Achieving Target 2 of the Global Strategy for Plant Conservation: building a preliminary assessment of vascular plant species using data from herbarium specimens

The Global Strategy for Plant Conservation calls for a preliminary assessment of the conservation status of all known plant species by the year 2010. To date insufficient progress has been made on meeting this target. New efforts to develop a preliminary list beyond using the full IUCN criteria in plant assessments are needed. Here we present an algorithm that provides a preliminary assessment of the conservation status of plant species using data from herbarium specimens. We use Hawaiian specimen data from the United States National Herbarium to calibrate the parameters of the algorithm and then use specimen data from the Arecaceae, Commelinaceae, Gesneriaceae and Heliconiaceae as examples of the application of the algorithm. The algorithm was calibrated to insure 95% accuracy in placing the Hawaiian plant species into previously and independently determined threatened categories. Our results indicate that 28% of the Hawaiian taxa, 27% of the species of Arecaceae, 45% of the species of Commelinaceae, 32% of the species of Gesneriaceae, and 35% of the species of Heliconiaceae are Not Threatened and will not need any further evaluation for the preliminary assessment. Species identified here as Potentially Extinct and Potentially Threatened can be further assessed by additional herbarium material and/or conservation specialists for final evaluation using other assessment strategies (e.g., regional and national lists, taxonomic expert assessment, etc.).     

Defining a role for herbarium data in Red List assessments: a case study of Plectranthus from eastern and southern tropical Africa

Red Lists are widely used to indicate species at risk of extinction. Specimen sheets in herbaria provide an important source of data relevant for Red List assessments. The aims of this paper are to establish which data can be sourced from specimen information to satisfy IUCN Red Data List criteria and to identify the specific criteria that can be used. Red List parameters are measured within a Geographical Information System (GIS), as this provides an objective and repeatable methodology which is less subjective than manual methods. Data used to explore this were gathered during the course of preparing a monograph on Plectranthus (Lamiaceae). Criteria relating to distribution (extent of occurrence, area of occupancy and fragmentation) and population profile (projected continuing decline and number of subpopulations) proved most suitable for assigning categories of threat. Estimates of mature individuals, generation length, population size, population reduction, extreme fluctuation and number of locations could not be derived from herbarium material without making inconsistent subjective decisions. In addition to comprehensively databased specimen information, extensive field knowledge is required to produce better estimates for assessing extinction risk. In order to enhance the usefulness of specimen information in the future, improvements in recording additional botanical data at the time of collection would be beneficial. Overall, herbaria provide a useful starting point for conservation-related work and can help to guide future work.     

Genetic variation in time and space: the use of herbarium specimens to reconstruct patterns of genetic variation in the endangered orchid Anacamptis palustris

Habitat alteration, fragmentation and destruction as a consequence of human impact are a global phenomenon. Here we document changes in genetic variation in the marsh orchid Anacamptis palustris as a consequence of such habitat changes. We examined historical specimens that were collected during the nineteenth and early twentieth centuries, prior to the most recent massive habitat changes affecting this species. Sequences of a hypervariable region in the plastid DNA, located in the tRNA^LEU intron, from herbarium vouchers were compared with those from a near-exhaustive survey of the extant A. palustris populations on the Italian peninsula. It was found that private haplotypes and alleles found in small, extant populations were once widespread and more common in historic populations and that alleles, once present in historic populations, have gone extinct. In addition, genetic differentiation among populations has increased over time and haplotype frequencies significantly differ among historic and extant populations. These results document that human induced habitat changes have reduced genetic diversity and increased the importance of random genetic drift in this species. It is concluded that the analysis of herbarium specimens may provide important insights into changes of genetic diversity over time and may be critical for correct inference of the evolutionary history of rare and endangered species.     

