Spatial metrics for detecting ecosystem degradation in the ridge-slough patterned landscape

Indicators of landscape condition should be selected based on their sensitivity to environmental changes and their capacity to provide early warning detection of those changes. We assessed the performance of a suite of spatial-pattern metrics selected to quantify the condition of the ridge-slough landscape in the Everglades (South Florida, USA). Spatial pattern metrics (n = 14) that describe landscape composition, geometry and hydrologic connectivity were enumerated from vegetation maps of twenty-five 2 × 2 km primary sampling units (PSUs) that span a gradient of hydrologic and ecological condition across the greater Everglades ecosystem. Metrics were assessed in comparison with field measurements from each PSU of landscape condition obtained from regional surveys of soil elevation, which have previously been shown to capture dramatic differences between conserved and degraded locations. Elevation-based measures of landscape condition included soil elevation bi-modality (BI_SE), a binary measure of landscape condition, and also the standard deviation of soil elevation (SD_SE), a continuous measure of condition. Metric performance was assessed based on the strength (sensitivity) and shape (leading vs. lagging) of the relationship between spatial pattern metrics and these elevation-based measures. We observed significant logistic regression slopes with BI_SE for only 4 metrics (slough width, ridge density, directional connectivity index – DCI, and least flow cost – LFC). More significant relationships (n = 8 metrics) were observed with SD_SE, with the strongest associations for slough density, mean ridge width, and the average length of straight flow, as well as for a suite of hydrologic connectivity metrics (DCI, LFC and landscape discharge competence – LDC). Leading vs. lagging performance, inferred from the curvature of the association obtained from the exponent of fitted power functions, suggest that only DCI was a leading metric of the loss of soil elevation variation; most metrics were indeterminate, though some were clearly lagging. Our findings support the contention that soil elevation changes from altered peat accretion dynamics precede changes in landscape pattern, and offer insights that will enable efficient monitoring of the ridge-slough landscape as part of the ongoing Everglades restoration effort.     

A testis‐specific gene within a widely expressed gene: Contrasting evolutionary patterns of two differentially expressed mammalian proteins encoded by a single gene,CAMK4

Understanding the patterns of genetic variations within fertility‐related genes and the evolutionary forces that shape such variations is crucial in predicting the fitness landscapes of subsequent generations. This study reports distinct evolutionary features of two differentially expressed mammalian proteins [CaMKIV (Ca²⁺/calmodulin‐dependent protein kinase IV) and CaS (calspermin)] that are encoded by a single gene, CAMK4. The multifunctional CaMKIV, which is expressed in multiple tissues including testis and ovary, is evolving at a relatively low rate (0.46–0.64 × 10^?9 nucleotide substitutions/site/year), whereas the testis‐specific CaS gene, which is predominantly expressed in post‐meiotic cells, evolves at least three to four times faster (1.48–1.98 × 10^?9 substitutions/site/year). Concomitantly, maximum‐likelihood‐based selection analyses revealed that the ubiquitously expressed CaMKIV is constrained by intense purifying selection and, therefore, remained functionally highly conserved throughout the mammalian evolution, whereas the testis‐specific CaS gene is under strong positive selection. The substitution rates of different mammalian lineages within both genes are positively correlated with GC content, indicating the possible influence of GC‐biased gene conversion on the estimated substitution rates. The observation of such unusually high GC content of the CaS gene (≈74%), particularly in the lineage that comprises the bovine species, suggests the possible role of GC‐biased gene conversion in the evolution of CaS that mimics positive selection.     

Identification of soil quality indicators for assessing the effect of different tillage practices through a soil quality index in a semi-arid environment

