Ecological vegetation maps

On ecological vegetation maps, the distribution of vegetation is related to one or more features of the environment. Tolerance, competition, map scales and the environment are discussed with regard to their bearing on the geographical distribution of phytocenoses and their portrayal on maps. There are two types of ecological vegetation maps: those relating the vegetation to one environmental quality, and those with two or more such qualities. The interpretation of ecological vegetation maps is relatively simple when plant communities are related to a single quality of the biotope and difficult but usually more useful when related to several qualities. Perfection is not possible but can be approached asymptotically.     

Using climatically based random forests to downscale coarse‐grained potential natural vegetation maps in tropical Mexico

Questions: Can the accuracy of coarse resolution potential vegetation maps be improved through downscaling to finer resolution climatic grids? Can output from random forests produce new insight into the climatic characteristics that are associated with the structural characteristics of the vegetation? Location: Southern Mexico. Methods: A potential vegetation map (National Atlas of Mexico) at a 1:4 000 000 scale, was downscaled to a 1 km² grid resolution using climatically based random forests models. The resulting map was then evaluated against 256 inventory plots sampled at the transition between different vegetation types in Southern Mexico. Results: Downscaling increased accuracy up to 0.40, as measured by the Kappa Index of Agreement. Multivariate analysis of the results allowed the association between Rzedowski's classification and climatic variation to be explored. This confirmed that many of the structural aspects of the vegetation that are used by the Rzedowski classification are closely associated with climate, but it also revealed weaknesses in the underlying basis of this classification system. Conclusions: Rzedowski's scheme for vegetation classification may require further modification in order to be an effective tool for research into vegetation–climate relationships.     

An evaluation of rapid methods for monitoring vegetation characteristics of wetland bird habitat

Wetland managers benefit from monitoring data of sufficient precision and accuracy to assess wildlife habitat conditions and to evaluate and learn from past management decisions. For large-scale monitoring programs focused on waterbirds (waterfowl, wading birds, secretive marsh birds, and shorebirds), precision and accuracy of habitat measurements must be balanced with fiscal and logistic constraints. We evaluated a set of protocols for rapid, visual estimates of key waterbird habitat characteristics made from the wetland perimeter against estimates from (1) plots sampled within wetlands, and (2) cover maps made from aerial photographs. Estimated percent cover of annuals and perennials using a perimeter-based protocol fell within 10 percent of plot-based estimates, and percent cover estimates for seven vegetation height classes were within 20 % of plot-based estimates. Perimeter-based estimates of total emergent vegetation cover did not differ significantly from cover map estimates. Post-hoc analyses revealed evidence for observer effects in estimates of annual and perennial covers and vegetation height. Median time required to complete perimeter-based methods was less than 7 percent of the time needed for intensive plot-based methods. Our results show that rapid, perimeter-based assessments, which increase sample size and efficiency, provide vegetation estimates comparable to more intensive methods.     

Past and present forest vegetation in NE Slovenia derived from old maps

Abstract. Using old military and cadastral maps and modern vegetation maps, the changes in land use over the past 230 yr were followed. The following maps were used: the military map from the second half of the 18th century, the cadastral map of the ‘Economic cadastral survey for regulation of land taxes’ from the first half of the 19th century, and a field map made in the 1980s. A vegetation map of the area was made on the basis of satellite images. We used basic classification techniques combined with extensive field inspections and aerial photographs. The output of this procedure was verified in the field. Additionally, a comparison of statistical data about land use categories is presented. It was established that the last remaining areas of inundated riverine forest disappeared 200 yr ago, and since then only minor changes in land use have occurred.     

Grid map analysis and its application for detecting vegetation changes in Japan

Abstract. Grid maps are used as a basic vegetation data base in Japan; they are simplified from vector-based vegetation maps. We estimated the frequency error or lack of information corresponding to reduced resolution and examined the reliable limits of this data base. We produced 10 grid maps on five different scales from 50 m to 1000 m using two different methods using both the whole cell (W-method) and only the central circle (C-method) from a vegetation map at scale 1: 25 000. We found that patches larger than the area of a cell on a vector-based map could be kept almost certainly on any map, but many patches of less than the cell size were lost. The number of missing patches with the C-method is fewer at every scale than those with the W-method. Though the value of Morisita's Cλ (p) index showed that the similarity with the original map was high - from the 50-m to the 200-m resolution - it was increasingly lower on the 400-m and 1000-m grid maps. The values of the Shannon index on the original map, 50-m and 100-m grid maps were not different, but they decreased from the 200-m to 1000-m grid maps. Because the vegetation data base of the Japanese Environment Agency used a 1000-m C-method grid map, we found that much information on patches less than 100 ha had disappeared. Information about dominant vegetation or large patches is almost accurate in this data base.     

