Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.     

Impact of soil types on sugarcane development monitored over time by remote sensing

Soil is one of the most important factors for agricultural production. In tropical regions, soil variability is considerable, with the most diverse combinations of physical and chemical characteristics, an influence factor in crop growth and productivity. In this research, the main objective was to identify how soil characteristics and parent material can influence sugarcane development over time using remote sensing. An area located in Sao Paulo, Brazil, of 182 ha (one point per ha with soil analysis), with high variability in the parent material and soil types, was selected. Images from the Sentinel2-MSI satellite were used to describe the spectral behavior of sugarcane over a period of one year. The NDRE (normalized difference red-edge index) was calculated for each image and then the leaf area index (LAI) was obtained from it. Maps of soil classes, soil properties at two depths (0–0.20 and 0.80–1.0 m), and parent material classes were related to sugarcane LAI variability over time. Production environment zones, which is a classification based on soil characteristics to support sugarcane development, were also obtained and related to LAI variability. Spectral signatures of the crop presented different behaviors through the season, soil types and soil attributes provided useful responses for this variability. At the beginning of the season, the surface and subsurface soil properties (texture and fertility) impacted differently on crop development. On the other hand, soil classes and parent material influenced LAI in all production environments studied. The results indicated that the soil types and their properties at different depths have a significant impact on sugarcane development. Furthermore, RS was able to monitor the plant evolution and be related to soil types which may assist in plant management. The results can bring light on how better sugarcane management can be conducted using remote sensing data and soils variability.

     

Soil organic carbon stocks in Veracruz State (Mexico) estimated using the 1:250,000 soil database of INEGI: biophysical contributions

Purpose

In this study, we quantified soil organic carbon (SOC) stocks and analyzed their relationship with biophysical factors and soil properties.

Materials and methods

The study region was Veracruz State, located in the eastern part of Mexico, covering an area of 72,410 km². A soil database that contains physicochemical analyses of soil horizons such as carbon concentration data was the source of information used in this study. The database consisted of 163 soil profiles representing 464 genetic horizons. Statistical analysis was used to investigate the effect of each factor (climate, altitude, slope) on SOC stock to 0.50 m depth and to assess differences in the distribution of SOC stock in terms of soil depth (0.0–0.20, 0.20–0.40, 0.40–0.60, 0.60–0.80, 0.80–1.0 m) and land use. In order to compute the spatial distribution of SOC stock to 0.50 m depth based on the soil sampling location, the kriging method was used.

Results and discussion

Results indicated that SOC stock (0.50 m depth) ranged between 0.44 and 41.2 kg C m^?2. Regression analysis showed that SOC stocks (0.50 m depth) are negatively correlated with temperature (r?=??0.38; P?<?0.001) and positively correlated with altitude (r?=?0.40; P?<?0.001) and slope (r?=?0.40; P?<?0.001). In addition, by multiple regression, temperature combined with precipitation explained more SOC stock variations (r?=?0.43; P?<?0.001) than the regression model with precipitation (r?=?0.13; P?=?0.16) alone. Also, slope combined with temperature and precipitation explained more SOC stock variations (r?=?0.46; P?<?0.001) than the regression model with slope alone. Forest lands, grasslands, and croplands have higher SOC stocks in the 0.0–0.20-m soil layer than in deeper layers. On average, forest lands, grasslands, croplands, and other lands (wetland and dunes) had a SOC stock of 13.6, 14.6, 15.1, and 8.5 kg C m^?2 at 1 m depth, respectively. Soil color correlated (?0.25 ≤ r ≤ ?0.89) with SOC content.

Conclusions

Overall, these results indicate the influence of major interactions between biophysical factors and SOC stocks. This research indicated that SOC stock decreased with soil depth, but with slight variations depending on land use. Thus, there remains a need for more SOC data that include an improved distribution of soil sampling points in order to entirely understand the contributions of biophysical factors to SOC stocks in Veracruz State.     

A framework for results‐based management in fisheries

We present a framework for results‐based management (RBM) of commercial fisheries. The core idea of RBM is to reduce micromanagement by delegating management responsibility to resource users. The RBM framework represents an industrial organization approach to co‐management and comprises three defining processes, conducted by three independent “agents”: (i) an “authority” defines specific and measurable and achievable objectives (outcome targets, OTs) for the utilization of fisheries resources, (ii) resource user organizations (termed “operators”) take responsibility for achieving these OTs and provide documentation that (iii) allows independent “auditors” to evaluate the achievement of OTs. Using incentive mechanisms, notably deregulation, RBM grants operators the flexibility to develop and implement innovative and cost‐effective ways to achieve OTs. The feasibility of implementing RBM in five European fisheries was investigated in cooperation with relevant stakeholders through artificial planning processes and computer simulations. The operators involved were enthusiastic, and new management plans were drafted based on the framework. These included socioeconomic OTs in addition to traditional stock objectives, encompassing an ecosystem approach. Several issues are in need of further research to consolidate the approach and prepare the ground for practical implementation, including: the specification of the legal and regulatory framework required to underpin RBM, details of transitional arrangements when shifting towards RBM (including cost‐sharing) and the development of necessary organizational capacity for operators. Initially, we therefore envisage the framework being applied to high‐value single‐species fisheries, with a limited number of participants, which are adequately represented by a competent organization.     

