Basin Populations Research Articles

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(N),H(alpha)) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.

Tyrrhenian basins of Ligury as a new peri-Mediterranean ichthyogeographic district? Population structure of Telestes muticellus (Osteichthyes, Cyprinidae), a primary freshwater fish

The phylogeographic structure of vairone (Telestes muticellus), a primary freshwater fish endangered in a large part of its distributional range, was assessed: (i) to reconstruct the complex dispersion pattern in the upper Tyrrhenian hydrographic basins of Ligury, actually not recognised as peri-Mediterranean ichthyogeographic district, and (ii) to evidence the shape of population genetic structure as useful tool for future conservation strategies. A partial fragment of mitochondrial DNA cytochrome b (497 bp) was sequenced in 109 specimens sampled from eight populations, along an east–west geographic gradient. Fourteen haplotypes were identified, confirming the evolutionary distance between the two co-generic species: T. muticellus as ‘Ligurian’ clade and T. souffia as ‘French’ clade. The Nested Clade Analysis (NCA), the population genetic variability and population structure suggested a natural colonization occurred throughout the crossing of Alpine and Apennine watershed. The hierarchical Analysis of Molecular Variance (AMOVA) confirmed a geographic distinction between the populations from western (WTL) and from eastern (ETL) Tyrrhenian basins of Ligury colonised through the river capture processes along the Maritime Alpine watershed (Padano-Venetian district) and along the Apennine watershed (Tuscano-Latium district), respectively. Our results, evidencing the lack of genetic contiguity among vairone populations of the upper Tyrrhenian hydrographic basins of Ligury, allowed to recognise the presence of two management units (MUs) for its conservation.

EMERGY ANALYSIS FOR ASSESSING THE ROLE OF RESOURCE AND ENVIRONMENT OF LOWER MEKONG RIVER BASIN

Emergy (spelled with an "m") concept is the basic for a science-based evaluation system representing both the environmental values and the economic values with a common measure. Emergy analysis of Lower Mekong River Basin (LMRB) was performed to show the important contribution of water and soil environmental resources and agricultural activities as well to its economic development. The most important renewable resource is the chemical potential of rain of 1429.23E+20 sej/yr. The second most important renewable resource is the chemical potential of river of 362.68E+20 sej/yr. About 49% of the total emergy used was derived from local resources. Agriculture is the main economic activity in LMRB with the contribution of 36% of total emergy used. The renewable carrying capacity was equal to 38% of the basin population. Based on emergy indices, the current status of LMRB is at the boundary between sustainability and unsustainability.

Historical trends affecting accumulation of sediment and phosphorus in Lake Pepin, upper Mississippi River, USA

This study was conducted to collect historical land use information that would help explain the historical patterns in accumulation of sediment and phosphorus in Lake Pepin documented by Engstrom et al. (J Paleolimnol, this issue). A wide range of historical factors including cropping systems, phosphorus applications from fertilizer and manure, human and animal populations, river flows and phosphorus discharges from waste water treatment plants were studied using statistical methods. Results showed that sediment losses from the Minnesota River basin are significantly correlated with historical increases in river flows, row crop production acreage and basin population. Total phosphorus accumulations in the sediments of Lake Pepin are significantly correlated with increased phosphorus discharges from metropolitan area wastewater treatment plants, and increases in row crop acreage and river flows. Total phosphorus inflows to Lake Pepin are significantly correlated with increases in river flows, row crop acreage and phosphorus fertilizer applied to agricultural lands.

Environmental Degradation, Livelihood and Conflicts: A Focus on the Implications of the Diminishing Water Resources of Lake Chad for North-Eastern Nigeria

Lake Chad has been a source of economic livelihood for millions of people inhabiting the catchment areas in the four riparian states, namely: Cameroon, Chad, Niger and Nigeria. However, in the last four decades, the size of the lake including its resources has continued to diminish. The impact of this depletion is being felt by Lake Chad basin population who depend on the lake for their means of livelihood. This paper focuses on the diminishing natural resources of Lake Chad as an empirical referent to analyse the relationship that can develop among natural resource diminution, livelihood and conflicts. Of particular attention is the incidence of conflict between and among fishermen, pastoralists, farmers and sometimes state security agents, and the tendency of the conflicts to degenerate into large scale intra-ethnic, intra-state and interstate conflicts. The paper further draws attention to the implications of the diminishing water resources of the lake for the North-East zone of Nigeria, and makes recommendations suggested by the analysis. African Journal on Conflict Resolution Vol. 8 (2) 2008: pp. 35-62

