Deficiency in African plant distribution data – missing pieces of the puzzle

Biodiversity is spatially unevenly distributed and so is the information on its spatial patterns. This uneven distribution of information on species occurrences is an important impediment to the conservation of biodiversity. Based on 185 427 collection records of 5873 plant species in sub-Saharan Africa, we analyse the availability of distribution data suitable for the GIS-based mapping of plant diversity patterns at a one-degree resolution. Using the bioclimatic model GARP, distribution ranges for each species were modelled. In order to identify data-deficient areas, the documented and modelled diversity patterns were compared. Only for a few, well-known centres of plant diversity are there comparatively many data collection records available. For several of the areas with very few collection records, such as the Guinean montane forests, the north-western Congolian lowland forests, and the southern Albertine Rift montane forests, the model predicts a species richness much higher than currently documented. In many of the data deficient areas, difficult conditions for scientific research appear to have limited collection activities for decades. Only strategic field collections can fill these gaps. Another cause of data deficiency is that data collected and digitized do not match the quality requirements for GIS-based work at the super-regional scale. In particular, regional databases documenting partial ranges of species are rarely connected. One challenge for the Global Strategy for Plant Conservation is therefore to establish international collaborative structures and technical standards that will allow analysis of biogeographical patterns across political boundaries.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 355–368.     

论植物园的活植物收集

对植物园活植物收集评价、引种中的取样方法和迁地保护种群大小等问题进行了论述.对活植物收集的评价包括科学性和代表性,最具有科学意义的是经过调查从野外收集的有完整记录的材料,其次是从植物园等机构 引种的有记录的材料,再次是从各地引种的基本上无记录的材料.根据收集物的代表性可分为具有保护意义的收集和保护性收集.取样技术主要针对保护性收集而言,要求收集样本能涵盖该物种95%以上、频率大于5%的等位基因.活植物收集种群的大小应从科学性和现实性二方面来考虑,对植物园里大量的具有保护意义的收集,其种群大小为乔木10～20株,灌木40～50株,草本100～200株;对于保护性收集则至少为乔木50～100株,灌木200株或更多,草本300～500株以上.另外,对当前植物园活植物收集圃建设的一些重要问题也进行了探讨.     

Annotated catalogue of the types of Indo-Burmese non-marine Gastropoda deposited in the Faculty of Tropical Medicine,Mahidol University,Thailand

ABSTRACT

Four decades after its publication, Rolf A.M. Brandt’s 1974 monograph on the non-marine molluscs of Thailand remains the main authority on freshwater and estuarine species for Southeast Asia and includes up to 165 new species of snails and bivalves described by Brandt and colleagues in the same book and preceding publications. All the holotypes are lodged at the Forschungsinstitut und Naturmuseum Senckenberg in Germany, and are largely inaccessible to Thai and other Southeast Asian researchers, who rely heavily on the Brandt collection as a key reference. Paratypes were, however, donated to various other collections, including some in Thailand. We present the first catalogue of 45 paratypes of gastropods of the Brandt collection, described from Thailand, Laos and Cambodia, which are lodged at the Faculty of Tropical Medicine, Mahidol University, Thailand.     

Improving representativeness of genebank collections through species distribution models, gap analysis and ecogeographical maps

An efficient germplasm collecting method was evaluated using six Lupinus species and the Spanish Lupinus collection as a study case. This method includes the application of geographic information systems, ecogeographical land characterization maps, species distribution models and gap analysis to identify prioritized collecting sites. To evaluate the efficiency of this collecting method, field collecting expeditions were carried out focusing on prioritized sites and the results of these collections were analyzed. Prioritized sites were identified using spatial and ecogeographical gaps, and potential species richness maps. The spatial gaps corresponded to populations non-included in the collection but recorded by other information sources while ecogeographical gaps corresponded to spatial gaps that were located in ecogeographical categories (obtained from the ecogeographical map) that were scarcely represented in the collection. A potential Lupinus species richness map was obtained by adding the information of single maps of Lupinus species distribution models. Subsequently, prioritized sites were obtained in ecogeographical gaps with high potential species richness values. Collecting expeditions were made in Spain in 2006, 2007 and 2008. Results showed that using the efficient germplasm collecting methodology was highly positive not only from a quantitative viewpoint (between 7.8 and 11% increase) but also in qualitative terms, focusing collection efforts in ecogeographical categories with low or null representation in the Spanish Lupinus collection (41% of the new accessions). Phenotypic differences related to adaptation to environment were observed in the field between the populations that grow in low or null represented categories and those that grow in highly represented categories.     

A gap analysis methodology for collecting crop genepools: a case study with phaseolus beans

Background

The wild relatives of crops represent a major source of valuable traits for crop improvement. These resources are threatened by habitat destruction, land use changes, and other factors, requiring their urgent collection and long-term availability for research and breeding from ex situ collections. We propose a method to identify gaps in ex situ collections (i.e. gap analysis) of crop wild relatives as a means to guide efficient and effective collecting activities.

Methodology/Principal Findings

The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps. We apply the gap analysis methodology to wild taxa of the Phaseolus genepool. Of 85 taxa, 48 (56.5%) are assigned high priority for collecting due to lack of, or under-representation, in genebanks, 17 taxa are given medium priority for collecting, 15 low priority, and 5 species are assessed as adequately represented in ex situ collections. Gap “hotspots”, representing priority target areas for collecting, are concentrated in central Mexico, although the narrow endemic nature of a suite of priority species adds a number of specific additional regions to spatial collecting priorities.

Conclusions/Significance

Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions. A more detailed prioritization of taxa and geographic areas for collection can be achieved by including in the analysis predictive threat factors, such as climate change or habitat destruction, or by adding additional prioritization filters, such as the degree of relatedness to cultivated species (i.e. ease of use in crop breeding). Furthermore, results for multiple crop genepools may be overlaid, which would allow a global analysis of gaps in ex situ collections of the world''s plant genetic resources.     

Regionalization of the avifauna of the Baja California Peninsula, Mexico: a parsimony analysis of endemicity and distributional modelling approach

Aim To analyse the distributional patterns of the Baja California Peninsula's resident avifauna, and to generate a regionalization based on a method that uses a parsimony analysis (parsimony analysis of endemicity, PAE) of point data and modelled potential distributions. Location The Baja California Peninsula, Mexico. Methods A data base was constructed containing records of 113 species of resident terrestrial birds present in the Baja California Peninsula. Records and localities were obtained from the literature and from specimens housed in scientific collections world‐wide. Raw data points and potential distribution maps obtained using the software Genetic Algorithms for Rule‐set Prediction (GARP), were analysed with PAE. Results The data base consisted of 4164 unique records (only one combination of species/locality) belonging to 113 terrestrial resident bird species, in a total of 809 localities. From the point distribution matrix, the analysis generated 500 equally parsimonious trees, from which a strict consensus cladogram with 967 steps was obtained. The cladogram shows a basal polytomy and some geographical correspondence of a few resolved groups obtained in the analysis. These results do not allow the recognition of areas defined by avifaunistic associations. From the potential distribution matrix, the analysis generated 501 equally parsimonious trees, and a strict consensus cladogram of 516 steps was obtained. The cladogram shows a higher resolution because of the number of resolved groups with better geographical correspondence and therefore regions are well‐defined. Main conclusions The correspondence of some groupings of species suggest their validity as areas with biogeographical (historical and/or ecological) meaning. This regionalization in the Baja California avifauna seems to be consistent with previous regionalizations for other groups. Hence, PAE is a useful tool for area categorization if reliable point records and prediction tools are available. Our results suggest that the geographical definition is much better using potential data generated by GARP, particularly when they are contrasted with the results from point data. Thus, this is an excellent alternative for developing biogeographical studies, as well as for improving the use of data from scientific collections and other sources of biodiversity information.     

Passalidae (Coleoptera: Scarabaeoidea) of the Biogeographical Province of Chocó and the West Andean Region of Colombia,with the Description of Two New Species

We present a synopsis of the Passalidae of the Chocó biogeographical province and the western slopes of the Western Andean range of Colombia as a result of field collections, examination of entomological collections, and review of the literature. We record a total of 41 species, provide an identification key, and, for the 39 species for which we were able to examine specimens, include a diagnosis and collecting data. Two new species of Passalus (Pertinax) are described and illustrated. The species of this region compose 42% of the passalid species known for Colombia. The richness of species and the high degree of endemism (34%) indicate the faunistic importance of this area, which is closely related to the fauna of lowland Central America.     

A new comprehensive database of alien plant species in Chile based on herbarium records

There is an urgent need for comprehensive national databases on alien plant species, especially in developing countries. Despite the fact that plant invasions are considered a major threat to biodiversity, they have been poorly studied or not considered a conservation priority in South America. We aim to assess alien plant distribution in Chile, using the first comprehensive public alien plant database, and discuss the implications of using herbarium records to develop national databases of alien plants. We used herbarium records to assemble a comprehensive national database of alien plants. We calculated the number of alien and native species and specimens recorded in each 10 × 10 km cell. We evaluated sampling efforts and tested for relationships between alien and native species collections, as well as other spatial patterns along the latitudinal gradient. Alien and native species richness was positively correlated. Alien plants were mostly collected in central Chile, with few species collected in both the extreme north and south. However, native plants were strongly collected in central Chile, as well as in both extremes of the country. Alien and native plants followed the same pattern of accumulation along the latitudinal gradient, with native plants being relatively more collected than alien plants. Herbarium records provide valuable baseline information to evaluate plant species distribution. However, there are important gaps in this database, (e.g. variable sampling effort for alien and native plants, incomplete information on life-history traits). Given scientists and land managers increasing demand for baseline information and the high cost of collecting such data in developing countries, herbarium records should be used more frequently for research and management of plant invasions.     

Analysing botanical collecting effort in Amazonia and correcting for it in species range estimation

Aim The aim of this study is to analyse the distribution pattern of the botanical collecting effort in Amazonia so that it can be accounted for when interpreting phytogeographical patterns such as inferred species ranges. We also develop a mechanistic and transparent method for taking into account the bias in collecting effort when estimating likelihoods of species occurrences. Location Amazonia, Neotropics. Methods We utilized electronic data sets of georeferenced herbarium collections (1,063,530 in total). We plotted collecting localities (68,246 in total) on maps overlaid with 1° and 0.5° square grids, and analysed collecting effort using a geographical information system (GIS). We also drew a map of Thiessen polygons, using collecting localities as polygon centres, to visualize collecting density in a scale‐independent way. We then created a ‘collecting activity landscape’ in which well‐collected areas appear as peaks and poorly studied areas as valleys. We demonstrate how this surface can be utilized when estimating species distributions. Results The data available to us confirm that botanical collecting activity is still severely biased in Amazonia. The uncollected area represents 43% of the total area of Amazonia, while another 28% is poorly collected and only 2% can be considered relatively well collected. The Thiessen polygon network represents an improvement in the presentation of collecting intensity compared with square grids. Main conclusions The maps of botanical collecting effort in the Neotropics should be used for visually correcting phytogeographical interpretations. With the help of GIS applications the observed spatial bias in collecting effort can be utilized in estimating the likelihood of occurrence of species in a repeatable manner. These estimates, in turn, can be used for various purposes in basic and applied science as well as in decision‐making. The biased collecting effort should, in the long run, be corrected by further field work in unexplored areas, which can be identified with the maps presented here.     

The Indochinese–Sundaic faunal transition at the Isthmus of Kra: an analysis of resident forest bird species distributions

Aim  To establish the geographical position of the biogeographical transition between Indochinese and Sundaic faunas using distributional data for the best-documented taxon, the birds.
Methods  Distributional data of 544 resident forest and forest edge bird species of Thailand and the Thai–Malay peninsula were examined at 45 sites spanning 15° of latitude from northern-most Thailand to the southern peninsular Malaysia. Sites were grouped into 23 degree or half-degree latitudinal zones and avifaunal similarity coefficients were calculated between each zone.
Results  A Mantel test revealed a significant transition between northern Indochinese and southern Sundaic (Indomalay) avifauna assemblages just north of the Isthmus of Kra (10°30' N). Northern and southern range limits of 152 species (> 269 species and subspecies combined) lie between 11° and 13° N.
Main conclusions  This transition between zoogeographical subregions is not coincident with the widely recognized transition between floristic provinces which is traditionally placed 400–500 km further south at the Kangar–Pattani line, but is associated with a change from wet seasonal evergreen dipterocarp rain forest to mixed moist deciduous forest north of the Isthmus of Kra in the northern Thai–Malay peninsula. Climatological and ecological factors associated with the distribution of forest types today are reviewed and it is hypothesized that the avian transition tracks the northern phytogeographical boundary. Palaeogeographical factors, including hypothetical Neogene seaways, which may account for the historical development of both phytogeographical and avifaunal transitions are also described.     

ITE Merlewood Land Classification of Great Britain

Abstract. The Institute of Terrestrial Ecology (ITE) has classified the 1 km squares in Great Britain (GB) into thirty-two environmental strata, termed land classes, as a basis for ecological survey. The classes have been used in biogeographical studies of the distribution of individual species and species assemblages. The concept behind the technique is that there is an association between the environmental character of land and ecological parameters. The initial classification was based on a sample of squares drawn from a regular grid. The data for the 12121 km squares classified were drawn from published maps; the number of squares was limited by the available computing power. Subsequently the availability of more powerful computers and the need to improve geographical definition have led to the allocation of every 1 km square to its appropriate class. This paper has been written to summarise the principles involved in the development of the system and indicate the range of projects for which it has been used. The extension of the classification from a sample to the complete coverage of GB revealed the importance of the structure and style of data used to produce the classification. The significance of these conclusions for future work is discussed, with particular reference to automated methods of data capture.     

Modelling the known and unknown plant biodiversity of the Amazon Basin

Aims The overall aim of this study is to provide the data needed for Amazonian conservation and the sustainable management of the region. To this end I model the hypothetical distribution of plant species richness across the Amazon Basin, the distribution of the proportion of this species richness that can be accounted for by described species, and hence the distribution of the biodiversity which remains unknown. Location Amazonia, Neotropics. Methods Species richness across the Amazon Basin is estimated by comparing the occurrences of 1584 species of Magnoliophyta whose taxonomy and geographical distributions are relatively well known. These data are used to collate checklists for squares of 1° latitude by 1° longitude. Comparison of the checklists allows estimation of the relative expected diversity in the vicinity of each degree square. Summing the distributions of the hypothetical real ranges gives the proportion of the biodiversity that can be accounted for by described species. Subtraction of the second distribution from the first gives a distribution of the contribution to the overall biodiversity that the model predicts, potentially, results from as yet undescribed species. Results Collections documented in recent botanical monographs show an extremely biased distribution with the best knowledge being found in a very few relatively well‐collected areas. At the degree square level, this model predicts that gamma biodiversity in the Amazon Basin is uniformly high across most of the basin. The model predicts that four large areas of the basin are particularly poorly known, and that they should contain large numbers of uncollected species. Main conclusions The model presented here highlights the difficulties of quantifying Amazonian plant diversity and its distribution. The low density of collections, and especially their extremely clumped distribution, undermines confidence in theories that seek to explain the apparent distribution of biodiversity. The model's prediction is substantially different from published predictions of the distribution of alpha diversity. Testing of this model in the areas identified as lacunae would require collecting programmes designed to collect fertile material of rare species. If the model's predictions are approximately accurate, the plant biodiversity of the Amazon Basin is considerably underestimated.     

植物核心种质研究进展

丰富的植物遗传资源为作物育种和遗传研究提供广阔的遗传基础,然而资源庞大的数量也给植物遗传资源的收集、保存、研究和利用带来了困难。Frankel首先提出并与Brown等人完善了核心种质(core collection)的概念,即通过一定的方法从整个种质资源中选择一部分样本,以最小的资源数量和遗传重复,尽可能最大限度的代表整个资源的多样性。核心种质的提出,为遗传资源的研究和利用提供了崭新的解决途径。目前,已在多年生野生大豆、硬粒小麦、花生等20种植物上开展了核心种质研究。本围绕核心种质具有四个显特点即代表性、实用性、有效性、动态性,介绍在不同植物构建核心种质时,所利用的数据、分组原则及取样方法等,并介绍了核心种质的评价进展。通过比较发现,不同植物在构建核心种质各有区别,但是以根据地理来源分组,按聚类法取样为主。目前,对植物核心种质的研究,多处于取样策略的研究阶段。对建成的核心种质评价研究较少,主要集中在农艺性状遗传多样性方面的验证,而时分子水平的验证较少,构建的核心种质还有待于实践的检验。     

Keep collecting: accurate species distribution modelling requires more collections than previously thought

Aim Species distribution models (SDMs) use the locations of collection records to map the distributions of species, making them a powerful tool in conservation biology, ecology and biogeography. However, the accuracy of range predictions may be reduced by temporally autocorrelated biases in the data. We assess the accuracy of SDMs in predicting the ranges of tropical plant species on the basis of different sample sizes while incorporating real‐world collection patterns and biases. Location Tropical South American moist forests. Methods We use dated herbarium records to model the distributions of 65 Amazonian and Andean plant species. For each species, we use the first 25, 50, 100, 125 and 150 records collected and available for each species to analyse changes in spatial aggregation and climatic representativeness through time. We compare the accuracy of SDM range estimates produced using the time‐ordered data subsets to the accuracy of range estimates generated using the same number of collections but randomly subsampled from all available records. Results We find that collections become increasingly aggregated through time but that additional collecting sites are added resulting in progressively better representations of the species’ full climatic niches. The range predictions produced using time‐ordered data subsets are less accurate than predictions from random subsets of equal sample sizes. Range predictions produced using time‐ordered data subsets consistently underestimate the extent of ranges while no such tendency exists for range predictions produced using random data subsets. Main conclusions These results suggest that larger sample sizes are required to accurately map species ranges. Additional attention should be given to increasing the number of records available per species through continued collecting, better distributed collecting, and/or increasing access to existing collections. The fact that SDMs generally under‐predict the extent of species ranges means that extinction risks of species because of future habitat loss may be lower than previously estimated.     

Species richness of the Cladocera (Branchiopoda: Anomopoda and Ctenopoda) in southern Thailand, and its complementarity with neighboring regions

Seventy-two cladoceran species from southern Thailand include eleven first records. Species accumulation curves were used to estimate the total number of species present, and Chaos estimator was used to extrapolate the species number observed in 212 samples to the total number present. This S*max amounted to 76.06 species, with a low ratio of variance/estimator. Cladoceran faunas were compared by a complementarity index at three levels: between habitat types, between different zones of Thailand, and between Thailand and other countries. The geographical gradient was quite strong, but because not all areas have been studied to the same degree and with the same taxonomic accuracy, some comparisons are robust while others are not.     

中国云南、泰国和越南木兰科植物新资料

报道了木兰科植物中国云南新记录 1亚种 1变种 ,泰国新记录 2种和越南新记录 1种 ,引证标本均保存于中国国家林业局云南珍稀濒特森林植物保护与繁育实验室标本馆 (YCP)     

The contribution of small collections to species distribution modelling: A case study from Fuireneae (Cyperaceae)

The recent and rapid digitization of biodiversity data from natural history collection (NHC) archives has enriched collections based data repositories; this data continues to inform studies of species' geographic distributions. Here we investigate the relative impact of plant data from small natural history collections (collections with < 100,000 specimens) on species distributional models in an effort to document the potential of data from small NHCs to contribute to and inform biodiversity research. We modelled suitable habitat of five test case species from Fuireneae (Cyperaceae) in the United States using specimen records available via the Global Biodiversity Information Facility and that of data ready to mobilize from two regional small herbaria. Data were partitioned into three datasets based on their source: 1) collections-based records from large NHCs accessed GBIF, 2) collections-based records from small NHCs accessed from GBIF, and 3) collections-based records from two small regional herbaria not yet mobilized to GBIF. We extracted and evaluated the ecological niche represented for each of the three datasets by applying dataset occurrences to 14 environmental factors, and we modelled habitat suitability using Maxent to compare the represented distribution of the environmental values among the datasets. Our analyses indicate that the data from small NHCs contributed unique information in both geographic and environmental space. When data from small collections were combined with data from large collections, species models of the ecological niche resulted in more refined predictions of habitat suitability, indicating that small collections can contribute unique occurrence data which enhance species distribution models by bridging geographic collection gaps and shifting modelled predictions of suitable habitat. Inclusion of specimen records from small collections in ongoing digitization efforts is essential for generating informed models of a species' niche and distribution.     