Mapping vegetation in an arid,mountainous region of Western Australia

Abstract. Predictive mapping of vegetation using models linking vegetation units to mapped environmental variables has been advocated for remote areas. In this study, three different types of model were employed (within a GIS) to produce vegetation maps of the Hamersley Ranges region of Western Australia. The models were: (1) decision trees; (2) statistical models; and (3) heuristic/conceptual models. Maps were produced for three different levels of a floristic classification, i.e. 16 communities in two community groups with eight subgroups. All models satisfactorily established relationships between the vegetation units and available predictor variables, except where the number of sites of a particular unit was small. The different models often made similar predictions, especially for more widespread vegetation units. Map accuracy (as determined by field testing of maps) improved with increasing level of abstraction, with plant community maps ca. 50 % correct, subgroup maps ca. 60 % correct and group maps 90 % correct. Map inaccuracies were due to several factors, including low sample numbers producing unrepresentative models, poor resolution of and errors in available maps of predictor variables, and available predictor variables not being able to differentiate between certain vegetation units, particularly at the plant community level. Of these factors, poor resolution of maps was seen as the most critical. One type of model could not be recommended over another; however the choice of model will be largely dependent on the nature of the data set and the type of map coverage required.     

Mapping global cropland and field size

A new 1 km global IIASA‐IFPRI cropland percentage map for the baseline year 2005 has been developed which integrates a number of individual cropland maps at global to regional to national scales. The individual map products include existing global land cover maps such as GlobCover 2005 and MODIS v.5, regional maps such as AFRICOVER and national maps from mapping agencies and other organizations. The different products are ranked at the national level using crowdsourced data from Geo‐Wiki to create a map that reflects the likelihood of cropland. Calibration with national and subnational crop statistics was then undertaken to distribute the cropland within each country and subnational unit. The new IIASA‐IFPRI cropland product has been validated using very high‐resolution satellite imagery via Geo‐Wiki and has an overall accuracy of 82.4%. It has also been compared with the EarthStat cropland product and shows a lower root mean square error on an independent data set collected from Geo‐Wiki. The first ever global field size map was produced at the same resolution as the IIASA‐IFPRI cropland map based on interpolation of field size data collected via a Geo‐Wiki crowdsourcing campaign. A validation exercise of the global field size map revealed satisfactory agreement with control data, particularly given the relatively modest size of the field size data set used to create the map. Both are critical inputs to global agricultural monitoring in the frame of GEOGLAM and will serve the global land modelling and integrated assessment community, in particular for improving land use models that require baseline cropland information. These products are freely available for downloading from the http://cropland.geo-wiki.org website.     

A composite linkage map from two crosses for the species complex Picea mariana × Picea rubens and analysis of synteny with other Pinaceae

Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. × Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homoeologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed. Electronic Supplementary Material Supplementary material is available for this article at     

Changes in a Wetland Ecosystem: A Vegetation Reconstruction Study Based on Historical Panchromatic Aerial Photographs and Succession Patterns

This paper presents the methodology and results of a vegetation reconstruction method based on botanical sampling, the knowledge of succession pattern, digital photograph-interpretation and automatic delineation via image segmentation. The aim is to provide a methodology for interpretation of archived black-and-white aerial photographs, which can be applied at other study sites. Our study area was the Nyíres-tó mire in the Bereg Plain (NE Hungary). Initially, botanical sampling was carried out, and this was followed by separation and identification of current vegetation types. In our study we selected automatic delineation using multi-resolution image segmentation as the method for vegetation mapping. Based on the present-day vegetation map produced and the known successional pathway of the mire, archive aerial photographs were analyzed separately in reverse chronological order to derive plant associations present at the different photograph acquisition dates. With this method we were able to make a chronological sequence of digital vegetation maps over a period of almost fifty years (1956–2002). The analysis of vegetation maps showed that forest cover increased steadily until 1988. After an artificial water supply was introduced (in 1986), the spread of tree-dominated associations became slower, and the relative cover of the different vegetation types reached a stable state.     

A Composite Linkage Map from Three Crosses Between Commercial Clones of Cacao, Theobroma cacao L.

In this paper, we report the construction of the first composite map of cacao from linkage data of one F₂ and two F₁ mapping populations with a high number of codominant markers in common. The combination of linkage information from all three maps results in the currently most precise estimates of marker locations and distances between markers, especially in densely marked areas. JoinMap®V4 software was used for all marker quality assessment and mapping. Individual (sub-composite) maps and the composite map contained 10 major linkage groups, corresponding to the number of cacao chromosomes. Homogeneity of marker placement was very high among sub-composite maps, the composite map, and the designated “reference” map. Care was exercised in the re-creation of sub-composite maps and the composite map to include only markers with acceptable mapping quality parameters. The composite map places more markers with higher precision than any individual map. This research clearly demonstrates for the first time a very high level of marker homogeneity among commercial cacao clones compared to other species. The observed homogeneity between different maps, including the composite one, is probably due to a narrow genetic base of commercial cacao clones. Markers linked to identified quantitative trait loci (QTLs) are more likely to retain linkage in other commercial clones, rendering the QTLs in cacao potentially more stable than in other species.     

