Consensus and Confusion in Molluscan Trees: Evaluating Morphological and Molecular Phylogenies

Mollusks are the most morphologically disparate living animal phylum, they have diversified into all habitats, and have a deep fossil record. Monophyly and identity of their eight living classes is undisputed, but relationships between these groups and patterns of their early radiation have remained elusive. Arguments about traditional morphological phylogeny focus on a small number of topological concepts but often without regard to proximity of the individual classes. In contrast, molecular studies have proposed a number of radically different, inherently contradictory, and controversial sister relationships. Here, we assembled a dataset of 42 unique published trees describing molluscan interrelationships. We used these data to ask several questions about the state of resolution of molluscan phylogeny compared to a null model of the variation possible in random trees constructed from a monophyletic assemblage of eight terminals. Although 27 different unique trees have been proposed from morphological inference, the majority of these are not statistically different from each other. Within the available molecular topologies, only four studies to date have included the deep-sea class Monoplacophora; but 36.4% of all trees are not significantly different. We also present supertrees derived from 2 data partitions and 3 methods, including all available molecular molluscan phylogenies, which will form the basis for future hypothesis testing. The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate published topologies. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The internodal distance is consistently short between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Other taxon pairs are rarely or never found in close proximity, such as the vermiform Caudofoveata and Bivalvia. Our results have specific utility for guiding constructive research planning in order to better test relationships in Mollusca as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach in a concerted assessment of potential genetic and anatomical homology, while unequivocally distant taxa will make the most constructive choices for exemplar selection in higher-level phylogenomic analyses.

Pool Evolution: A Parallel Pattern for Evolutionary and Symbolic Computing

We introduce a new parallel pattern derived from a specific application domain and show how it turns out to have application beyond its domain of origin. The pool evolution pattern models the parallel evolution of a population subject to mutations and evolving in such a way that a given fitness function is optimized. The pattern has been demonstrated to be suitable for capturing and modeling the parallel patterns underpinning various evolutionary algorithms, as well as other parallel patterns typical of symbolic computation. In this paper we introduce the pattern, we discuss its implementation on modern multi/many core architectures and finally present experimental results obtained with FastFlow and Erlang implementations to assess its feasibility and scalability.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

The emergence of bone technologies at the end of the pleistocene in Southeast Asia:Regional and evolutionary implications

For many decades Palaeolithic research viewed the development of early modern human behaviour as largely one of progress down a path towards the modernity of the present. The European Palaeolithic sequence the most extensively studied was for a long time the yard-stick against which records from other regions were judged. Recent work undertaken in Africa and increasingly Asia, however, now suggests that the European evidence may tell a story that is more parochial and less universal than previously thought. While tracking developments at the large scale (the grand narrative) remains important, there is growing appreciation that to achieve a comprehensive understanding of human behavioural evolution requires an archaeologically regional perspective to balance this. One of the apparent markers of human modernity that has been sought in the global Palaeolithic record, prompted by finds in the European sequence, is innovation in bonebased technologies. As one step in the process of re-evaluating and contextualizing such innovations, in this article we explore the role of prehistoric bone technologies within the Southeast Asian sequence, where they have at least comparable antiquity to Europe and other parts of Asia. We observe a shift in the technological usage of bone from a minor component to a medium of choice during the second half of the Last Termination and into the Holocene. We suggest that this is consistent with it becoming a focus of the kinds of inventive behaviour demanded of foraging communities as they adapted to the far-reaching environmental and demographic changes that were reshaping this region at that time. This record represents one small element of a much wider, much longerterm adaptive process, which we would argue is not confined to the earliest instances of a particular technology or behaviour, but which forms part of an on-going story of our behavioural evolution. © 2012 The McDonald Institute for Archaeological Research.

Does chemical composition of individual Scots pine trees determine the biodiversity of their associated ground vegetation?

