The use of herbarium specimens in DNA phylogenetics: Evaluation and improvement

During the last few years we have been confronted with the need to use herbarium specimens in the molecular phylogeny studies, since it is generally difficult to obtain living material of some rare species. Ancient DNA has been sequenced, and there are also reports on successful DNA amplification from herbarium specimens. However, it is not easy to obtain amplified DNA from the first herbarium sample tested. In this paper, experiments are described about trials of DNA amplification from two to 151-year-old herbarium specimens of plant species we needed for our projects. Of the 17 herbarium samples tested only two allowed DNA amplification under standard DNA isolation conditions. Different types of PCR inhibiting activities were demonstrated in DNA extracts. In some of the extracts there was extremely low concentration of template with satisfactory quality. In some instances, PCR inhibiting activities were successfully removed by treating them either with insoluble polyvinylpyrrolidone or by adding bovine serum albumin (BSA) to the amplification mixture. However, some PCR-inhibiting activities were resistant to the treatments described above. When the concentration of template was very low, a second PCR amplification with internal primers was necessary to increase the amount of DNA for sequencing. Nevertheless, contamination of either DNA extract or amplification mixture were sometimes observed, and consequently precautions were taken to minimize them. Finally, successful amplification was obtained in eight samples out of the 17 examined.     

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.).     

Weed invasion in East Africa: insights from herbarium records

The invasion process was documented from data on the labels of specimens stored in the East African Herbarium at the National Museums of Kenya. We analysed data from seven abundant alien plant species: Ageratum conyzoides L. (Asteraceae), Capsella bursa‐pastoris (L.) Med . (Brassicaceae ) , Datura stramonium L. (Solanaceae), Galinsoga parviflora Cav. (Asteraceae), Tagetes minuta L. (Asteraceae), Spergula arvensis L. (Caryophyllaceae) and Stellaria media (L.) Vill. (Caryophyllaceae) and compared these data with the spread of two native weeds: Cynoglossum coeruleum A.DC. (Boraginaceae) and Senecio discifolius Oliv. (Asteraceae). Although all investigated species had been already recorded before the Second World War, most specimens were collected between 1960 and 1980. This regional spread is correlated with a change in the agricultural systems of Kenya. The early records of alien weeds were restricted to higher altitudes. With the increasing human population and the associated increase of agricultural activities (e.g. irrigation in arid areas) the weed species from South America were able to spread to lower altitudes.     

Sampling procedures and species estimation: testing the effectiveness of herbarium data against vegetation sampling in an oceanic island

Questions: What is the relationship between species assemblages in herbarium collections and species abundances in the field, and how trustworthy are herbarium data in vegetation science? Location: Guadalupe Island, Baja California, Mexico. Methods: We compared species‐abundance distribution and evenness in 110 vegetation plots in Guadalupe Island against data from four herbaria. We tested whether the relative frequencies derived from herbarium specimens differed significantly from species frequencies in the field. We compared the rarefaction curves for both field and herbarium data sets, and tested whether taxonomic collectors accumulated new species at a higher rate than that observed in ecological plot sampling. Results: At any given sampling effort, the total number of observed species was higher in herbarium data. The relative abundance of common species in the field was higher, and the evenness of the distribution was lower, than in herbarium data. There was no significant correlation between species abundances in the field and in the herbaria. By selectively targeting rare species, collectors accumulate previously unseen species much faster than through ecological sampling. Conclusions: Because collectors aim for the rarer species and avoid the more common ones, the relative abundance of species in herbarium collections cannot be interpreted as a predictor of their true abundance in the field. Any statistical procedure that requires the sample to be representative of the true abundance distribution is likely to show errors when applied to herbarium data. However, because collectors actively search for rare species their rate of species accumulation is higher and their floristic lists are more complete than those obtained through ecological field sampling.     

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.     