Tillage is known to potentially affect soil quality in various ways. In this study, a soil quality index (SQI) was developed by quantifying several soil attributes either sensitive or insensitive to physical disturbance, using factor analysis as a dimension reduction technique, in order to discriminate different tillage systems. Soil properties including physical (MWD), chemical (pH, organic C, total N, available P and POM contents) and microbial (MBC, MBN, PCM, PNM and three enzymes) parameters were measured to establish a minimum data set (MDS) for the assessment of overall SQI. The soil attributes were determined on samples (0–20 cm depth) collected under moldboard (MP) and disk (DP) plows as conventional tillage (CT), and rotary (RP) and chisel (CP) plows as reduced tillage (RT) systems with a similar plant C input rate and cover crop over a period of six years (2005–2011) in a semi-arid calcareous soil (Calcixerepts) from Central Iran. Results indicated a clear difference in soil quality among the tillage systems with a significant increase of SQI under RT over time, particularly under CP practices. Although RT improved most soil microbial attributes, not all attributes contributed to SQI because of their close interrelationship. The final SQI consisted only of geometric mean of microbial activity (GMA, the square root of the product of PCM and PNM) and geometric mean of enzyme activity (GME, the cube root of the product of enzyme activities). Soil GME and GMA were found to be as key indicators contributing 55% and 36% to SQI, respectively. Therefore, the GME and GMA were the most important indicators effectively discriminating tillage systems, and could be used to monitor the enhancement of soil quality under RT in this semiarid environment. The influence of tillage year on SQI was greater than that of tillage practices. In conclusion, RT systems were characterized by a higher value of SQI, suggesting a good recovery of soil capacity and functions after abandoning CT in the studied area. Smallholder farmers should therefore be aware of the potential for high soil quality in future as a result of continuing RT systems, especially with surface tillage using CP practices.     

Energy budgeting and emergy synthesis of rainfed maize–wheat rotation system with different soil amendment applications

Soil is a non-renewable resource and its preservation is essential for food security, ecosystem services and our sustainable future. Simultaneously, it is a major challenge to substitute non-renewable fossil based resources with renewable resources to reduce environmental load. In order to check soil erosion vis-a-vis degradation of sloppy lands of rainfed maize–wheat rotation system, fertilization with organic manure supplemented with inorganic fertilizers is required. In order to address these issues, substitution of 50% NPK through four organic manures viz. farmyard manure (FYM), vermicompost (VC), poultry manure (PM) and in situ green manuring (GM) of sunnhemp (Crotalaria juncea L.) were evaluated against 100% NPK through inorganic fertilizers and through FYM for energy budgeting and emergy synthesis during 2009–2014. Integrated use of FYM along with 50% NPK fertilizers could maintain the highest energy ratio (7.3), human energy profitability (142.4), energy productivity (0.22 kg MJ⁻¹), and energy profitability (6.3 MJ ha⁻¹) over other treatments. However, GM and inorganic fertilizers on equal NPK basis maintained the highest energy intensiveness (24.61 MJ US $⁻¹) and exhibited higher emergy yield ratio (2.66) and lower emergy investment ratio (0.60) and environmental loading ratio (3.74) which resulted into higher environmental sustainability index (0.71) over other treatments. Fertilization with organic manure (FYM) alone could not compete with other fertilized options to energy budgeting and emergy synthesis except specific energy. The study demonstrated that innovative integrated nutrient management of chemical fertilizers and organic manures particularly FYM for energy budgeting and GM for emergy synthesis may be considered as feasible and environment-friendly options for soil conservation, thereby benefiting a 50% saving on costly chemical fertilizers in non-OPEC countries which import most of its phosphorus and potassium fertilizers.     

Alpine vascular plant species richness: the importance of daily maximum temperature and pH

Species richness in the alpine zone varies dramatically when communities are compared. We explored (i) which stress and disturbance factors were highly correlated with species richness, (ii) whether the intermediate stress hypothesis (ISH) and the intermediate disturbance hypothesis (IDH) can be applied to alpine ecosystems, and (iii) whether standing crop can be used as an easily measurable surrogate for causal factors determining species richness in the alpine zone. Species numbers and standing crop were determined in 14 alpine plant communities in the Swiss Alps. To quantify the stress and disturbance factors in each community, air temperature, relative air humidity, wind speed, global radiation, UV-B radiation, length of the growing season, soil suction, pH, main soil nutrients, waterlogging, soil movement, number of avalanches, level of denudation, winter dieback, herbivory, wind damage, and days with frost were measured or observed. The present study revealed that 82% of the variance in␣vascular species richness among sites could be explained by just two abiotic factors, daily maximum temperature and soil pH. Daily maximum temperature and pH affect species richness both directly and via their effects on other environmental variables. Some stress and disturbance factors were related to species richness in a monotonic way, others in an unimodal way. Monotonic relationships suggest that the harsher the environment is, the fewer species can survive in such habitats. In cases of unimodal relationships (ISH and IDH) species richness decreases at both ends of the gradients due to the harsh environment and/or the interaction of other environmental factors. Competition and disturbance seemed only to play a secondary role in the form of fine-tuning species richness in specific communities. Thus, we concluded that neither the ISH nor the IDH can be considered useful conceptual models for the alpine zone. Furthermore, we found that standing crop can be used as an easily measurable surrogate for causal factors determining species richness in the alpine zone, even though there is no direct causality.     

