1,106 research outputs found
Circular Networks from Distorted Metrics
Trees have long been used as a graphical representation of species
relationships. However complex evolutionary events, such as genetic
reassortments or hybrid speciations which occur commonly in viruses, bacteria
and plants, do not fit into this elementary framework. Alternatively, various
network representations have been developed. Circular networks are a natural
generalization of leaf-labeled trees interpreted as split systems, that is,
collections of bipartitions over leaf labels corresponding to current species.
Although such networks do not explicitly model specific evolutionary events of
interest, their straightforward visualization and fast reconstruction have made
them a popular exploratory tool to detect network-like evolution in genetic
datasets.
Standard reconstruction methods for circular networks, such as Neighbor-Net,
rely on an associated metric on the species set. Such a metric is first
estimated from DNA sequences, which leads to a key difficulty: distantly
related sequences produce statistically unreliable estimates. This is
problematic for Neighbor-Net as it is based on the popular tree reconstruction
method Neighbor-Joining, whose sensitivity to distance estimation errors is
well established theoretically. In the tree case, more robust reconstruction
methods have been developed using the notion of a distorted metric, which
captures the dependence of the error in the distance through a radius of
accuracy. Here we design the first circular network reconstruction method based
on distorted metrics. Our method is computationally efficient. Moreover, the
analysis of its radius of accuracy highlights the important role played by the
maximum incompatibility, a measure of the extent to which the network differs
from a tree.Comment: Submitte
Identifying environmental versus phylogenetic correlates of behavioural ecology in gibbons: implications for conservation management of the world's rarest ape.
For conservation of highly threatened species to be effective, it is crucial to differentiate natural population parameters from atypical behavioural, ecological and demographic characteristics associated with human disturbance and habitat degradation, which can constrain population growth and recovery. Unfortunately, these parameters can be very hard to determine for species of extreme rarity. The Hainan gibbon (Nomascus hainanus), the world's rarest ape, consists of a single population of c.25 individuals, but intensive management is constrained by a limited understanding of the species' expected population characteristics and environmental requirements. In order to generate a more robust evidence-base for Hainan gibbon conservation, we employed a comparative approach to identify intrinsic and extrinsic drivers of variation in key ecological and behavioural traits (home range size, social group size, mating system) across the Hylobatidae while controlling for phylogenetic non-independence
A Note on Encodings of Phylogenetic Networks of Bounded Level
Driven by the need for better models that allow one to shed light into the
question how life's diversity has evolved, phylogenetic networks have now
joined phylogenetic trees in the center of phylogenetics research. Like
phylogenetic trees, such networks canonically induce collections of
phylogenetic trees, clusters, and triplets, respectively. Thus it is not
surprising that many network approaches aim to reconstruct a phylogenetic
network from such collections. Related to the well-studied perfect phylogeny
problem, the following question is of fundamental importance in this context:
When does one of the above collections encode (i.e. uniquely describe) the
network that induces it? In this note, we present a complete answer to this
question for the special case of a level-1 (phylogenetic) network by
characterizing those level-1 networks for which an encoding in terms of one (or
equivalently all) of the above collections exists. Given that this type of
network forms the first layer of the rich hierarchy of level-k networks, k a
non-negative integer, it is natural to wonder whether our arguments could be
extended to members of that hierarchy for higher values for k. By giving
examples, we show that this is not the case
Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity
Evidence-based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of c.25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na=2.27, Ar=2.24, He =0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of c.30% from historical levels (Na=3.36, Ar=3.29, He =0.63). Significant differentiation is seen between current and historical samples (FST =0.156, P=0.0315), and the current population exhibits extremely small Ne (current Ne =2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical Ne =1162.96). Individuals in the current population are related at the level of half- to full-siblings between social groups, and full-siblings or parent-offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential
Quarnet Inference Rules for Level-1 Networks