The contribution of common and rare species to plant species richness patterns: the effect of habitat type and size of sampling unit

Understanding how overall patterns of spatial variation in species richness are affected by distributional patterns of species has been an area of growing concern. In the present study, we investigated the relative importance of common and rare species as contributors in overall plant species richness. We further examined if the effects of common or rare species in richness patterns are affected by the size of the sampling units and if the observed patterns hold at different habitats. We used a dataset of 5,148 higher plant species distributed across 16,114 sampling plots located in 240 sites of the NATURA 2000 network of Greece. We ranked all species based on the number of sites they occupied and we developed a common to rare and a rare to common sequence. We correlated those sequences with cumulative species distributions. We performed this analysis in nine different sizes of sampling units and in three different datasets referring to (a) all habitat types together, (b) coniferous habitats only and (c) alpine habitats only. Our analysis showed that despite the proportionally higher numbers of restricted species, widespread species make a greater contribution to overall richness patterns and that this observed pattern does not depend on the size of the sampling units. Moreover, the observed pattern stands for different habitat types. Our findings support the generality of this pattern and highlight the importance of widespread species as adequate indicators of biodiversity patterns at various habitat types. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The relationship between percentage of singletons and sampling effort: A new approach to reduce the bias of richness estimates

Estimate the richness of a community with accuracy despite differences in sampling effort is a key aspect to monitoring high diverse ecosystems. We compiled a worldwide multitaxa database, comprising 185 communities, in order to study the relationship between the percentage of species represented by one individual (singletons) and the intensity of sampling (number of individuals divided by the number of species sampled). The database was used to empirically adjust a correction factor to improve the performance of non-parametrical estimators under conditions of low sampling effort. The correction factor was tested on seven estimators (Chao1, Chao2, Jack1, Jack2, ACE, ICE and Bootstrap). The correction factor was able to reduce the bias of all estimators tested under conditions of undersampling, while converging to the original uncorrected values at higher intensities. Our findings led us to recommend the threshold of 20 individuals/species, or less than 21% of singletons, as a minimum sampling effort to produce reliable richness estimates of high diverse ecosystems using corrected non-parametric estimators. This threshold rise for 50 individuals/species if non-corrected estimators are used which implies in an economy of 60% of sampling effort if the correction factor is used.     

Sampling effort and common species: Optimizing surveys of understorey fruit-feeding butterflies in the Central Amazon

Surveys on tropical invertebrates must gather as much information as possible over the shortest period, mainly because of financial limitations and hyperdiversity. Fruit-feeding butterflies in the subfamilies Biblidinae, Charaxinae, Nymphalinae and Satyrinae (Nymphalidae) are attracted to decaying material and can be sampled with standardized methodologies, but (1) some groups can be difficult to collect, despite being quite common in Amazonian forest understorey; moreover, (2) the duration of the sampling period is not consistent among studies and (3) the sufficient effort for financially limited projects remains unknown. With this study, we aimed to fulfill points 1–3 in order to recommend a less costly protocol for monitoring purposes in the Amazon. In 25 km² of rainforest in the state of Amazonas, Brazil, we evaluated the performance of sampling schemes for these butterflies (four, three, two and one visit in 250 m-long plots), using both nets and bait traps, while considering reductions in sampling effort and the removal of rare and infrequent taxa to optimize field and laboratory work. Reduced-effort schemes are only validated if they reflect both taxonomic and ecological information provided by the maximum effort. Procrustes superimposition was used to estimate the dissimilarity in the spatial distribution of species between schemes. Spatial turnover in herb, liana, palm tree and diameter-at-breast-height > 10 cm tree species composition was used as predictor for the butterfly community through linear regressions. The three-visit scheme was sufficient to retrieve high species similarity and the ecological patterns observed with maximum effort. The two-visit scheme lost a significant amount of information on species composition similarity, but recovered stronger environmental relationships than those observed with the four-visit scheme. The removal of uncommon species did not affect the ecological response of the community, thereby suggesting that common species are driving the spatial patterns of the studied butterflies. Thus, large reductions in costs by reducing sampling effort could be achieved with relatively little loss of information on the species turnover of butterflies and their relationships with the environment. The proposed sampling protocols with reduced effort will allow projects to use their time and financial supply more effectively, showing that cost-effective shortcuts for biodiversity assessments can be useful for conservation, biomonitoring and land use management.     