Differences in spatial predictions among species distribution modeling methods vary with species traits and environmental predictors

Prediction maps produced by species distribution models (SDMs) influence decision‐making in resource management or designation of land in conservation planning. Many studies have compared the prediction accuracy of different SDM modeling methods, but few have quantified the similarity among prediction maps. There has also been little systematic exploration of how the relative importance of different predictor variables varies among model types and affects map similarity. Our objective was to expand the evaluation of SDM performance for 45 plant species in southern California to better understand how map predictions vary among model types, and to explain what factors may affect spatial correspondence, including the selection and relative importance of different environmental variables. Four types of models were tested. Correlation among maps was highest between generalized linear models (GLMs) and generalized additive models (GAMs) and lowest between classification trees and GAMs or GLMs. Correlation between Random Forests (RFs) and GAMs was the same as between RFs and classification trees. Spatial correspondence among maps was influenced the most by model prediction accuracy (AUC) and species prevalence; map correspondence was highest when accuracy was high and prevalence was intermediate (average prevalence for all species was 0.124). Species functional type and the selection of climate variables also influenced map correspondence. For most (but not all) species, climate variables were more important than terrain or soil in predicting their distributions. Environmental variable selection varied according to modeling method, but the largest differences were between RFs and GLMs or GAMs. Although prediction accuracy was equal for GLMs, GAMs, and RFs, the differences in spatial predictions suggest that it may be important to evaluate the results of more than one model to estimate the range of spatial uncertainty before making planning decisions based on map outputs. This may be particularly important if models have low accuracy or if species prevalence is not intermediate.     

利用3S技术对梅里雪山地区植被制图的精度检验分析

在野外考察的基础上,应用3S技术,完成了云南西北部梅里雪山地区的1：50000的植被图．对已完成的植被图通过野外收集的GPS点进行校正,GPS样点数的多少依据统计学抽样调查的样本大小计算而得,用这些校正样点数建立混淆矩阵进行植被图精度计算,最后利用计算成数方差进行检验．混淆矩阵计算得出植被图总的判对精度即整体精度OA为84．7％,利用计算成数方差检验,结果表明大部分类型为90％以上．基于3S技术完成的植被图精度取决于区域面积大小和植被分类等级,而利用遥感技术来划分的植被等级与传统的植被分类等级不完全一致．     

Validation of the Greater Hunter Native Vegetation Mapping as it pertains to the Upper Hunter region of New South Wales

Reliable vegetation maps are an important component of any long‐term landscape planning initiatives. A number of approaches are available but one, in particular, pattern recognition (segmentation) combined with modelling from floristic site data, is currently being used to map vegetation across NSW. An independent assessment of this approach based on a review of the Greater Hunter Native Vegetation Mapping (GHM_v4) was undertaken in order to assess its ability to cater for regional, local, strategic and landscape planning. The validation process tested 2151 locations across the Upper Hunter Valley region of New South Wales (NSW), Australia. The results suggest that mapping at the coarsest level of NSW vegetation classification, the Formation, is generally poor, with only Dry Sclerophyll Forest and Woodland modelled with some level of reliability. The modelled mapping of individual plant community types (PCTs) was found to be highly inaccurate with only 17% of validation points attributed as ‘correct’ and a further 13% ‘essentially correct’. Therefore, a majority of PCTs were mapped with an accuracy of less than 30%. The results of this validation suggest that the GHM_v4 is of such a low level of accuracy within the upper Hunter as to be inherently unusable for broad‐scale regional and local landscape planning or environmental assessment, including locating compensatory offsets for the loss of native vegetation due to developments. The GHM_v4 methods of pattern recognition of mainly SPOT5 satellite imagery combined with modelling from plot data have not produced reliable vegetation maps of plant community types. Yet this mapping programme is extending across NSW and could be misused for environmental decisions or as a regulation.     

Iteratio: calculating environmental indicator values for species and relevés

Question: Is it possible to translate vegetation maps into reliable thematic maps of site conditions? Method: This paper presents a new method, called Iteratio, by which a coherent spatial overview of specific environmental conditions can be obtained from a comprehensive vegetation survey of a specific area. Iteratio is a database application which calculates environmental indicator values for vegetation samples (relevés) on the basis of known indicator values of a limited number of plant species. The outcome is then linked to a digitalized vegetation map (map of plant communities) which results in a spatial overview of site conditions. Iteratio requires the indicator values of a minimum of 10–20% of the species occurring. The species are given a relative weight according to their amplitudes: species with a narrow range are weighted stronger, species with a broad range are weighted weaker. Conclusion: The method presented here enables a coherent assessment of site conditions on the basis of a vegetation survey and the indicator values of a limited number of plant species.     

