Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either ‘conventional’ estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h²=0.05) and moderate heritability (h²=0.30). GEBV were calculated for different accuracies (r_mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r_g=0.5 to 1.0. For both traits (h²=0.05 and 0.30) and r_mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r_g=0.5), and for highly accurate GEBV for natural service bulls (r_mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.     

Effects of data structure on the estimation of covariance functions to describe genotype by environment interactions in a reaction norm model

Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of environmental parameters and non-random use of sires on expected breeding values and estimated genetic variances across environments. Breeding values were simulated as a linear function of simulated herd effects. The definition of environmental parameters hardly influenced the results. In situations with random use of sires, estimated genetic correlations between the trait expressed in different environments were 0.93, 0.93 and 0.97 while simulated at 0.89 and estimated genetic variances deviated up to 30% from the simulated values. Non random use of sires, poor genetic connectedness and small herd size had a large impact on the estimated covariance functions, expected breeding values and calculated environmental parameters. Estimated genetic correlations between a trait expressed in different environments were biased upwards and breeding values were more biased when genetic connectedness became poorer and herd composition more diverse. The best possible solution at this stage is to use environmental parameters combining large numbers of animals per herd, while losing some information on genotype by environment interaction in the data.     

Rapid evolution and range expansion of an invasive plant are driven by provenance–environment interactions

To improve our ability to prevent and manage biological invasions, we must understand their ecological and evolutionary drivers. We are often able to explain invasions after they happen, but our predictive ability is limited. Here, we show that range expansions of introduced Pinus taeda result from an interaction between genetic provenance and climate and that temperature and precipitation clines predict the invasive performance of particular provenances. Furthermore, we show that genotypes can occupy climate niche spaces different from those observed in their native ranges and, at least in our case, that admixture is not a main driver of invasion. Genotypes respond to climate in distinct ways, and these interactions affect the ability of populations to expand their ranges. While rapid evolution in introduced ranges is a mechanism at later stages of the invasion process, the introduction of adapted genotypes is a key driver of naturalisation of populations of introduced species.     

栖息地环境对种群营养生态位的影响——以黄颡鱼为例

生态位是生态学研究的基础,目前关于环境指标是否直接影响营养生态位的分析研究很少。以高营养级鱼类黄颡鱼为研究对象,利用稳定同位素分析和相关分析,在太湖贡湖湾研究了氨氮、亚硝酸盐氮、硝酸盐氮、总氮、溶解性总氮、溶解性正磷酸盐、总磷、溶解性总磷、叶绿素等多个栖息地水环境因子对鱼类种群营养生态位的影响。结果表明,栖息地水环境对黄颡鱼总营养生态位影响不大,但部分栖息地水环境因子对分项营养生态位(包括浮游、底栖与肉食性)有影响。研究得知,栖息地水环境因子中氨氮、硝酸盐氮、总氮、溶解性总氮及溶解性总磷与浮游食性营养生态位显著正相关,氨氮、硝酸盐氮、总氮、溶解性总氮及溶解性总磷与肉食性营养生态位显著负相关,而底栖食性则主要受溶解性总磷的影响,与其显著正相关。水环境因子的季节变化影响水体中饵料资源的分布,进而影响鱼类的食物组成。     

基于水文地貌法模型的城市湿地水环境功能评估——以南京仙林典型湿地为例

我国正处于快速城市化发展过程中,许多湿地被改造利用成为城市湿地。如何科学评估城市湿地功能及其改变程度,是科学认识城市湿地的重要内容。基于水文地貌法,通过选取区域受城市化影响小、生态系统结构与功能接近于自然湿地的湿地作为参考湿地,利用遥感和GIS的手段以及野外实地调查方法,从湿地水环境功能角度,对南京仙林区域内典型城市湿地的水环境特征与功能进行评估。结果表明:(1)城市湿地水环境功能明显降低,其蓄水功能、净水功能、水文调节功能明显低于参考湿地;(2)受城市化景观复杂性影响,城市湿地水环境功能的改变程度呈现个性化特征,纪家边、采月湖和西湖西这3个湿地可以作为城市化过程中湿地改造的典范。这一结论可为城市化区域内湿地的合理开发利用以及湿地的保护、恢复提供科学依据。     

