Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

The Notch ankyrin domain is a repeat protein whose folding has been characterized through equilibrium and kinetic measurements. In previous work, equilibrium folding free energies of truncated constructs were used to generate an experimentally determined folding energy landscape (Mello and Barrick, Proc Natl Acad Sci USA 2004;101:14102–14107). Here, this folding energy landscape is used to parameterize a kinetic model in which local transition probabilities between partly folded states are based on energy values from the landscape. The landscape‐based model correctly predicts highly diverse experimentally determined folding kinetics of the Notch ankyrin domain and sequence variants. These predictions include monophasic folding and biphasic unfolding, curvature in the unfolding limb of the chevron plot, population of a transient unfolding intermediate, relative folding rates of 19 variants spanning three orders of magnitude, and a change in the folding pathway that results from C‐terminal stabilization. These findings indicate that the folding pathway(s) of the Notch ankyrin domain are thermodynamically selected: the primary determinants of kinetic behavior can be simply deduced from the local stability of individual repeats.     

Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula

To examine the generality of population-level impacts of ancient vicariance identified for numerous arid-adapted animal taxa along the Baja peninsula, we tested phylogeographical hypotheses in a similarly distributed desert plant, Euphorbia lomelii (Euphorbiaceae). In light of fossil data indicating marked changes in the distributions of Baja floristic assemblages throughout the Holocene and earlier, we also examined evidence for range expansion over more recent temporal scales. Two classes of complementary analytical approaches — hypothesis-testing and hypothesis-generating — were used to exploit phylogeographical signal from chloroplast DNA sequence data and genotypic data from six codominant nuclear intron markers. Sequence data are consistent with a scenario of mid-peninsular vicariance originating c. 1 million years ago (Ma). Alternative vicariance scenarios representing earlier splitting events inferred for some animals (e.g. Isthmus of La Paz inundation, c. 3 Ma; Sea of Cortez formation, c. 5 Ma) were rejected. Nested clade phylo-geographical analysis corroborated coalescent simulation-based inferences. Nuclear markers broadened the temporal spectrum over which phylogeographical scenarios could be addressed, and provided strong evidence for recent range expansions along the north–south axis of the Baja peninsula. In contrast to previous plant studies in this region, however, the expansions do not appear to have been in a strictly northward direction. These findings contribute to a growing appreciation of the complexity of organismal responses to past climatic and geological changes — even when taxa have evolved in the same landscape context.     

Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense)

A major goal of landscape genetics is to understand how landscapes structure genetic variation in natural populations. However, landscape genetics still lacks a framework for quantifying the effects of landscape features, such as habitat type, on realized gene flow. Here, we present a methodology for identifying the costs of dispersal through different habitats for the California tiger salamander ( Ambystoma californiense ), an endangered species restricted to grassland/vernal pool habitat mosaics. We sampled larvae from all 16 breeding ponds in a geographically restricted area of vernal pool habitat at the Fort Ord Natural Reserve, Monterey County, California. We estimated between-pond gene flow using 13 polymorphic microsatellite loci and constructed GIS data layers of habitat types in our study area. We then used least-cost path analysis to determine the relative costs of movement through each habitat that best match rates of gene flow measured by our genetic data. We identified four measurable rates of gene flow between pairs of ponds, with between 10.5% and 19.9% of larvae having immigrant ancestry. Although A. californiense is typically associated with breeding ponds in grassland habitat, we found that dispersal through grassland is nearly twice as costly as dispersal through chaparral and that oak woodland is by far the most costly habitat to traverse. With the increasing availability of molecular resources and GIS data, we anticipate that these methods could be applied to a broad range of study systems, particularly those with cryptic life histories that make direct observation of movement challenging.     

干旱区不同景观单元土壤盐分的变化特征

针对内陆河流域空间土壤盐渍化问题,以新疆三工河流域为例,通过调查、取样分析,研究了冲洪积扇和冲洪积平原2个水文地质带上一个生长季5-10月0～10、10～20cm土壤盐分积聚特征及其主导因素.结果表明:冲洪积扇土壤盐分含量明显低于冲洪积平原,盐分含量的变异系数均>100%,属于强变异性;灌溉景观土壤盐分的聚积在冲洪积扇和冲洪积平原相似,盐分含量均减小,而非灌溉景观的差异较大,冲洪积扇区土壤盐分含量减小,土壤盐渍化程度减弱;而冲洪积平原区土壤盐分含量升高,盐渍化程度增强.冲洪积扇区土层间盐分变化关系紧密相关(P<0.01),降雨和灌溉对盐分都具有淋洗作用,促进了盐分含量的减少;冲洪积平原区,蒸发对非灌溉景观0～10 cm土层盐分聚积起到促进作用,而10～20 cm土层盐分聚积受上层土壤盐分和地下水位共同作用.

