Genetic differentiation and cryptic speciation in natural populations of Drosophila lacertosa

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two ge

Molecular genetic basis for the rhino mouse from Chinese KM subcolony

Both the rhino mouse and hairless mouse resulted from hairless gene mutation, but they show different phenotypes of skin physiology. The rhino mouse has more similar histological characters to human papular alopecia. Therefore rhino mouse is a good experimental animal model for human papular alopecia. This study reports a hairless mouse named rhino KIZ, arose from KM colony in Kunming Institue of Zoology, by systematic studies on morphology, skin histopathology, gene sequence, pedigree and protein domain analysis. The results demonstrate that a C-to-T transition in exon 11 of hr gene (The mutant gene has been applied for a Chinese patent (patent No. 03135280)) results in the rhino KIZ. The rhino KIZ with clear genetic mechanism will be a useful animal model.

Feeding habits and trophic levels of some demersal fish species in the Persian Gulf (Bushehr Province) using Ecopath model

A trophic study was carried out in February of 2012 to January 2013 on the ecosystem in the Persian Gulf, Bushehr provience. A total of 2,948 samples of stomach contents were analyzed based on the weight and number of food items and were identified about 40 preys. Crustacean and bony fish were as a main prey in most of the stomach contents . The mean average trophic level was estimated at 3.6 by Ecopath software. In this research, the mean level were studied between eight species varied from 3.47 to 4.61, Saurida tumbil occupy the highest and the Argyrops spinifer was the lowest level. The ranges of total mortality varied from 0.7 to 3.05 per years. The food consumption rate was estimated about 69.82 per year. The overlap index showed that the prey items such as fish, crustacean, bivalve and echinoderm were shared about 65, 15, 15 and 6 percent in all stomach of individual in respectively. Mixed trophic analysis indicates that benthos have a positive effect on most of the fish species. Most species have a negative impact on themselves, interpreted here as reflecting increased with in group competition for resources. This preliminary model can be helpful to determine the gaps in the present knowledge about demersal system of the Persian Gulf.

Report of the Indian Mackerel Working Group Meeting, Colombo, Sri Lanka, 28-29 May, 2012

Stock structure approaches and consequences of management in the eight member countries. Indian mackerel (Rastrelliger kanagurta) genetic stock studies and workplan

Report of the hilsa fisheries assessment working group meeting, Kolkata, India, 26-28 November, 2014

The items discussed at the meeting included; capacity development assessment techniques, development of a hilsa fishery management plan; development of a standardised model framework for stock assessment; development of a Strategic Action Plan (SAP) for ecosystem health and resource evaluation; priority fishery management recommendations; and stock status advice for hilsa in BOBLME region .

Survey of exist specifications morphometric, meristic and inter species molecular genetic on Bream (Abramis brava orientalis) in Anzali wetland, southern coast of Caspian Sea, Aras Dam Lake and Azerbijan Republic