基于综合生物标志物响应指数法评估近岸海洋环境压力——以广西西部沿海为例

2011-2012年,在广西西部沿海设置5个站点,以野生文蛤作为指示生物进行3次采样监测.从个体、细胞和分子水平选择了钻沙所需时间、吞噬能力、溶酶体膜稳定性、血浆三价铁还原力、乙酰胆碱酯酶活性及彗星率6项指标,利用综合生物标志物响应指数模型(IBR),整合上述生物标志物指标,并转化为形象直观的星状图,对调查站点的环境状况进行风险评估.结果表明: 各站点的综合生物标志物响应指数值(IBR/n)介于2.30~8.68,茅尾海的环境压力最大,北仑河口最小.虽然不同的生物标志物对污染压力的响应存在差异,但利用IBR可以有效区分文蛤所在区域的环境压力状况.利用生物标志物的监测结果与化学监测结果基本吻合.     

森林景观变化的地理环境因素整合分析——以伊洛河流域洛宁县为例

运用景观生态学的基本原理,借助于地理信息系统技术,整合分析了地理环境因素对伊洛河流域洛宁县森林景观动态变化的影响。结果显示,应用地理环境因素影响指数可以很好地从整体上分析地理环境因素,如高程、坡度、距离居民点中心的距离、与森林边缘距离等地理环境因子对区域森林景观动态变化的影响。1983和1999年,伊洛河流域洛宁县森林景观在地理环境因素影响指数上的优势分布区间(Pie1)分别为1230和1030,即在中高地理环境因素影响指数分布区间内,且有向低地理环境因素影响指数分布区间略为移动的趋势。森林景观类型保持不变部分、森林景观转化为非森林景观类型部分和非森林景观转化为森林景观类型部分所对应的在地理环境因素影响指数上的优势分布区间(Pie1)分别为1130、18和613。通过建立森林景观动态变化与地理环境因素影响指数的相互关系,表明森林景观动态变化与地理环境因素影响指数(特别是在地理环境因素影响指数的优势分布区间内)有显著相关关系。     

Interactions between environmental factors can hide isolation by distance patterns: a case study of Ctenomys rionegrensis in Uruguay

Identifying the factors responsible for the structuring of genetic diversity is of fundamental importance for biodiversity conservation. However, arriving at such understanding is difficult owing to the many factors involved and the potential interactions between them. Here, we present an example of how such interactions can preclude us from arriving at a complete characterization of the demographic history and genetic structure of a species. Ctenomys rionegrensis is a species with restricted dispersal abilities and, as such, should exhibit an isolation by distance (IBD) pattern, which previous studies were unable to uncover. It was therefore concluded that this species underwent a recent population expansion. Using a novel hierarchical Bayesian method, we show that the inability to detect the IBD pattern is due to the interaction between elevation and geographical distance. We posit that populations in low areas suffer periodic floods that may reduce local population sizes, increasing genetic drift, a process that masks the effect of distance on genetic differentiation. Our results do not refute the possibility that the populations of C. rionegrensis underwent a recent population expansion but they indicate that an alternative scenario described by a metapopulation model at or near migration-drift equilibrium cannot be excluded either.     

面向城市热环境格局时空演变的多重分形模式——以郑州市为例

与单分形相比,多重分形模型赋予了更多描述客观世界中复杂现象和事物的参数和手段,为更加准确和精细地刻画自然界中普遍存在的非线性现象和过程提供了一种有效途径。以河南省郑州市为研究对象,选取三期Landsat5-TM影像反演城市地表温度,并采用多重分形的理论与方法定量地探讨和研究城市热环境场纹理结构及其在时空中的分布特征,以及在不同的标度区间内热环境场与NDVI之间的关系。研究结果表明:20年间郑州市热场景观的多重分形谱奇异性指数最大值与最小值之差"α由0.6716减小为0.6419,奇异性指数最小值αmin和最大值αmax分别由1.4644、2.136减小为1.4304和2.0723,背景场奇异值α(fmax)由2.0111减小为2.0083,纹理测度最大值与最小值的分维数f(αmin)和f(αmax)分别由0.2354、1.4877增大为0.3412和1.734,意味着随着近20年经济的发展和城镇化率的提高,研究区域的热场纹理信息量不断减少,结构趋于简单,而纹理测度最大值、最小值和研究区温度有增大的趋势。对于位于郑州市不同位置且由不同景观斑块类型构成的区域,市区区域纹理测度波动幅度最小,而水体区域最大;市区纹理测度最大值和最小值的分维数最大,不同等级纹理像元数量分布比较均匀,空间簇聚程度高,而水体则相反,另从市区样本的多重分形参数来看,新开发的区域比老市区具有更小的αmin值和D2值。区域温度均值与多重分形参数之间呈现较强的线性相关性,而区域标准差与多重分形参数之间的相关性更强,线性变化的顺序依次为水体、农业用地、城郊和市区。另外,还利用C-A(浓度-面积)模型把2011年热场图像纹理结构分割为3个标度不变性区间,在此基础上讨论了奇异性指数α对区域温度与NDVI(归一化植被指数)之间关系的影响,发现斑块边缘的地表温度对NDVI最为敏感,且奇异性指数对不同标度区间的地表温度的本底值贡献是正向的,这些结论对热环境场的尺度转换研究具有一定的参考意义。     