Linkage maps for the Pacific abalone (genus Haliotis) based on microsatellite DNA markers

This study presents linkage maps for the Pacific abalone (Haliotis discus hannai) based on 180 microsatellite DNA markers. Linkage mapping was performed using three F1 outbred families, and a composite linkage map for each sex was generated by incorporating map information from the multiple families. A total of 160 markers are placed on the consolidated female map and 167 markers on the male map. The numbers of linkage groups in the composite female and male maps are 19 and 18, respectively; however, by aligning the two maps, 18 linkage groups are formed, which are consistent with the haploid chromosome number of H. discus hannai. The female map spans 888.1 cM (Kosambi) with an average spacing of 6.3 cM; the male map spans 702.4 cM with an average spacing of 4.7 cM. However, we encountered several linkage groups that show a high level of heterogeneity in recombination rate between families even within the same sex, which reduces the precision of the consolidated maps. Nevertheless, we suggest that the composite maps are of significant potential use as a scaffold to further extend the coverage of the H. discus hannai genome with additional markers.     

Construction of a high-density,high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.     

Mapping mountain vegetation using species distribution modeling,image‐based texture analysis,and object‐based classification

Objective: The objective of this study was to map vegetation composition across a 24 000 ha watershed. Location: The study was conducted on the western slope of the Sierra Nevada mountain range of California, USA. Methods: Automated image segmentation was used to delineate image objects representing vegetation patches of similar physiognomy and structure. Image objects were classified using a decision tree and data sources extracted from individual species distribution models, Landsat spectral data, and life form cover estimates derived from aerial image‐based texture variables. Results: A total of 12 plant communities were mapped with an overall accuracy of 75% and a χ‐value of 0.69. Species distribution model inputs improved map accuracy by approximately 15% over maps derived solely from image data. Automated mapping of existing vegetation distributions, based solely on predictive distribution model results, proved to be more accurate than mapping based on Landsat data, and equivalent in accuracy to mapping based on all image data sources. Conclusions: Results highlight the importance of terrain, edaphic, and bioclimatic variables when mapping vegetation communities in complex terrain. Mapping errors stemmed from the lack of spectral discernability between vegetation classes, and the inability to account for the confounding effects of land use history and disturbance within a static distribution modeling framework.     

Across the grain: Multi-scale map comparison and land change assessment

Changes in the spatial distribution of land cover and land use can have significant impacts on ecological processes at multiple scales; estimating these changes provides critical data for both monitoring and understanding land-use effects on these processes. One approach to mapping landcover changes, particularly useful over longer periods of time, is comparison of existing landcover maps, (post-classification change analysis). The accuracy of these maps is often unknown and varies depending on data sources and interpretation techniques; therefore, separating change on the ground from differences attributable to sensors and methods is both critical and problematic. Through a novel map comparison method applying major axis regression at multiple spatial grains of analysis, this study partitioned accuracy into components of bias and precision in comparing maps, which aided selection of an optimal analytical grain size. Comparisons between contemporaneous maps showed the magnitude and distribution of error alone, while between-period analyses indicated both cumulative map error and change on the ground. These methods enable exploration of the nature of error and identification of differences between maps, while accounting for the imprecision and bias inherent in the source documents. Mapping landcover change delineates landscapes under recent disturbance pressure, and these measures are more effective as performance indicators for broad-scale evaluation of natural heritage policies and habitat restoration initiatives when error in the data is identified and accounted for.     

A potato molecular-function map for carbohydrate metabolism and transport

Molecular-linkage maps based on functional gene markers (molecular-function maps) are the prerequisite for a candidate-gene approach to identify genes responsible for quantitative traits at the molecular level. Genetic linkage between a quantitative trait locus (QTL) and a candidate-gene locus is observed when there is a causal relationship between alleles of the candidate gene and the QTL effect. Functional gene markers can also be used for marker-assisted selection and as anchors for structural and functional comparisons between distantly related plant species sharing the same metabolic pathways. A first molecular-function map with 85 loci was constructed in potato based on 69 genes. Priority was given to genes operating in carbohydrate metabolism and transport. Public databases were searched for genes of interest from potato, tomato, or other plant species. DNA sequence information was used to develop PCR-based marker assays that allowed the localization of corresponding potato genes on existing RFLP linkage maps. Comparing the molecular-function map for genes operating in carbohydrate metabolism and transport with a QTL map for tuber starch content indicates a number of putative candidate genes for this important agronomic trait. Received: 19 March 2000 / Accepted: 16 May 2000