Patterns of alien plant distribution at multiple spatial scales in a large national park: implications for ecology, management and monitoring

Aim Spatial scale is critical for understanding and managing biological invasions. In providing direction to managing alien plant invasions, much emphasis is placed on collecting spatially explicit data. However, insufficient thought is often given to how the data are to be used, frequently resulting in the incompatibility of the data for different uses. This paper explores the role of spatial scale in interpreting, managing and monitoring alien plant invasions in a large protected area. Location Kruger National Park, South Africa. Methods Using 27,000 spatially‐explicit records of invasive alien plants for the Kruger National Park (> 20,000 km²) we assessed alien plant species richness per cell at nine different scales of resolution. Results When assessing the patterns of alien plants at the various scales of resolution, almost identical results are obtained when working at scales of quarter‐degree grids and quaternary watersheds (the fourth level category in South Africa's river basin classification system). Likewise, insights gained from working at resolutions of 0.1–0.5 km and 1–5 km are similar. At a scale of 0.1 × 0.1 km cells, only 0.4% of the Kruger National Park is invaded, whereas > 90% of the park is invaded when mapped at the quarter‐degree cell resolution. Main conclusions Selecting the appropriate scale of resolution is crucial when evaluating the distribution and abundance of alien plant invasions, understanding ecological processes, and operationalizing management applications and monitoring strategies. Quarter‐degree grids and quaternary watersheds are most useful at a regional or national scale. Grid cells of 1 to 25 km² are generally useful for establishing priorities for and planning management interventions. Fine‐scale data are useful for informing management in areas which are small in extent; they also provide the detail appropriate for assessing patterns and rates of invasion.     

Comparative leaf anatomy, FTIR discrimination and biogeographical analysis of Camellia section Tuberculata (Theaceae) with a discussion of its taxonomic treatments

A comparative anatomical and FTIR study on the leaves of 18 disputed species of section Tuberculata (Camellia, Theaceae) combined with their biogeographical distribution have been conducted in order to investigate interspecific variations which are useful in species taxonomic treatment and systematic evolution. All Tuberculata species have bifacial and hypostomatic leaves, contain sclereids and crystals. Multivariate analysis of leaf FTIR data shows a visualization of the degree of affinity among the species in this section, which is consistent with the distribution of synonymous Tuberculata species indicated in the biogeographical maps. Our study indicates that the combination of characters based on leaf comparative anatomy, FTIR analysis and biogeographical distribution are useful in species revision. The results determine 11 species in section Tuberculata and provide the evolutionary trends in Tuberculata, which originated in three-river region of Guizhou province and spread to Guizhou, Guangxi, Yunnan, Sichuan, Chongqing, Hunan and probably Hubei provinces of China.     

Filling gaps in species distributions through the study of biological collections: 415 new distribution records for Neotropical Cryptinae (Hymenoptera,Ichneumonidae)

Filling gaps in species distributions is instrumental to increase our understanding of natural environments and underpin efficient conservation policies. For many hyperdiverse groups, this knowledge is hampered by insufficient taxonomic information. Herein we provide 415 new distribution records for the parasitic wasp subfamily Cryptinae (Hymenoptera, Ichneumonidae) in the Neotropical region, based on examination of material from 20 biological collections worldwide. Records span across 227 sites in 24 countries and territories, and represent 175 species from 53 genera. Of these, 102 represent new country records for 74 species. A distinct “road pattern” was detected in the records, at least within Brazil, where 50.2% of the records fall within 10 km of federal roads, an area that occupies only 11.9% of the surface of the country. The results help to identify priority areas that remain poorly sampled and should be targeted for future collecting efforts, and highlight the importance of biological collections in yielding new information about species distributions that is orders of magnitude above what is provided in most individual studies.