scholarly journals Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): inference from transcriptome-wide coalescence analyses

2015 ◽  
Author(s):  
Beate Nurnberger ◽  
Konrad Lohse ◽  
Anna Fijarczyk ◽  
Jacek M Szymura ◽  
Mark L Blaxter
Keyword(s):  
De Novo ◽  
Adaptive Divergence ◽  
Small Scale ◽  
Parameter Estimates ◽  
Test Case ◽  
Hybrid Zones ◽  
Confidence Sets ◽  
Environmental Perturbations ◽  
Distribution Ranges ◽  
Bombina Bombina

Ancient origins, profound ecological divergence and extensive hybridization make the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Narrow Bombina hybrid zones erect barriers to neutral introgression whose strength has been estimated previously. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Krakow transect. We developed a software pipeline to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihoods calculations. There was clear evidence for post-divergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small-scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.

scholarly journals Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

2013 ◽  
Author(s):  
Nicola Nadeau ◽  
Mayte Ruiz ◽  
Patricio Salazar ◽  
Brian Counterman ◽  
Jose Alejandro Medina ◽  
...  
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Reference Sequence ◽  
Colour Pattern ◽  
Adaptive Divergence ◽  
Population Divergence ◽  
Hybrid Zones ◽  
Data Alignment ◽  
Parallel Hybrid ◽  
Genomic Regions

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on colour pattern. The co-mimetic species H. erato and H. melpomene have parallel hybrid zones where both species undergo a change from one colour pattern form to another. We use restriction associated DNA sequencing to obtain several thousand genome wide sequence markers and use these to analyse patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data; alignment to a reference genome and de novo assembly, and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ~15% divergent) related to the reference sequence. Our results confirm that the colour pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to colour pattern differences. We also use association mapping to identify previously unmapped colour pattern loci, in particular the Ro locus. Finally, we identify within our sample a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.

scholarly journals Tadpoles of hybridising fire-bellied toads (B. bombina and B. variegata) differ in their susceptibility to predation

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0231804
Author(s):  
Radovan Smolinský ◽  
Vojtech Baláž ◽  
Beate Nürnberger
Keyword(s):  
Direct Evidence ◽  
Adaptive Divergence ◽  
Differential Adaptation ◽  
Risk Of Predation ◽  
Distribution Ranges ◽  
Bombina Bombina ◽  
Recent Debate ◽  
The Subject ◽  
Genomic Regions

The role of adaptive divergence in the formation of new species has been the subject of much recent debate. The most direct evidence comes from traits that can be shown to have diverged under natural selection and that now contribute to reproductive isolation. Here, we investigate differential adaptation of two fire-bellied toads (Anura, Bombinatoridae) to two types of aquatic habitat. Bombina bombina and B. variegata are two anciently diverged taxa that now reproduce in predator-rich ponds and ephemeral aquatic sites, respectively. Nevertheless, they hybridise extensively wherever their distribution ranges adjoin. We show in laboratory experiments that, as expected, B. variegata tadpoles are at relatively greater risk of predation from dragonfly larvae, even when they display a predator-induced phenotype. These tadpoles spent relatively more time swimming and so prompted more attacks from the visually hunting predators. We argue in the discussion that genomic regions linked to high activity in B. variegata should be barred from introgression into the B. bombina gene pool and thus contribute to gene flow barriers that keep the two taxa from merging into one.

scholarly journals Tadpoles of hybridising fire-bellied toads (B. bombina and B. variegata) differ in their susceptibility to predation

2020 ◽  
Author(s):  
Radovan Smolinský ◽  
Vojtech Baláž ◽  
Beate Nürnberger
Keyword(s):  
Direct Evidence ◽  
Adaptive Divergence ◽  
Differential Adaptation ◽  
Risk Of Predation ◽  
Distribution Ranges ◽  
Bombina Bombina ◽  
Recent Debate ◽  
The Subject ◽  
Genomic Regions

AbstractThe role of adaptive divergence in the formation of new species has been the subject of much recent debate. The most direct evidence comes from traits that can be shown to have diverged under natural selection and that now contribute to reproductive isolation. Here, we make the case for differential adaptation of two fire-bellied toads (Anura, Bombinatoridae) to two types of aquatic habitat. Bombina bombina and B. variegata are two anciently diverged taxa that now reproduce in predator-rich ponds and ephemeral aquatic sites, respectively. Nevertheless, they hybridise extensively wherever their distribution ranges adjoin. We show in laboratory experiments that, as expected, B. variegata tadpoles are at relatively greater risk of predation from dragonfly larvae, even when they display a predator-induced phenotype. These tadpoles spent relatively more time swimming and so prompted more attacks from the visually hunting predators. We predict that genomic regions linked to high activity in B. variegata are barred from introgression into the B. bombina gene pool and thus contribute to gene flow barriers that keep the two taxa from merging into one.