Herbarium records in Arctic dwarf shrub dendrochronology: Methodological approach and perspectives

Our work aims to investigate whether herbaria resources can be used for the extension of Arctic dwarf shrub chronologies. The current use of herbaria reaches far beyond their initially aims; among the new applications, phenology observations and conservation biology can be mentioned. However, to this date, no studies on the use of herbarium specimens for dendrochronological research have been published. Examples of perennial plants from herbarium sheets that could potentially be used for such studies are dwarf shrubs, samples of which often consist of whole specimens, including the root system, the root collar and branches. Here, we present a protocol for the selection and processing of historical material. Based on the collections from Kew and Copenhagen, which are among of the largest herbaria with Arctic plants, a database of 25 areas from the Atlantic sector of the Arctic was created. Material from the following most common species was collected: grey willow (Salix glauca L.), polar willow (Salix polaris Wahlenb.), dwarf willow (Salix herbacea L.), net-leaved willow (Salix reticulata L.), arctic willow (Salix arctica Pall.), mountain avens (Dryas octopetala L.), dwarf birch (Betula nana L.). We present the preliminary results of a case study using historical samples of Salix arctica from the Thule (Qaanaaq) area, NW Greenland. Dwarf shrubs can commonly reach the age of 80–100 years or beyond, while herbaria resources may allow the extension of such series over the last centuries. Therewith, these resources may provide an excellent proxy data source on the changing natural environment beyond the northern and upper tree limits, where well-replicated proxy time-series remain sparse.     

Alien vascular plants in Iceland: Diversity,spatial patterns,temporal trends,and the impact of climate change

The present study provides first comprehensive and up-to-date results on alien plant taxa in Iceland since 1967. We evidenced the presence of 336 alien vascular plant taxa, including 277 casuals and 59 naturalised taxa, two being invasive. The distribution of the alien flora exhibits a clear spatial pattern showing hotspots of occurrence and diversity within areas of major settlement centres. Altitude above sea level and temperature-related variables proved to be the most important factors shaping alien plant distribution in Iceland. Predictive modelling evidenced that arctic areas of Iceland and the Central Highlands are under serious risk of alien plant invasion due to climate change. The results provide crucial information for alien and invasive plant management and contribute data for meta-analyses of invasion processes worldwide.     

Spiny invaders – Patterns and determinants of cacti invasion in Europe

In this paper, we analyse the patterns and determinants of cacti invasion in 22 European countries. We compiled a checklist for each country. Cacti were classified for each country according to their invasion status as casuals, locally established (1–5 localities of small population size) and widely established (>5 localities of considerable population size).We used generalised linear models (GLM) from the Poisson family with a log-link function and a set of seven country-specific explanatory variables to account for geographical, climatic, habitat-related and economic determinants to test which features of the recipient area determine invasion success and if distribution patterns of species at different invasion stages are governed by the same interplay of explanatory variables. Separate models were fitted with the same predictor variables for casual, locally established, widely established and all cacti. Further, we analysed the temporal invasion trend, and tested if niche breadth (expressed as the number of habitat types colonized) is influenced by the range size (measured as the number of countries invaded). Finally, we reviewed the consequences of cacti invasion for nature conservation.In total, 26 cacti species have been recorded in Europe. Ten species are more widespread and occur in at least three countries, Opuntia humifusa (six countries) being the most widespread species. The country with most cacti is Spain (21 species), whereas in 13 countries no cactus species have been recorded. By far the most important genus is Opuntia with 20 alien species. The temporal invasion pattern shows an exponential increase of the cumulative number of invasion events, increasing from three (1801–50) to nine (1951–2000) invasion events over a 50-year period.Regardless of the invasion stage, the factor explaining most of the variance in the models is the presence of the Mediterranean biogeographic region, and a significant positive effect of the country size on species numbers was identified.Considering the invasion stage, some interesting deviations in the models can be observed. Invasion of casual cacti is only influenced by the presence of the Mediterranean biogeographic region. For locally established cacti, precipitation is negatively correlated with the invasion rate, and the presence of the Alpine biogeographic region is positively correlated; the latter is due the local occurrence of few hardy cacti (Opuntia phaeacantha, O. humifusa) in low-lying valleys of the Alps. As all widely established cactus species are restricted to the Mediterranean region, only this factor was included in the model.All cacti are confined to dry, open habitats on acid siliceous bedrock. Thus, the predominant habitats invaded are rock vegetation, dry grassland, open Mediterranean scrub and dry ruderal habitats. The niche breadth of cacti increases with the numbers of countries colonized. Further, the niche breadth of cacti exhibits a geographic gradient towards the Mediterranean region.Until the 19th century, the dominant pathway of invasion was agriculture, as some cactus species had been introduced for the production of forage and fruits. However, in the last decades horticulture and deliberate planting in the wild have become the dominant pathways.The invasion of cacti in natural and semi-natural habitats in the Mediterranean region changes habitat structure and species composition. However, dense and extensive stands of cacti are restricted to few species (e.g. Opuntia ficus-indica).     