Abstract：

Aiming at the problem of soil salinization in inland river basin, a case study was con-ducted in the Sangong River catchment of Xinjiang, China. The characteristics and dominant af-fecting factors of salt accumulation in 0-10 cm and 10-20 cm soil layers in two hydro-geological zones, i. e. , alluvial-proluvial delta and alluvial plain, were studied in a growth season (from May to October), and the precipitation, evaporation, groundwater table, and irrigation were also taken into account. The soil salt content was obviously lower in alluvial-proluvial delta than in al-luvial plain, but its coefficient of variation in the two zones was all higher than 100%, indicating a great variability. The soil salt accumulation in irrigated landscape in the two zones had a similar decreasing trend, but that in non-irrigated landscape had greater difference, with a decreased soil salinization in alluvial-proluvial delta, and an increased soil salinization in alluvial plain. In allu-vial-proluvial delta, the salt contents in 0-10 cm and 10-20 cm soil layers had a close relation-ship (P <0. 01), and there was a clear process of salt leaching by precipitation and irrigation, leading to the decrease of soil salt content. In alluvial plain, the salt accumulation in 0-10 cm soil layer in non-irrigated landscape was promoted by evaporation, and that in 10-20 cm soil lay-er was co-affected by the salt content in 0-10 cm soil layer and the groundwater table.     

四川小相岭山系植被景观的斑块特征分析

利用3S技术与景观生态学相结合的方法,分别从斑块的基本特征、形状特征、聚集与散布特征以及多样性特征4个方面对四川小相岭山系的植被景观空间格局进行了详细分析。研究结果表明：1）该山系存在9种植被类型,斑块数为1849,斑块面积约186951hm^2。其中,针阔叶混交林分布面积与密度最大,是山系的基质植被类型;而次生落叶阔叶林面积最少,景观地位最弱。2）常绿落叶阔叶混交林形状最为简单,但聚集度高;而针阔叶混交林形状最不规则,边界最为复杂;另外,次生落叶阔叶林连接性最弱,高山草甸斑块聚集程度最高。3）该山系斑块的多样性、优势度、均匀度指数值分别为1．54、0．66和0．67,植被类型丰富多样、植被错综复杂、各植被斑块间镶嵌度较好。     

Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: a catchment analysis of mitochondrial DNA sequences and nuclear microsatellites

Catchment population structure and divergence patterns of the rainbow darter Etheostoma caeruleum (Percidae: Teleostei), an eastern North American benthic fish, are tested using a landscape genetics approach. Allelic variation at eight nuclear DNA microsatellite loci and two mitochondrial DNA regions [cytochrome (cyt) b gene and control region; 2056 aligned base pairs (bp)] is analysed from 89 individuals and six sites in the Lake Erie catchment (Blanchard, Chagrin, Cuyahoga and Grand Rivers) v. the Ohio River catchment (Big Darby Creek and Little Miami River). Genetic and geographic patterning is assessed using phylogenetic trees, pair‐wise F_ST analogues, AMOVA partitioning, Mantel regression, Bayesian assignment, 3D factorial correspondence and barrier analyses. Results identify 34 cyt b haplotypes, 22 control region haplotypes and 137 microsatellite alleles whose distributions demonstrate marked genetic divergence between populations from the Lake Erie and Ohio River catchments. Etheostoma caeruleum populations in the Lake Erie and Ohio River catchments diverged c. 1·6 mya during the Pleistocene glaciations. Greater genetic separations characterize the Ohio River populations, reflecting their older habitat age and less recent connectivity. Divergence levels within the Lake Erie catchment denote more recent post‐glacial origins. Notably, the western Lake Erie Blanchard River population markedly differs from the three central basin tributary samples, which are each genetically distinguishable using microsatellites. Overall relationships among the Lake Erie sites refute a genetic isolation by geographic distance hypothesis. Etheostoma caeruleum populations thus exchange few genes and have low migration among tributaries and catchments.     

Local and ecoregion effects on fish assemblage structure in tributaries of the Rio Paraíba do Sul, Brazil

1.  We examined the effects of physical and chemical habitat variables and ecoregions on species occurrence and fish assemblage structure in streams of the Paraíba do Sul basin, in southeast Brazil.
2.  Fish and environmental data were collected from 42 sites on 26 first to fourth order streams (1 : 50 000 map scale) in three ecoregions. The sites occurred in one valley and two plateau ecoregions at altitudes of 40–1080 m and distances of 0.1–188 km from the main channel of the Rio Paraíba do Sul. Physical habitat (substratum, riparian cover, habitat types) and water quality (dissolved oxygen, pH, temperature and conductivity) variables were measured at each sampling site.
3.  A total of 2684 individuals in 16 families and 59 species were recorded.
4.  Ecoregion was a better predictor of the fish assemblage than the other environmental variables, according to the differences between the mean within-class and mean between-class similarities in assemblage data.
5.  Differing landscape characteristics were associated with differing local variables and thereby with differing fish assemblage structures. Riffles, shrub, grass, dissolved oxygen, conductivity and temperature were closely related to fish assemblage structure.
6.  Fish assemblages in sites far from the main river and at higher altitudes also differed from those near the Paraíba do Sul main channel, presumably as a result of differences in connectivity, covarying environmental factors and anthropogenic influence.
7.  These results reinforce the importance of understanding how stream communities are influenced by processes and patterns operating at local and regional scales, which will aid water resource managers to target those factors in their management and rehabilitation efforts.     