scholarly journals Using a Groundwater Adjusted Water Balance Approach and Copulas to Evaluate Spatial Patterns and Dependence Structures in Remote Sensing Derived Evapotranspiration Products

2021 ◽  
Vol 13 (5) ◽  
pp. 853
Author(s):  
Mohsen Soltani ◽  
Julian Koch ◽  
Simon Stisen
Keyword(s):  
Remote Sensing ◽  
Water Balance ◽  
Spatial Pattern ◽  
Spatial Patterns ◽  
Principal Component ◽  
Small Scale ◽  
Dependence Structure ◽  
Test Case ◽  
Catchment Scale ◽  
Balance Approach

This study aims to improve the standard water balance evapotranspiration (WB ET) estimate, which is typically used as benchmark data for catchment-scale ET estimation, by accounting for net intercatchment groundwater flow in the ET calculation. Using the modified WB ET approach, we examine errors and shortcomings associated with the long-term annual mean (2002–2014) spatial patterns of three remote-sensing (RS) MODIS-based ET products from MODIS16, PML_V2, and TSEB algorithms at 1 km spatial resolution over Denmark, as a test case for small-scale, energy-limited regions. Our results indicate that the novel approach of adding groundwater net in water balance ET calculation results in a more trustworthy ET spatial pattern. This is especially relevant for smaller catchments where groundwater net can be a significant component of the catchment water balance. Nevertheless, large discrepancies are observed both amongst RS ET datasets and compared to modified water balance ET spatial pattern at the national scale; however, catchment-scale analysis highlights that difference in RS ET and WB ET decreases with increasing catchment size and that 90%, 87%, and 93% of all catchments have ∆ET < ±150 mm/year for MODIS16, PML_V2, and TSEB, respectively. In addition, Copula approach captures a nonlinear structure of the joint relationship with multiple densities amongst the RS/WB ET products, showing a complex dependence structure (correlation); however, among the three RS ET datasets, MODIS16 ET shows a closer spatial pattern to the modified WB ET, as identified by a principal component analysis also. This study will help improve the water balance approach by the addition of groundwater net in the ET estimation and contribute to better understand the true correlations amongst RS/WB ET products especially over energy-limited environments.

A Web-Accessible Robotics Monitoring System Powered by a Thermoelectric Generator Connected to a Battery

2014 ◽  
Author(s):  
Robert Dell ◽  
Runar Unnthorsson ◽  
C. S. Wei ◽  
William Foley
Keyword(s):  
Peak Power ◽  
Thermoelectric Generator ◽  
Small Scale ◽  
Test Case ◽  
Test Bed ◽  
Robot System ◽  
Source Power ◽  
Power Generator ◽  
The Stability ◽  
Electrical Supply

In small source power generation scenarios in industrial or remote settings a viable small electrical supply for security and monitoring systems is often problematic due to the variability of the energy sources and the stability of the power generated. These small scale systems lack the advantages of a larger power grid. Therefore peak power requirements can be beyond the power generator necessitating energy storage such as batteries. The authors have developed and documented a reliable thermoelectric generator and a test bed. The generator was combined with a battery in order to meet peak power requirements beyond the unassisted range of the generator. This paper presents a test case result with the thermoelectric generator powering a complete web accessible mobile robot system. The robot system can be used for monitoring, physical manipulation of the environment, routine maintenance and in emergencies.

scholarly journals De-novo protein function prediction using DNA binding and RNA binding proteins as a test case

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Sapir Peled ◽  
Olga Leiderman ◽  
Rotem Charar ◽  
Gilat Efroni ◽  
Yaron Shav-Tal ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Function ◽  
Binding Proteins ◽  
Rna Binding ◽  
De Novo ◽  
Rna Binding Proteins ◽  
Protein Function Prediction ◽  
Function Prediction ◽  
Test Case

scholarly journals Assessment of the Challenges in Policy Implementation in the Small Scale Gold Mining Sector in Ghana – A Case Study

2017 ◽  
Vol 17 (1) ◽  
pp. 54-63 ◽  
Author(s):  
P. Arroja Eshun ◽  
E. Okyere
Keyword(s):  
Policy Implementation ◽  
Gold Mining ◽  
Small Scale ◽  
Mining District ◽  
Test Case ◽  
Mining Sector ◽  
Social Challenges ◽  
Mining Sites ◽  
Adequate Knowledge ◽  
Acquisition Processes