Despite plant secondary metabolites being major determinants of species interactions and ecosystem processes, their role in the maintenance of biodiversity has received little attention. In order to investigate the relationship between chemical and biological diversity in a natural ecosystem, we considered the impact of chemical diversity in individual Scots pine trees (Pinus sylvestris) on species richness of associated ground vegetation. Scots pine trees show substantial genetically determined constitutive variation between individuals in concentrations of a group of secondary metabolites, the monoterpenes. When the monoterpenes of particular trees were assessed individually, there was no relationship with species richness of associated ground flora. However, the chemical diversity of monoterpenes of individual trees was significantly positively associated with the species richness of the ground vegetation beneath each tree, mainly the result of an effect among the non-woody vascular plants. This correlation suggests that the chemical diversity of the ecosystem dominant species has an important role in shaping the biodiversity of the associated plant community. The extent and significance of this effect, and its underlying processes require further investigation.

The imprint of the geographical, evolutionary and ecological context on species-area relationships

Species-area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.

Are Alaskan trees found in locally more favourable sites in marginal areas?

Aim Species generally become rarer and more patchily distributed as the margins of their ranges are approached. We predicted that in such marginal sites, tree species would tend to occur where some key environmental factors are at particularly favourable levels, compensating in part for the low overall suitability of marginal sites.

Location The article considers the spatial distributions of trees in Southeast Alaska (the Alaskan 'panhandle').

Methods We quantified range marginality using spatial distributions of eight tree species across more than one thousand surveyed sites in Southeast Alaska. For each species we derived a site core/margin index using a three-dimensional trend surface generated from logistic regression on site coordinates. For each species, the relationships between the environmental factors slope, aspect and site marginality were then compared for occupied and unoccupied sets of sites.

Results We found that site slope is important for more Alaskan tree species than aspect. Three out of eight had a significant core/margin by occupied/unoccupied interaction, tending to be present in significantly shallower-sloped (more favourable) sites in the marginal areas than the simple core/margin trend predicted. For site aspect, one species had a significant interaction, selecting potentially more favourable northerly aspects in marginal areas. A finer-scale analysis based on the same data came to the same overall conclusions.

Conclusions There is evidence that several tree species in Alaska tend to occur in especially favourable sites in marginal areas. In these marginal areas, these species amplify habitat preferences shown in core areas.

Modelling Duqu 2.0 Malware using Attack Trees with Sequential Conjunction

In this paper we identify requirements for choosing a threat modelling formalisation for modelling sophisticated malware such as Duqu 2.0. We discuss the gaps in current formalisations and propose the use of Attack Trees with Sequential Conjunction when it comes to analysing complex attacks. The paper models Duqu 2.0 based on the latest information sourced from formal and informal sources. This paper provides a well structured model which can be used for future analysis of Duqu 2.0 and related attacks.

Partially Ordered Preferences in Decision Trees: Computing Strategies with Imprecision in Probabilities

Partially ordered preferences generally lead to choices that do not abide by standard expected utility guidelines; often such preferences are revealed by imprecision in probability values. We investigate five criteria for strategy selection in decision trees with imprecision in probabilities: “extensive” Γ-maximin and Γ-maximax, interval dominance, maximality and E-admissibility. We present algorithms that generate strategies for all these criteria; our main contribution is an algorithm for Eadmissibility that runs over admissible strategies rather than over sets of probability distributions.

Compact Routing Messages in Self-Healing Trees

Existing compact routing schemes, e.g., Thorup and Zwick [SPAA 2001] and Chechik [PODC 2013], often have no means to tolerate failures, once the system has been setup and started. This paper presents, to our knowledge, the first self-healing compact routing scheme. Besides, our schemes are developed for low memory nodes, i.e., nodes need only O(log2 n) memory, and are thus, compact schemes.
We introduce two algorithms of independent interest: The first is CompactFT, a novel compact version (using only O(log n) local memory) of the self-healing algorithm Forgiving Tree of Hayes et al. [PODC 2008]. The second algorithm (CompactFTZ) combines CompactFT with Thorup-Zwick’s treebased compact routing scheme [SPAA 2001] to produce a fully compact self-healing routing scheme. In the self-healing model, the adversary deletes nodes one at a time with the affected nodes self-healing locally by adding few edges. CompactFT recovers from each attack in only O(1) time and ∆ messages, with only +3 degree increase and O(log∆) graph diameter increase, over any sequence of deletions (∆ is the initial maximum degree).
Additionally, CompactFTZ guarantees delivery of a packet sent from sender s as long as the receiver has not been deleted, with only an additional O(y log ∆) latency, where y is the number of nodes that have been deleted on the path between s and t. If t has been deleted, s gets informed and the packet removed from the network.