Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables easily installable, integrable in workflow environments, and parallelizable when possible. Moreover, Go is a compiled language, which accelerates computations compared to interpreted languages. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386) on GitHub at https://github.com/evolbioinfo/gotree, Bioconda and DockerHub.

Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales)

ABSTRACTAmong many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.

Gotree/Goalign : Toolkit and Go API to facilitate the development of phylogenetic workflows

Besides computer intensive steps, phylogenetic analysis workflows are usually composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables efficient, easily installable, integrable in workflow environments, and parallelizable when possible. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386). Sources and binaries are available on GitHub at https://github.com/evolbioinfo/{gotree|goalign} , Bioconda, and DockerHub.

Efficient Approaches to the Mixture Distance Problem

The ancestral mixture model, an important model building a hierarchical tree from high dimensional binary sequences, was proposed by Chen and Lindsay in 2006. As a phylogenetic tree (or evolutionary tree), a mixture tree created from ancestral mixture models, involves the inferred evolutionary relationships among various biological species. Moreover, it contains the information of time when the species mutates. The tree comparison metric, an essential issue in bioinformatics, is used to measure the similarity between trees. To our knowledge, however, the approach to the comparison between two mixture trees is still unknown. In this paper, we propose a new metric named the mixture distance metric, to measure the similarity of two mixture trees. It uniquely considers the factor of evolutionary times between trees. If we convert the mixture tree that contains the information of mutation time of each internal node into a weighted tree, the mixture distance metric is very close to the weighted path difference distance metric. Since the converted mixture tree forms a special weighted tree, we were able to design a more efficient algorithm to calculate this new metric. Therefore, we developed two algorithms to compute the mixture distance between two mixture trees. One requires O(n2) and the other requires O(nh1h2) computational time with O(n) preprocessing time, where n denotes the number of leaves in the two mixture trees, and h1 and h2 denote the heights of these two trees.

Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms

Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host–parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae’s fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.

­­­Multi-locus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletales)

Among many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subgenus Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multi-locus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate the taxon O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multi-locus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity within the genus.

‘He passed away because of cutting down a fig tree’: The similarity between people and trees in Jewish symbolism, mysticism and halakhic practice

Comparing people to trees is a customary and common practice in Jewish tradition. The current article examines the roots and the development of the image of people as trees in Jewish sources, from biblical times to recent generations (Bible, classical rabbinical literature, medieval to modern rabbinic literature and popular culture), as related to the prohibition against destroying fruit trees. The similarity between humans and trees in the Jewish religion and culture was firstly suggested in biblical literature as a conceptual-symbolic element. However, since the Amoraic period (3rd–5th centuries CE), this similarity was transformed to a resemblance bearing mystical and Halakhic (Jewish Law) implications. Various sources in rabbinical literature describe trees as humans that may be spoken to or yelled at to produce fruit. Cutting down a tree was perceived by the rabbis of the Talmud (3rd–5th centuries CE) not only as an unethical act or vandalism, but also as a hazard: the death of the tree corresponds to the death of the person who resembles it. All societies, cultures and religions have a system of values and practices that are aimed at shaping people, society and the environment according to a certain worldview.Contribution: The discussion in this article on the relationship between religion-culture and nature (plants) indicates how the Jewish religion shaped believers’ attitude to the world of flora over the generations by transforming the man-tree comparison into one with binding and even threatening practical religious meaning.

Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees

Motivation The Robinson–Foulds (RF) metric is widely used by biologists, linguists and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies the number of bipartition splits that occur in both trees—but this conservative approach ignores potential similarities between almost-identical splits, with undesirable consequences. ‘Generalized’ RF metrics address this shortcoming by pairing splits in one tree with similar splits in the other. Each pair is assigned a similarity score, the sum of which enumerates the similarity between two trees. The challenge lies in quantifying split similarity: existing definitions lack a principled statistical underpinning, resulting in misleading tree distances that are difficult to interpret. Here, I propose probabilistic measures of split similarity, which allow tree similarity to be measured in natural units (bits). Results My new information-theoretic metrics outperform alternative measures of tree similarity when evaluated against a broad suite of criteria, even though they do not account for the non-independence of splits within a single tree. Mutual clustering information exhibits none of the undesirable properties that characterize other tree comparison metrics, and should be preferred to the RF metric. Availability and implementation The methods discussed in this article are implemented in the R package ‘TreeDist’, archived at https://dx.doi.org/10.5281/zenodo.3528123. Supplementary information Supplementary data are available at Bioinformatics online.

Generating Trees for Comparison

Tree comparisons are used in various areas with various statistical or dissimilarity measures. Given that data in various domains are diverse, and a particular comparison approach could be more appropriate for specific applications, there is a need to evaluate different comparison approaches. As gathering real data is often an extensive task, using generated trees provides a faster evaluation of the proposed solutions. This paper presents three algorithms for generating random trees: parametrized by tree size, shape based on the node distribution and the amount of difference between generated trees. The motivation for the algorithms came from unordered trees that are created from class hierarchies in object-oriented programs. The presented algorithms are evaluated by statistical and dissimilarity measures to observe stability, behavior, and impact on node distribution. The results in the case of dissimilarity measures evaluation show that the algorithms are suitable for tree comparison.

A combined approach of fine Role-Based Access Control and dynamic/static parse tree comparison to mediate SQL Injection Attacks within a selected West African case system and context

Business legacy systems, when migrated to the Web, often face increased chances of Structured Query Language (SQL) injection attacks; these attacks are compounded when this system lacks proper security mechanisms and security training for its staff. This study seeks to determine how the researcher’s new theory of amalgamating two established techniques for defence namely; fine-grained Role-Based Access Control (RBAC) and static/dynamic parse tree comparison; can be combined to form a single centralized defence in order to effectively mitigate SQL injection attacks in a web-based environment, using a selected recently migrated legacy system as an exemplar. This proposed defence first involves redefining existing RBAC security to a fine-grained RBAC to act as the first tier of defence. Those queries, legitimate or not, which successfully pass through the first tier are analysed by the second tier of defence that is designed to both do a static and dynamic parse tree analysis and comparison of the queries in order to identify legitimate queries from illegitimate queues. During the study, it was discovered that the basic RBAC in control system and the fine grained RBAC could only mitigate a fraction of the selected test cases and thereby generated a number of false positives but no false negatives. However, those false positives were successfully identified and mitigated by the second tier of static/dynamic parse tree comparison. As such the measurement of performance using precision, recall and f-measure were determined in three cases namely basic RBAC defence in control with 31% precision,100% recall and f-measure of 32%; Fine grained RBAC without dynamic parse tree comparism with 54% precision ,100% recall and fmeaure of 54% and hybrid defence of fine grained RBAC and dynamic parse tree comparism with 100 % precision with a 100 % recall and f-measure of 100% with the test cases used in a repeated experimentation. However extensive real-world testing might expose weaknesses not observed during experimentation and such is the recommendation of the study. This entire approach is centralized in a security aspect in order to easily incorporate it into vulnerable newly migrated legacy systems to the web which requires minimal training of security staff for deployment. The hybrid was then tested using a case sample system that represents the West African context of inadequate security mechanisms and poor staff training. Standard test cases were used to test each defence tier in the hybrid as well as the individual tiers. This testing detected and halted illegitimate SQL queues and demonstrated this aspect’s effectiveness and suitability for the West African context.