An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Fast protein sequencing of monoclonal antibody by real-time digestion on emitter during nanoelectrospray

Growth in the pharmaceutical industry has led to an increasing demand for rapid characterization of therapeutic monoclonal antibodies. The current methods for antibody sequence confirmation (e.g., N-terminal Edman sequencing and traditional peptide mapping methods) are not sufficient; thus, we developed a fast method for sequencing recombinant monoclonal antibodies using a novel digestion-on-emitter technology. Using this method, a monoclonal antibody can be denatured, reduced, digested, and sequenced in less than an hour. High throughput and satisfactory protein sequence coverage were achieved by using a non-specific protease from Aspergillus saitoi, protease XIII, to digest the denatured and reduced monoclonal antibody on an electrospray emitter, while electrospray high voltage was applied to the digestion mixture through the emitter. Tandem mass spectrometry data was acquired over the course of enzyme digestion, generating similar information compared to standard peptide mapping experiments in much less time. We demonstrated that this fast protein sequencing method provided sufficient sequence information for bovine serum albumin and two commercially available monoclonal antibodies, mouse IgG1 MOPC21 and humanized IgG1 NISTmAb. For two monoclonal antibodies, we obtained sequence coverage of 90.5–95.1% for the heavy chains and 98.6–99.1% for the light chains. We found that on-emitter digestion by protease XIII generated peptides of various lengths during the digestion process, which was critical for achieving sufficient sequence coverage. Moreover, we discovered that the enzyme-to-substrate ratio was an important parameter that affects protein sequence coverage. Due to its highly automatable and efficient design, our method offers a major advantage over N-terminal Edman sequencing and traditional peptide mapping methods in the identification of protein sequence, and is capable of meeting an ever-increasing demand for monoclonal antibody sequence confirmation in the biopharmaceutical industry.     

基于地理探测器的宁夏贺兰山植被覆盖度时空分异及驱动因子

监测区域植被覆盖变化并分析其驱动因子,有利于实现生态环境的可持续发展。本研究以1989—2021年Landsat 5/8遥感影像为数据源,利用像元二分模型获取宁夏贺兰山植被覆盖度,基于地理探测器量化了环境和人为等10个因子对其时空分布的影响。结果表明: 1989—2021年间,宁夏贺兰山平均植被覆盖度为35.8%,时间尺度上总体呈增加趋势,平均增幅为0.043·(10 a)^-1,空间尺度上呈现从西南向东北递减的分布特征;研究区58.1%的区域植被覆盖度未来将持续性改善,但仍有30.7%的植被存在退化的潜在风险。降水是影响植被分布的主要环境因子,与单因子相比,环境因子和人为因子的交互作用对植被覆盖度的解释力更强,降水与其他因子的交互作用处于主导作用。     

宁夏东部风沙区沙化草地土壤水分和植被的空间特征

土壤水分作为土壤-植被-大气连续体的关键因子,对沙化草地的演化过程具有重要作用。为探讨宁夏东部风沙区沙化草地土壤水分、物种丰富度指数及植被盖度的空间变异及其相互关系,以哈巴湖自然保护区沙化草地为对象,采用样线法自潜在沙化草地至重度沙化草地进行植被调查和土壤取样,通过经典统计学和地统计学分析,得出以下结果：0—100 m各土层土壤水分含量、植被盖度和物种丰富度指数的分布范围分别为0.82%—28.22%、41.00%—93.00%和0.82—2.80,变异系数范围为0.20—0.48,均属于中等变异。各土层土壤水分和物种丰富度指数表现为中等的空间自相关性,植被盖度则表现为强烈的空间自相关性。Kriging插值结果表明,0—100 cm各土层土壤水分和植被盖度的空间插值图呈条带状和斑块状的梯度变化,物种丰富度呈斑块分布,自潜在沙化草地至重度沙化草地,表现为逐渐降低的趋势。相关分析表明,植被盖度与0—40 cm各土层土壤水分呈显著正相关,与40—100 cm各土层土壤水分呈极显著正相关。宁夏东部风沙区沙化草地土壤水分含量总体较低,由于结构因素和随机因素的共同作用,随草地沙化程度的加重,表现为...     

