Analyzing species distributions among temporary ponds with a permutation test approach to the join-count statistic

The Bluff Springs Sand Ponds (BSSPs) are a set of closely-spaced temporary ponds of varying hydroperiod, depth and surface area. We sampled crustacean communities of 15 ponds throughout hydroperiods in 1996 to examine species distributions among ponds. Although ponds were closely spaced (within ca. 16 ha), most species were present in subsets of the 15 ponds. We then analyzed spatial patterns of 12 crustacean species for complete spatial randomness (CSR) using join-count statistics. However, the join-count was designed for large-samples (n>50), so we further analyzed (by simulation) the join-count and a variation of the join-count (Cliff & Ord, 1981) for small-scale reliability. Simulation results revealed that neither testing distribution was reliable for n<30. We then used a permutation test to analyze species distributions and concluded that some species were distributed non-randomly. Therefore, further investigations of mechanisms causing species distributions (e.g., hydroperiod, physical/chemical conditions, biotic interactions) are clearly prescribed. The permutation test should be useful for studies of species distribution patterns among other temporary waters, and can help focus studies on causal mechanisms of distributions among small numbers of temporary aquatic habitats.     

红松存在/不存在数据的多尺度空间分布格局

红松属小兴安岭地区地带性植被优势种,该地区也是其分布的北缘。在景观尺度上开展红松的分布格局研究有利于进一步了解红松分布机理、未来迁移过程等问题,对其经营和保护有重要意义。将景观指数法与点格局分析法结合,设定8个空间尺度,利用红松存在/不存在数据,通过计算各空间尺度上红松聚集程度和景观指数,分析小兴安岭地区红松种群在多尺度上的分布格局。研究结果表明,小尺度上红松聚集分布明显,随机分布区多处于其聚集分布区的边缘,均匀分布区则散布在其聚集分布区内。景观指数研究表明,通过景观指数可判断红松聚集分布格局趋势,而不能判断均匀分布、随机分布格局趋势,因为它们在多尺度下景观指数波动大,不能用景观指数来描述分布格局。研究得出如下结论:1)红松主要分布在其分布区的核心区域内,在分布区边缘和过渡带上呈随机分布,2)存在/不存在数据能够用来分析种群的多尺度空间分布格局,3)空间尺度的变化会引起树种分布格局的变化,随机分布随尺度增加,边缘化程度加强,4)单一尺度上,景观格局指数不能完全描述种群分布格局;而在多尺度上,变化趋势稳定的景观指数表明聚集分布存在,而波动剧烈的景观指数常与随机分布和均匀分布联系在一起,5)地形因子中,红松对坡度和海拔两个因子变化敏感。     

Verifying zero-infestation in pest control: A simple sequential test based on the succession of zero-samples

A simple sequential test based on the succession of ‘zero's or uninfested sampling units is proposed for use in verifying zero-infestation in pest control surveys. The method is applicable efficiently to both finite and infinite populations. Problems concerning its efficiency on application are discussed.     

Genome-wide patterns of large-size presence/absence variants in sorghum

The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.     

Comparing patterns of spatial autocorrelation of assemblages of benthic invertebrates in upland rivers in south-eastern Australia

Patterns of spatial autocorrelation of biota may reveal much about underlying ecological and biological forces responsible for generating the patterns. Operationally, ecological work and many applied problems (e.g., impact detection, ecosystem health assessment using reference sites) require statistical knowledge of autocorrelation patterns. Here, we report on assemblage-level autocorrelation in the benthic-invertebrate assemblages of riffles in two adjacent, relatively pristine rivers in south-eastern Victoria, Australia (40 km reaches of the Wellington and Wonnangatta rivers). The assemblages of the Wellington River were strongly autocorrelated, but those of the Wonnangatta River showed a distance-independent pattern. There was no effect of taxonomic resolution, rarity protocols or whole-assemblage surrogates on the inferred levels of autocorrelation. We conclude that there is little evidence that one can assume the pattern of spatial relationships among invertebrate faunas within a river, and this probably holds true for the usual set of taxonomic resolutions and subsets used to discern changes wrought by human impacts.     

