Origins of Shared Genetic Variation in African Cichlids

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of 160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.

Phylogeography of silver pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression, and riverine barriers

The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.

Genetic consequences of habitat fragmentation during a range expansion

We investigate the effect of habitat fragmentation on the genetic diversity of a species experiencing a range expansion. These two evolutionary processes have not been studied yet, at the same time, owing to the difficulties of deriving analytic results for non-equilibrium models. Here we provide a description of their interaction by using extensive spatial and temporal coalescent simulations and we suggest guidelines for a proper genetic sampling to detect fragmentation. To model habitat fragmentation, we simulated a two-dimensional lattice of demes partitioned into groups (patches) by adding barriers to dispersal. After letting a population expand on this grid, we sampled lineages from the lattice at several scales and studied their coalescent history. We find that in order to detect fragmentation, one needs to extensively sample at a local level rather than at a landscape level. This is because the gene genealogy of a scattered sample is less sensitive to the presence of genetic barriers. Considering the effect of temporal changes of fragmentation intensities, we find that at least 10, but often >100, generations are needed to affect local genetic diversity and population structure. This result explains why recent habitat fragmentation does not always lead to detectable signatures in the genetic structure of populations. Finally, as expected, long-distance dispersal increases local genetic diversity and decreases levels of population differentiation, efficiently counteracting the effects of fragmentation.

Evidence for selection on coloration in a Panamanian poison frog: a coalescent-based approach

Aim The strawberry poison frog, Oophaga pumilio, has undergone a remarkable radiation of colour morphs in the Bocas del Toro archipelago in Panama. This species shows extreme variation in colour and pattern between populations that have been geographically isolated for < 10,000 years. While previous research has suggested the involvement of divergent selection, to date no quantitative test has examined this hypothesis. Location Bocas del Toro archipelago, Panama. Methods We use a combination of population genetics, phylogeography and phenotypic analyses to test for divergent selection in coloration in O. pumilio. Tissue samples of 88 individuals from 15 distinct populations were collected. Using these data, we developed a gene tree using the mitochondrial DNA (mtDNA) d-loop region. Using parameters derived from our mtDNA phylogeny, we predicted the coalescence of a hypothetical nuclear gene underlying coloration. We collected spectral reflectance and body size measurements on 94 individuals from four of the populations and performed a quantitative analysis of phenotypic divergence. Results The mtDNA d-loop tree revealed considerable polyphyly across populations. Coalescent reconstructions of gene trees within population trees revealed incomplete genotypic sorting among populations. The quantitative analysis of phenotypic divergence revealed complete lineage sorting by colour, but not by body size: populations showed non-overlapping variation in spectral reflectance measures of body coloration, while variation in body size did not separate populations. Simulations of the coalescent using parameter values derived from our empirical analyses demonstrated that the level of sorting among populations seen in colour cannot reasonably be attributed to drift. Main conclusions These results imply that divergence in colour, but not body size, is occurring at a faster rate than expected under neutral processes. Our study provides the first quantitative support for the claim that strong diversifying selection underlies colour variation in the strawberry poison frog.

Dynamic computer simulations of electrophoresis: a versatile research and teaching tool

Software is available, which simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. These dynamic models are based upon equations derived from the transport concepts such as electromigration, diffusion, electroosmosis and imposed hydrodynamic buffer flow that are applied to user-specified initial distributions of analytes and electrolytes. They are able to predict the evolution of electrolyte systems together with associated properties such as pH and conductivity profiles and are as such the most versatile tool to explore the fundamentals of electrokinetic separations and analyses. In addition to revealing the detailed mechanisms of fundamental phenomena that occur in electrophoretic separations, dynamic simulations are useful for educational purposes. This review includes a list of current high-resolution simulators, information on how a simulation is performed, simulation examples for zone electrophoresis, ITP, IEF and EKC and a comprehensive discussion of the applications and achievements.

Comparison of actual surgical outcomes and 3-dimensional surgical simulations

PURPOSE: The advent of imaging software programs has proved to be useful for diagnosis, treatment planning, and outcome measurement, but precision of 3-dimensional (3D) surgical simulation still needs to be tested. This study was conducted to determine whether the virtual surgery performed on 3D models constructed from cone-beam computed tomography (CBCT) can correctly simulate the actual surgical outcome and to validate the ability of this emerging technology to recreate the orthognathic surgery hard tissue movements in 3 translational and 3 rotational planes of space. MATERIALS AND METHODS: Construction of pre- and postsurgery 3D models from CBCTs of 14 patients who had combined maxillary advancement and mandibular setback surgery and 6 patients who had 1-piece maxillary advancement surgery was performed. The postsurgery and virtually simulated surgery 3D models were registered at the cranial base to quantify differences between simulated and actual surgery models. Hotelling t tests were used to assess the differences between simulated and actual surgical outcomes. RESULTS: For all anatomic regions of interest, there was no statistically significant difference between the simulated and the actual surgical models. The right lateral ramus was the only region that showed a statistically significant, but small difference when comparing 2- and 1-jaw surgeries. CONCLUSIONS: Virtual surgical methods were reliably reproduced. Oral surgery residents could benefit from virtual surgical training. Computer simulation has the potential to increase predictability in the operating room.

