The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but …
Viral nervous necrosis (VNN) is a severe neuropathological disease affecting a broad variety of finfish species worldwide. The causative agent of VNN is a small virus with a bi-segmented RNA genome known as betanodavirus. At least four genotypes with distinct, but yet insufficiently characterized, epidemiological features are recognized. The …
Almost 90% of global bird extinctions have occurred on islands. The loss of endemic species from island systems can dramatically alter evolutionary trajectories of insular species biodiversity, resulting in a loss of evolutionary diversity important for species adaptation to changing environments. The Western Indian Ocean islands have been the …
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza …
The emergence of the influenza (H1N1) 2009 virus provided a unique opportunity to study the evolution of a pandemic virus following its introduction into the human population. Virological and clinical surveillance in the UK were comprehensive during the first and second waves of the pandemic in 2009, with extensive …
Arguments about conservation are almost always arguments about species. Lists are compiled of endangered species, conservation schemes are prioritised on how many species are preserved, and legislation is phrased in terms of species. In the political economy of biodiversity, species are the currency. Despite this central role, the very …
Conservation genetics - and indeed conservation in general - falls into the two broad areas of the identification and preservation of (1) endangered species and (2) habitats with high biodiversity. Most research has been towards the first aim, with hard-won findings on the importance of genetic variation in population management, but …
Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely …
Linkage disequilibrium is an ubiquitous biological phenomenon. However a common metric for disequilibrium — the index of association or IA – is dependent on sample size. In this paper we present a modification of IA that removes this dependency. This method has been implemented in a software package.
Agapow & Burt …
The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature …
Groundwater bacterial rRNA sequences extracted from the natural nuclear reactor region of Gabon are used to demonstrate the application of phylogenetic methods to biodiversity assessment. Clones were provisionally placed in 'genera' using either the genus of the closest named EMBL entry, or by grouping clones at least 97.5 …