近20年来京津冀地区土壤风蚀扬尘颗粒物排放变化

京津冀地区是我国大气污染严重区域,土壤扬尘颗粒物排放变化研究对于改善京津冀地区空气质量具有重要意义。收集2000-2019年京津冀地区气候、土壤、植被覆盖数据,分析近20年来京津冀地区土壤扬尘颗粒物排放变化,揭示其变化的影响因素。结果显示2000-2019年京津冀地区土壤扬尘源总悬浮颗粒物（TSP）排放系数均值为1.79 t km^-2 a^-1,其中PM10占8.99%,PM2.5占0.25%。近20年土壤扬尘源TSP排放系数具有下降趋势,PM10和PM2.5排放系数变化过程与TSP一致。上述变化主要受气候因子变化影响,其次受植被覆盖度影响。分析发现近20年来京津冀地区土壤扬尘源TSP排放系数变化主要受年降水量影响。沧州市、天津市和石家庄市土壤扬尘源TSP、PM10和PM2.5排放系数均值较高,张家口市、保定市和沧州市土壤扬尘源TSP排放量占京津冀地区总量的19.18%、12.98%和11.63%。耕地土壤扬尘排放量最大占京津冀地区总量的59.83%,是抑制土壤扬尘源颗粒物排放的重点关注对象,其次为草地占15.66%。2019年邢台市土壤扬尘源PM10排放占观测值比例最高为12.66%,石家庄市和天津市占比也较高分别为11.09%和10.30%,沧州市和邯郸市占比分别为8.63%和8.02%。上述地区环境管理部门均应关注土壤扬尘源颗粒物排放对空气质量的影响。     

植被覆盖度对夏季降温效应的影响——以内蒙古为例

随着全球变暖的加剧,区域热环境问题日益凸显,植被的降温作用逐渐得到广泛关注。目前已有的研究多从样地尺度分析不同类型植被的降温效应。而区域尺度的研究多从定性的角度揭示地表温度与植被覆盖的关系,对评估植被的实际降温效应具有一定的局限性。以内蒙古为研究区,以MODIS地表温度数据为基础,采用近邻分析法,将森林、灌丛和草地的MODIS地表温度与相邻5km范围内的低覆盖地表作为对照,分析植被的降温效应以及植被覆盖度对降温效应的影响。从2015年7月地表温度平均值的结果来看,降温度数在蒙东、蒙中和蒙甘区均呈现森林>灌丛>草地。森林的降温范围在0.67-1.03℃,灌丛为0.60-0.95℃,草地为0.47-0.86℃。植被降温度数与植被覆盖度的回归拟合为对数分布,均呈显著正相关（P<0.01）。且在不同的植被覆盖度范围内植被降温效应具有显著差异,植被覆盖度水平较低时（<40%）,植被覆盖度的增加能更显著地降低地表温度。从整体来看,植被覆盖度每增加10%,森林降温0.12-0.39℃;灌丛降温0.1-0.2℃;草地降温0.049-0.075℃。综上,内蒙古作为全球气候变化最为敏感的区域之一,研究植被的夏季降温效应能够为内蒙古的气候调节服务评估提供重要的理论支撑及案例参考。     