In recent times, stakeholders in the mining sector have expressed concerns about the environmental degradation and the social impacts of uncontrolled Small Scale Mining (SSM) activities in Ghana despite the existence of legislative instruments that define the procedures required for the acquisition of licences and operations of SSM activities in the country. This paper assesses the challenges in policy implementation in the small scale gold mining sector of Ghana by reviewing policies on regularisation and environmental management. It further identifies challenges faced by small scale mining operators in adhering to laid down policies for the smooth operation of the sector and furthermore assesses the views of some principal stakeholders on the benefits and challenges of small scale mining using the Dunkwa mining district as a test case. The methods employed include: field visits to some  small scale mining sites within the Dunkwa mining district; interviews and questionnaire administration; and statistical and content analysis of data. The study reveals the following factors, among others, to have contributed largely to the difficulty in regularisation, environmental and social challenges that have plagued the SSM sector: low level of education of majority of miners; bureaucracies and centralisation of licence acquisition processes; lack of sources of finance for SSM projects; lack of geological information on mineable areas; and lack of adequate knowledge of the laws and regulations on mining and environment. In addressing the challenges the following recommendations are made: decentralisation of the regularisation processes to simplify licence acquisition; adequate geological investigations should be undertaken on SSM blocked-out areas to reduce the try and error mining approach adopted by miners; and continuous education and training of miners on good mining and environmental practices. Keywords: Small Scale Mining, Mineral Policies, Environmental Impact, Regularisation, Challenges

scholarly journals Accurate long-read de novo assembly evaluation with Inspector

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Chen ◽  
Yixin Zhang ◽  
Amy Y. Wang ◽  
Min Gao ◽  
Zechen Chong
Keyword(s):  
Genome Assembly ◽  
De Novo Assembly ◽  
In Silico ◽  
Large Scale ◽  
De Novo ◽  
Small Scale ◽  
De Novo Genome Assembly ◽  
Consensus Sequences ◽  
Assembly Evaluation ◽  
Long Read

AbstractLong-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors.

Adjoint-Based Aerodynamic Shape Optimization for Low Reynolds Number Airfoils

2015 ◽  
Vol 138 (2) ◽  
Author(s):  
Juanmian Lei ◽  
Jiandong He
Keyword(s):  
Reynolds Number ◽  
Shape Optimization ◽  
Low Reynolds Number ◽  
Boundary Layer Separation ◽  
Small Scale ◽  
Test Case ◽  
Aerodynamic Shape Optimization ◽  
Aerodynamic Shape ◽  
Aerial Vehicles ◽  
Low Reynolds

In the past decades, most of the research studies on airfoil shape design and optimization were focused on high Reynolds number airfoils. However, low Reynolds number airfoils have attracted significant attention nowadays due to their vast applications, ranging from micro-aerial vehicles (MAVs) to small-scale unmanned aerial vehicles. For low Reynolds number airfoils, the unsteady effects caused by boundary layer separation cannot be neglected. In this paper, we present an aerodynamic shape optimization framework for low Reynolds number airfoil that we developed based on the unsteady laminar N–S equation and the adjoint method. Finally, using the developed framework, we performed a test case with NACA0012 airfoil as a baseline configuration and the inverse of lift to drag ratio as the cost function. The optimization was carried out at Re = 10,000 and Ma = 0.2. The results demonstrate the effectiveness of the framework.

scholarly journals Measurement of Dioxin Emissions from a Small-Scale Waste Incinerator in the Absence of Air Pollution Controls

2019 ◽  
Vol 16 (7) ◽  
pp. 1267 ◽  
Author(s):  
Gang Zhang ◽  
Xiangxuan Huang ◽  
Wenbo Liao ◽  
Shimin Kang ◽  
Mingzhong Ren ◽  
...  
Keyword(s):  
Air Pollution ◽  
Solid Waste ◽  
De Novo ◽  
Dominant Role ◽  
Small Scale ◽  
Waste Incinerator ◽  
Bag Filter ◽  
Mean Values ◽  
Carbon Injection ◽  
Waste Incinerators

Polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/Fs) emissions from basic small-scale waste incinerators (SWI) may cause health risks in nearby people and are thus subject to stringent regulations. The aim of this study was to evaluate PCDD/F emission and reduction of a basic SWI in the absence of air pollution controls (APCs). The results indicated that the stack gas and fly ash presented average PCDD/F levels and emission factors of 3.6 ng international toxic equivalent (I-TEQ)/Nm3 and 189.31µg I-TEQ/t and 6.89 ng I-TEQ/g and 137.85µg I-TEQ/t, respectively, much higher than those from large municipal solid waste incinerators (MSWI). PCDD/Fs congener fingerprints indicated that de novo synthesis played a dominant role in the low-temperature post-combustion zone and increased the presence of high-chlorine substituted congeners. On the basis of the emission factor 327.24 µg I-TEQ/t-waste, approximately 3000 g I-TEQ dioxins might be generated in total through basic SWIs and open burning. After refitting an SWI by adding activated carbon injection with a bag filter (ACI+BG), the PCDD/F emissions decreased to mean values of 0.042 ng I-TEQ/Nm3, far below the standard of 0.1 ng I-TEQ/Nm3, and the removal efficiency reached 99.13% in terms of I-TEQ. Therefore, it is entirely feasible to considerably reduce PCDD/F emissions by refitting basic SWI, which is positive for the future development of rural solid waste (RSW (RSW) disposal by SWI.

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