Title: Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses
Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such as selecting event costs and selecting representative reconciliations. Next, recent advances to address these challenges are discussed followed by a discussion of several established and recent software tools. more »« less
Abstract Summary We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences. Availability and implementation eMPRess is freely available at http://www.cs.hmc.edu/empress. Supplementary information Supplementary data are available at Bioinformatics online.
LeMay, Matthew; Wu, Yi-Chieh; Libeskind-Hadas, Ran
(, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021))
Carbone, Alessandra; El-Kebir, Mohammed
(Ed.)
The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics.
Hassan, Md Mahadi; Salvador, John; Santu, Shubhra_Kanti Karmaker; Rahman, Akond
(, Proceedings of the ACM on Software Engineering)
In infrastructure as code (IaC), state reconciliation is the process of querying and comparing the infrastructure state prior to changing the infrastructure. As state reconciliation is pivotal to manage IaC-based computing infrastructure at scale, defects related to state reconciliation can create large-scale consequences. A categorization of state reconciliation defects, i.e., defects related to state reconciliation, can aid in understanding the nature of state reconciliation defects. We conduct an empirical study with 5,110 state reconciliation defects where we apply qualitative analysis to categorize state reconciliation defects. From the identified defect categories, we derive heuristics to design prompts for a large language model (LLM), which in turn are used for validation of state reconciliation. From our empirical study, we identify 8 categories of state reconciliation defects, amongst which 3 have not been reported for previously-studied software systems. The most frequently occurring defect category is inventory, i.e., the category of defects that occur when managing infrastructure inventory. Using an LLM with heuristics-based paragraph style prompts, we identify 9 previously unknown state reconciliation defects of which 7 have been accepted as valid defects, and 4 have already been fixed. Based on our findings, we conclude the paper by providing a set of recommendations for researchers and practitioners.
An entanglement-based continuous variable (CV) QKD scheme is proposed, performing information reconciliation over an entanglement-assisted link. The same entanglement generation source is used in both raw key transmission and information reconciliation. The entanglement generation source employs only low-cost devices operated in the C-band. The proposed CV-QKD scheme with information reconciliation over an entanglement-assisted link significantly outperforms the corresponding CV-QKD scheme with information reconciliation over an authenticated public channel. It also outperforms the CV-QKD scheme in which a classical free-space optical communication link is used to perform information reconciliation. An experimental demonstration over the free-space optical testbed established at the University of Arizona campus indicates that the proposed CV-QKD can operate in strong turbulence regimes. To improve the secret key rate performance further, adaptive optics is used.
Hosner, Peter A; Zhao, Min; Kimball, Rebecca T; Braun, Edward L; Burleigh, J Gordon
(, Ornithology)
Abstract Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially “splits, lumps, and shuffles,” presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to more than 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase’s system of taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to more than 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates.
Ran Libeskind-Hadas. Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses. Retrieved from https://par.nsf.gov/biblio/10337462. Life 12.443 Web. doi:10.3390/life12030443.
Ran Libeskind-Hadas. Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses. Life, 12 (443). Retrieved from https://par.nsf.gov/biblio/10337462. https://doi.org/10.3390/life12030443
@article{osti_10337462,
place = {Country unknown/Code not available},
title = {Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses},
url = {https://par.nsf.gov/biblio/10337462},
DOI = {10.3390/life12030443},
abstractNote = {Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such as selecting event costs and selecting representative reconciliations. Next, recent advances to address these challenges are discussed followed by a discussion of several established and recent software tools.},
journal = {Life},
volume = {12},
number = {443},
author = {Ran Libeskind-Hadas},
editor = {Dona, Jorge and Sweet, Andrew and Tamura, Koichiro}
}
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