Revisiting the evolutionary history of pigs via de novo mutation rate estimation by deep genome sequencing on a three-generation pedigree

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and brought potential bias in inferring the evolutionary history of pig, an essential domesticated agricultural animal. Herein, we estimated de novo mutation rate of pigs using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. The estimated mutation rate was 3.6 × 10−9 per site per generation, corresponding to 1.2 × 10−9 per site per year. Using this mutation rate, we re-investigated the evolutionary history of pigs. Our estimates agreed to the divergence time of ~10 kiloyears ago (Kya) between European wild and domesticated pigs, which was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggested that: Sus speciation occurred ~1.36 Million years ago (Mya); European pigs split up with Asian ones only around 219 Kya; South and North Chinese wild boars split about 25 Kya. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, North China, approximately 20 Kya, supporting the possibly independent domestication in North China along the middle Yellow River. We also found the maximum effective population size of pigs was ~6 times larger than the previous estimate. Notably by simulation, we confirmed an archaic migration from other Sus species originating ~2 Mya to European pigs during western colonization of pigs, which possibly interfered with the previous demographic inference. Our findings advance the understanding of pig evolutionary history.

A Study on Water and Salt Transport, and Balance Analysis in Sand Dune–Wasteland–Lake Systems of Hetao Oases, Upper Reaches of the Yellow River Basin

Desert oases are important parts of maintaining ecohydrology. However, irrigation water diverted from the Yellow River carries a large amount of salt into the desert oases in the Hetao plain. It is of the utmost importance to determine the characteristics of water and salt transport. Research was carried out in the Hetao plain of Inner Mongolia. Three methods, i.e., water-table fluctuation (WTF), soil hydrodynamics, and solute dynamics, were combined to build a water and salt balance model to reveal the relationship of water and salt transport in sand dune–wasteland–lake systems. Results showed that groundwater level had a typical seasonal-fluctuation pattern, and the groundwater transport direction in the sand dune–wasteland–lake system changed during different periods. During the crop-growth period (5 May–27 October), the average evapotranspiration values of the sand dune, wasteland–sand dune junction, and wasteland were 31–42% of the reference evapotranspiration. The water consumption of sand dune was 1.95 times that of the wasteland–sand dune junction, and 1.88 times that of wasteland. Water loss of the lake was 761.25–869.05 mm (5 May–27 October). The lake is facing the risk of drying up. The vertical salt transport of groundwater at the sand-dune site was 1.13 times that at the wasteland–sand dune junction site, and 1.82 times that at the wasteland site. Of the groundwater salt of the sand dune, 54% was accumulated in the groundwater of the wasteland–sand dune junction. Of the groundwater salt of the wasteland–sand dune junction, 53% was accumulated in wasteland groundwater, and the remaining 47% was accumulated in the lake. Salt storage of the 1 m soil layer of the sand dune was 85% that of the wasteland–sand dune junction, and 82% that of the wasteland. Research results provide a theoretical basis for the ecohydrology of the Hetao plain.

Dynamic Monitoring of Surface Water Area during 1989–2019 in the Hetao Plain Using Landsat Data in Google Earth Engine

The spatio-temporal change of the surface water is very important to agricultural, economic, and social development in the Hetao Plain, as well as the structure and function of the ecosystem. To understand the long-term changes of the surface water area in the Hetao Plain, we used all available Landsat images (7534 scenes) and adopted the modified Normalized Difference Water Index (mNDWI), Enhanced Vegetation Index (EVI), and Normalized Difference Vegetation Index (NDVI) to map the open-surface water from 1989 to 2019 in the Google Earth Engine (GEE) cloud platform. We further analyzed precipitation, temperature, and irrigated area, revealing the impact of climate change and human activities on long-term surface water changes. The results show the following. (1) In the last 31 years, the maximum, seasonal, and annual average water body area values in the Hetao Plain have exhibited a downward trend. Meanwhile, the number of maximum, seasonal, and permanent water bodies displayed a significant upward trend. (2) The variation of the surface water area in the Hetao Plain is mainly affected by the maximum water body area, while the variation of the water body number is mainly affected by the number of minimum water bodies. (3) Precipitation has statistically significant positive effects on the water body area and water body number, which has statistically significant negative effects with temperature and irrigation. The findings of this study can be used to help the policy-makers and farmers understand changing water resources and its driving mechanism and provide a reference for water resources management, agricultural irrigation, and ecological protection.

