THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/1/EVO_846_sm_FigS3A.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/2/EVO_846_sm_legend.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/3/EVO_846_sm_FigS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/4/j.1558-5646.2009.00846.x.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/5/EVO_846_sm_FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/6/EVO_846_sm_FigS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/7/EVO_846_sm_FigS3B.pd

The genetic architecture of divergence between threespine stickleback species.

The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution

Modelling road hazards and the effect on AV safety of hazardous failures

Autonomous vehicles (AV) are about to appear on our roads within the next few years. However, to achieve the final breakthrough, not only functional progress is required, but also fundamental safety questions must be solved. Among those, a question demanding special attention is the need to assess the overall safety of an AV and quantify that it is safe enough to take part in normal traffic despite its inherent imperfections. Therefore, this paper describes a probabilistic model, which allows to study how imperfections of an AV perception system and of mechanisms responsible for AV safety (e.g., Safety Monitors), can impact AV safety in the presence of road hazards. We also demonstrate how the model can be used to validate if the AV is safe enough, to understand the criticality of (perception) errors, and to identify areas/parameters that have more influence on safety than others

The high-precision, charge-dependent Bonn nucleon-nucleon potential (CD-Bonn)

We present a charge-dependent nucleon-nucleon (NN) potential that fits the world proton-proton data below 350 MeV available in the year of 2000 with a chi^2 per datum of 1.01 for 2932 data and the corresponding neutron-proton data with chi^2/datum = 1.02 for 3058 data. This reproduction of the NN data is more accurate than by any phase-shift analysis and any other NN potential. The charge-dependence of the present potential (that has been dubbed `CD-Bonn') is based upon the predictions by the Bonn Full Model for charge-symmetry and charge-independence breaking in all partial waves with J <= 4. The potential is represented in terms of the covariant Feynman amplitudes for one-boson exchange which are nonlocal. Therefore, the off-shell behavior of the CD-Bonn potential differs in a characteristic and well-founded way from commonly used local potentials and leads to larger binding energies in nuclear few- and many-body systems, where underbinding is a persistent problem.Comment: 69 pages (RevTex) including 20 tables and 9 figures (ps files

System for deployment of groups of unmanned micro aerial vehicles in GPS-denied environments using onboard visual relative localization

A complex system for control of swarms of micro aerial vehicles (MAV), in literature also called as unmanned aerial vehicles (UAV) or unmanned aerial systems (UAS), stabilized via an onboard visual relative localization is described in this paper. The main purpose of this work is to verify the possibility of self-stabilization of multi-MAV groups without an external global positioning system. This approach enables the deployment of MAV swarms outside laboratory conditions, and it may be considered an enabling technique for utilizing fleets of MAVs in real-world scenarios. The proposed visual-based stabilization approach has been designed for numerous different multi-UAV robotic applications (leader-follower UAV formation stabilization, UAV swarm stabilization and deployment in surveillance scenarios, cooperative UAV sensory measurement) in this paper. Deployment of the system in real-world scenarios truthfully verifies its operational constraints, given by limited onboard sensing suites and processing capabilities. The performance of the presented approach (MAV control, motion planning, MAV stabilization, and trajectory planning) in multi-MAV applications has been validated by experimental results in indoor as well as in challenging outdoor environments (e.g., in windy conditions and in a former pit mine)

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse") at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

<p>Abstract</p> <p>Background</p> <p>Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as <it>reticulate evolutionary events</it>, result in <it>networks</it>, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.</p> <p>Results</p> <p>In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or <it>evolutionary networks</it>, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.</p> <p>Conclusion</p> <p>The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.</p

Annealing multicomponent supramolecular gels

Annealing is widely used as a means of changing the physical properties of a material. The rate of heating and cooling used in the annealing process controls the final properties. Annealing can be used as a means of driving towards the, or at least a, thermodynamic minimum. There is surprisingly little information on annealing kinetically-trapped supramolecular gels. Here, we show that annealing multicomponent gels can be used to prepare materials with tunable mechanical properties. We show that annealing in a two-component gel leads to a self-sorted network, which has significantly different mechanical properties to the asprepared gels. Whilst the fibres are self-sorted, we show that the annealing of this system leads to significant change in the network level of assembly, and it is this that leads to the increase in storage modulus. We also show that it is possible to selectively anneal only a single component in the mixtureAMFC thanks the University of Glasgow for funding. FPGF acknowledges an Erasmus traineeship. DJA thanks the EPSRC for a Fellowship (EP/L021978/1), which funded BD. MarvinSketch 16.11.28.0 was used for naming chemical structures. This work benefitted from SasView software, originally developed by the DANSE project under NSF award DMR-0520547. SasView also contains code developed with funding from the EU Horizon 2020 programme under the SINE2020 project Grant No. 654000. The X-ray scattering apparatus was purchased under (EP/K035746/1)