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.     

Invasive alien plants in China: diversity and ecological insights

China’s current invasive alien plant species were analyzed with regard to their floristic status, biological attributes and invasion status elsewhere. Most of the 270 species identified were annuals, followed by perennial herbs. Woody perennials made only about 10% of the species. The invasives were comprised of 59 families, the largest being Asteraceae, Poaceae, and Brassicaceae. The genera with most invasive species were Amaranthus, Ipomoea, and Solanum. Most of the species originated from the New World, notably from South America. About one-third of the species were serious invaders of natural habitats in countries other than China. The proportion of invasive alien plants in province floras ranged from 0.5 to 3.8%, absolute numbers from nine to 117 species per province. Density of invasive species was correlated positively with native species density at provincial scale. The results demonstrate that in China invasive plants are present throughout the country, with a particularly high species richness in the Southeast. The ecological diversity of invasive plants suggests wide ranging impacts which need to be assessed.     

The historical spread of Ambrosia artemisiifolia L. in France from herbarium records

Aim The problems in public health and field management in France caused by Ambrosia artemisiifolia L. require a better knowledge of the introduction and naturalization of this species in both the past and present. Location France. Methods The pattern of spread of A. artemisiifolia was investigated through the study of herbarium specimens. More than 1200 specimens were found in 58 herbaria and virtual herbaria in France and in bordering countries. The spread was analysed by mapping the localities for each 30‐year period since 1863. Specific indications as ‘new plant’ were used to determine the timing of the introduction of the species into a new area. Results It seems that the spread of A. artemisiifolia is not linked to its presence in botanical gardens. The study of specimen labels indicates that this species has been introduced in France in seed crops at various independent geographical points and at various times since its introduction in natural habitats. Commercial trade and American troops have contributed to its spread. Main conclusions The spread of the species in area and in time over France showed no clear front: new localities separated by large distances were colonized simultaneously. Cumulative numbers of localities show a continuous increase during the twentieth century. Herbarium specimens can be used to follow the spread of A. artemisiifolia.     

Alien and native plants show contrasting responses to climate and land use in Europe

Aim We tested whether the distribution and cover of alien plant species in Europe was related to human disturbance and microclimate. Location Surveys were conducted at 13 sites across Europe, each containing a pair of landscapes with different land‐use intensities. Methods Sampling locations were chosen based on land use and microclimate at two scales: land use was characterized at the patch and landscape scale; climate was expressed as regional and local temperature. The slope of each sample location was derived from a digital elevation model. Cover of plant species was measured using point counts and analysed using mixed effect models. Species were classified as native, archaeophytes and neophytes (pre‐ versus post‐ad 1500 immigrants). Due to the zero inflation observed in the alien groups, their cover was analysed conditional on their presence. Results Anthropogenic disturbance was a significant explanatory variable, increasing the presence and cover of alien species and decreasing the cover of native species. Alien presence was increased in sites under agricultural management, while their cover responded to land use at both local and landscape scales (and to their interaction), such that only natural habitats in semi‐natural landscapes had low alien cover. Microclimate was important for neophytes, with presence concentrated around mesic conditions. Slope was relevant for archaeophytes and native species, suppressing the former group and promoting the latter one. Main conclusions We found that, at the European scale, the distribution of alien plants is related to anthropogenic disturbance more than to microclimatic differences. The presence of neophytes, however, was influenced by climate at local and regional scales, with the highest incidence under mesic conditions. The different patterns observed for the presence and cover of alien species suggest different mechanisms acting during their establishment and spread. They also suggest that to counteract the expansion of alien species natural habitats may need to be maintained at landscape scales.     

Down under the southeastern Pacific: marine non-indigenous species in Chile

This article presents the first compilation of marine non-indigenous species (NIS) of algae and macro-invertebrates invading Chilean waters. A total of 32 cosmopolitan and non-cosmopolitan species are reported. Among them there are six species considered as extending their southern range of distribution in connection with El Niño events. The article highlights negative and positive impacts caused by marine NIS invasions. Among the first are Codium fragile var. tomentosoide, considered as a pest in Gracilaria chilensis aquaculture facilities in northern Chile, and Ciona intestinalis, a pest in scallop aquaculture installations. Among the second are bio-engineers species, such as the ascidian Pyura praeputialis and the sea grass Heterozostera tasmanica, which have caused an increase in local biodiversity and enhancement of nursery grounds via the creation of new habitats. Further more, invaders such as the algae Mastocarpus papillosus, Porphyra linearis and P. pseudolinearis represent new exploitable resources, extracted by coastal food gatherers along the coast (M. papillosus) or potential species to develop aquaculture. Additional information is presented on the anemone Anemonia alicemartinae, which appears to be a native species (?), having shown in the past 40–50 years, a geographical southward range extension of approximately 1900 km. The number of NIS reported for Chile is compared with those published for the southwestern Atlantic, South Africa, North America (Atlantic and Pacific coasts) and New Zealand. It is suggested that probably the low number of Chilean NIS is due to the fact that the Chilean coasts are environmentally less stressed than other coasts in the world, due to the scarcity of estuaries, gulfs, enclosed bays, lagoons and low human populations. These kinds of sheltered areas have been suggested as centers for bio-invasions, due to the high rate of human-mediated transfer and increase of pollutants. Furthermore, none of NIS reported from Chile show a fast geographical expansion rate (exception of A. alicemartinae), nor invading strategies such as those described for marine NIS in other latitudes, where notorious ecological unbalances following invasions have been observed. An alternative hypothesis is that the low number of marine NIS invading Chile is underestimated, since the modern list of species generated through specific taxonomically intensive port and harbor surveys is still lacking. Fifteen species (five invertebrate and 10 fish) have been deliberately imported to Chile for aquaculture. The invertebrates appear to be controlled within aquaculture facilities and have not established naturalized populations or caused direct ecological impacts on local communities. On the contrary, several millions of salmoniforms (and rainbow trout) have escaped from farming facilities in southern Chile and established naturalized populations. Studies on ecological impacts are lacking. These escapees are also playing a role in the enhancement of artisanal and sport fishery activities.     

A case study to quantify the value of voucher specimens for invertebrate conservation: ant records in Lower Austria

Ant records for Lower Austria date back to 1802. Since then, the number of presently recognized central European ant species has increased from 34 to 165. Taxonomic changes and former misidentifications have unfortunately made published historical data unreliable. Therefore, in preparing for the publication of the Red List of Ants of Lower Austria, all voucher specimens from the available major collections were redetermined at the species level. This amounted to a total of 18500 pre-1980 specimens, and 42000 post-1980 specimens. Currently, there are 111 ant species recorded for Lower Austria (including three introduced species). Twelve of these are published here for the first time for Lower Austria, six for all Austria, and one of these is a so far unknown species, discovered among historic voucher specimens. Voucher specimens provide information on the pre-1980 situation of 108 (=97% of the known) species and 32% of the surface area of Lower Austria.     