The association of tryptophan and phenylalanine are associated with arsenic-induced skin lesions in a Chinese population chronically exposed to arsenic via drinking water: a case–control study

ObjectivesWe investigated the association of specific serum amino acids (AAs) with the odds of arsenic-induced skin lesions (AISL) and their ability to distinguish patients with AISL from people chronically exposed to arsenic.DesignCase–control study.SettingThree arsenic-exposed villages in Wuyuan County, Hetao Plain, Inner Mongolia, China were evaluated.ParticipantsAmong the 450 residents aged 18–79 years, who were chronically exposed to arsenic via drinking water, 56 were diagnosed as having AISL (defined as cases). Another 56 participants without AISL, matched by gender and age (±1 year) from the same population, were examined as controls.Main outcome measures and methodsAA levels were determined by ultra-high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry-based metabolomics analysis. Potential confounding variables were identified via a standardised questionnaire and clinical examination. Multivariable conditional logistic regression model and receiver operating characteristic curve analyses were performed to investigate the relationship between specific AAs and AISL.ResultsTryptophan and phenylalanine levels were negatively associated with AISL (p<0.05). Compared with that in the first quartile, the adjusted OR of AISL in the second, third and fourth quartiles were decreased by 44%, 88% and 79% for tryptophan and 30%, 80% and 80% for phenylalanine, respectively. The combination of these two higher-level AAs showed the lowest OR for AISL (OR=0.08; 95% CI 0.02 to 0.25; p<0.001). Furthermore, both AAs showed a moderate ability to distinguish patients with AISL from the control, with the area under the curve (AUC; 95% CI) as 0.67 (0.57 to 0.77) for tryptophan and 0.70 (0.60 to 0.80) for phenylalanine (p<0.05). The combined pattern with AUC (95% CI) was 0.72 (0.62 to 0.81), showing a sensitivity of 76.79% and specificity of 58.93% (p<0.001).ConclusionsSpecific AAs may be linked to AISL and play important roles in early AISL identification.Trial Registration numberNCT02235948.

Performance of Winter-Seeded Spring Wheat in Inner Mongolia

Growing spring wheat in Inner Mongolia is challenging because of the short growing period, dry-hot winds, and heat-forced maturity. There are also problems with growing winter wheat varieties, such as frost damage, spring droughts, and “late spring cold”. These factors have restricted efforts to increase yields. In order to address these challenges, this study adopted a “spring wheat winter-sowing” planting model for growing wheat in the Hetao Plain Irrigation District in Inner Mongolia and studied wheat varieties with different vernalization requirements through three consecutive field trials. The effects of different sowing dates were analyzed on seed germination and seedling emergence, growth, material accumulation, and yield formation, and the differences were characterized from traditional spring wheat. The results indicated that delaying the sowing date increased the spring emergence rate of the wheat varieties. The winter-seeded spring wheat germinated and ripened after three and seven days, respectively, earlier than the spring-seeded. The grain yield for the winter-seeded wheat was parallel to the spring-seeded wheat. Compared with the spring-seeded wheat, the winter-seeded wheat displayed less panicles, but greater grains per spike, and a 1000-grain weight. When seeded in winter, Yongliang 4 performed better than Ningdong 11 and Henong 7106 in terms of the emergence rate, material accumulation, and grain yield. The best seeding time for the winter-seeded spring wheat in the Hetao Irrigation District of Inner Mongolia is early November.