Mitochondrial DNA sequence diversity in three ethnic populations from the South-west Iran: a preliminary study

To investigate the genetic structure of human populations in the South-west region of Iran, mitochondrial first hypervariable DNA sequences were obtained from 50 individuals representing three different ethnic groups from Khuzestan Province. Studied groups were Shushtari Persians and Chahar Lang Bakhtiyaries from Indo-European-speaking populations and Bani Torof Arabs from Semitic-speaking linguistic families. Genetic analysis of mtDNA data showed high similarity of Chahar Lang Bakhtiyaries with other Iranian Indo-European-speaking populations while Shushtaries and Bani Torofs had a closer affinity with Semitic-speaking groups rather than to other Iranian populations. The relationship of Chahar Lang Bakhtiyaries and Bani Torof Arabs with their neighbor populations can be explained by linguistic and geographic proximity. Whereas, the greater similarity of Shushtari Persians with West Asian Arabs is probably according to high gene flow between them. This article represents a preliminary study of three major ethnic groups of South-west Iran which investigates the potential genetic substructure of the region.     

Variation in larval black fly populations at three sites in a stream system over five years (Diptera:Simuliidae)

Five years of monthly samples taken from three sites in the Broad Cove River, two at lake outlets and one a kilometer downstream from an outlet were analyzed. Considerable variations in the population of each species between sites and years were observed. Fluctuations in the populations were not always consistent from site to site or between species at the same site from one year to the next. As all sites were on the same stream and within 3 km of each other with only slight altitude differences climatic factors were not a major factor producing variations observed between sites. Also the previous years population level did not appear to be directly related to the following seasons population level. Apparently localized conditions at a site were exerting a marked influence on the larval simuliid population at each site.     

Climate change and bird phenology: a long-term study in the Iberian Peninsula

Many studies in recent years have demonstrated long‐term temporal trends in biological parameters that can only be explained by climate change. Bird phenology has received great attention, as it studies one of the most conspicuous, popular, and easily observable phenomena in nature. There are many studies of long‐term changes in spring arrival dates, most of which concur with earlier records from the last few decades. However, few data are available for autumn departures or length of stays. Furthermore, existing data offer an equivocal picture. In this study, we analysed a huge database of about 44 000 records for five trans‐Saharan bird species (Ciconia ciconia, Cuculus canorus, Apus apus, Hirundo rustica and Luscinia megarhynchos). Data were collected from over 1300 sites around Spain during the period 1944–2004. Common spring arrival patterns were found in all species. Spring arrival dates have tended to advance since the mid‐1970s. Current dates are similar to those from the 1940s (except for C. ciconia). Thus, the advance of spring migration over the last three decades could be seen as a return to the initial timing of arrival dates, after abnormally delayed arrivals during the 1970s. A strong negative relationship with temperature in Spain at arrival time was observed in all species. A negative relationship with the Sahel Index (a measurement of precipitation in the African Sahel area during the rainy season) for the previous year was also found in C. canorus, A. apus and H. rustica. Regarding autumn departures, all species showed common interdecadal fluctuations, but only H. rustica is leaving earlier Spain at present. All species departed earlier in years that had higher temperatures during their reproductive period. However, only for H. rustica the relation between Spanish temperatures at departure time and the last sightings of individuals was significant. A heterogeneous temporal response for the length of stay was also found: C. ciconia increased, A. apus did not change and H. rustica decreased its stay. This is the first study, based on an extensive bird phenology observational network covering a large region, that shows the most complete and thorough analysis available for the Mediterranean region.     

Linking root morphology, longevity and function to root branch order: a case study in three shrubs

Root branching order supports a powerful approach to understanding complex root systems; however, how the pattern of root morphological characteristics, tissue carbon (C) and nitrogen (N) concentrations, and root lifespan are related to anatomical features of variable root orders for mature shrubs (～19 years old) in sandy habitats is still unclear. In this study, these relationships were investigated for three typical shrubs in Horqin Sand Land, Northeast China. Root diameter, individual root length, tissue carbon concentration, C:N ratio, root lifespan, root cross-sectional area (CSA), stele CSA, proportion of stele in root CSA, mean xylem vessel CSA and the number of xylem vessels all increased with root order for the three shrubs, while specific root length and nitrogen concentration decreased with root order. The combined root biomass of the first two orders accounted for more than 63% of the first–fourth order root biomass for all the three shrubs. Proportion of stele to root CSA and number of xylem vessels of third-order root segments were significantly higher than that of the first two orders, and third-order roots showed secondary development with a continuous cork layer. All first-order and most second-order roots exhibited primary development, had an intact cortex, a lower proportion of stele to root CSA, and a smaller number of vessels. Our research suggests that the first two order roots of shrubs in sandy habitats are responsible mainly for absorption, and that they play a major role in root turnover and C and N flux in the soil organic matter pool due to their high proportion of biomass and N concentration, as well as their short lifespan.     

