Dominic J. Bennett

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization,” to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.

Distribution and population structure of the anther smut Microbotryum silenes-acaulis parasitizing an arctic-alpine plant.

Cold‐adapted organisms with current arctic–alpine distributions have persisted during the last glaciation in multiple ice‐free refugia, leaving footprints in their population structure that contrast with temperate plants and animals. However, pathogens that live within hosts having arctic–alpine distributions have been little studied. Here, we therefore investigated the geographical range and population structure of a fungus parasitizing an arctic–alpine plant. A total of 1437 herbarium specimens of the plant Silene acaulis were examined, and the anther smut pathogen Microbotryum silenes‐acaulis was present throughout the hosts geographical range. There was significantly greater incidence of anther smut disease in more northern latitudes and where the host locations were less dense, indicating a major influence of environmental factors and/or host demographic structure on the pathogen distribution. Genetic analyses with seven microsatellite markers on recent collections of 195 M. silenes‐acaulis individuals revealed three main genetic clusters, in North America, northern Europe and southern Europe, likely corresponding to differentiation in distinct refugia during the last glaciation. The lower genetic diversity in northern Europe indicates postglacial recolonization northwards from southern refugia. This study combining herbarium surveys and population genetics thus uniquely reveals the effects of climate and environmental factors on a plant pathogen species with an arctic–alpine distribution.

Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates

Abstract. As a label for a distinct category of life, “living fossil” is controversial. The term has multiple definitions, and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective in which a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: Does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation ratesmust have been unequally distributed among species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determinewhether extinction rates also show an unequal distribution, we developed a tree-growth model in which the probability of speciation and extinction is a function of a tips ED. We simulated thousands of trees in which the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations in which the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.

Protecting Free-Living Dormice: Molecular Identification of Cestode Parasites in Captive Dormice (Muscardinus avellanarius) Destined for Reintroduction.

The success of any population translocation programme relies heavily on the measures implemented to control and monitor the spread of disease. Without these measures, programmes run the risk of releasing immunologically naïve species or, more dangerously, introducing novel infectious agents to native populations. As a precaution, a reintroduction programme for the common or hazel dormouse, Muscardinus avellanarius, in England screens dormice before release following captive breeding. Using PCR sequencing of a range of genes, we tested whether the same species of tapeworm(s) were present in captive and free-living dormice. Whilst only Rodentolepis straminea were identified in free-living dormice, cestode ova found in a captive individual produced a molecular match closely related to Hymenolepis microstoma and a previously unrecorded Rodentolepis species. To prevent putting at risk the free-living population, we recommended the continued treatment of dormice showing tapeworm infection before release. Our work demonstrates how molecular techniques can be used to inform reintroduction programmes, reduce risk from disease and increase chances of reintroduction success.

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

BackgroundPhylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees—in terms of adding or removing tips—is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks.ResultsWe present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes.ConclusionsWe present three use cases—pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover—that demonstrate the new package’s speed and simplicity.

Phylogenetic factorization of compositional data

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization”, to re-analyze datasets from human body and soil microbial communities, demonstrating how phylofactorization can be a dimensionality-reducing tool, an ordination-visualization tool, and also mass-produce inferences on the edges in the phylogeny in which meaningful differences arose.

Quantifying the living fossil concept

“Living fossil” is a contentious label, often used to identify clades that have experienced particularly little evolutionary change. Many of the problems associated with the term are due to a lack of a clear definition. To date, most work on the phenomenon has been primarily qualitative, leading to a list of living fossils each selected for different sets of reasons. This non-uniformity in living fossil identification makes the ubiquity, clarity and potential causes of the phenomenon difficult to assess. An alternative approach is to use a quantitative metric that matches the most common interpretations of “living fossil” to generate a less subjective listing. Here, we present the Evolutionary Performance Index (EPI); this metric is calculable across the entire tree of life and allows for fair comparisons between taxonomic groups. With this index, we calculated the performance scores for over 24,000 clades within Metazoa and Embryophyta. Many well-known living fossils featured among the lowest performing clades, e.g. coelacanths, gingko, tuataras, as well as groups that have previously been overlooked. By grounding the definition in a strictly quantitative framework, future researchers will be better able to test the causes and relevance of the phenomenon.