Mirroring co-evolving trees in the light of their topologies

Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain families through maximizing the similarity between trimmed versions of their phylogenetic trees. Since maximization of any natural similarity score is computationally difficult, many approaches employ heuristics to maximize the distance matrices corresponding to the tree topologies in question. In this paper we devise an efficient deterministic algorithm which directly maximizes the similarity between two leaf labeled trees with edge lengths, obtaining a score-optimal alignment of the two trees in question. Our algorithm is significantly faster than those methods based on distance matrix comparison: 1 minute on a single processor vs. 730 hours on a supercomputer. Furthermore we have advantages over the current state-of-the-art heuristic search approach in terms of precision as well as a recently suggested overall performance measure for mirrortree approaches, while incurring only acceptable losses in recall. A C implementation of the method demonstrated in this paper is available at http://compbio.cs.sfu.ca/mirrort.htmComment: 13 pages, 2 figures, Iman Hajirasouliha and Alexander Sch\"onhuth are joint first author

Estimating phylogenetic trees from genome-scale data

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic methods known as "species tree methods" have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting or deep coalescence that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Although such methods are gaining in popularity, they are being adopted with caution in some quarters, in part because of an increasing number of examples of strong phylogenetic conflict between concatenation or supermatrix methods and species tree methods. Here we review theory and empirical examples that help clarify these conflicts. Thinking of concatenation as a special case of the more general model provided by the multispecies coalescent can help explain a number of differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences, base compositional heterogeneity and long branch attraction. We show that approaches such as binning, designed to augment the signal in species tree analyses, can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods that incorporate biological realism are a key to phylogenetic analysis of whole genome data.Comment: 39 pages, 3 figure

Environmentally Influenced Duplication Patterns Followed by Functional Shifts Fueling the Evolution of Metazoan Sensory Systems

In this thesis, some of the methods by which animals use their sensory systems to interact with their environment have been extensively studied. How gene duplications have played an important role in sensory evolution by duplication followed by functional shifts resulting in neofunctionalisation has been analysed. This extensive neofunctionalisation allows for an expansion in the number of environmental signals the animal can detect. In the following chapters, some of the ways gene duplication has effected sensory perception have been shown in detail, in particular by the expansion and specialisation of sensory receptor repertoires. Chapter two describes an extensive study performed on the duplication and neofunctionalisation of opsins in animals as a result of environmental signals, leading to the evolution of colour vision. This study of vision is expanded upon in chapter three by looking at how the duplication of an entire visual pathway has led to the emergence of a new cell type and visual function in the rod and cone cells of vertebrates. Finally, in chapter four, large-scale analyses were performed of some massively expanded gene families used for olfactory and gustatory discrimination, showing the effects of extreme cases of gene duplication on animal sensory perception

Comparing Patterns of Natural Selection across Species Using Selective Signatures

Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell

A practical guide to design and assess a phylogenomic study

Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of 'big data' molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phy- logenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of 'more genes, more robustness' often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when plan- ning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the tech- nical robustness of phylogenomic studies or improve the experimental design of a project

Diversification and coexistence in the Madagascar olive (Noronhia, Oleaceae)

The long-isolated island of Madagascar provides a suitable setting for studying species diversification, with most groups of organisms there both radiating and showing a high level of endemism. Noronhia is one of these groups and represents the most successful radiation of the olive family (Oleaceae) in Madagascar, with ca. 80 species. In this study, using plastid and nuclear DNA sequences obtained from a comprehensive sampling both within Noronhia and the family, I show that Noronhia, together with Indian Ocean species of Chionanthus, form a monophyletic clade sister to African Chionanthus. The diversification of Noronhia followed a likely Cenozoic dispersal from Africa. Within Noronhia, phylogenetic relationships are mostly unresolved despite the species showing considerable ecological and phenotypic diversity. In most cases, analyses of bioclimatic, molecular and morphological data, interpreted in phylogenetic and geographic contexts, show support for my initial species hypotheses and offer new insights into species boundaries. Morphological data provide the strongest support while bioclimatic ones are the least informative, suggesting that the broad-scale variation in bioclimatic data does not adequately capture the ecological processes driving the diversification of this genus. However, attempts to understand spatial patterns of richness and coexistence among species of Noronhia show that mountainous areas in the island harbor the highest concentrations of species and the highest endemism. Habitat heterogeneity likely explains how diversity is promoted and maintained in these topographically complex regions. Furthermore, analyses focused on a smaller spatial scale, the Montagne d’Ambre massif, again indicate that habitat heterogeneity plays an important role. Different groups of species grow in different habitats on the mountain, suggesting environmental filtering associated with rainfall and soil nutrient gradients. Overall, the integrative approach applied in this study highlights the importance of using different kinds of data analyzed at various scales to understand species diversification

TREBUCHET: Fully Homomorphic Encryption Accelerator for Deep Computation

Secure computation is of critical importance to not only the DoD, but across financial institutions, healthcare, and anywhere personally identifiable information (PII) is accessed. Traditional security techniques require data to be decrypted before performing any computation. When processed on untrusted systems the decrypted data is vulnerable to attacks to extract the sensitive information. To address these vulnerabilities Fully Homomorphic Encryption (FHE) keeps the data encrypted during computation and secures the results, even in these untrusted environments. However, FHE requires a significant amount of computation to perform equivalent unencrypted operations. To be useful, FHE must significantly close the computation gap (within 10x) to make encrypted processing practical. To accomplish this ambitious goal the TREBUCHET project is leading research and development in FHE processing hardware to accelerate deep computations on encrypted data, as part of the DARPA MTO Data Privacy for Virtual Environments (DPRIVE) program. We accelerate the major secure standardized FHE schemes (BGV, BFV, CKKS, FHEW, etc.) at >=128-bit security while integrating with the open-source PALISADE and OpenFHE libraries currently used in the DoD and in industry. We utilize a novel tile-based chip design with highly parallel ALUs optimized for vectorized 128b modulo arithmetic. The TREBUCHET coprocessor design provides a highly modular, flexible, and extensible FHE accelerator for easy reconfiguration, deployment, integration and application on other hardware form factors, such as System-on-Chip or alternate chip areas.Comment: 6 pages, 5figures, 2 table

Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. Results: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). Conclusions: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.NHM Repositor

Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea,which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. Results: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). Conclusions: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth“arms race”.Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis