Leaf morphological analyses in four European oak species (Quercus) and their hybrids: A comparison of traditional and geometric morphometric methods

Abstract

In this study, leaf morphology was assessed in a mixed oak stand (western France) using two geometric morphometric (landmark and outline) datasets and one dataset of 19 leaf measures. Adult oaks (817 oaks), comprising four white oak species (Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica), were sampled for DNA extraction and genetic analysis (nuclear microsatellites). Leaf morphology was assessed on 336 oaks, comprising pure species and hybrids as determined by genetic assignment. This comparative study of oak leaf morphology, based on the use of two free size geometric morphometric methods and a set of leaf measurements, combined with the genetic assignment of individuals to pure species or hybrids, provided information about the differences among species and the intermediate leaf morphology of their hybrids.     

Geometric morphometric analyses of leaf variation in four oak species of the subgenus Quercus (Fagaceae)

Abstract

This paper defines a protocol for the study of leaf morphology and morphometric relationships among Quercus frainetto, Quercus robur, Quercus petraea and Quercus pubescens. Leaf shapes were investigated in an attempt to characterize and discriminate among these four species. Landmark and outline data were compared in order to ascertain their relative efficacy for describing variation in leaf morphology. MANOVA was performed to assess intra‐specific differentiation and to compare the distribution of variance in individuals, populations and species. A strong correlation was found between landmark and outline datasets of the four species: both methods proved capable of discriminating among the four species. Finally, a Two‐Block Partial Least‐Squares analysis was performed for each species in order to assess the correlation between intra‐specific shape variation and environmental factors.     

竞争-耐胁迫-杂草型植物对策理论及其应用研究进展

竞争-耐胁迫-杂草型植物(CSR)对策理论主要研究植物对环境胁迫和干扰的适应性特化。从功能生态学角度讲,CSR理论是通过解释各种功能性状协同变异的主导维度来反映植物的生态对策。而物种所采取的生态对策将决定其在群落中的生态位,并最终会影响生态系统过程与功能。自1974年Grime首次提出CSR对策的概念以来,CSR对策思想就受到了生态学家很大的关注,经过近半个世纪的发展,目前已经形成了比较完整的理论和研究方法体系。试图在回顾CSR理论及其研究方法发展的基础上,阐述其基本内涵,并重点从功能性状变异空间、植物适应性、群落过程和生态系统特性等4个方面概述CSR理论及其分析模型的验证及应用,梳理其最新研究进展。CSR理论已经得到了很多研究的广泛验证并应用于多种尺度上的植物生态学研究,但仍有一些方面值得进一步发展完善,如第四区缺失问题、功能性状变异主轴以外的变异、CSR对策与功能性状种内变异和谱系关系的联系等方面需要深入研究。     

高寒草地植物生存策略地理分布特征及其影响因素

植物性状能够反映植物的生存策略,是植物生态学的研究热点之一。植物CSR策略模型将植物物种分为3类:在资源丰富环境中能够最大程度提高生物量的物种(竞争型物种:C策略);在干扰频率较高的环境中能够快速摄取资源并繁殖的物种(投机取巧型物种:R策略);在资源贫瘠环境中能够保持个体生存的物种(耐受型物种:S策略)。植物叶片性状对环境梯度具有适应性的改变,性状的改变对植物生存策略产生影响,但是青藏高原植物叶片性状是如何影响植物CSR生存策略的,其机制尚不清楚。该研究探究了高寒草地植物CSR生存策略的分布特征,以及环境因子对CSR生存策略的影响机制。2020年7–8月,对青藏高原高寒草地53个样点进行了调查,测定植物叶片叶面积、叶片鲜质量和叶片干质量等性状,并计算C、S、R值。然后,分析关键地理环境要素对植物CSR策略影响的主要因子和作用机理。结果表明:(1)在青藏高原高寒草地,植物的生存策略主要以S策略(41.6%–96.7%)为主。(2)随着经度的增加,青藏高原高寒草地C策略植物所占比例自西向东逐渐上升;在海拔梯度上,高寒草地C策略植物所占比例随着海拔的升高而降低。(3)随机森林分析结果显示降水...     