Oxidative stress and antioxidant responses in juvenile Brazilian flounder <Emphasis Type="Italic">Paralichthys orbignyanus</Emphasis> exposed to sublethal levels of nitrite

This study evaluated the effects of short-term exposure to sublethal levels of nitrite on oxidative stress parameters and histology of juvenile Brazilian flounder Paralichthys orbignyanus. An assessment of fish recovery was also performed. Fish were exposed to 0.08 (control), 5.72, 10.43, and 15.27 NO₂-N mg L^?1 for 10 days followed by the same recovery time. Gill, liver, and muscle samples were collected after 1, 5, and 10 days of exposure and after recovery for the measurement of antioxidant capacity against peroxyl radicals (ACAP), glutathione-S-transferase (GST) activity, content of non-protein (NPSH) and protein thiols (PSH), and lipid peroxidation levels by thiobarbituric acid-reactive substances (TBARS) content. Nitrite exposure induced alterations which compromised the overall antioxidant system (reduced ACAP and GST activity) and enhanced oxidative damage in lipids and proteins. Increases in GST activity and NPSH and PSH contents were also demonstrated. The recovery period allowed for resumption of basal levels for all (treatment 5.72 NO₂-N mg L^?1) or some of the evaluated parameters (other treatments). In conclusion, exposure to nitrite concentrations from 5.72 to 15.27 NO₂-N mg L^?1 induced oxidative stress and antioxidant responses in juvenile Brazilian flounder. The 10-day recovery period was sufficient for a complete resumption of basal physiological condition of fish exposed to concentrations of up to 5.72 NO₂-N mg L^?1.     

Intake and ingestive behavior of lambs fed diets containing ammoniated buffel grass hay

This study aimed to evaluate the effect of diets with ammoniated buffel grass hay on the ingestive behavior of feedlot lambs. Thirty-two sheep of no defined breed with an average body weight of 17.7?±?1.8 kg were used. A completely randomized design with four treatments (0, 18, 36, and 54 g/kg dry matter (DM) basis) and eight repetitions was used. Ingestive behavior, rumination, and idle time were similar (P?>?0.05) among the diets containing ammoniated buffel grass hay, with mean values of 294.5, 554.44, and 594.25 min per day, respectively. Regarding the chews, all of the variables resulted in similar behavior (P?>?0.05). The quadratic effect (P?<?0.05) observed for daily intake can be explained based on the amount of DM and neutral detergent fiber (NDF) per meal per rumination. There was no effect of urea levels from the ammoniation (P?>?0.05) on the efficiency of DM and NDF consumption. However, the rumination efficiency of DM and NDF showed a quadratic effect (P?<?0.05). Thus, the use of ammoniated buffel grass hay with urea in lamb diet affects the ingestive behavior by increasing the rumination efficiency, increased intake, and feed utilization.     

Seroprevalence and risk factors for leptospirosis in cattle,sheep, and goats at consorted rearing from the State of Piauí, northeastern Brazil

Leptospirosis is an endemic disease in Latin America, caused by pathogenic bacteria of the genus Leptospira. It is considered one of the main causes responsible for the negative economic impact on global livestock by causing reproductive problems. The research aimed to determine the prevalence of leptospirosis in cattle, sheep, and goats at consorted rearing in the micro-region of Teresina, Piauí state, northeastern Brazil, as well as to identify prevalent serovars and risk factors associated with seroprevalence. Serum samples were analyzed in 336 sheep, 292 goats, and 253 cattle using microscopic agglutination test (MAT). Overall, 378 samples were positive to MAT, with seroprevalence of 42.9%. The prevalences in cattle, sheep, and goats were 50.5, 40.5, and 34.6%, respectively. All herds presented at least one seropositive animal; the Hardjo/Wolffi serovar association was the most common in cattle and Icterohaemorrhagiae in goats and sheep. Beef production (OR?=?4.9), cattle herd over 35 animals (OR?=?4.0), feeding on pasture (OR?=?6.4), weir and/or stream as water source (OR?=?2.1), and no veterinary services (OR?=?2.9) were risk factors for cattle infection. For sheep, intensive management system (OR?=?5.3), suspended slatted facilities (OR?=?2.2), more than 20 sheep in reproductive age (OR?=?1.9), and absence of deworming (OR?=?3.5) were the risk factors, while for goats, the identified risk factors were sheep herd over 52 animals (OR?=?1.9) and no veterinary services (OR?=?1.8). We conclude that the infection was spreading in consorted herds in this region. Thus, it would be interesting and important to conduct educative activities to farmers on the economic impacts of this disease and the need of preventive and control strategies mainly focused on sanitary measures and animal handling.     

Cover Image,Volume 73, Issue 1

The cover image, by Oscar Fernando Santos‐Amaya et al., is based on the Research Article Fitness costs and stability of Cry1Fa resistance in Brazilian populations of Spodoptera frugiperda, DOI: 10.1002/ps.4312 . Photo Credit: Dr. Oscar Santos‐Amaya.