Community ecology of absent species: hidden and dark diversity

Community ecologists have so far focused mainly on species identified at a site. I suggest that we can understand better patterns and their underlying processes in ecological communities if we also examine those species absent from the sampled community. However, there are various types of absences, which all harbour different information. Hidden diversity comprises species that are absent from our sight: dormant or locally very rare species overlooked by traditional sampling. Fortunately, modern DNA‐based techniques can help us to find hidden species when analysing environmental samples. Depending on habitat type and sampling scale, a large number of co‐existing species might be hidden. Dark diversity comprises absent species that constitute the habitat‐specific species pool. Dark diversity can be determined based on data on species distribution, dispersal potential and ecological requirements. If we know both observed and dark diversity, we can estimate community completeness and infer those processes that determine which species in the species pool actually co‐exist locally. In addition, most species in the world do not actually belong to the habitat‐specific species pool of the community: their ecological requirements differ or their distribution area is elsewhere. Such other absent species are usually not directly relevant to a particular community. However, knowing ecologically suitable species from other regions can give early warning of possible future invasion of alien species (alien dark diversity). To conclude, species presences have meaning only if there are absences (and vice versa). Methods to detect absent species are rapidly developing and will soon form a standard toolbox for community ecology.     

Identification and characterization of Colletotrichum species associated with anthracnose on persimmon in Brazil

Persimmon (Diospyros kaki) anthracnose is a major threat in production areas worldwide. Most of the studies are focused on Colletotrichum horii, but other species have been reported as well. The association of distinct Colletotrichum species present in Brazilian persimmon production regions as well as their host ranges are yet elusive. The aims of this work were to identify and characterize Colletotrichum species associated with the persimmon anthracnose. In a survey performed in four production regions of Brazil, 88.7% and 11.3% out of 231 isolates were identified as members of Colletotrichum gloeosporioides species complex (Cgc) or Colletotrichum acutatum species complex (Cac), respectively. A subset of 18 isolates were identified through multilocus phylogenetic analysis, using ITS-rDNA region and two loci, namely GAPDH and TUB2. This study revealed the presence of four species: C. horii (38.8%) and Colletotrichum fructicola (27.7%) from the Cgc and Colletotrichum nymphaeae (27.7%) and Colletotrichum melonis (5.8%), from the Cac. Additionally, 13 isolates were selected for morphological, physiological, and pathogenic analyses. Contrasting characteristics were observed among species of the Cgc and Cac complexes. The optimal temperature for mycelial growth and germination were higher for Cgc species. The percentage of appressoria melanisation also varied across complexes. All the identified species were able to cause anthracnose-like symptoms on persimmon fruit, leaves, shoots, and sepals. Colletotrichum species from persimmon were also able to infect apple and pear. The findings will support decisions to manage anthracnose of persimmon under high infection risk due to multiple host susceptibility.     

Taxonomy and species delimitation in Cryptosporidium

Amphibians, reptiles, birds and mammals serve as hosts for 19 species of Cryptosporidium. All 19 species have been confirmed by morphological, biological, and molecular data. Fish serve as hosts for three additional species, all of which lack supporting molecular data. In addition to the named species, gene sequence data from more than 40 isolates from various vertebrate hosts are reported in the scientific literature or are listed in GenBank. These isolates lack taxonomic status and are referred to as genotypes based on the host of origin. Undoubtedly, some will eventually be recognized as species. For them to receive taxonomic status sufficient morphological, biological, and molecular data are required and names must comply with the rules of the International Code for Zoological Nomenclature (ICZN). Because the ICZN rules may be interpreted differently by persons proposing names, original names might be improperly assigned, original literature might be overlooked, or new scientific methods might be applicable to determining taxonomic status, the names of species and higher taxa are not immutable. The rapidly evolving taxonomic status of Cryptosporidium sp. reflects these considerations.     

Population structure and diversity in cultivated and wild Luffa species

1. Download : Download full-size image

     

Medicinal plant conservation and management: distribution of wild and cultivated species in eight countries

In order to understand the particular challenges that medicinal plant conservation and management raise at the global level, it is necessary to address issues pertaining their distribution and the environments where they grow. When reviewing medicinal plant studies from eight countries in four regions we found that a high proportion of the reported medicinal plants had wide distributions across countries and continents. Most plants are found wild (40.5%) or naturalized (33.9%), while only 3.3% are cultivated. Since many species are distributed in wild conditions, cultivated and naturalized in several continents, conservation and management interventions would be best served through collaboration between host countries.     