Geometric morphometrics in entomology: Basics and applications

The recent expansion of a variety of morphometric tools has brought about a revolution in the comparison of morphology in the context of the size and shape in various fields including entomology. First, an overview of the theoretical issues of geometric morphometrics is presented with a caution about the usage of traditional morphometric measurements. Second, focus is then placed on two broad approaches as tools for geometric morphometrics; that is, the landmark‐based and the outline‐based approaches. A brief outline of the two methodologies is provided with some important cautions. The increasing trend of entomological studies in using the procedures of geometric morphometrics is then summarized. Finally, information is provided on useful toolkits such as computer software as well as codes and packages of the R statistical software that could be used in geometric morphometrics.     

Parallels between the foraging strategies of ants and plants

Animal and plant ecologists generally follow separate paths. This often leads to disjointed approaches to solving similar ecological problems. In the past 20 years, two related, but unconnected, research fields have undergone rapid development: modular demography, with its morphological and functional analysis of resource capture, until now basically the domain of plant ecology; and foraging theory, traditionally applied and developed in animal ecology. The results of recent research on the foraging strategies of ants and clonal plants, however, outline a general framework of functional parallels between both types of organisms that could link important aspects of animal and plant foraging ecology.     

Weak whole‐plant trait coordination in a seasonally dry South American stressful environment

A core question involving both plant physiology and community ecology is whether traits from different organs are coordinated across species, beyond pairwise trait correlations. The strength of within‐community trait coordination has been hypothesized to increase along gradients of environmental harshness, due to the cost of adopting ecological strategies out of the viable niche space supported by the abiotic conditions. We evaluated the strength of trait relationship and coordination in a stressful environment using 21 leaf and stem traits of 21 deciduous and evergreen woody species from a heath vegetation growing on coastal sandy plain in northeastern South America. The study region faces marked dry season, high soil salinity and acidity, and poor nutritional conditions. Results from multiple factor analyses supported two weak and independent axes of trait coordination, which accounted for 25%–29% of the trait variance using phylogenetically independent contrasts. Trait correlations on the multiple factor analyses main axis fit well with the global plant economic spectrum, with species investing in small leaves and dense stems as opposed to species with softer stems and large leaves. The species’ positions on the main functional axis corresponded to the competitor‐stress‐tolerant side of Grime's CSR triangle of plant strategies. The weak degree of trait coordination displayed by the heath vegetation species contradicted our expectation of high trait coordination in stressful environmental habitats. The distinct biogeographic origins of the species occurring in the study region and the prevalence of a regional environmental filter coupled with local homogeneous conditions could account for prevalence of trait independence we observed.     

Geographical variation in shell shape of the pod razor shell Ensis siliqua (Bivalvia: Pharidae)

The present study assessed the existence of variation in the shell shape of the pod razor shell (Ensis siliqua) throughout its distributional range in the north-eastern Atlantic. Shells of E. siliqua caught at seven collecting sites (three in Portugal, three in Spain and one in Ireland) were studied by geometric morphometric methods, using both landmark- and contour-based methods. Both approaches (landmarks inside the valves and shell outline) discriminated the shells from Aveiro (centre of Portugal) and Strangford Lough (Ireland) from those caught in the nearby localities (remaining Portuguese and Spanish sites, maximum distance of 550 km by sea). Landmark analysis revealed that shells from Aveiro were more similar to shells from Ireland (~1,500 km far away). Contour analysis revealed that shells from Aveiro had a shape with a comparatively larger height-to-width ratio, whereas shells from Ireland showed a slightly more curved outline than in the remaining sites. Landmark- and contour-based methods provided coherent complementary information, confirming the usefulness of geometric morphometric analyses for discerning differences in shell shape among populations of E. siliqua. A brief review of previous applications of geometric morphometric methods to modern bivalve species is also provided.     

