results obtained for each candidate polyculture according to stakeholder priorities; (ii) assessing differentiation between candidate species combinations based on these weighted results; and (iii) ranking differentiated candidate polycultures. We applied our procedure on three test cases of fish polycultures in recirculated aquaculture systems. These test cases each focused on a target species (two on Sander lucioperca and one on Carassius auratus), which were reared in two or three different alternative candidate fish polycultures. For each test case, our procedure aimed at ranking alternative combinations according to their benefits for production and/or welfare of the target species. These benefits were evaluated based on survival rate as well as morphology, behavioral, and physiological traits. Three scenarios of stakeholder priorities were considered for weighting evaluation results: placing a premium on production, welfare, or both for the target species. A comparison of our procedure results between these scenarios showed that the ranking changed for candidate polycultures in two test cases. This highlights the need to carefully consider stakeholder priorities when choosing fish polycultures.

Dataset Information

Best match graphs and reconciliation of gene trees with species trees.

Publications

Best match graphs and reconciliation of gene trees with species trees.

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