Multilocus sequence analysis of homologous recombination and diversity in Arthrobacter sensu lato named species and glacier-inhabiting strains

Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato. We also collected a total of 31 cold-adapted Arthrobacter sensu lato strains from two cold glaciers located in northwest China and two temperate glaciers in southwest China, and evaluated their diversity and population structure by MLSA. The glacier strains displayed high diversity, but rates of recombination among the four glacier groups were quite low, indicating that barriers to homologous recombination formed in the past among the populations on different glaciers. Our findings indicate that historical glaciation events shaped the contemporary distributions, taxonomic relationships, and phylogeographic patterns of Arthrobacter sensu lato species on glaciers.     

Why georeferencing matters: Introducing a practical protocol to prepare species occurrence records for spatial analysis

Species Distribution Models (SDMs) are widely used to understand environmental controls on species’ ranges and to forecast species range shifts in response to climatic changes. The quality of input data is crucial determinant of the model's accuracy. While museum records can be useful sources of presence data for many species, they do not always include accurate geographic coordinates. Therefore, actual locations must be verified through the process of georeferencing. We present a practical, standardized manual georeferencing method (the Spatial Analysis Georeferencing Accuracy (SAGA) protocol) to classify the spatial resolution of museum records specifically for building improved SDMs. We used the high‐elevation plant Saxifraga austromontana Wiegand (Saxifragaceae) as a case study to test the effect of using this protocol when developing an SDM. In MAXENT, we generated and compared SDMs using a comprehensive occurrence dataset that had undergone three different levels of georeferencing: (1) trained using all publicly available herbarium records of the species, minus outliers (2) trained using herbarium records claimed to be previously georeferenced, and (3) trained using herbarium records that we have manually georeferenced to a ≤ 1‐km resolution using the SAGA protocol. Model predictions of suitable habitat for S. austromontana differed greatly depending on georeferencing level. The SDMs fitted with presence locations georeferenced using SAGA outperformed all others. Differences among models were exacerbated for future distribution predictions. Under rapid climate change, accurately forecasting the response of species becomes increasingly important. Failure to georeference location data and cull inaccurate samples leads to erroneous model output, limiting the utility of spatial analyses. We present a simple, standardized georeferencing method to be adopted by curators, ecologists, and modelers to improve the geographic accuracy of museum records and SDM predictions.     

Molecular systematics of pinniped hookworms (Nematoda: Uncinaria): species delimitation,host associations and host-induced morphometric variation

Hookworms of the genus Uncinaria have been widely reported from juvenile pinnipeds, however investigations of their systematics has been limited, with only two species described, Uncinaria lucasi from northern fur seals (Callorhinus ursinus) and Uncinaria hamiltoni from South American sea lions (Otaria flavescens). Hookworms were sampled from these hosts and seven additional species including Steller sea lions (Eumetopias jubatus), California sea lions (Zalophus californianus), South American fur seals (Arctocephalus australis), Australian fur seals (Arctocephalus pusillus), New Zealand sea lions (Phocarctos hookeri), southern elephant seals (Mirounga leonina), and the Mediterranean monk seal (Monachus monachus). One hundred and thirteen individual hookworms, including an outgroup species, were sequenced for four genes representing two loci (nuclear ribosomal DNA and mitochondrial DNA). Phylogenetic analyses of these sequences recovered seven independent evolutionary lineages or species, including the described species and five undescribed species. The molecular evidence shows that U. lucasi parasitises both C. ursinus and E. jubatus, whereas U. hamiltoni parasitises O. flavescens and A. australis. The five undescribed hookworm species were each associated with single host species (Z. californianus, A. pusillus, P. hookeri, M. leonina and M. monachus). For parasites of otarids, patterns of Uncinaria host-sharing and phylogenetic relationships had a strong biogeographic component with separate clades of parasites from northern versus southern hemisphere hosts. Comparison of phylogenies for these hookworms and their hosts suggests that the association of U. lucasi with northern fur seals results from a host-switch from Steller sea lions. Morphometric data for U. lucasi shows marked host-associated size differences for both sexes, with U. lucasi individuals from E. jubatus significantly larger. This result suggests that adult growth of U. lucasi is reduced within the host species representing the more recent host–parasite association. Intraspecific host-induced size differences are inconsistent with the exclusive use of morphometrics to delimit and diagnose species of Uncinaria from pinnipeds.     