Genetic structure of the Imperial Eagle (Aquila heliaca) population in Slovakia

Genetic structure of the Imperial Eagle (Aquila heliaca) population in SlovakiaThe distribution of the Imperial Eagle (Aquila heliaca) in the Carpathian Basin is not continuous, since western and eastern breeding pairs are separated by 150 km from each other in Slovakia, and 70 km in Hungary. In the present study our aim was to examine whether this geographical distance has resulted in any genetic separation between the Western and Eastern Slovak breeding groups. We have used 132 shed feathers and 128 blood samples collected in the fields geographically representing the whole of the Slovak breeding population, and included all juveniles ringed between 2004 and 2006. After successful DNA extractions we have determined the sex, microsatellite DNA-profiles and mtDNA control region haplotypes of the specimens. Data were integrated in a common Hungarian-Slovak "DNA-fingerprint" database, making identification of the same specimen possible when recaptured. Based on a subsample of the collected individuals, the genetic structure of the Slovak population was tested using ten microsatellite loci and mtDNA control region haplotypes, and marginally significant genetic differentiation was found between western and eastern subpopulations. These results suggest that, in spite of the large dispersal capacity of the species, a relatively small geographic distance can also decrease the exchange rate of individuals between subpopulations. As this result involves only samples from the northern part of the breeding area, major conclusions concerning genetic structure and gene flow of Imperial Eagles in the entire Carpathian Basin population cannot be drawn without sampling and analysing the southern subpopulations in Hungary.

Genetic Stock Composition of Subyearling Chinook Salmon in Seasonal Floodplain Wetlands of the Lower Willamette River, Oregon

AbstractWe used genetic identification methods to examine the stock composition of subyearling Chinook salmon Oncorhynchus tshawytscha in floodplain wetland and main‐stem habitats of the lower Willamette River, Oregon. Using a microsatellite DNA baseline of 13 standardized loci and 30 Columbia River basin populations, we analyzed 280 subyearlings collected in winter and spring 2005‐2006 from wetland and main‐stem river sites. Genetic stock identification analysis indicated that spring Chinook salmon originating from the Willamette River made up a substantial proportion of the samples and contributed 16‐71% to sample mixtures representing the wetland habitat sites. Fall Chinook salmon from lower Columbia River sources were also present and contributed 58% of winter samples. Spring Chinook salmon from lower Columbia River populations were present in both wetland (17%) and river (16%) samples in spring 2005, and subyearlings from summer‐fall‐run populations in the middle and upper Columbia River contributed to spring wetland samples in 2006 (26%). The results suggest that floodplain restoration projects intended to improve fish habitats during winter and spring periods in the lower Willamette River may benefit Chinook salmon populations from the upper Willamette River, lower Columbia River, and upper Columbia River summer‐fall evolutionarily significant units.

“Pharm‐Ecology” of Diet Shifting: Biotransformation of Plant Secondary Compounds in Creosote (Larrea tridentata) by a Woodrat Herbivore,Neotoma lepida

Diet switching in mammalian herbivores may necessitate a change in the biotransformation enzymes used to process plant secondary compounds (PSCs). We investigated differences in the biotransformation system in the mammalian herbivore, Neotoma lepida, after a radical shift in diet and secondary compound composition. Populations of N. lepida in the Mojave Desert have evolved over the past 10,000 years to feed on creosote (Larrea tridentata) from an ancestral state of consuming juniper (Juniperus osteosperma). This dietary shift represents a marked change in the dietary composition of PSCs in that creosote leaves are coated with phenolic resin, whereas juniper is high in terpenes but lacks phenolic resin. We quantified the enzyme activity of five major groups of biotransformation enzymes (cytochrome P450s, NAD(P)H:quinone oxidoreductase, glutathione conjugation, sulfation, and glucuronidation) recognized for their importance to mammalian biotransformation for the elimination of foreign compounds. Enzyme activities were compared between populations of Mojave and Great Basin woodrats fed control and creosote diets. In response to creosote, the Mojave population had greater levels of cytochrome P450s (CYP2B, CYP1A) and glutathione conjugation liver enzymes compared with the Great Basin population. Our results suggest that elevated levels of cytochrome P450s and glutathione conjugation enzymes in the Mojave population may be the underlying biotransformation mechanisms that facilitate feeding on creosote.

Geographic variation in Parauchenoglanis ngamensis (Boulenger 1911), (Siluriformes: Auchenoglanididae)

ABSTRACT The catfish, Parauchenoglanis ngamensis (Auchenoglanididae), is distributed in the Kasai and upper Zambezi-Okavango basins in southern Africa. The Kasai Basin population can be distinguished from the upper Zambezi-Okavango basins population by a less robust humeral process of the cleithrum, a longer external mandibular barbel, and less pigmentation on the body and fins. A population at Lake Calundo, appears to represent a portion of a cline within the species or a hybrid zone between two forms in the Kasai and upper Zambezi-Okavango basins.

English

  Random amplified polymorphic DNA (RAPD) marker analyses were used to profile the ‘ecological explosion’ of the introduced Oreochromis niloticus in the basins of Lakes Victoria and Kyoga in comparison to its putative origin of Lakes Edward, George and Albert.  O. niloticus is currently the dominant tilapiine in Lakes Victoria and Kyoga basins following its introductions from the Lakes Albert and Edward starting in the 1920s. The populations from the Lake Victoria basin were more similar to the putative source population of Lake Edward, while the populations from Lake Kyoga were more similar to the Lake Albert population. Lake Kyoga basin populations were less diverse than those of Lake Victoria basin, consistent with the hypothesis that introductions into Kyoga were more recent and/or that a more diverse set of introductions contributed to those of Victoria basin. Wider differences between Lake George and Lake Edward populations relative to distant populations was attributed to the direct transplant of Albert strain into George by a fish processing establishment in the 1970s. RAPDs offered a quick and inexpensive molecular tool to discern fish populations that could be adopted for management of the fisheries given the recent volatile species/populations changes and/or losses in Lake Victoria Region.   Key words: RAPDs, Oreochromis niloticus, Lakes Victoria, Kyoga, Edward, Albert, George.

A profile of the introduced Oreochromis niloticus (Pisces: Teleostei) populations in Lake Victoria Region in relation to its putative origin of Lakes Edward and Albert (Uganda - E. Africa) based on random amplified polymorphic DNA analysis

Random amplified polymorphic DNA (RAPD) marker analyses were used to profile the ‘ecological explosion’ of the introduced Oreochromis niloticus in the basins of Lakes Victoria and Kyoga in comparison to its putative origin of Lakes Edward, George and Albert. O. niloticus is currently the dominant tilapiine in Lakes Victoria and Kyoga basins following its introductions from the Lakes Albert and Edward starting in the 1920s. The populations from the Lake Victoria basin were more similar to the putative source population of Lake Edward, while the populations from Lake Kyoga were more similar to the Lake Albert population. Lake Kyoga basin populations were less diverse than those of Lake Victoria basin, consistent with the hypothesis that introductions into Kyoga were more recent and/or that a more diverse set of introductions contributed to those of Victoria basin. Wider differences between Lake George and Lake Edward populations relative to distant populations was attributed to the direct transplant of Albert strain into George by a fish processing establishment in the 1970s. RAPDs offered a quick and inexpensive molecular tool to discern fish populations that could be adopted for management of the fisheries given the recent volatile species/populations changes and/or losses in Lake Victoria Region.

Comparative experimental electron density and electron localization function study of thymidine based on 20 K X-ray diffraction data

From a high-resolution X-ray data set (sin theta/lambda = 1.1 A(-1)) measured at 20 K the electron-density distribution of the nucleoside thymidine was derived by a classical multipole refinement and by application of the invariom formalism. Owing to the presence of the heteroaromatic thymine ring system two invariom models were compared which considered the nearest and next-nearest neighbors for the invariom assignments. Differences between the two invariom models were small for the bond topological and atomic properties - about five times smaller than differences with the classical multipole refinement. Even the latter differences are in the uncertainty ranges which are commonly observed in experimental charge-density work and were found in molecular regions involved in intermolecular contacts. The application of the constrained wavefunction-fitting approach allowed the electron localization function (ELF) to be obtained from the experimental X-ray data, which was graphically represented and topologically analyzed. ELF basin populations were derived from experiment for the first time. The electron populations in the disynaptic valence basins were related quantitatively to bond orders.

Stereoelectronic Effects in N−C−S and N−N−C Systems: Experimental andab InitioAIM Study

The energy of stereoelectronic interactions in N-C-S and N-N-C systems in tetrahydro[1,3,4]thiadiazolo[3,4- c][1,3,4]thiadiazole was estimated by means of R. W. Bader's quantum theory of "atoms in molecules" (AIM) and natural bond orbital analysis (NBO). The results were compared with those obtained by analysis of rho( r) derived from high-resolution X-ray diffraction data. The analysis of the data obtained allowed one to find a correlation between geometric characteristics of the stereoelectronic interactions, NBO mixing energies and the AIM properties of atoms. Significant variations of nitrogen atom atomic basin populations in different conformers were explained by sterical interactions between their electron lone pairs.

Isoenzymatic Characterization of Phlebotomus papatasi (Diptera: Psychodidae) of the Marrakech Area, Morocco

This study reports the genetic characterization of urban and rural populations of Phlebotomus (Phlebotomus) papatasi Scopoli (Diptera: Psychodidae) in Marrakech, Morocco. Using isoenzymatic analysis, four Moroccan populations were compared with other Mediterranean basin populations from Spain, Cyprus, and Syria. Morphological anomalies were noted in the male genitalia of 5.3% of the specimens collected from Marrakech area. Qualitative analysis of zymogram profiles revealed nine polymorphic enzymes (HK, PGM, PGI, 6PGD, MDH1, MDH2, ICD2, FUM, and ACO) and three monomorphic enzymes (ME, ICD1, and αGPDH). Genetic distances clearly separated the populations of western Mediterranean countries (Morocco and Spain) from eastern countries (Syria and Cyprus), but they could not be used to differentiate between urban and rural populations in Marrakech area.

Isoenzymatic Characterization of <I>Phlebotomus papatasi</I> (Diptera: Psychodidae) of the Marrakech Area, Morocco

This study reports the genetic characterization of urban and rural populations of Phlebotomus (Phlebotomus) papatasi Scopoli (Diptera: Psychodidae) in Marrakech, Morocco. Using isoenzymatic analysis, four Moroccan populations were compared with other Mediterranean basin populations from Spain, Cyprus, and Syria. Morphological anomalies were noted in the male genitalia of 5.3% of the specimens collected from Marrakech area. Qualitative analysis of zymogram profiles revealed nine polymorphic enzymes (HK, PGM, PGI, 6PGD, MDH1, MDH2, ICD2, FUM, and ACO) and three monomorphic enzymes (ME, ICD1, and alphaGPDH). Genetic distances clearly separated the populations of western Mediterranean countries (Morocco and Spain) from eastern countries (Syria and Cyprus), but they could not be used to differentiate between urban and rural populations in Marrakech area.

Shannon Entropies of Atomic Basins and Electron Correlation Effects

Electron correlation effects on atomic basin populations of AIM theory and the resulting de/localization of the basin charge and momentum densities, as measured by local Shannon entropies and basin kinetic energies, are discussed for a series of ten- , fourteen- and eighteen-electron molecules. These results are related to the nature of the chemical environment. Correlation effects on global Shannon entropies and kinetic energies are also examined.