Resprouting in the Mediterranean‐type shrub Erica australis afffected by soil resource availability

Abstract. Soil resource availability may affect plant regeneration by resprouting in disturbed environments directly, by affecting plant growth rates, or indirectly by determining allocation to storage in the resprouting organs. Allocation to storage may be higher in stressful, low resource‐supply soils, but under such conditions plant growth rates may be lower. These factors could act in opposite directions leading to poorly known effects on resprouting. This paper analyses the role played by soil resources in the production and growth of resprouts after removal of above‐ground plant tissues in the Mediterranean shrub Erica australis. At 13 sites, differing in substrate, we cut the base of the stems of six plants of E. australis and allowed them to resprout and grow for two years. Soils were chemically analysed and plant water potential measured during the summer at all sites to characterize soil resource availability. We used stepwise regression analysis to determine the relationships between the resprouting response [mean site values of the number of resprouts (RN), maximum length (RML) and biomass (RB)] and soil nutrient content and plant water potential at each site. During the first two years of resprouting there were statistically significant differences among sites in the variables characterizing the resprouting response. RML was always different among sites and had little relationship with lignotuber area. RN was less different among sites and was always positively correlated with lignotuber area. RB was different among sites after the two years of growth. During the first months of resprouting, RN and RML were highly and positively related to the water status of the plant during summer. At later dates soil fertility variables came into play, explaining significant amounts of variance of the resprouting variables. Soil extractable cations content was the main variable accounting for RML and RB. Our results indicate that resprout growth of E. australis is positively affected by high water availability at the beginning of the resprouting response and negatively so by high soil extractable cation content at later periods. Some of these factors had previously shown to be related, with an opposite sign, to the development of a relatively larger lignotuber. Indeed, RML and RB measured in the second year of resprouting were significantly and negatively correlated with some indices of biomass allocation to the lignotuber at each site. This indicates that sites favouring allocation to the resprouting organ may not favour resprout growth.     

Functional Diversity and Evolution of the Drosophila Sperm Proteome

Spermatozoa are central to fertilization and the evolutionary fitness of sexually reproducing organisms. As such, a deeper understanding of sperm proteomes (and associated reproductive tissues) has proven critical to the advancement of the fields of sexual selection and reproductive biology. Due to their extraordinary complexity, proteome depth-of-coverage is dependent on advancements in technology and related bioinformatics, both of which have made significant advancements in the decade since the last Drosophila sperm proteome was published. Here, we provide an updated version of the Drosophila melanogaster sperm proteome (DmSP3) using improved separation and detection methods and an updated genome annotation. Combined with previous versions of the sperm proteome, the DmSP3 contains a total of 3176 proteins, and we provide the first label-free quantitation of the sperm proteome for 2125 proteins. The top 20 most abundant proteins included the structural elements α- and β-tubulins and sperm leucyl-aminopeptidases. Both gene content and protein abundance were significantly reduced on the X chromosome, consistent with prior genomic studies of X chromosome evolution. We identified 9 of the 16 Y-linked proteins, including known testis-specific male fertility factors. We also identified almost one-half of known Drosophila ribosomal proteins in the DmSP3. The role of this subset of ribosomal proteins in sperm is unknown. Surprisingly, our expanded sperm proteome also identified 122 seminal fluid proteins (Sfps), proteins originally identified in the accessory glands. We show that a significant fraction of ‘sperm-associated Sfps’ are recalcitrant to concentrated salt and detergent treatments, suggesting this subclass of Sfps are expressed in testes and may have additional functions in sperm, per se. Overall, our results add to a growing landscape of both sperm and seminal fluid protein biology and in particular provides quantitative evidence at the protein level for prior findings supporting the meiotic sex-chromosome inactivation model for male-specific gene and X chromosome evolution.