A computer program to simulate multilocus genotype data with spatially autocorrelated allele frequencies

Many models for inference of population genetic parameters are based on the assumption that the data set at hand consists of groups displaying within-group Hardy-Weinberg equilibrium at individual loci and linkage equilibrium between loci. This assumption is commonly violated by the presence of within-group spatial structure arising from nonrandom mating of individuals due to isolation by distance (IBD). This paper proposes a model and simulation method implemented in a computer program to flexibly simulate data displaying such patterns. The program permits displaying of smooth spatial variations of allele frequencies due to IBD and more abrupt variations due to presence of strong barriers to gene flow. It is useful in assessing performance of various statistical inference methods and in designing spatial sampling schemes. This is shown by a simulation study aimed at assessing the extent to which IBD patterns affect accuracy of cluster inferences performed in models assuming panmixia. The program is also used to study the effects of spatial sampling scheme (e.g. sampling individuals in clumps or uniformly across the spatial domain). The accuracy of such inferences is assessed in terms of number of inferred populations, assignment of individuals to populations and location of borders between populations. The effect of spatial sampling was weak while the effect of IBD may be substantial, leading to the inference of spurious populations, especially when IBD was strong with respect to the size of the sampling domain. The model and program are new and have been embedded in the R package Geneland, for user convenience and compliance with existing data formats.     

Biomass and seed yields of big bluestem, switchgrass, and intermediate wheatgrass in response to manure and harvest timing at two topographic positions

A principle attribute of perennial grasses for biomass energy is the potential for high yields on marginal lands. Objectives of this study were to compare biomass and seed production of intermediate wheatgrass ( Thinopyrum intermedium [Host] Barkworth and D.R. Dewey), big bluestem ( Andropogon gerardii Vitman), and switchgrass ( Panicum virgatum L.) as affected by harvest timing and manure application on two topographic positions (footslope and backslope). Footslope is the hillslope position that forms the inclined surface at the base of a slope and backslope forms the steepest, middle position of the hillslope. Grasses were harvested for biomass at anthesis (summer), after a killing frost (autumn), or the following spring after overwintering in the field. Seed was harvested at maturity during 2003 and 2004. Two rates of beef cattle ( Bos taurus L.) manure (target rates of 0 and 150 kg total-N ha⁻¹) were surface applied annually. Maximum annual biomass yield ranged from 4.4 to 5.2, 2.7 to 4.2, and 3.7 to 5.6 Mg ha⁻¹ for intermediate wheatgrass, big bluestem, and switchgrass, respectively. Biomass yields were not different between fall and spring harvest treatments. Biomass yields of big bluestem and switchgrass at the backslope position were 86% and 96% of biomass yields at the footslope position with normal precipitation, respectively. Manure application increased biomass yield approximately 30% during the second year on both topographic positions. The highest seed yield was obtained from intermediate wheatgrass, followed by switchgrass and big bluestem. Utilizing these management practices in our environment, it appears that switchgrass and big bluestem could be allowed to overwinter in the field without suffering appreciable loss of biomass.     

Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog, Atelopus varius

Aim Understanding how heterogeneous landscapes shape genetic structure not only sheds light on processes involved in population divergence and speciation, but can also guide management strategies to promote and maintain genetic connectivity of populations of endangered species. This study aimed to (1) identify barriers and corridors for gene flow among populations of the endangered frog, Atelopus varius and (2) assess the relative contributions of alternative landscape factors to patterns of genetic variation among these populations in a hypothesis testing framework. Location This study took place in western Panama and included all nine of the remaining known populations of A. varius at the time of study. Methods The influence of landscape variables on gene flow among populations was examined by testing for correlations between alternative landscape‐resistance scenarios and genetic distance. Fifteen alternative hypotheses about the influence of (1) riparian habitat corridors, (2) steep slopes, and (3) climatic suitability on patterns of genetic structure were tested in a causal modelling framework, using Mantel and partial‐Mantel tests, along with an analysis of molecular variation. Results Only the hypothesis attributing resistance to dispersal across steep slopes (genetic isolation by slope distance) was fully supported by the causal modelling approach. However, the analysis of molecular variance and the paths of least‐slope among populations suggest that riparian habitat connectivity may influence genetic structure as well. Main conclusions These results suggest that patterns of genetic variation among A. varius populations are affected by the slope of the landscape such that areas with steep slopes act as barriers to gene flow. In contrast, areas of low slope, such as streams and mountain ridges, appear to be important corridors for gene flow, especially among high elevation populations. These results engender important considerations for the management of this critically endangered species.