Nested collagen matrices: a new model to study migration of human fibroblast populations in three dimensions

Fibroblast-3D collagen matrix culture provides a model system to analyze cell physiology under conditions that more closely resemble tissue than conventional 2D cell culture. Previous work has focused primarily on remodeling and contraction of collagen matrices by fibroblasts, and there has been little research on migration of cell populations within the matrix. Here, we introduce a nested collagen matrix model to analyze migration of fibroblasts in 3D collagen matrices. Nested collagen matrices were prepared by embedding contracted cell-containing matrices (also called dermal equivalents) inside cell-free matrices; migration occurred from the former to the latter. Control experiments with human dermal fragments in place of dermal equivalents confirmed the reliability of the model. Human fibroblast migration in nested collagen matrices occurred after a lag phase of 8-16 h, and cells migrating out of the inner matrices were bipolar with leading dendritic extensions. Migration was myosin II, Rho kinase and metalloproteinase-dependent but did not require plasma fibronectin. Platelet-derived growth factor but not lysophosphatidic acid or serum stimulated cell migration, although all three of these physiological agonists promote matrix remodeling and contraction. The nested collagen matrix model is a relatively easy, rapid and quantitative method to measure migration of cell populations. Our studies using this model demonstrate important differences between regulation of fibroblast migration and remodeling in collagen matrices.     

Linking recruitment to trophic factors: revisiting the Beverton--Holt recruitment model from a life history and multispecies perspective

The Beverton--Holt recruitment model can be derived from arguments about evolution of life history traits related to foraging and predation risk, along with spatially localized and temporarily competitive relationships in the habitats where juvenile fish forage and face predation risk while foraging. This derivation explicitly represents two key biotic factors, food supply (I) and predator abundance (R), which appear as a risk ratio (R/I) that facilitates modelling of changes in trophic circumstances and analysis of historical data. The same general recruitment relationship is expected whether the juvenile life history is simple or involves a complex sequence of stanzas; in the complex case, the Beverton--Holt parameters represent weighted averages or integrals of risk ratios over the stanzas. The relationship should also apply in settings where there is complex, mesoscale variation in habitat and predation risk, provided that animals sense this variation and move about so as to achieve similar survival at all mesoscale rearing sites. The model predicts that changes in food and predation risk can be amplified violently in settings where juvenile survival rate is low, producing large changes in recruitment rates over time.     

ABC as a flexible framework to estimate demography over space and time: some cons,many pros

The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human‐induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data‐analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.     

Adapting to winter in wheat: a long-term study follows parallel phenotypic and genetic changes in three experimental wheat populations

Drawing a direct connection between adaptive evolution at the phenotypic level and underlying genetic factors has long been a major goal of evolutionary biologists, but the genetic characterization of adaptive traits in natural populations is notoriously difficult. The study of evolution in experimental populations offers some help — initial conditions are known and changes can be tracked for extended periods under conditions more controlled than wild populations and more realistic than laboratory or greenhouse experiments. In this issue of Molecular Ecology , researchers studying experimental wheat populations over a 12-year period have demonstrated evolution in a major adaptive trait, flowering time, and parallel changes in underlying genetic variation ( Rhoné et al . 2008 ). Their work suggests that cis -regulatory mutations at a single gene may explain most of the flowering time variation in these populations.     

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long‐lived tree endemic to Hainan Island,China

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long‐lived trees. Dracaena cambodiana is an endangered, long‐lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter‐simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat‐private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.     

Using broad-scale, community survey data to compare species conservation strategies across regions: A case study of the Koala in a set of adjacent 'catchments'

Summary   Managers of wildlife populations with a wide geographical range are understandably interested in the question of whether they can manage a broader population with a single conservation strategy (e.g. covering a set of adjacent management regions, referred to as 'catchments' in Australia) or whether separate strategies are required for individual catchments. We addressed this question using data from a statewide, community wildlife survey to quantify Koala ( Phascolarctos cinereus ) habitat relationships in the catchments of four adjacent Catchment Management Authorities or CMA (>10 000 km²) of New South Wales, Australia and then tested whether these habitat relationships were similar across catchments. Although the results were constrained by the coarse resolution of the community survey and environmental data, we were able to model broad-scale patterns of habitat use. Model explanatory power and cross-regional predictability was low, but consistent with Koala ecology. Two environmental variables emerged as having a strong relationship with Koala presence – mean elevation and percentage of fertile soils – the importance of which varied among catchments depending on land-use patterns. The results highlight the need for local wildlife management plans, not a single plan covering multiple catchments.     

Chemically enhanced phytoextraction of risk elements from a contaminated agricultural soil using Zea mays and Triticum aestivum: performance and metal mobilization over a three year period

Enhanced phytoextraction using EDTA for the remediation of an agricultural soil contaminated with less mobile risk elements Cd and Pb originating from smelting activities in Príbram (Czech Republic) was assessed on the laboratory and the field scale. EDTA was applied to the first years crop Zea mays. Metal mobilization and metal uptake by the plants in the soil were monitored for two additional years when Triticum aestivum was planted. The application ofEDTA effectively increased water-soluble Cd and Pb concentrations in the soil. These concentrations decreased over time. Anyhow, increased concentrations could be still observed in the third experimental year indicating a low possibility of groundwater pollution after the addition of EDTA during and also after the enhanced phytoextraction process under prevailing climatic conditions. EDTA-applications caused phytotoxicity and thereby decreased biomass production and increased Cd and Pb uptake by the plants. Phytoextraction efficiency and phytoextraction potential were too low for Cd and Pb phytoextraction in the field in a reasonable time frame (as less than one-tenth of a percent of total Cd and Pb could be removed). This strongly indicates that EDTA-enhanced phytoextraction as implemented in this study is not a suitable remediation technique for risk metal contaminated soils.     

Relationships between boron concentrations and trout in the Firehole River, Wyoming: historical information and preliminary results of a field study

The Firehole River (FHR) in Yellowstone National Park (YNP) is a world-renowned recreational fishery that predominantly includes rainbow trout (RBT,Oncorhynchus mykiss) and brown trout (BNT,Salmo trutta). The trout populations apparently are closed to immigration and have been self-sustaining since 1955. Inputs from hot springs and geysers increase the temperature and mineral content of the water, including elevating the boron (B) concentrations to a maximum of 1 mg B/L. Both RBT and BNT reside in warm-water reaches, except when the water is extremely warm (≥25°C) during midsummer. They spawn in late fall and early winter, with documented spawning of BNT in the cold-water reach upstream from the Upper Geyser Basin and of RBT in the Lower Geyser Basin reach, where water temperatures presumably are the warmest; however, successful recruitment of RBT in waters containing 1 mg B/L has not been demonstrated conclusively. Thus, we began investigating the relationships among temperature, B concentrations, other waterquality parameters, and the distribution and reproduction of trout in the FHR in spring 1997. However, atypical high water flows and concomitant lower than historical temperatures and B concentrations during summer 1997 preclude conclusions about avoidance of high B concentrations.     

Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout ( Salmo trutta ) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with nonlocal strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation by distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation by distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analysing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.     

Reconstruction of ancestral FGLamide-type insect allatostatins: a novel approach to the study of allatostatin function and evolution

Allatostatins (ASTs) are a class of regulatory neuropeptides, with diverse functions, found in an array of invertebrate phyla. ASTs have complex gene structure, in which individual ASTs are cleaved from a precursor peptide. Little is known about the molecular evolution of AST structure and function, even in extensively studied groups such as cockroaches. This paper presents the application of a novel technique for the analysis of this system, that of ancestral reconstruction, whereby ancestral amino acid sequences are resurrected in the laboratory. We inferred the ancestral sequences of a well-characterized peptide, AST 7, for the insect ancestor, as well as several cockroach ancestors. Peptides were assayed for in vitro inhibition of JH production in Diploptera punctata and Periplaneta americana. Our results surprisingly, indicate a decrease in potency of the ancestral cockroach AST7 peptide in comparison with more ancient ones such as the ancestral insect peptide, as well as more recently evolved cockroach peptides. We propose that this unexpected decrease in peptide potency at the cockroach ancestor may be related to the concurrent increase in peptide copy number in the lineages leading to cockroaches. This model is consistent with current physiological data, and may be linked to the increased role of ASTs in the regulation of reproductive processes in the cockroaches.     

Projected climate impacts to South African maize and wheat production in 2055: a comparison of empirical and mechanistic modeling approaches

Crop model‐specific biases are a key uncertainty affecting our understanding of climate change impacts to agriculture. There is increasing research focus on intermodel variation, but comparisons between mechanistic (MMs) and empirical models (EMs) are rare despite both being used widely in this field. We combined MMs and EMs to project future (2055) changes in the potential distribution (suitability) and productivity of maize and spring wheat in South Africa under 18 downscaled climate scenarios (9 models run under 2 emissions scenarios). EMs projected larger yield losses or smaller gains than MMs. The EMs’ median‐projected maize and wheat yield changes were ?3.6% and 6.2%, respectively, compared to 6.5% and 15.2% for the MM. The EM projected a 10% reduction in the potential maize growing area, where the MM projected a 9% gain. Both models showed increases in the potential spring wheat production region (EM = 48%, MM = 20%), but these results were more equivocal because both models (particularly the EM) substantially overestimated the extent of current suitability. The substantial water‐use efficiency gains simulated by the MMs under elevated CO₂ accounted for much of the EM?MM difference, but EMs may have more accurately represented crop temperature sensitivities. Our results align with earlier studies showing that EMs may show larger climate change losses than MMs. Crop forecasting efforts should expand to include EM?MM comparisons to provide a fuller picture of crop–climate response uncertainties.     

