PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Global marine bacterial diversity peaks at high latitudes in winter.

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms

The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical, and thoracic muscles

The body masses of cats (Mammalia, Carnivora, Felidae) span a ~300‐fold range from the smallest to largest species. Despite this range, felid musculoskeletal anatomy remains remarkably conservative, including the maintenance of a crouched limb posture at unusually large sizes. The forelimbs in felids are important for body support and other aspects of locomotion, as well as climbing and prey capture, with the assistance of the vertebral (and hindlimb) muscles. Here, we examine the scaling of the anterior postcranial musculature across felids to assess scaling patterns between different species spanning the range of felid body sizes. The muscle architecture (lengths and masses of the muscle‐tendon unit components) for the forelimb, cervical and thoracic muscles was quantified to analyse how the muscles scale with body mass. Our results demonstrate that physiological cross‐sectional areas of the forelimb muscles scale positively with increasing body mass (i.e. becoming relatively larger). Many significantly allometric variables pertain to shoulder support, whereas the rest of the limb muscles become relatively weaker in larger felid species. However, when phylogenetic relationships were corrected for, most of these significant relationships disappeared, leaving no significantly allometric muscle metrics. The majority of cervical and thoracic muscle metrics are not significantly allometric, despite there being many allometric skeletal elements in these regions. When forelimb muscle data were considered in isolation or in combination with those of the vertebral muscles in principal components analyses and MANOVAs, there was no significant discrimination among species by either size or locomotory mode. Our results support the inference that larger felid species have relatively weaker anterior postcranial musculature compared with smaller species, due to an absence of significant positive allometry of forelimb or vertebral muscle architecture. This difference in strength is consistent with behavioural changes in larger felids, such as a reduction of maximal speed and other aspects of locomotor abilities

Protracted speciation revitalizes the neutral theory of biodiversity.

Understanding the maintenance and origin of biodiversity is a formidable task, yet many ubiquitous ecological patterns are predicted by a surprisingly simple and widely studied neutral model that ignores functional differences between species. However, this model assumes that new species arise instantaneously as singletons and consequently makes unrealistic predictions about species lifetimes, speciation rates and number of rare species. Here, we resolve these anomalies - without compromising any of the original models existing achievements and retaining computational and analytical tractability - by modelling speciation as a gradual, protracted, process rather than an instantaneous event. Our model also makes new predictions about the diversity of incipient species and rare species in the metacommunity. We show that it is both necessary and straightforward to incorporate protracted speciation in future studies of neutral models, and argue that non-neutral models should also model speciation as a gradual process rather than an instantaneous one

When the Dead are Not Silent: The Investigation of Cultural Perspectives Concerning Improper Burials in Northern Uganda

This thesis presents the findings of a qualitative examination of the effects of improper burials and the associated cultural impacts on the Acholi population of northern Uganda. Since independence in 1962 Uganda has experienced several internal conflicts, including the notorious struggle between the Lord’s Resistance Army and the Ugandan government. This conflict, which disproportionately affected the Acholi ethnic group, resulted in tens of thousands of deaths and culturally inappropriate burials. These burials are particularity problematic because the Acholi maintain continual ties to the dead through ancestor veneration with proper burial being one of the most important conciliatory rites. In the negotiation between the living and the dead, the social infrastructure that is built around and on mortuary practices is part of the active creation of social relationships and ways of being. Improper burials are, therefore, an obstacle to post-war recovery efforts, as these interments violate beliefs within the Acholi religious system as to how the dead should be treated. As a consequence of this mistreatment these spirits, known as cen, become angry and cause disease, death, possession, nightmares, and other misfortunes. This research utilizes a psychosocial framework based in grounded theory to explore the impact of improper burials within Acholi communities, the cultural consequences of these interments, local perceptions of what should be done about this issue, and how such endeavors should be accomplished. Additionally, this study also assessed the appropriateness of forensic excavation and DNA identification as a potential solution to improper burials. Though the findings revealed that improper burials and the associated cen are a significant problem, the desired approach for addressing this issue depends upon whether communities practices tradition Acholi cosmology or Christianity. Based on these results I argue that religion and cosmology are vital coping strategies for addressing cen on local and institutional levels within northern Uganda. Furthermore, future psychosocial interventions aimed at post-conflict recovery would benefit from a more comprehensive understanding and inclusion of religious beliefs and their effects on local perceptions and needs

THE EFFECT OF TEMPERATURE AND EXTRACTION TECHNIQUE ON THE BINDING INTERACTIONS AND HYDROLYSIS OF β-LACTOGLOBULIN WITH MILK FAT GLOBULE MEMBRANE (MFGM)