Atomistic simulations of 2D bicomponent self-assembly: from molecular recognition to self-healing

Supramolecular two-dimensional engineering epitomizes the design of complex molecular architectures through recognition events in multicomponent self-assembly. Despite being the subject of in-depth experimental studies, such articulated phenomena have not been yet elucidated in time and space with atomic precision. Here we use atomistic molecular dynamics to simulate the recognition of complementary hydrogen-bonding modules forming 2D porous networks on graphite. We describe the transition path from the melt to the crystalline hexagonal phase and show that self-assembly proceeds through a series of intermediate states featuring a plethora of polygonal types. Finally, we design a novel bicomponent system possessing kinetically improved self-healing ability in silico, thus demonstrating that a priori engineering of 2D self-assembly is possible.

Retrieval simulations of the vertical profiles of water vapour and other chemical species in the Martian atmosphere using PACS

Water vapour, despite being a minor constituent in the Martian atmosphere with its precipitable amount of less than 70 pr. μm, attracts considerable attention in the scientific community because of its potential importance for past life on Mars. The partial pressure of water vapour is highly variable because of its seasonal condensation onto the polar caps and exchange with a subsurface reservoir. It is also known to drive photochemical processes: photolysis of water produces H, OH, HO2 and some other odd hydrogen compounds, which in turn destroy ozone. Consequently, the abundance of water vapour is anti-correlated with ozone abundance. The Herschel Space Observatory provides for the first time the possibility to retrieve vertical water profiles in the Martian atmosphere. Herschel will contribute to this topic with its guaranteed-time key project called "Water and related chemistry in the solar system". Observations of Mars by Heterodyne Instrument for the Far Infrared (HIFI) and Photodetector Array Camera and Spectrometer (PACS) onboard Herschel are planned in the frame of the programme. HIFI with its high spectral resolution enables accurate observations of vertically resolved H2O and temperature profiles in the Martian atmosphere. Unlike HIFI, PACS is not capable of resolving the line-shape of molecular lines. However, our present study of PACS observations for the Martian atmosphere shows that the vertical sensitivity of the PACS observations can be improved by using multiple-line observations with different line opacities. We have investigated the possibility of retrieving vertical profiles of temperature and molecular abundances of minor species including H2O in the Martian atmosphere using PACS. In this paper, we report that PACS is able to provide water vapour vertical profiles for the Martian atmosphere and we present the expected spectra for future PACS observations. We also show that the spectral resolution does not allow the retrieval of several studied minor species, such as H2O2, HCl, NO, SO2, etc.

High-resolution electrophoretic simulations: performance characteristics of one-dimensional simulators

Three comprehensive one-dimensional simulators were used on the same PC to simulate the dynamics of different electrophoretic configurations, including two migrating hybrid boundaries, an isotachophoretic boundary and the zone electrophoretic separation of ten monovalent anions. Two simulators, SIMUL5 and GENTRANS, use a uniform grid, while SPRESSO uses a dynamic adaptive grid. The simulators differ in the way components are handled. SIMUL5 and SPRESSO feature one equation for all components, whereas GENTRANS is based on the use of separate modules for the different types of monovalent components, a module for multivalent components and a module for proteins. The code for multivalent components is executed more slowly compared to those for monovalent components. Furthermore, with SIMUL5, the computational time interval becomes smaller when it is operated with a reduced calculation space that features moving borders, whereas GENTRANS offers the possibility of using data smoothing (removal of negative concentrations), which can avoid numerical oscillations and speed up a simulation. SPRESSO with its adaptive grid could be employed to simulate the same configurations with smaller numbers of grid points and thus is faster in certain but not all cases. The data reveal that simulations featuring a large number of monovalent components distributed such that a high mesh is required throughout a large proportion of the column are fastest executed with GENTRANS.

Variations of the Atlantic meridional overturning circulation in control and transient simulations of the last millennium

The variability of the Atlantic meridional overturing circulation (AMOC) strength is investigated in control experiments and in transient simulations of up to the last millennium using the low-resolution Community Climate System Model version 3. In the transient simulations the AMOC exhibits enhanced low-frequency variability that is mainly caused by infrequent transitions between two semi-stable circulation states which amount to a 10 percent change of the maximum overturning. One transition is also found in a control experiment, but the time-varying external forcing significantly increases the probability of the occurrence of such events though not having a direct, linear impact on the AMOC. The transition from a high to a low AMOC state starts with a reduction of the convection in the Labrador and Irminger Seas and goes along with a changed barotropic circulation of both gyres in the North Atlantic and a gradual strengthening of the convection in the Greenland-Iceland-Norwegian (GIN) Seas. In contrast, the transition from a weak to a strong overturning is induced by decreased mixing in the GIN Seas. As a consequence of the transition, regional sea surface temperature (SST) anomalies are found in the midlatitude North Atlantic and in the convection regions with an amplitude of up to 3 K. The atmospheric response to the SST forcing associated with the transition indicates a significant impact on the Scandinavian surface air temperature (SAT) in the order of 1 K. Thus, the changes of the ocean circulation make a major contribution to the Scandinavian SAT variability in the last millennium.

Climate forcing reconstructions for use in the PMIP simulations of the last millennium

Simulations of climate over the Last Millennium (850–1850 CE) have been incorporated into the third phase of the Paleoclimate Modelling Intercomparison Project (PMIP3). The drivers of climate over this period are chiefly orbital, solar, volcanic, changes in land use/land cover and some variation in greenhouse gas levels. While some of these effects can be easily defined, the reconstructions of solar, volcanic and land use-related forcing are more uncertain. We describe here the approach taken in defining the scenarios used in PMIP3, document the forcing reconstructions and discuss likely implications.