A three‐dimensional geometric morphometric study of the development of sulcus versus shell outline in Permian neospiriferine brachiopods

The morphological variation of the sulcal development and shell outline in large Permian neospiriferine brachiopods including Fasciculatia Waterhouse, 2004 is investigated using geometric morphometrics. The sulcal tongues of spiriferide brachiopods can be, in a qualitative sense, categorized into three types according to the degree of their development: short sulcal tongue, long sulcal tongue and geniculated sulcal tongue. All three types have been noted within Fasciculatia striatoparadoxa, regardless of the nature of the substrate which they originally inhabited. To quantify its morphological variation both in sulcal development and shell outline, 51 brachiopod shells were scanned with a three‐dimensional (3‐D) surface imaging device, and their 3‐D models were reconstructed. Using two landmarks and 58 semilandmarks designated on the surface of the reconstructed 3‐D models, a landmark‐based morphometric analysis was performed. Our result demonstrates a significant intraspecific variation of sulcal development in F. striatoparadoxa and its relatives. Local environmental factors, especially the intensity of ambient water flow, are invoked as the most likely cause for this intraspecific variation. Additionally, this study also shows that there are considerable interspecific distinctions in shell outline among Fasciculatia species, independent of the high variation in the sulcal development. The strong stability of overall shell outline at species level implies a decoupled morphological development between sulcal tongue and whole shell outline. The 3‐D morphometric approach applied here demonstrates its great utility as a tool for quantifying and analysing the morphological variation of highly convex brachiopod shells.     

Suites of plant traits in species from different stages of a Mediterranean secondary succession

The aim of this study was to detect suites of traits related to whole plant and seed morphology, phenology and resource use – including water – in species differing in successional status. Twenty traits were measured on 55 species representative of 5 successional stages in Mediterranean southern France, including eight pertaining to phenology and five to water economy. Suites of traits that changed along succession in agreement with the acquisition/conservation trade-off were completed by continuous changes in phenology. Early successional species had leaves with a high specific leaf area that were produced and lost continuously through the growing season. Late-successional species were taller with long-lived, high δ¹³C leaves produced during short periods, most of them persisting during summer, and produced large seeds requiring a long ripening period. Replacement of species occurred with change in strategies of drought survival: early successional species escaped drought by dying before summer; later herbaceous species maintained favourable water status in relation to leaf shedding during summer; late successional trees with a large body allowing access to a large pool of resources, produced dense leaves that could tolerate desiccation. These changes occurred concomitantly with a shift in CSR strategies, using traits related to resource use, plant size and flowering phenology: ruderal herbs were replaced by more stress-tolerant herbs and shrubs throughout the succession, with competitive trees dominating the latest successional stage. These results suggest that the breadth of functional variability found in natura is not predicted by the CSR framework, and calls for a more integrated view of whole plant functioning.     

黄土丘陵区植物叶片与细根功能性状关系及其变化

通过植物叶片功能性状(比叶面积、叶组织密度、叶氮含量)和细根功能性状(比根长、根组织密度、根氮含量)间的相互关系,分析植物对环境的适应途径;然后根据性状间的差异进行了层次聚类,将物种划分为3大功能型,并分析了不同功能型对环境的适应策略.结果表明:黄土丘陵区延河流域149种植物的叶氮含量与比叶面积和根氮含量正相关、与叶组织密度负相关,比根长与根组织密度负相关,除了根氮含量,其余根性状与叶性状不相关.此外,功能性状间关系变化和适应策略在不同功能型之间也存在差异.功能型1的植物具有最强的耐旱力和防御力;功能型3的植物具有最强的养分维持能力用以对抗营养贫瘠的环境;功能型2的植物居中,生长速率最高,具有较强的竞争力、分布最广;根据C-S-R理论,功能型1和3属于“胁迫忍耐型”策略(S策略),功能型2则属于“竞争型”(C)和“干扰型”(R)策略的综合.研究结果为黄土丘陵区植被恢复规划及物种配置等提供依据.     