Two markers and one history: phylogeography of the edible common sea urchin Paracentrotus lividus in the Lusitanian region

Benthic marine invertebrates with long-lived larvae are believed to have dispersal capabilities that contribute to maintaining genetic uniformity among populations over large geographical scales. However, both hydrological and biological factors may limit the actual dispersal of such larvae. We studied the population genetic structure of the edible common sea urchin Paracentrotus lividus (Lamarck, 1816), to explore its dispersal patterns in the Atlanto-Mediterranean region and, more specifically, to ascertain the role of the Strait of Gibraltar in shaping the genetic structure of this species. For this purpose, we analysed 158 individuals for the mitochondrial 16S rRNA gene and 151 of these for the nuclear single-copy intron adenine nucleotide transporter (ANT) from 16 localities from the Atlantic and Mediterranean basins, spanning over 4,000 km. Mitochondrial 16S rRNA shows higher genetic diversity in the Mediterranean than in the Atlantic and reveals a sharp break between the populations of both basins, probably as a consequence of the barrier imposed by the Almería–Orán hydrological front, situated east of the Strait of Gibraltar. Both markers suggest that a recent population expansion has taken place in both basins, most probably following the Messinian salinity crisis.

Phylogeography of a threatened freshwater fish (Mogurnda adspersa) in eastern Australia: conservation implications

Phylogeography is a field that has the potential to provide an integrative approach to the conservation of threatened species. The southern purple spotted gudgeon, Mogurnda adspersa, is a small freshwater fish that was once common and widely distributed throughout south-eastern Australia. However, habitat alteration has dramatically reduced the size and the range of Murray–Darling Basin populations, which are now classified as endangered. Here patterns of genetic structure and evolutionary history of M. adspersa in southern Queensland and the Murray–Darling Basin are elucidated using three regions of the mitochondrial DNA, the ATPase 6 and 8 and the control region. Murray–Darling Basin populations are characterised by lineages with highly localised endemism, very low genetic diversity and restricted gene flow. Phylogenetic reconstructions show that Murray–Darling Basin populations comprise a monophyletic clade that possibly originated by range expansion from the coast around 1.6 million years ago. It is proposed that the divergent Murray–Darling Basin clade is of high conservation priority and requires separate management. The present study further exemplifies the role of drainage rearrangement in driving evolutionary diversification in Australian freshwater fishes, an historical process with profound implications for conservation management.

Clinal Variation in Ohio River Basin Populations of the Redfin Shiner (Lythrurus umbratilis)

Abstract Prior to this study, undocumented morphological variation in Lythrurus umbratilis (Redfin Shiner) has impaired identification of many samples of eastern populations of the species. Meristics, morphometrics, tuberculation, pigmentation, and nuptial male coloration of over 700 specimens of L. umbratilis were examined in order to assess patterns of geographic variation and species limits in the Ohio River basin. Principle component and spatial autocorrelation analyses of these data demonstrate that morphological variation in L. umbratilis is clinal along most of the length of the Ohio River basin. Specimens from eastern populations have less black in the dorsal fin of breeding males, have lower mean scale counts, and are more slender than western populations. The cline does not extend into central and northern Ohio, as populations have relatively high meristic counts and more robust males. These analyses suggest that recognition of an additional species in the Ohio River basin is not warranted at th...

Multi‐marker phylogeny of three evergreen oaks reveals vicariant patterns in the Western Mediterranean

Nuclear (AFLPs and ITSs) and chloroplast DNA markers (cpDNA) were analysed in Quercus suber L., Q. ilex L. and Q. coccifera L. in order to detect vicariant patterns in the Western Mediterranean Basin populations. Clustering methods, i.e., parsimony, minimum spanning network, UPGMA and PCO, were used to obtain robust phylogenies. The Mantel test was used to check the geographic structure of the populations. Nuclear markers’ based phylogenies showed high bootstrap values at basal nodes of clusters indicative of species. Within species, Q. suber and Q. ilex showed three and two groups respectively with strong geographic structure for cytoplasmic and nuclear markers. In contrast, Q. coccifera had overlapping cpDNA lineages and nuclear markers did not show any group with strong geographic structure. Taxonomic assignation of the species was well‐supported by our data. Ongoing allopatric speciation was inferred for Q. suber and Q. ilex derived from Pliocene vicariant events. Quercus coccifera showed a more homogeneous genetic pattern in the Western Mediterranean.