基于多源遥感数据的城市热环境响应与归因分析——以深圳市为例

城市热环境是城市局部气候与环境的综合表现,它与土地利用格局密切相关,但是相应的机制研究还不充分。以深圳市为例,首先基于2018年LANDSAT 8遥感影像,采用支持向量机方法和线性光谱混合模型提取土地利用与覆盖度信息,分析了城市土地覆盖对地表温度以及热量收支状况的影响。基于2003-2018的MODIS地表温度数据,进一步研究了深圳市城市热岛现象的时空变化,从地表能量的角度分析城市热岛变化背后的形成机制。结果表明,深圳市地表温度从西北到东南逐渐降低,城市不透水面温度显著高于植被覆盖区域,城市热岛效应明显。不透水面和城市植被共同影响深圳市的地表温度与热量收支状况,不透水地表与感热具有较好的相关性,城市植被与潜热具有较好的相关性。长时间序列分析表明深圳的城市热岛现象在夏季较高而冬季较低,月均热岛强度为2.14℃;对于年际变化,深圳在2003-2018表现出显著的下降趋势。归因分析显示感热通量的影响在深圳起主导作用,这一模式在全年和季节上都较为明显。结果表明深圳市经过高速扩张阶段,目前发展方向是提高建成区的利用效率,该现象强调了热传输在加强城市热岛效应过程中对近地面湍流的干扰作用。本研究可以为缓解热岛效应与景观格局优化研究提供借鉴。     

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: a case study using molecular approaches

In Middle European suburban environments green algae often cover open surfaces of artificial hard substrates. Microscopy reveals the Apatococcus/Desmococcus morphotype predominant over smaller coccoid forms. Adverse conditions such as limited water availability connected with high PAR and UV irradiance may narrow the algal diversity to a few specialists in these subaerial habitats. We used rRNA gene cloning/sequencing from both DNA extracts of the biofilms without culturing as well as cultures, for the unambiguous determination of the algal composition and to assess the algal diversity more comprehensively. The culture independent approach revealed mainly just two genera (Apatococcus, Trebouxia) for all study sites and five molecular operational taxonomic units (OTUs) for a particular study site, which based on microscopic observation was the one with the highest morphological diversity. The culture approach, however, revealed seven additional OTUs from five genera (Chloroidium, Coccomyxa, Coenochloris, Pabia, Klebsormidium) and an unidentified trebouxiophyte lineage for that same site; only two OTUs were shared by both approaches. Two OTUs or species were recovered for which references have been isolated only from Antarctica so far. However, the internal transcribed spacer (ITS) sequence differences among them supported they are representing distinct populations of the same species. Within Apatococcus five clearly distinct groups of ITS sequences, each putatively representing a distinct species, were recovered with three or four such ITS types co‐occurring at the same study site. Except for the streptophyte Klebsormidium only members of Trebouxiophyceae were detected suggesting these algae may be particularly well‐adapted to subaerial habitats.     

Management and conservation of the land crab Cardisoma guanhumi (Crustacea: Gecarcinidae) based on environmental and fishery factors: a case study in Brazil

Wetlands Ecology and Management - A mangrove ecosystem encompasses two environments, a larger flooding area with a characteristic wetland forest, and a less flooded area, more saline with little or...     