CSR analysis of plant functional types in highly diverse tropical grasslands of harsh environments

The classification of plant species according to the CSR ecological strategy scheme has been proposed as a common language that allows comparison among species, communities, and floras. Although several studies on European continent have demonstrated a consistent association between CSR strategies and key ecosystem processes, studies of this type are still lacking in other ecoregions worldwide. For the first time, the CSR strategy scheme is applied in a tropical plant community. In a Brazilian mountain grassland ecosystem characterized by both high biodiversity and environmental stress, we sampled various functional traits of 48 herbaceous species in stony and sandy grasslands, and evaluated the relationship between CSR strategies and functional traits with several environmental parameters. The extremely infertile soils in the two studied habitats may have acted as a major environmental filter leading to a clear predominance of the stress-tolerant strategy in both communities. However, fine-scale environmental differences between the two communities resulted in the filtering of distinct functional trait values. The sites with coarser soil texture, lower percentage of plant cover and (paradoxically) higher mineral nutrient concentrations favored plants with narrower leaves, higher stress tolerance, lower competitiveness, and higher sclerophylly (i.e., lower specific leaf area and higher leaf dry matter content). The comparison between the functional character of stony and sandy communities evidenced the influence of soil texture and water availability in the environmental filtering. This study highlighted the validity of the CSR classification outside the temperate region where it was originally developed and corroborated.     

Artificial neural networks and geometric morphometric methods as a means for classification: A case‐study using teeth from Carcharhinus sp. (Carcharhinidae)

Over the past few decades, geometric morphometric methods have become increasingly popular and powerful tools to describe morphological data while over the same period artificial neural networks have had a similar rise in the classification of specimens to preconceived groups. However, there has been little research into how well these two systems operate together, particularly in comparison to preexisting techniques. In this study, geometric morphometric data and multilayer perceptrons, a style of artificial neural network, were used to classify shark teeth from the genus Carcharhinus to species. Three datasets of varying size and species differences were used. We compared the performance of this combination with geometric morphometric data in a linear discriminate function analysis, linear measurements in a linear discriminate function analysis, and a preexisting methodology from the literature that incorporates linear measurements and a two‐layered discriminate function analysis. Across datasets, geometric morphometric data in a multilayer perceptron tended to yield modest accuracies but accuracies that varied less across species whereas other methods were able to achieve higher accuracies in some species at the expense of lower accuracies in others. Further, the performance of the two‐layered discriminate function analysis illustrates that constraining what material is classified can increase the accuracy of a method. Based on this tradeoff, the best methodology will then depend on the scope of the study and the amount of material available. J. Morphol. 278:131–141, 2017. ©© 2016 Wiley Periodicals,Inc.     

Nutrient conservation strategies in native Andean‐Patagonian forests

Abstract. Nutrient conservation in vegetation affects rates of litter decomposition and soil nutrient availability. Although resorption has been traditionally considered one of the most important plant strategies to conserve nutrients in temperate forests, long leaf life‐span and low nutrient requirements have been postulated as better indicators. We aimed at identifying nutrient conservation strategies within characteristic functional groups of NW Patagonian forests on Andisols. We analysed C‐, N‐, P‐, K‐ and lignin‐concentrations in mature and senescent leaves of ten native woody species within the functional groups: broad‐leaved deciduous species, broad‐leaved evergreens and conifers. We also examined mycorrhizal associations in all species. Nutrient concentration in mature leaves and N‐ resorption were higher in broad‐leaved deciduous species than in the other two functional groups. Conifers had low mature leaf nutrient concentrations, low N‐resorption and high lignin/N ratios in senescent leaves. P‐ and K‐resorptions did not differ among functional groups. Broad‐leaved evergreens exhibited a species‐dependent response. Nitrogen in mature leaves was positively correlated with both N resorption and soil N‐fertility. Despite the high P‐retention capacity of Andisols, N appeared to be the more limiting nutrient, with most species being proficient in resorbing N but not P. The presence of endomycorrhizae in all conifers and the broad‐leaved evergreen Maytenus boaria, ectomycorrhizae in all Nothofagus species (four deciduous, one evergreen), and cluster roots in the broad‐leaved evergreen Lomatia hirsuta, would be possibly explaining why P is less limiting than N in these forests.     