Molecular taxonomy and species delimitation in Andean Schistocerca (Orthoptera: Acrididae)

The acridian genus Schistocerca comprises about 50 species which are endemic to the New World, except the Old World locust S. gregaria. Their morphological identification is rendered difficult by phase polyphenism, geographical overlap due to migrations or swarming, the difficulty to easily differentiate genitalia and the occurrence of interspecific hybrids. The three species reported from Peru include the swarming species S. interrita, a pest that can be recognized only by taxonomists. We show that it can be unambiguously identified using a mitochondrial DNA fragment known to have barcoding properties in this genus. We used several methods to delimitate Peruvian species. While S. interrita and S. pallens were well characterized, S. piceifrons peruviana was split into several taxa by a phylogeny-based method, whereas a combination of population genetics methods led one to identify only the three nominal species. A tentative reconstruction of the species history shows that several populations of S. piceifrons peruviana have recently increased in number, while exchanging some migrants, whereas an isolated population at the northern margin of the species range is substantially differentiated while exchanging no migrants with the others. This complex history has resulted in an atypical lineage pattern that appears to have confounded the standard assumptions underlying available species delimitation methods. Because of its behavioral property which tends to keep it panmictic, the identification of the swarming S. interrita remained unaffected.     

Foraging ecology and reproductive biology of the Stonechat Saxicola torquata: comparison between a revitalized, intensively cultivated and a historical, traditionally cultivated agro-ecosystem

An effective strategy to reintegrate biodiversity within otherwise intensively cultivated agroecosystems is to create set-aside and wildflower areas. It remains largely unknown, however, whether the ecological performance of an agroecosystem revitalized in this manner is comparable—from a species’ population biology perspective—to traditionally exploited farmland. To address this question we compared, during two successive years, the trophic ecology and breeding performance of an insectivorous, indicator passerine (the Stonechat Saxicola torquata) in a revitalized intensively cultivated farmland (RIC) and a traditional, extensively cultivated farmland (TEC) in southern Switzerland. The chicks' diet and prey abundance did not differ between the RIC and TEC, with orthopterans, caterpillars (Lepidoptera) and coleopterans predominating (approx. 80% of diet biomass). Although Stonechat pairs initiated more broods in TEC than in the RIC, reproductive success (number of fledglings/territory × year) did not differ significantly between the TEC and RIC. The chicks’ condition (body mass) was slightly better in TEC than in RIC, while no such effect could be shown for chick constitution (tarsus length) in either year. The inter-site (RIC vs. TEC) variation fell well within the inter-annual variation of breeding parameters, indicating that environmental stochasticity could be a greater determinant of reproductive output and young quality than agroecosystem type. Although in need of replication, these results suggest that incentives for setting aside farmland and creating wildflower areas within agroecosystems may not only enhance plant and invertebrate diversity, as has been demonstrated earlier, but can also support functioning populations of vertebrates situated at higher trophic levels along the food chain.     

The Paxillus involutus (Boletales, Paxillaceae) complex in Europe: Genetic diversity and morphological description of the new species Paxillus cuprinus, typification of P. involutus s.s., and synthesis of species boundaries

Paxillus involutus is a model species for ecological or physiological studies of ectomycorrhizal agaricomycetes. Three to six groups or species linked to it have been ecologically and morphologically distinguished. Phylogenetic studies have revealed the existence of four species in Europe: Paxillus ammoniavirescens, Paxillus obscurisporus, P. involutus, and a fourth as yet not described species. We studied 47 collections from 24 French and Italian locations, supplemented with GenBank data, in order to genetically and taxonomically delineate these species. Phylogenetic analyses of three nuclear DNA regions (rDNA internal transcribed spacer (ITS), tef1-α, and gpd) confirmed the four European species. Morphology, culture, and ecology features allowed us to delineate species boundaries and to describe the fourth species we named Paxillus cuprinus since it turns coppery with age. As there is no existing original herbarium specimen for P. involutus, one of our collections was chosen as the epitype. The low genetic diversity found in P. cuprinus correlates with stable morphological traits (basidiome colour, ovoid–amygdaliform spores with an apical constriction) and with ecological preferences (association with Betulaceae in open and temperate areas). In contrast, P. ammoniavirescens is characterized by a high genetic diversity and a high variation of its morphological and ecological features.     