Environment and dispersal paths override life strategies and residence time in determining regional patterns of invasion by alien plants

We describe a novel dissimilarity framework to analyze spatial patterns of species diversity and illustrate it with alien plant invasions in Northern Portugal. We used this framework to test the hypothesis that patterns of alien invasive plant species richness and composition are differently affected by differences in climate, land use and landscape connectivity (i.e. Geographic distance as a proxy and vectorial objects that facilitate dispersal such as roads and rivers) between pairs of localities at the regional scale. We further evaluated possible effects of plant life strategies (Grime's C-S-R) and residence time. Each locality consisted of a 1 km² landscape mosaic in which all alien invasive species were recorded by visiting all habitat types.Multi-model inference revealed that dissimilarity in species richness is more influenced by environmental distance (particularly climate), whereas geographic distance (proxies for dispersal limitations) is more important to explain dissimilarity in species composition, with a prevailing role for ecotones and roads. However, only minor differences were found in the responses of the three C-S-R strategies. Some effect of residence time was found, but only for dissimilarity in species richness. Our results also indicated that environmental conditions (e.g. climate conditions) limit the number of alien species invading a given site, but that the presence of dispersal corridors determines the paths of invasion and therefore the pool of species reaching each site. As geographic distances (e.g. ecotones and roads) tend to explain invasion at our regional scale highlights the need to consider the management of alien invasions in the context of integrated landscape planning. Alien species management should include (but not be limited to) the mitigation of dispersal pathways along linear infrastructures. Our results therefore highlight potentially useful applications of the novel multimodel framework to the anticipation and management of plant invasions.     

Increasing the Understanding of Plant Invasions in Southern South America: First Symposium on Alien Plant Invasions in Chile

The first symposium on Alien Plant Invasions in Chile was held in southern Chile in November of 2002. Chile represents an interesting setting to study biological invasions because of its long history of introductions, and its high rate of endemisms that makes it more prone to invasions. However, little is known about plant invasions in Chile and the country lacks a clear policy on alien species. The speakers at the symposium discussed their research on several aspects of alien plant invasions in southern Chile and Argentina. They also elaborated a list of future challenges of plant invasion ecology for the area. The package of recommendations may be useful for other developing countries with similar state of knowledge of their flora and similar environmental and economic issues. We expect that this type of meeting will help to stimulate the scientific debate about invasion ecology and the development of coordinated research to answer local questions, while contributing to find generalities in plant invasion patterns and processes.     

Differential rates of invasion in three related alien oak gall wasps (Cynipidae: Hymenoptera)

Abstract. Three related species of oak gall wasps, Andricus corruptrix (Schlechtendal), A. kollari (Hartig) and A. lignicola (Hartig) have entered Britain since the introduction of Turkey oak, Quercus cerris L. in 1735. Their lifecycles involve alternating generations between an agamic generation on the native oak species (Q. petraea, Q. robur and their hybrid Q. x. rosacea), and a smaller, sexual generation on the alien Q. cerris. In examining the distributions of these insects and Q. cerris, we hypothesized that: (1) the invasion will spread more rapidly in places where both host trees are equally abundant than through regions where one of the tree species is substantially less common than the other; (2) interspecific competition between these bud‐galling species will lead to a negative correlation between their abundances at a particular site; (3) differential recruitment of natural enemies from the native hymenopteran fauna will slow the rate of spread in a species‐specific manner. A. kollari arrived nearly 200 years ago and is now found throughout the British Isles, wherever Turkey oak is grown. A. lignicola and A. corruptrix have been here for 30 years, after establishing in S.E. England. A. lignicola is in its final rapid stages of range expansion across England, southern Scotland and N.E. Scotland. A. corruptrix is just beginning to spread through Central and S.W. England. It has occupied proportionally fewer sites behind its invasion front than have the other two species, but is no less abundant at these sites. Nevertheless, distance leaps of up to 50 km were identified in A. lignicola in N.E. Scotland, and the possibility of long‐distance transport of infected trees through the horticulture and forestry trades remains. The co‐occurrence of mature individuals of both host Quercus species does appear to have increased their rates of colonization in A. lignicola and A. corruptrix. There is no evidence, however, to suggest that interspecific competition between the three alien gall formers is an important factor in determining their distributions and abundance within their invaded ranges. All three species have recruited parasitoids and inquilines rapidly from the native fauna; attack rates were highly variable, but showed no evidence of density dependence across sites.