库布齐沙漠南缘风沙-植被相互作用及其景观效应

干旱区尤其沙漠边缘地区的风沙与植被相互作用对塑造地表景观具有重要意义。选择库布齐沙漠南缘的油蒿灌丛地为研究区,开展了植被调查、风沙流观测和表层沉积物粒度采样测试,分析了顺风向植被盖度、风沙流结构与沉积物特征的沿程变化,探讨了风沙-植被相互作用及其对地表景观格局的影响。结果表明,风沙流与植被相互作用方式的改变使植物生长状况与地表蚀积模式发生变化,进而导致顺风向景观表现出明显的空间异质性。自上风向裸地过渡到均匀分布的新生油蒿和油蒿灌丛再至斑块状分布的灌丛沙堆,植被盖度与覆沙厚度先增大后减小,空气动力学粗糙度沿程不断增加且在过渡时其增幅最大,输沙率与沉积物粒度呈先减小后增大趋势,并在植被盖度与覆沙厚度最大处出现最小值。在沙漠边缘剥蚀高原上,起初适量风沙堆积促进油蒿定植与生长,均匀分布的油蒿灌丛进一步促进沙物质堆积,但当堆积厚度超过油蒿耐沙埋深度时发生退化,灌丛出现斑块状分布且风沙流在丘间地处侵蚀。据此,可理解为剥蚀高原风沙区景观异质性是风沙与植被相互协同与抑制作用的结果。     

青海祁连瑞香狼毒的光谱差异特征提取

瑞香狼毒是分布在青海省高寒草甸的主要毒害草之一,近年来其迅速蔓延对当地畜牧业危害严重并使草地生态系统日趋退化.在海北州祁连县选取狼毒分布的典型退化草甸,采用2012—2014年狼毒盛花期获取的实测光谱数据,分析狼毒与牧草的光谱差异性.结果表明： 在350~900 nm的可见光 近红外波段,狼毒顶花的光谱反射特征明显异于狼毒叶片和同期牧草等绿色背景,顶花与绿色背景的光谱反射率差异主要体现在红谷和蓝谷.随着盖度的增加,狼毒群落光谱反射率整体升高,在近红外反射峰处狼毒群落与牧草群落光谱反射率具有最大差值,且不同盖度狼毒群落之间的差异性最明显.顶花与绿色背景以及狼毒群落与牧草群落的一阶导数光谱差异均体现在黄边幅值和蓝边幅值.狼毒群落盖度与光谱特征参量的线性回归分析表明,红谷与狼毒群落盖度的相关性最好(R²=0.94),反演狼毒群落盖度的精度最高.盛花期区分狼毒与牧草的主要光谱特征参量为红谷、蓝谷与近红外反射峰,其对应的红、蓝及近红外波段的组合可用于构建狼毒提取的敏感指数.     

松嫩平原农业区土壤理化性质与真菌代谢产物——球囊霉素相关土壤蛋白的关系

对不同土壤深度的真菌特征代谢产物球囊霉素相关土壤蛋白(glomalin-related soil protein,GRSP)与土壤理化性质相关关系的研究,有助于揭示土壤真菌在不同土壤深度对养分的调节作用。本研究在松嫩平原农田5个土层(0~100 cm)采集360个土样,分析了易提取球囊霉素相关土壤蛋白(EE-GRSP)、总提取球囊霉素相关土壤蛋白(T-GRSP)含量和11个土壤理化性质指标及其相关关系。结果表明:表层EE-GRSP和T-GRSP平均含量为0.74和6.0 mg·g-1,随土层加深均呈显著下降趋势;深层土壤养分储量较大,有机碳、全氮、全磷、全钾、碱解氮、速效磷和速效钾储量在深层(40~100 cm)占总储量的41.2%~62.8%;土壤p H、容重、含水量和电导率也表现了明显的垂直变化规律;各理化性质在不同土层与GRSP的相关关系不同,有机碳在全部深度与GRSP均有显著的相关关系,而p H与GRSP均在20~100 cm深度有极显著的相关性(P0.01),且与EE-GRSP、T-GRSP显著相关的理化性质指标分别在60~80、20~60 cm最多,在表层最少;GRSP在深层土壤与各指标的相关性与表层不同,可能会影响GRSP对不同土壤深度养分的调节功能;鉴于深层土壤中GRSP与养分显著相关,本研究提出,种植与土壤真菌具有共生关系的深根性植物是对富集养分的深层土壤进行生物修复的有效方法。