Estimating index of population trend by re-sampling techniques (jackknife and bootstrap) and its application to the life table study of rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

Taking a published natural population life table of rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), as an example, we estimated the population trend index, I, via re‐sampling methods (jackknife and bootstrap), determined its statistical properties and illustrated the application of these methods in determining the control effectiveness of bio‐agents and chemical insecticides. Depending on the simulation outputs, the smoothed distribution pattern of the estimates of I by delete‐1 jackknife is visually distinguishable from the normal density, but the smoothed pattern produced by delete‐d jackknife, and logarithm‐transformed smoothed patterns produced by both empirical and parametric bootstraps, matched well the corresponding normal density. Thus, the estimates of I produced by delete‐1 jackknife were not used to determine the suppressive effect of wasps and insecticides. The 95% percent confidence intervals or the narrowest 95 percentiles and Z‐test criterion were employed to compare the effectiveness of Trichogramma japonicum Ashmead and insecticides (powder, 1.5% mevinphos + 3% alpha‐hexachloro cyclohexane) against the rice leaf roller based on the estimates of I produced by delete‐d jackknife and bootstrap techniques. At α= 0.05 level, there were statistical differences between wasp treatment and control, and between wasp and insecticide treatments, if the normality is ensured, or by the narrowest 95 percentiles. However, there is still no difference between insecticide treatment and control. By Z‐test criterion, wasp treatment is better than control and insecticide treatment with P‐value < 0.01. Insecticide treatment is similar to control with P‐value > 0.2 indicating that 95% confidence intervals procedure is more conservative. Although similar conclusions may be drawn by re‐sampling techniques, such as the delta method, about the suppressive effect of trichogramma and insecticides, the normality of the estimates can be checked and guaranteed, and the correlation among sequential life stages of rice leaf roller is also considered in the estimation. Judged by the P‐values from Z‐test, the delta method is more conservative.     

PIT telemetry as a method to study the habitat requirements of fish populations: application to native and stocked trout movements

Passive integrated transponder (PIT) technology was used to study the behaviour of fishes during the summer season in two headwater streams of northeastern Portugal. A total of 71 PIT tags (12 mm long × 2.1 mm diameter) were surgically implanted in 1⁺ stocked (39) and native (32) brown trout of two size classes (<20.0 and ≥20.0 cm). Eight independent antennae, connected to a multi-point decoder (MPD reader) unit, were placed in different microhabitats, selected randomly every 3 days during the observation period (29 August–9 September in Baceiro stream and 19 September–4 October in Sabor stream). The results confirmed this method as a suitable, labour efficient tool to assess the movement and habitat use of sympatric stocked and native trout populations. About 76.9% of stocked and 59.4% of native PIT tagged trouts were detected. Multivariate techniques (CCA, DFA and classification tree) showed a separation in habitat use between the two sympatric populations. Stocked trout mainly used the microhabitats located in the middle of the channel with higher depths and without cover. Furthermore, these fishes displayed a greater mobility and a diel activity pattern different to native trout populations.     

Population size and structure of three mussel species (Bivalvia: Unionidae) in a northeastern German river with special regard to influences of environmental factors

Unionid mussels are of great ecological importance in running and standing waters, however their populations declined continually during the 20th century. In order to collect more data on the situation of these mussels in running waters, the populations of Anodonta anatina, Anodonta cygnea, and Unio tumidus (Unionidae) were investigated in the northeastern German river Ryck from 1996 to 1998. At three sampling stations along the river, the mussel stocks as well as sediment and water properties were analyzed. In this river abundances of up to 138.7 indiv./m² were detected. The average population densities varied from 10.9 to 34.9 indiv./m². More critically however, the age structures showed significant signs of irregular reproductive success and overaging. Consequently, the mussel stocks are going to decline, and furthermore, U.tumidus should be listed as an endangered species in the Ryck river. Negative influences on bivalves can be expected from sporadically occurring low oxygen and high ion concentrations in the water. But after all, the conditions within the sediments seem to be decisive for the survival of juvenile mussels and thus for the age structure of the populations.