A comparison of statistical approaches for modelling fish species distributions

SUMMARY 1. The prediction of species distributions is of primary importance in ecology and conservation biology. Statistical models play an important role in this regard; however, researchers have little guidance when choosing between competing methodologies because few comparative studies have been conducted. 2. We provide a comprehensive comparison of traditional and alternative techniques for predicting species distributions using logistic regression analysis, linear discriminant analysis, classification trees and artificial neural networks to model: (1) the presence/absence of 27 fish species as a function of habitat conditions in 286 temperate lakes located in south‐central Ontario, Canada and (2) simulated data sets exhibiting deterministic, linear and non‐linear species response curves. 3. Detailed evaluation of model predictive power showed that approaches produced species models that differed in overall correct classification, specificity (i.e. ability to correctly predict species absence) and sensitivity (i.e. ability to correctly predict speciespresence) and in terms of which of the study lakes they correctly classified. Onaverage, neural networks outperformed the other modelling approaches, although all approaches predicted species presence/absence with moderate to excellent success. 4. Based on simulated non‐linear data, classification trees and neural networks greatly outperformed traditional approaches, whereas all approaches exhibited similar correct classification rates when modelling simulated linear data. 5. Detailed evaluation of model explanatory insight showed that the relative importance of the habitat variables in the species models varied among the approaches, where habitat variable importance was similar among approaches for some species and very different for others. 6. In general, differences in predictive power (both correct classification rate and identity of the lakes correctly classified) among the approaches corresponded with differences in habitat variable importance, suggesting that non‐linear modelling approaches (i.e. classification trees and neural networks) are better able to capture and model complex, non‐linear patterns found in ecological data. The results from the comparisons using simulated data further support this notion. 7. By employing parallel modelling approaches with the same set of data and focusing on comparing multiple metrics of predictive performance, researchers can begin to choose predictive models that not only provide the greatest predictive power, but also best fit the proposed application.     

一个获得与缺失变异(PAV)调控甜瓜果实苦味

甜瓜苦味物质严重影响其口感和品质。本研究利用不苦的薄皮甜瓜品系C69和苦的薄皮甜瓜品系C14构建了一个包含100个单株的F2群体。首先利用2b-RAD测序构建一个遗传连锁图谱。其次,结合群体的苦味性状进行全基因组的QTL定位和关联分析。然后,利用2b-RAD测序特有的技术优势进行群体的获得与缺失变异(PAV)的挖掘。最后,利用亲本的重测序信息确定控制苦味性状的关键基因。结果发现,F1的果实表现出强烈的苦味,F2群体中苦与不苦的单株分别为81个和19个,符合3∶1的分离比(χ^2=1.92,P=0.1659),表型表明所用甜瓜材料的苦味主要是由一个显性的基因位点控制。利用477个SNP标记构建一张包含10个连锁群的连锁图谱,总长为337.79 cM,标记间平均间隔0.71 cM。全基因组QTL定位在8号连锁群(对应9号染色体),检测到一个解释表型变异为20%的甜瓜苦味QTL。全基因组关联分析检测到7个SNPs与苦味性状相关,全部位于9号染色体苦味QTL的基因组区域。通过PAV分型分析仅发现一个特有的大片段缺失(21707702~21743072 bp),位于QTL区域,且在所有的不苦株系中存在,而苦的株系中不存在。基于两个亲本材料的深度重测序信息,发现这个PAV的区域更大,约为62 Kb,共涉及到9个连续的基因(MELO3C005601、MELO3C005602、MELO3C005603、MELO3C005604、MELO3C005605、MELO3C005606、MELO3C005607、MELO3C005608和MELO3C005609),其中5个是细胞色素P450基因。构建的系统发育树表明,这5个细胞色素P450基因与参与葫芦素C/B/E合成的细胞色素P450基因簇CYP81Q58、CYP81Q59和CYP712D8在一个进化枝,可能行使类似的功能,为潜在的类似于黄瓜葫芦素C合成的基因簇的一部分。前人通过比较基因组学研究获得的2个控制葫芦素B合成的bHLH转录因子CmBr(MELO3C005610)和CmBt(MELO3C005611)同在9号染色体,与本研究检测到的PAV紧密挨在一起。我们的研究结果为后续不苦甜瓜的育种提供了新的理论支撑和分子辅助育种目标。