Tropical rain forest fragmentation and its ecological and species diversity changes in southern Yunnan

Three fragmented rain forests and one primary forest in southern Yunnan were plotted. The microclimate and soil conditions of these forests were also studied. The following conclusions were drawn: (1) The microclimatic differences between inside and outside forest are less in the fragmented forests than in the primary forest, which indicates that the buffer effects to climatic change have been reduced in the fragmented forests. The soil has deteriorated to some extent due to forest fragmentation. (2) In species composition, especially the abundance of some species and the dominant ranks of some families have changed with fragmentation. Barringtonia macrostachya, the most dominant species in the control primary forest, disappeared from the fragmented forests, while Antiaris toxicaria, which is a characteristic but not dominant species in the primary forest, is dominant in fragmented forests. (3) The total number of species per plot was reduced in the fragmented forests and the more seriously disturbed the fragment was, the more the species richness diminished. (4) In life form spectra, the liana and microphanerophyte species increased, but epiphyte, megaphanerophyte, mesophanerophyte and chamaephyte species decreased in the fragmented forests. (5) The plant species diversity is generally lower in the fragmented forests than in the primary forest, although for some life forms it could be higher. (6) The tree species with small populations could be lost first in the process of rain forest fragmentation. (7) The heliophilous or pioneer tree species increased and the shade-tolerant species were reduced in the fragmented forests.     

Thermal ecology of five Cnemidophorus species (Squamata: Teiidae) in east coast of Brazil

In this study we compared the body temperature of 16 populations belonging to five species of the genus Cnemidophorus from restinga habitats along the eastern coast of Brazil in order to evaluate the importance of how some environmental factors affect lizard body temperatures. Cloacal body temperatures (T_b) were taken immediately after capture with a quick-reading thermometer (Schultheis). Substrate temperatures (T_s) and air temperatures (T_a; approximately 1 cm above the substrate) were taken as close as possible to the point when each lizard was initially sighted. Most of the mean body temperatures in activity of the different populations and species of Cnemidophorus along the coast of Brazil ranged from 36.5 to 39.3 °C, except for Cnemidophorus lacertoides (T_b=35.2 °C) in the restinga of Joaquina, SC and for Cnemidophorus ocellifer (T_b=34.8 °C ) in the restinga of Praia do Porto, SE. Some studies show that the body temperature of lizards is more related to phylogenetic than ecological factors, suggesting that species of the same genus tend to have similar body temperatures even occurring in different types of environments. In general, regardless of the locality and latitude along the eastern coast of Brazil, the different species of lizards of the genus Cnemidophorus and their respective populations have similar body temperatures in activity and the apparent differences result from the influence of the local thermal environment of each restinga.     

Outcrossing and hybridization in wild and cultivated foxtail millets: consequences for the release of transgenic crops

Summary Outcrossing rates within the wild green foxtail, Setaria viridis, and the cultivated foxtail millet, S. italica, are very low. However, spontaneous interspecific hybridizations in the experimental garden occurred in both directions at rates ranging from 0.002% to 0.6% according to plant density and distance between parents. Offtypes found in farmers' fields where foxtail millet is cultivated were shown to have originated from such interspecific crosses. Differences in the EcoR1 patterns of chloroplast DNA between cultivated and wild plants indicated that reciprocal crosses do occur in the field. These findings indicate that even a largely selfing cultivated species may exchange genetic information with wild relatives at rates that may cause problems if transgenic cultivars are released.     

A toolbox for integrative species delimitation in Machilis jumping bristletails (Microcoryphia: Machilidae)

Accurate species delimitation is fundamental for many fields of biology. Although a wide range of evolutionary-biological patterns are known to promote failure in species delimitation when any single information source is considered, the majority of species characterisations are still based on single disciplines. Using Alpine jumping bristletails we here showcase the establishment of morphological and molecular tools for multi-source species delimitation in a taxonomically problematic arthropod group and stress its advantages over single-discipline approaches. Once sound species delimitations have been achieved, Alpine jumping bristletails will be available as a prime model system for addressing questions related to the emergence of endemism and parthenogenesis.     

Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR

Agrobacteria are common soil bacteria that interact with plants as commensals, plant growth promoting rhizobacteria or alternatively as pathogens. Indigenous agrobacterial populations are composites, generally with several species and/or genomic species and several strains per species. We thus developed a recA-based PCR approach to accurately identify and specifically detect agrobacteria at various taxonomic levels. Specific primers were designed for all species and/or genomic species of Agrobacterium presently known, including 11 genomic species of the Agrobacterium tumefaciens complex (G1-G9, G13 and G14, among which only G2, G4, G8 and G14 still received a Latin epithet: pusense, radiobacter, fabrum and nepotum, respectively), A. larrymoorei, A. rubi, R. skierniewicense, A. sp. 1650, and A. vitis, and for the close relative Allorhizobium undicola. Specific primers were also designed for superior taxa, Agrobacterium spp. and Rhizobiaceace. Primer specificities were assessed with target and non-target pure culture DNAs as well as with DNAs extracted from composite agrobacterial communities. In addition, we showed that the amplicon cloning-sequencing approach used with Agrobacterium-specific or Rhizobiaceae-specific primers is a way to assess the agrobacterial diversity of an indigenous agrobacterial population. Hence, the agrobacterium-specific primers designed in the present study enabled the first accurate and rapid identification of all species and/or genomic species of Agrobacterium, as well as their direct detection in environmental samples.     

Plant species diversity in cape fynbos: Gamma and delta diversity

Summary This paper reports the number of plant species on circumscribed fynbos areas (gamma diversity), ranging in size from 0.27 km² (a site with 364 species) to 471 km² (2351 species). The composition of the floras of four of these sites was analysed to measure delta diversity, the change in flora from one site to the next. Maximum gamma diversity values fitted a species-area curve log S=2.69+0.25 log A. Gamma diversity is apparently higher than in any of the world's biogeographic zones except perhaps the tropical rain forest, and in other South African sites of areas around 1.0 km², which have about as many species. High delta diversities are reflected in differences between fynbos floras of 50 to 70 %, in spite of relative proximity; this degree of diversity is apparently unmatched anywhere. The results support the conventional view that fynbos plant diversity is partly a consequence of the peculiar geography of the zone, and of palaeo-climatic change, which have favoured geographic speciation.This paper would not have been possible without the conscientious work of staff at Jonkershoek, especially that of R.A. Haynes and E.F. Kruger. The information on the floras of each area studied here has been built up through decades of field work by various collectors. Identifications of the many difficult taxa are due to taxonomists at the National Herbarium, at the Compton Herbarium, Kirstenbosch and at the Bolus Herbarium, University of Cape Town. M. F. Thompson and E. E. Esterhuysen contributed materially in this respect.Paper presented at the Annual Congress of the South African Association of Botanists, Stellenbosch, January 1979.This work is based partly on the results of the conservation research programme of the South African Department of Forestry and the Botanical Research Institute's programme on fynbos phytosociology, and is published with permission of our respective heads of Departments.     

History and conservation of wild and cultivated plant diversity in Uganda: forest species and banana varieties as case studies

The history of wild and cultivated plant diversity in Uganda is reviewed, taking forest species and bananas as examples. Palynological research into past human influences on forests is reassessed. The evidence suggests that crops were first introduced into the country at about 1,000 BCE, farming communities practicing slash and burn agriculture started to significantly influence the floristic composition of forests during the 1st millennium BCE and there was a major episode of forest reduction at about 1,000 CE related to socio economic change. Bananas were probably introduced in the early centuries CE. The colonial era from 1894 saw the introduction of new concepts of land ownership and the establishment of forest reserves and agricultural stations. Forests and banana diversity are currently under threat, Uganda having a very high rate of deforestation and endemic banana varieties proving susceptible to introduced pests and diseases. It is suggested that, under these circumstances, conservationists take an opportunistic approach to field engagement, making use of favourable local conditions as they arise. Partnerships should be sought with elements of society concerned with sustainable use, provision of ecosystem services and cultural survival to widen the social base of plant conservation. International organisations involved in conservation of plant genetic resources and wild plant species should collaborate with one another to develop the conceptual basis of plant conservation, to make it more relevant to countries like Uganda.