Relationships between food quality and fitness in the desert locust, Schistocerca gregaria, and its distribution over habitats on the Red Sea coastal plain of Sudan

The effect of millet, Pennisetum typhoideum Rich. (Poaceae), leaf nitrogen content on fitness parameters of the desert locust, Schistocerca gregaria Forsk. (Orthoptera: Acrididae), was studied under laboratory conditions. Locusts reared on high‐nitrogen leaves were larger, developed faster, had higher survival, reproduced more and earlier, and showed greater synchronization than those fed on low‐nitrogen leaves. Active and passive cannibalism contributed to mortality when locusts were reared on low‐nitrogen leaves, but not when reared on high‐nitrogen leaves. Elevated leaf nitrogen content of host plants increased net reproduction and intrinsic rate of increase, and lowered generation time. The findings show that nitrogen content of host plants affects the potential for population increase in the desert locust. Leaf samples of common plant species were collected in the Heliotropium arbainense (Fresen.) (Boraginaceae) and Panicum turgidum (Forssk.) (Poaceae) plant communities on the Red Sea coastal plain of Sudan during the winters of 1999 and 2000. The levels of leaf nitrogen in host plants were comparable to those in the laboratory studies and consistently higher in plant samples from the Heliotropium community than in samples from the Panicum community. Both in 1999 and 2000, locust densities were much higher in the Heliotropium than in the Panicum plant community. It should be assessed whether the desert locust would be attracted to sites where host plants have high leaf nitrogen content, as this would not only increase their fitness, but also the likelihood of gregarization and outbreaks.     

Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding,genotyping, and disease diagnostics from fungal and oomycete samples

The ubiquity, high diversity and often‐cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods (NaOH, Rapid one‐step extraction (ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8S/ITS2 from various fungal cultures and sporocarps; single‐copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe‐based P. ramorum detection from leaves. Several methods were effective for most of the applications, with NaOH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and NaOH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol‐chloroform extracts for TaqMan diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. NaOH extracts exhibited lower yield and size than CTAB/phenol‐chloroform extracts; however, NaOH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use.     

Elliptic Fourier analysis of leaf shape in southern African Strychnos section Densiflorae (Loganiaceae)

Leaves can be a useful source of taxonomic information in plants particularly when flowers and fruits are absent during certain periods of the year. In this study, we applied an elliptic Fourier analysis (EFA)‐based morphometric technique to assess leaf morphological divergence among four species of southern African Strychnos section Densiflorae. Using leaf specimen images from field and herbarium collections, we extracted six shape variables [i.e. principal components (PCs)] from the Fourier coefficients and used these variables to describe leaf outline among the species. Our results indicate that the symmetric component of a leaf is the main source of shape differences accounting for 90.25% of total leaf shape variation and captures the more obvious range of observed shapes. PC1 of the symmetric variables describes a wide range of visually observable leaf shape among the species. MANOVA revealed significant interspecific differences except between S. innocua and S. madagascariensis, which could not be separated by outline analysis. A cross‐validated group classification suggests that S. gerrardii, with a classification rate of 88.4%, is distinct from S. madagascariensis, contrary to some taxonomic treatments. We discuss the value of geometric morphometrics at detecting subtle morphological variations and the evolutionary implications of such variations, which may be undetectable to the human eye. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 542–553.     