Bream (Abramis brava orientalis) is one of Cyprindae the Caspian Sea and its basin which has a special ecological, biological and economical role. Stock of this fish in the Caspian Sea has reduced during several years for different reason the over fishing, different industrial, agriculture, urban pollution and destroy of the spawning habitat. So that fishery company decided to recover the stock of this fish by the way of artificial reproduction of a Bream couple hunted from south coast of the Caspian Sea (Iran) and setting the fingerling to the rivers and inflow wetlands of the Caspian Sea.This activity has due to 20 tons Bream annual fishing in the Iranian South coast of the Caspian Sea (Gilan province coast and Anzali wetland), The artificial reproduction has decreased Bream population diversity of Caspian sea and Anzali wetland.So it has been declined to improve Braem population diversity by the entrance of Azerbijan republic Bream and encounter to the Caspian sea Bream. Meanwhile there is Bream in the Aras Dam Lake which had been forgotten by the Fishery Company of Iran .For this reason specifications morphometric, meristic and inter species Molecular Genetic have been surveyed in Anzali wetland,Southern coast of Caspian Sea ,Aras Darn Lake and Azerbijan republic during 2003-2005. According to the research on specifications of Morphometric and Meristic of Anzali wetland(120 species),Southern coast of Caspian Sea(90 species), Aras Dam Lake(110 species) and Azerbijan Republic(125 species)has Morphometric and Meristic differences. So that average weight and total length of Anzali wetland Bream respectively was 167 g and 23/76 cm, 102 g and 27/62 cm in Caspian Sea , 461 g and 3 5/38 cm in Aras Darn Lake and 3 4189 g and 15/21 cm in Azerbijan republic (We forced to use 1 year Bream of artificial reproduction in Iran). Also variation coefficient average Morphometric, Morphometric specification Ration and meristic in Anzali wetland Bream was 17/45, 21/56 and 4/63, in Caspian Sea bream 22/58, 15/27 and 3124, in Aras Dam lake Lake 17145. 1.5/27 and 3/57 and Azerbaijan republic Bream 22/29, 19/66 and 4/22. Also Bream of these four regions in general status had Morphometric significant differences based on One Way ANOVA Analysis. Meanwhile Anzali wetland Bream with Caspian Sea Bream from 41 Morphometric surveyed factors in 33 factors, with Aras Darn Lake Bream in 41 factors, with Azerbkjan republic Bream in 41 factors,Caspian Sea Bream with Aras Darn Lake Bream in 36 factors,with Azerbijan republic B ream in 40 factors and A ras Dam L ake Bream with Azerbijan republic Bream in 38 factors had significant statistical differences. These four regions Bream had differences according to the Morphomertric specification ration based on One Way ANOVA Analysis. Also Anzali wetland Bream was surveyed with Caspian Sea Bream from 37 factors i n 27 factors, Anzali wetland Bream with Aras Dam 1ake in 37 factors Anzali wetland Bream with Azerbijan republic Bream in 32 factors,Caspian sea bream with Arsa Dam Lake Bream in 26 factors, Caspian Sea Bream with Azerbijan republic Bream in 29 factors and Aras Dam Lake Bream with Azerbijan republic Bream in 34 factor had significant statistical differences. Based on Meristic factor of four regions bream in 16 surveyed factors in 10 factors had meaningful differences according to the One Way ANOVA Analysis. While Anzali wetland Bream was surveyed with Caspian Sea Bream from in 3 factors,Anzali wetland Bream with Aras Dam lake in 8 factors,Anzali wetland Bream with Azerbijan republic B ream in 6 factors,Caspian Sea bream with Arsa Dam Lake Bream in 6 factors,Caspian sea Bream with Azerbijan republic Bream in 3 factors and Aras Dam Lake Bream with Azerijan republic Bream in 8 factor had significant statistical differences.Meanwihle based on Factor Analysis and Discriminant Breams had differences. Also according to the resrarchs Anzali wetland Bream in 0+ age group till 5+ (6 age groups),Caspian Sea bream in 1+ - 5+(5 age groups),Aras Darn Lake Bream in 1+ - 7+ (7 age groups) and Azerbijan republic Bream for Morphometric and Meristic studies in 1+age group and for molecular Genetic reaserch were in 8+and 9+ age groups. According to the research 4 ecosystems Bream in status of same age, Aras lake Bream were bigger according to weight and length.Also in this research genetic diversity between four population was researched by PCR-RFLP technic on a piece of mitochondrion genome with the length of 3500bp contain of tRNA-leu,tRNA-glu,ND5/6,Cytb. Between 17 used enzyme. 4 enzyme, Dral, Bc11, Haefll and Banff showed diversity in totally 6 composite haplotype was detected. Maximum nucleotide diversity by the value% 0/58 in Azerbijan republic Bream by all haplotype. Aras darn Lake Bream had 2 haplotype and nucleotide diversity of %0/35.Anzali wetland and Caspian Sea Bream had no diversity. Statistical analysis by the usage of Monte Carlo with 1000 repeat showed significant differences between Azerbaijan Bream and other Bream(P<0/0001) but there was no significant difference between 3 regions Bream(P>0/5).

Genetic status of selected fish taxa in relation to conservation of genetic and species diversity in the Victoria and Kyoga Lake basins

Cichlids are known for their explosive radiation especially in the African Great Lakes marked with a high level of lake endemism. These fishes have been characterized mainly along trophic and habitat differences, by variation in morphological structures such as teeth and jaws and by differences in body shape and coloration. Cichlids are important as a microcosm of macroevolution. The explosive radiation, young evolutionary scale, and the isolation of groups characterized with high levels of endemism and presence of living fossils makes the group important for evolutionary and genetic studies. Lake Victoria region cichlids which are isolated and relatively more recent in evolution were the last to be appreciated in their diversity. Recently Ole Seehausen has found scores of rock fishes in Lake Victoria which were up to then thought to be absent from the Lake and only known to occur in Lakes Malawi and Tanganyika. Greenwood put together the species groups of Lake Victoria, and later in the early 1980's revised the classification of haplochromine species to reflect the phyletic origin and interrelationship of the various groups in Lake Victoria region. Melan Stiassny has been interested in early evolution of cichlids while the likes of Paul Fuerst and Lees Kaufman and Axel Meyer have been interested and are working to explain the speciation mechanisms responsible for the explosive radiation and evolution of cichlids. Locally S.B Wandera and his student Getrude Narnulemo are spearheading the biodiversity and taxonomic studies of cichlids in Lake Victoria region

Mechanism of pile group settlement in liquefiable soils

This paper examines the settlement of instrumented 2 × 2 model pile groups in liquefiable soil based on the results of dynamic centrifuge tests. The piles are end-bearing in dense sand, and are instrumented such that base, shaft and total pile load components can be measured. The data suggest that the overall co-seismic group settlement is accrued from incremental settlements of the individual piles as the group rocks under the action of the kinematic and inertial lateral loads. A Newmarkian framework for describing this behaviour is presented in which permanent settlement is incremented whenever the load in any of the piles exceeds the capacity of the soil to support the pile. This bearing capacity of the piles in liquefied soil is estimated based on measured dynamic soil properties during shaking and observations of the changes in load carried by the piles. The contribution of the pile cap in reducing settlement is also discussed. © 2008 ASCE.