Genetic differentiation among populations of an oceanic island: The case of Metrosideros boninensis, an endangered endemic tree species in the Bonin Islands

Conservation of endemic species on oceanic islands is an essential issue for biodiversity conservation. Metrosideros boninensis (Myrtaceae) is an endangered tree species endemic to the Bonin Islands of the western North Pacific Ocean. This species is considered to be extremely rare with less than 400 adult individuals, a number that has fluctuated between the 1880s and 1980s through human influence. We analyzed the genetic diversity and genetic structure of this species using amplified fragment length polymorphism markers and microsatellite markers. Genetic diversity of M. boninensis was extremely low compared to related taxa and similar endemic species from small islands. This low genetic diversity might be attributed to a stepwise colonization process with repeated founder bottlenecks in the dispersal pathway to the Bonin Islands. Populations of M. boninensis showed significant genetic differentiation and isolation by distance over a small geographical scale, despite the fact that this species should have extensive gene dispersal ability. This genetic differentiation might be caused by limited gene flow via pollen and seed among populations and genetic drift amid a small number of remnant individuals. Taken together, these findings suggest that the genetic diversity and connectivity of tree populations on islands are more vulnerable to habitat fragmentation than previously thought. We offer some recommendations for management to ameliorate habitat fragmentation and biological invasion.     

Heterogeneity in dynamic species abundance models: the selective effect of extinction processes

There is often large variation in traits across the species of a community. In particular, variation in life history traits affecting population dynamics is likely to affect the species abundance distribution. Applying a dynamic and heterogeneous species abundance model we study how differences in extinction time for species in a community act as a force changing the distribution of dynamic parameters across species. This process may generate communities that are more heterogeneous then the heterogeneity measured as the species enter the community. Analytical results for some versions of the lognormal and gamma species abundance model are given as exemplifications of this process, together with stochastic simulations demonstrating the temporal changes in number of species and community heterogeneity through time.     

Improving the assessment of species compositional dissimilarity in a priori ecological classifications: evaluating map scale,sampling intensity and improvement in a hierarchical classification

Question: Can species compositional dissimilarity analyses be used to assess and improve the representation of biodiversity patterns in a priori ecological classifications? Location: The case study examined the northern‐half of the South‐east Queensland Bioregion, eastern Australia. Methods: Site‐based floristic presence–absence data were used to construct species dissimilarity matrices (Kulczynski metric) for three levels of Queensland's bioregional hierarchy – subregions (1:500 000 scale), land zones (1:250 000 scale) and regional ecosystems (1:100 000 scale). Within‐ and between‐class dissimilarities were compiled for each level to elucidate species compositional patterns. Randomized subsampling was used to determine the minimum site sampling intensity for each hierarchy level, and the effects of lumping and splitting illustrated for several classes. Results: Consistent dissimilarity estimates were obtained with five or more sites per regional ecosystem, 10 or more sites per land zone, and more than 15 sites per subregion. On average, subregions represented 4% dissimilarity in floristic composition, land zones approximately 10%, and regional ecosystems over 19%. Splitting classes with a low dissimilarity increased dissimilarity levels closer to average, while merging ecologically similar classes with high dissimilarities reduced dissimilarity levels closer to average levels. Conclusions: This approach demonstrates a robust and repeatable means of analysing species compositional dissimilarity, determining site sampling requirements for classifications and guiding decisions about ‘lumping’ or ‘splitting’ of classes. This will allow more informed decisions on selecting and improving classifications and map scales in an ecologically and statistically robust manner.     

Drosophilids (Diptera) from Mayotte island: an annotated list of species collected in 2013 and comments on the colonisation of Indian Ocean Islands

Summary. The Indian Ocean Islands are a most interesting region for evolutionary studies of terrestrial organisms and, among insects, the Drosophilidae family occupies a privileged position. The Comoros archipelago was, up to now, the least explored place among all the islands. We present here the results of a collection on one of the four main islands, Mayotte. From 4500 collected flies, 25 species were distinguished. The biology, ecology and biogeography of each species are discussed. Considering the extant known species from all islands, five evolutionary scenarios are proposed, ranging from the invasive, cosmopolitan, man-transported species to endemic species restricted to a single island. Some species raise a puzzling problem: despite having a very narrow and specialised ecological niche, they are broadly distributed on most islands and also on the African mainland.     

Inclusion of phytosociological data in an index of vegetation fire danger: application and mapping on the Karst area around Trieste (Italy)

In this paper we propose a method to produce maps of fire danger index (FDI). The index includes in the formula a vegetation pyrogenic potential index (VPPI) based on floristic phytosociological data. The map of FDI is produced by integrating available phytosociological maps of vegetation, geomorphology and climate, using the Geographic Information System technology. The method is applied to an area of the coastal Classical Karst (NE-Italy). While fire risk maps based on the incidence of previous fires are useful for facilitating emergency operations, e.g. the allocation of fire fighting resources, we conclude that the proposed index offers an effective tool to plan actions for fire prevention.     