Whey protein, containing predominately b-Lactoglobulin (b-LG), is a popular choice among consumers looking for an excellent protein source. Likewise, fat is a natural component in milk and dairy products. Lipids are packaged within a membrane called the Milk Fat Globule Membrane (MFGM). The MGFM contains a variety of lipids and proteins. Although b-LG has been extensively characterized, the function of the protein is largely unknown. The objectives of this study were to assess the enzymatics of b-LG in an isolated system, evaluate the propensity of b-LG to bind to MFGM, determine the effects of temperature and fat extraction method on the conformation of b-LG, assess the antigenicity of b-LG in an isolated system, and determine the effects of temperature and fat extraction method on the antigenicity of b-LG peptides. Time course hydrolysis of b-LG reveled only slight differences in cleavage rate. A Mass Spectrometry method was developed to detect b-LG peptides. Whey Protein Isolate (WPI) digests in an isolated system yielded on average 8.67 ± 0.33 unique peptides and a protein sequence coverage of 43.67 % ± 1.33. When WPI was a component in a complex system of washed cream, it was found that there was an interaction between temperature and fat extraction method (P=0.001) in the individual peptide release. However, it was found that the total number of peptides released was dependent on the extraction method (P2resulted in a decrease in antigenicity. Investigating the binding complex of b-LG and MFGM, utilizing a sensitive analytical instrument and technique, illustrates how b-LG peptides can be accurately detected, quantified, and how conformational changes within the structure protein can be used to infer information regarding the function of the protein

The Biogeography of Putative Microbial Antibiotic Production

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics

Independent Evolution of Leaf and Root Traits within and among Temperate Grassland Plant Communities

In this study, we used data from temperate grassland plant communities in Alberta, Canada to test two longstanding hypotheses in ecology: 1) that there has been correlated evolution of the leaves and roots of plants due to selection for an integrated whole-plant resource uptake strategy, and 2) that trait diversity in ecological communities is generated by adaptations to the conditions in different habitats. We tested the first hypothesis using phylogenetic comparative methods to test for evidence of correlated evolution of suites of leaf and root functional traits in these grasslands. There were consistent evolutionary correlations among traits related to plant resource uptake strategies within leaf tissues, and within root tissues. In contrast, there were inconsistent correlations between the traits of leaves and the traits of roots, suggesting different evolutionary pressures on the above and belowground components of plant morphology. To test the second hypothesis, we evaluated the relative importance of two components of trait diversity: within-community variation (species trait values relative to co-occurring species; α traits) and among-community variation (the average trait value in communities where species occur; β traits). Trait diversity was mostly explained by variation among co-occurring species, not among-communities. Additionally, there was a phylogenetic signal in the within-community trait values of species relative to co-occurring taxa, but not in their habitat associations or among-community trait variation. These results suggest that sorting of pre-existing trait variation into local communities can explain the leaf and root trait diversity in these grasslands

Managing neotropical oil palm expansion to retain phylogenetic diversity

Summary: The expansion of tropical agriculture is a major driver of the extinction crisis. A key question is whether biodiversity losses can be minimized by restricting future expansion to low-productivity farmland and retaining forest fragments, especially in rapidly changing Neotropical landscapes. We investigated these methods in the context of avian phylogenetic diversity, which summarizes the evolutionary history preserved within communities. Evidence suggests that phylogenetic diversity plays an important role in maintaining key ecosystem functions. We collected data on avian communities in the Colombian Llanos, a region highlighted as being optimal for the expansion of oil palm, at the expense of existing habitats including forest remnants and improved cattle pastures. PD, a measure of phylogenetic richness, and MPD, a measure of the phylogenetic distance between individuals in a community in deep evolutionary time, were significantly higher in forest than in oil palm or pasture, but did not differ significantly between oil palm and pasture. MNTD, a measure of distance between individuals in a community at the intra-familial and intra-generic level, was significantly higher in oil palm and pasture than in forest. However, median evolutionary distinctiveness (ED) was highest in pasture, partly due to the abundance of distinct waterbirds, but did not differ between oil palm and forest. PD in oil palm and pasture increased with the extent of remnant forest cover. Synthesis and applications. The PD (a measure of phylogenetic richness) and MPD (a measure of the phylogenetic distance) of bird communities in this region can best be conserved by ensuring that new oil palm plantations replace pasturelands rather than forest. A secondary benefit of preserving forest would be the enhancement of PD in the surrounding agricultural landscape. This strategy will need to be coupled with measures to either reduce pasture demand or to intensify existing cattle production to ensure that forest is not replaced by pasture elsewhere

Tropical secondary forest regeneration conserves high levels of avian phylogenetic diversity

Secondary forests are promoted as having pivotal roles in reversing the tropical extinction crisis. While secondary forests recover carbon and species over time, a key question is whether phylogenetic diversity—the total evolutionary history across all species within a community—also recovers. Conserving phylogenetic diversity protects unique phenotypic and ecological traits, and benefits ecosystem functioning and stability. We examined the extent to which avian phylogenetic diversity recovers in secondary forests in the Colombian Chocó-Andes. sesPD, a measure of phylogenetic richness corrected for species richness, recovered to old-growth forest levels after ~ 30 years, while sesMPD, a measure of the phylogenetic distance between individuals in a community, recovered to old-growth levels even within young secondary forest. Mean evolutionary distinctiveness also recovered rapidly in secondary forest communities. Our results suggest that secondary forests can play a vital role in conserving distinct evolutionary lineages and high levels of evolutionary history. Focusing conservation and carbon-based payments for ecosystem services on secondary forest recovery and their subsequent protection thus represent a good use of scarce conservation resources