Convex approaches to model wavelet sparsity patterns

Statistical dependencies among wavelet coefficients are commonly represented by graphical models such as hidden Markov trees (HMTs). However, in linear inverse problems such as deconvolution, tomography, and compressed sensing, the presence of a sensing or observation matrix produces a linear mixing of the simple Markovian dependency structure. This leads to reconstruction problems that are non-convex optimizations. Past work has dealt with this issue by resorting to greedy or suboptimal iterative reconstruction methods. In this paper, we propose new modeling approaches based on group-sparsity penalties that leads to convex optimizations that can be solved exactly and efficiently. We show that the methods we develop perform significantly better in de-convolution and compressed sensing applications, while being as computationally efficient as standard coefficient-wise approaches such as lasso. © 2011 IEEE.

A path-following driver-vehicle model with neuromuscular dynamics, including measured and simulated responses to a step in steering angle overlay

An existing driver-vehicle model with neuromuscular dynamics is improved in the areas of cognitive delay, intrinsic muscle dynamics and alpha-gamma co-activation. The model is used to investigate the influence of steering torque feedback and neuromuscular dynamics on the vehicle response to lateral force disturbances. When steering torque feedback is present, it is found that the longitudinal position of the lateral disturbance has a significant influence on whether the drivers reflex response reinforces or attenuates the effect of the disturbance. The response to angle and torque overlay inputs to the steering system is also investigated. The presence of the steering torque feedback reduced the disturbing effect of torque overlay and angle overlay inputs. Reflex action reduced the disturbing effect of a torque overlay input, but increased the disturbing effect of an angle overlay input. Experiments on a driving simulator showed that measured handwheel angle response to an angle overlay input was consistent with the response predicted by the model with reflex action. However, there was significant intra-and inter-subject variability. The results highlight the significance of a drivers neuromuscular dynamics in determining the vehicle response to disturbances. © 2012 Copyright Taylor and Francis Group, LLC.

Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach.

We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population. Most existing approaches for local ancestry estimation ignore the latent genetic relatedness between ancestral populations and treat them as independent. In this article, we exploit such information by building an inheritance model that describes both the ancestral populations and the admixed population jointly in a unified framework. Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each ancestral population and further extend it to generate the admixed population. Through an effective utilization of the population structural information under a principled nonparametric Bayesian framework, the resulting model is significantly less sensitive to the choice and the amount of training data for ancestral populations than state-of-the-art algorithms. We also improve the robustness under deviation from common modeling assumptions by incorporating population-specific scale parameters that allow variable recombination rates in different populations. Our method is applicable to an admixed population from an arbitrary number of ancestral populations and also performs competitively in terms of spurious ancestry proportions under a general multiway admixture assumption. We validate the proposed method by simulation under various admixing scenarios and present empirical analysis results from a worldwide-distributed dataset from the Human Genome Diversity Project.

Case study on a deep excavation in soft ground by centrifuge model tests

This paper provides a case study on the deepest excavation carried out so far in the construction of the metro network in Shanghai, which typically features soft ground. The excavation is 38 m deep with retaining walls 65 m deep braced by 9 levels of concrete props. To obtain a quick and rough prediction, two centrifuge model tests were conducted, in which one is for the 'standard' section with green field surrounding and the other with an adjacent piled building. The tests were carried out in a run-stop-excavation-run style, in which excavation was conducted manually. By analyzing the lateral wall displacement, ground deformation, bending moment and earth pressure, the test results are shown to be reasonably convincing and the design and construction were validated. Such industry orientated centrifuge modeling was shown to be useful in understanding the performance of geotechnical processes, especially when engineers lack relevant field experience. © 2010 Taylor & Francis Group, London.

Improving model quality through computer controlled saturation

In dynamic centrifuge modelling, fluids with enhanced viscosity are often used to correct for the discrepancy in time scaling. However, great care must be taken when using a high viscosity fluid that hydraulic gradients during saturation do not become high enough to cause excessive model disturbance. This paper introduces the CAM-Sat system which aims to improve the saturation process by continually controlling the fluid flow into the model, limiting it to rates low enough to avoid model disturbance. A new method for measuring the fluid flow rate is then described, and its implementation & improvement to the system is discussed. © 2010 Taylor & Francis Group, London.