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set X of species from a collection of trees, each having leaf-set some subset of X. In the 1980s, Colonius and Schulze gave certain inference rules for deciding when a collection of 4-leaved trees, one for each 4-element subset of X, can be simultaneously displayed by a single supertree with leaf-set X. Recently, it has become of interest to extend this and related results to phylogenetic networks. These are a generalization of phylogenetic trees which can be used to represent reticulate evolution (where species can come together to form a new species). It has recently been shown that a certain type of phylogenetic network, called a (unrooted) level-1 network, can essentially be constructed from 4-leaved trees. However, the problem of providing appropriate inference rules for such networks remains unresolved. Here, we show that by considering 4-leaved networks, called quarnets, as opposed to 4-leaved trees, it is possible to provide such rules. In particular, we show that these rules can be used to characterize when a collection of quarnets, one for each 4-element subset of X, can all be simultaneously displayed by a level-1 network with leaf-set X. The rules are an intriguing mixture of tree inference rules, and an inference rule for building up a cyclic ordering of X from orderings on subsets of X of size 4. This opens up several new directions of research for inferring phylogenetic networks from smaller ones, which could yield new algorithms for solving the supernetwork problem in phylogenetics
Comparison of knowledge scores of medical students in problem-based learning and traditional curriculum on public health topics
BACKGROUND: The purpose of the study was to compare the knowledge scores of medical students in Problem-based Learning and traditional curriculum on public health topics. METHODS: We planned a cross-sectional study including the fifth and sixth year medical students of Dokuz Eylul University in Turkey. The fifth year students (PBL group, n = 56) were the pioneers educated with PBL curriculum since the 1997–1998 academic year. The sixth year students (traditional education group, n = 78) were the last students educated with traditional education methods. We prepared 25 multiple-choice questions in order to assess knowledge scores of students on selected subjects of Public Health. Our data were collected in year 2002. RESULTS: Mean test scores achieved in PBL and traditional groups were 65.0 and 60.5 respectively. PBL students were significantly more successful in the knowledge test (p = 0.01). The knowledge scores of two topics were statistically higher among PBL students. These topics were health management and chronic diseases. CONCLUSION: We found that mean total evaluation score in the PBL group was 4.5 points higher than in the traditional group in our study. Focusing only on the knowledge scores of students is the main limitation of our study. Upon the graduation of the first PBL students in the 2002–2003 academic year, we are planning additional studies regarding the other functions of a physician such as skill, behaviour and attitude
Abundance and Diversity of Dockerin-Containing Proteins in the Fiber-Degrading Rumen Bacterium, Ruminococcus flavefaciens FD-1
Peer reviewedPublisher PD
Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1
Peer reviewedPublisher PD
Quantitative imaging of concentrated suspensions under flow
We review recent advances in imaging the flow of concentrated suspensions,
focussing on the use of confocal microscopy to obtain time-resolved information
on the single-particle level in these systems. After motivating the need for
quantitative (confocal) imaging in suspension rheology, we briefly describe the
particles, sample environments, microscopy tools and analysis algorithms needed
to perform this kind of experiments. The second part of the review focusses on
microscopic aspects of the flow of concentrated model hard-sphere-like
suspensions, and the relation to non-linear rheological phenomena such as
yielding, shear localization, wall slip and shear-induced ordering. Both
Brownian and non-Brownian systems will be described. We show how quantitative
imaging can improve our understanding of the connection between microscopic
dynamics and bulk flow.Comment: Review on imaging hard-sphere suspensions, incl summary of
methodology. Submitted for special volume 'High Solid Dispersions' ed. M.
Cloitre, Vol. xx of 'Advances and Polymer Science' (Springer, Berlin, 2009);
22 pages, 16 fig
Vapour pressure deficit modulates hydraulic function and structure of tropical rainforests under nonlimiting soil water supply
This is the final version. Available on open access from Wiley via the DOI in this recordData availability:
All data are available from the Terrestrial Ecosystem Research Network (TERN) Data Portal: https://portal.tern.org.au/metadata/TERN/db33762b-1199-4dbd-b151-b6ce8d5ad042. doi: https://doi.org/10.25901/86yk-5m77.Atmospheric conditions are expected to become warmer and drier in the future, but little is known about how evaporative demand influences forest structure and function independently from soil moisture availability, and how fast-response variables (such as canopy water potential and stomatal conductance) may mediate longer-term changes in forest structure and function in response to climate change. We used two tropical rainforest sites with different temperatures and vapour pressure deficits (VPD), but nonlimiting soil water supply, to assess the impact of evaporative demand on ecophysiological function and forest structure. Common species between sites allowed us to test the extent to which species composition, relative abundance and intraspecific variability contributed to site-level differences. The highest VPD site had lower midday canopy water potentials, canopy conductance (gc ), annual transpiration, forest stature, and biomass, while the transpiration rate was less sensitive to changes in VPD; it also had different height-diameter allometry (accounting for 51% of the difference in biomass between sites) and higher plot-level wood density. Our findings suggest that increases in VPD, even in the absence of soil water limitation, influence fast-response variables, such as canopy water potentials and gc , potentially leading to longer-term changes in forest stature resulting in reductions in biomass.Australian Research Council (ARC)Catalan science and technology grant, Beatriu de Pinó
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