自然保护区居民福祉的历时性——以陕西佛坪国家级自然保护区为例

生态系统管理的一个重要挑战是在区域尺度上管理生态系统服务并提高当地居民福祉。选择陕西佛坪国家级自然保护区居民福祉进行历时性研究。构建了不同于较大范围和行政区域尺度的福祉指标测量体系,包括了主、客观福祉和千年生态系统评估下的人类福祉,然后对保护区居民从1995经2005至2015年的主、客观福祉和人类福祉指标进行了定量评估和特征刻画。历时数据结果表明:总体上看,保护区居民福祉有明显提升,2005—2015年阶段比1995—2005年阶段的增幅更多;居民主、客观福祉在各方面有了明显提升;人类福祉在基本生活与服务、安全、选择和行动的自由等方面有显著提高,健康方面有显著下滑。通过回归分析的结果表明:受访者居住地与保护区的距离等部分人口特征对提升居民主、客观福祉和人类福祉有着显著的积极影响。结合陕西省佛坪县实际情况,针对如何提升保护区居民福祉,提出了巩固生态系统服务成果、经济发展共建共享、社区共管助力旅游开发、提升教育水平促进旅游就业等建议。     

生态系统服务与居民收入的耦合关系及影响因素——以丽江拉市海流域为例

生态保护与社会经济发展的耦合关系极大地影响当地可持续性能力。以丽江拉市海流域为例,研究一个流域内生态系统服务与居民收入的耦合关系及其影响因素。文章运用In VEST模型和实地调研访谈方法计算流域内各自然村2015年生态系统服务供给数量和农民人均总收入,引入耦合协调度定量化衡量二者的耦合关系,并通过相关分析,探究流域内差异化的生计方式和生计资本对生态系统服务与居民收入耦合关系的影响。研究结果表明:(1)生态系统服务的供给存在空间差异,流域内水源涵养、土壤保持、森林固碳服务集中在流域上游;(2)流域内自然村间的生态系统服务与居民收入的耦合关系存在空间差异和一定的规律,湖泊东面的自然村能够通过特定的生计方式,获取生态系统的产品供给和文化服务所带来的收益,总体呈现较优的耦合协调关系;(3)当地居民的生计方式中,生态旅游与耦合关系具有显著正相关关系,而外出务工与耦合关系具有显著的负相关关系。尽管外出务工对于直接提高当地居民收入的促进作用较小,但其可能通过"智力回流"的方式提高了当地居民开展新型生计的能力。自然资本中人均耕地面积等可利用的自然资本与耦合关系显著正相关。金融、人力、社会资本的相关性尽管不显著,但其系数符号表明,该类生计资本的存量可能对促进生态系统服务与居民收入的耦合协调有积极作用。基础设施中的路网密度与耦合协调度呈显著负相关,在具有生态脆弱性、重要性的区域建设公路时需谨慎评估对生态系统结构和功能的影响。     

Species richness, environmental heterogeneity and area: a case study based on land snails in Skyros archipelago (Aegean Sea, Greece)

Aim To test the performance of the choros model in an archipelago using two measures of environmental heterogeneity. The choros model is a simple, easy‐to‐use mathematical relationship which approaches species richness as a combined function of area and environmental heterogeneity. Location The archipelago of Skyros in the central Aegean Sea (Greece). Methods We surveyed land snails on 12 islands of the archipelago. We informed the choros model with habitat data based on natural history information from the land snail species assemblage. We contrast this with habitat information taken from traditional vegetation classification to study the behaviour of choros with different measures of environmental heterogeneity. R² values and Akaike's information criterion (AIC) were used to compare the choros model and the Arrhenius species–area model. Path analysis was used to evaluate the variance in species richness explained by area and habitat diversity. Results Forty‐two land snail species were recorded, living in 33 different habitat types. The choros model with habitat types had more explanatory power than the classic species–area model and the choros model using vegetation types. This was true for all islands of the archipelago, as well as for the small islands alone. Combined effects of area and habitat diversity primarily explain species richness in the archipelago, but there is a decline when only small islands are considered. The effects of area are very low both for all the islands of the archipelago, and for the small islands alone. The variance explained by habitat diversity is low for the island group as a whole, but significantly increases for the small islands. Main conclusions The choros model is effective in describing species‐richness patterns of land snails in the Skyros Archipelago, incorporating ecologically relevant information on habitat occupancy and area. The choros model is more effective in explaining richness patterns on small islands. When using traditional vegetation types, the choros model performs worse than the classic species–area relationship, indicating that use of proxies for habitat diversity may be problematic. The slopes for choros and Arrhenius models both assert that, for land snails, the Skyros Archipelago is a portion of a larger biogeographical province. The choros model, informed by ecologically relevant habitat measures, in conjunction with path analysis points to the importance of habitat diversity in island species richness.     