Agrobacterium tumefaciens mediated transient expression of plant cell wall‐degrading enzymes in detached sunflower leaves

For biofuel applications, synthetic endoglucanase E1 and xylanase (Xyn10A) derived from Acidothermus cellulolyticus were transiently expressed in detached whole sunflower (Helianthus annuus L.) leaves using vacuum infiltration. Three different expression systems were tested, including the constitutive CaMV 35S‐driven, CMVar (Cucumber mosaic virus advanced replicating), and TRBO (Tobacco mosaic virus RNA‐Based Overexpression Vector) systems. For 6‐day leaf incubations, codon‐optimized E1 and xylanase driven by the CaMV 35S promoter were successfully expressed in sunflower leaves. The two viral expression vectors, CMVar and TRBO, were not successful although we found high expression in Nicotiana benthamiana leaves previously for other recombinant proteins. To further enhance transient expression, we demonstrated two novel methods: using the plant hormone methyl jasmonic acid in the agroinfiltration buffer and two‐phase optimization of the leaf incubation temperature. When methyl jasmonic acid was added to Agrobacterium tumefaciens cell suspensions and infiltrated into plant leaves, the functional enzyme production increased 4.6‐fold. Production also increased up to 4.2‐fold when the leaf incubation temperature was elevated above the typical temperature, 20°C, to 30°C in the late incubation phase, presumably due to enhanced rate of protein synthesis in plant cells. Finally, we demonstrated co‐expression of E1 and xylanase in detached sunflower leaves. To our knowledge, this is the first report of (co)expression of heterologous plant cell wall‐degrading enzymes in sunflower. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:905–915, 2014     

N‐P utilization of Acer mono leaves at different life history stages across altitudinal gradients

The relationship between plants and the environment is a core area of research in ecology. Owing to differences in plant sensitivity to the environment at different life history stages, the adaptive strategies of plants are a cumulative result of both their life history and environment. Previous research on plant adaptation strategies has focused on adult plants, neglecting saplings or seedlings, which are more sensitive to the environment and largely affect the growth strategy of subsequent life stages. We compared leaf N and P stoichiometric traits of the seedlings, saplings, and adult trees of Acer mono Maxim and different altitudes and found significant linear trends for both life history stages and altitude. Leaf N and P content by unit mass were greatly affected by environmental change, and the leaf N and P content by unit area varied greatly by life history stage. Acer mono leaf N‐P utilization showed a significant allometric growth trend in all life history stages and at low altitudes. The adult stage had higher N‐use efficiency than the seedling stage and exhibited an isometric growth trend at high altitudes. The N‐P utilization strategies of A. mono leaves are affected by changing environmental conditions, but their response is further dependent upon the life history stage of the plant. Thus, this study provides novel insights into the nutrient use strategies of A. mono and how they respond to the environmental temperature, soil moisture content along altitude and how these changes differ among different life history stages, which further provide the scientific basis for the study of plant nutrient utilization strategy on regional scale.     

崇明东滩湿地芦苇种群内功能性状及生态对策变异分析

植物种群功能性状及生态对策变异对其自身环境适应能力及群落结构具有重要影响。该文基于崇明东滩湿地芦苇(Phragmites australis)种群内3个小种群不同发育时期分株集合的多项性状指标,分析了其性状及生态对策变异,并基于CSR、LHS生态对策体系,对各小种群的生态对策进行了排序。结果表明, 3个芦苇小种群的21项性状指标及C、R对策得分均存在显著差异。在LHS体系中,以比叶面积(11.5 mm2/mg)、株高(175 cm)和花序干质量(4 g)为分界线,可对3个小种群进行区分。处于生殖生长期的芦苇分株具有更大的植株大小、更高的叶片干物质含量及S对策得分,而处于营养生长期的分株则具有较小的植株大小、较大的比叶面积及R对策得分。总体而言,崇明东滩湿地3个芦苇小种群间及各小种群内处于不同生长发育阶段的分株集合间,都存在显著的性状差异及生态对策差异,且二者的差异模式基本吻合。芦苇种内性状及生态对策变异特征,可为该区芦苇种群的生态保育和恢复实践提供重要的理论参考和技术支撑。