Relationships among fire frequency, rainfall and vegetation patterns in the wet–dry tropics of northern Australia: an analysis based on NOAA-AVHRR data

Aim To quantify the regional‐scale spatio‐temporal relationships among rainfall, vegetation and fire frequency in the Australian wet–dry tropics (AWDT). Location Northern Australia: Cape York Peninsula, central Arnhem, central Kimberly, Einasleigh Uplands, Gulf Fall Uplands and northern Kimberley. Methods Monthly ‘fraction of photosynthetic active radiation absorbed by green vegetation’ (fAPAR) was decomposed into monthly evergreen (EG) and monthly raingreen (RG) components using time‐series techniques applied to monthly normalized difference vegetation index (NDVI) data from Advanced Very High Resolution Radiometer (AVHRR) imagery. Fire affected areas were independently mapped at the same spatio‐temporal resolution from AVHRR imagery. Weather station records were spatially interpolated to create monthly rainfall surfaces. Vegetation structural classes were derived from a digitized map of northern Australian vegetation communities (1 : 1,000,000). Generalized linear models were used to quantify relationships among the fAPAR, EG and RG signals, vegetation structure, rainfall and fire frequency, for the period November 1996–December 2001. Results The fAPAR and EG signals are positively correlated with annual rainfall and canopy cover, notably: EG_{closed forest} > EG_{open heathland} > EG_{open forest} > EG_woodland > EG_{open woodland} > EG_{low woodland} > EG_{low open woodland} > EG_{open grassland}. Vegetation height and fAPAR are positively correlated, excluding the special case of open heathland. The RG signal is highest where intermediate annual rainfall and strong seasonality in rainfall coincide, and is associated with vegetation structure as follows: RG_{open grassland} > RG_woodland > RG_{open forest} > RG_{open heathland} > RG_{low woodland} > RG_{open woodland} > RG_{low open woodland} > RG_{closed forest}. Monthly RG tracks monthly rainfall. Annual proportion of area burnt (PB) is maximal where high RG coincides with low EG (open grassland, several woodland communities). PB is minimal in vegetation where both RG and EG are low (low open woodland); and in vegetation where EG is high (closed forest, open heathland). Conclusions The RG–EG scheme successfully reflects digitally mapped tree and grass covers in relation to rainfall. RG–EG patterns are strongly associated with fire frequency patterns. PB is maximal in areas of high RG, where high biomass production during the wet season supports abundant fine fuel during the dry season. PB is minimal in areas with high EG, where relatively moist fuel limits fire ignition; and in areas with low EG and RG, where a relative short supply of fuel limits fire spread.     

Individual identification and distribution assessment of otters (Lutra lutra) through non-invasive genetic sampling: Recovery of an endangered species in the Basque Country (Northern Spain)

Non-invasive genetic techniques have proven to be cost-effective for monitoring and studying otter populations, largely due to the linearity of otter territories and the marking behavior of the species. After a severe decline, in the 60, the Eurasian otter is recovering in the Iberian Peninsula. However, the recovery pattern is not homogeneous and the species is still considered “Threatened” in many regions. During 2007–2010 a systematic non-invasive genetic sampling effort was carried out to determine the spatial distribution and to estimate the population size of an endangered otter population in northern Iberian Peninsula (Basque Country). Samples were identified to species level by sequencing a 226 bp mtDNA fragment prior to genotyping. Among the 132 obtained samples, 127 (98.4%) belonged to the study species, one sample was genetically identified as European mink (Mustela lutreola) and one as American mink (Neovison vison) while genetic species confirmation was not possible in the three remaining samples. These results provided novel and accurate data on species distribution, highlighting an overall increase of 25% in 10 × 10 UTM grids occupied by otter and a clear pattern of re-colonization upstream of the main rivers. All samples corresponding to otter were subsequently individually genotyped using a novel multiplex panel of 11 microsatellite markers and sexed by typing the sex-chromosome-related gene ZFX/ZFY. We obtained a complete individual genetic profile for 55 samples (genotyping success 43%), corresponding to 20 different individuals (11 females, 6 males, and 3 individuals of unknown gender). The mean otter density in occupied areas estimated to be 0.09 (0.06–0.12) individuals per river kilometer. The present study enabled us to obtain updated and relevant information about this elusive species’ distribution and population size, essential to define population status and to design successful and effective management and conservation programs.