黄土高原沟壑区生态环境状况遥感动态监测——以陕西省富县为例

基于主成分分析耦合植被指数、湿度指数、地表温度和裸土指数4个遥感评价指标,对黄土高原丘陵沟壑区陕西省富县1995—2014年的生态环境质量进行评价.结果表明: 基于主成分分析确定权重的遥感生态指数能客观定量揭示区域生态环境的变化;富县生态环境现状整体上属于良好级别,植被覆盖度较高,生物多样性较丰富;1995—2014年,富县生态环境总体上得到了较大改善,生态环境质量综合指数由3.17上升到3.53,牛武镇的生态环境质量整体状况最好,全县由西北方向到东南方向,生态环境质量改善的幅度逐渐递增,其中,交道镇和南道德乡变化最大;研究期间,生态环境质量等级下降地区的面积占全县总面积的16.7%,生态质量等级提高的面积占富县总面积的42.7%,生态环境等级提高的地区主要分布在县域中部的高塬和丘陵沟壑地、县东北部的土石低山区、西南的子午岭自然保护区.     

基于MaxEnt模型的生态系统服务需求及其簇的空间分异——以陕西省米脂县为例

从微观土地利用主体视角量化并明确生态系统服务需求的空间格局对于改善资源依赖地区农户福祉具有重要意义。以地处黄土丘陵沟壑区的米脂县为例,基于参与式制图与MaxEnt模型实现10类生态系统服务需求空间评估;同时,采用K-means聚类识别村域服务需求簇,并探究环境变量对服务需求及其簇空间分布的影响。结果如下：(1)各类服务需求空间分异明显。供给服务中粮食和肉类供给均呈现中部高东西低的空间格局,水果供给空间分布规律相反;调节服务中土壤保持和空气净化高需求区均分布于高海拔区域,水源涵养高需求区分布于无定河流域;4类文化服务均呈现高、中、低需求区相间分布的空间格局但各等级需求区面积占比差异明显。(2)研究区有食物供给需求簇、文化娱乐需求簇和生态保育需求簇等3类。其中,食物供给需求簇是当地主导的需求簇,主要分布在研究区北部和南部;文化娱乐需求簇主要集中在无定河两岸;生态保育需求簇在研究区南部紧邻文化娱乐需求簇,在北部则较为分散。(3)影响各类服务需求空间分布的主导环境因子各不相同;影响食物供给需求簇的环境变量排序为：土地利用>海拔>距水体距离,影响文化娱乐需求簇的环境变量排序为：距居民...     

基于MFA和DEA的区域经济环境效率评价-以辽宁省为例

对经济与环境效率的科学评价是实现区域可持续发展的前提。运用物质流分析将辽宁省经济系统中数据进行物质化处理,再利用改进的数据包络分析模型对环境和经济效率进行综合评价。结果表明:辽宁省物资消费不主要依赖于进口,向其它地区物质输出量大;环境效率评价的综合效率主要受规模因素影响而显著低于纯技术效率,而整体经济的综合效率却主要受纯技术效率影响而下降。第二产业比重依然偏大的产业结构特征是导致上述结果的主因。进一步改造提升传统产业,发展战略性新兴产业,提高第三产业发展水平,扩大环保规模,促进居民生活质量水平全面提升,将是辽宁省以及与之相似的资源依赖型区域可持续发展的方向。     

基于碳足迹的传统农业系统环境影响评价——以青田稻鱼共生系统为例

现代农业在带来粮食高产的同时也产生许多生态环境问题,这促使人们再次把目光转向传统农业系统。一些传统农业系统不仅具有突出的经济、社会和文化价值,还具有多种重要的生态功能,如温室气体减排。然而,已有研究缺乏对传统农业系统整个生命周期的固碳减排能力的测算及其环境影响的评价。为此,基于农户调研数据,运用生命周期评价法对青田稻鱼共生系统的碳足迹进行了测算,并与当地水稻单作系统进行比较。研究发现:(1)青田稻鱼共生系统和水稻单作系统碳足迹分别为6266.7 kgCO₂-eq/hm²和7520.0 kgCO₂-eq/hm²,单位产值碳足迹分别为0.12 kgCO₂-eq/元和0.21 kgCO₂-eq/元。与水稻单作系统相比,稻鱼共生系统排放的温室气体更少,环境影响更小,生态和经济效益更高。(2)农业生产过程中积累的CH₄是碳足迹的最主要来源,农业生产资料投入中的化肥是碳足迹的的第二大来源。农业生产资料投入中的饲料则是稻鱼共生系统碳足迹的另一重要来...