Population baseline data for monitoring genetic diversity loss for 2010: A case study for Brassica species in the UK

The Convention on Biological Diversity and the subsequent International Treaty on Plant Genetic Resources for Food and Agriculture have proved a watershed in plant genetic resources (PGR) conservation and consequent initiatives have set various PGR conservation targets to be met by 2010. The aim of our paper is to develop ideas and issues concerning the monitoring of natural genetic resources: particularly in terms of developing a baseline from which to measure levels of genetic diversity. Three species of Brassica (B. nigra, B. oleracea, B. rapa) found wild in the UK were assessed for levels of genetic diversity using AFLP. The relationship between genetic distribution and ecogeographic distribution was considered for each species to determine patterns that may be useful in formulating conservation strategies. Genetic distance between populations of B. nigra and B. rapa were correlated to geographic distance. Levels of genetic polymorphism in B. oleracea were correlated to soil pH while in B. rapa they were correlated to soil coarseness. In terms of PGR conservation these findings may suggest an emphasis toward in situ conservation of a selection of disparate populations would be appropriate where possible as such adaptations may be lost in ex situ collections.     

How important is clonal recruitment for population maintenance in rare plant species?: the case of the narrow endemic cactus, Stenocereus eruca, in Baja California, México

Stenocereus eruca is a postrate columnar cactus whose regeneration seems to occur mainly through clonal propagation. It is a narrow endemic species of the Sonoran desert in Baja California Sur and currently considered as threatened under Mexican legislation. In this paper we describe the demography of ramets in four populations along its distribution range and the demography of genets in one population during a 3-year-study period in order to evaluate its conservation status. We also analyze the relative contribution of sexual reproduction and clonal propagation to population maintenance and provide guidelines for the formulation of conservation programs. Elasticity analyses were used to explore the relative contribution of sexual and clonal recruitment to projected population growth rate (λ). During the three years of study, regeneration occurred only through clonal propagation while sexually derived seedlings were not detected within or outside the permanent plots. Our demographic data showed that the four population of S. eruca are in equilibrium (λ ≈ 1), and elasticity analyses showed that the relative contribution to λ of clonal recruitment was larger than sexual recruitment, at least during the analyzed ecological time scale. Simulations showed that removing sexual recruitment had a minor impact on λ, but the absence of clonal propagation alone was sufficient to keep below unity. We propose the establishment of at least one reserve with adequate protection from human disturbance to conserve S. eruca.     

How well does a botanical garden collection of a rare palm capture the genetic variation in a wild population?

Conservation is increasingly central to the botanic garden mission. Living plant collections are important components of conservation. Critical evaluation of living conservation collections with population genetic analysis can directly inform ex situ conservation strategy. Here, we quantify the degree of genetic variation captured through a population-based collection protocol, and explore optimal sampling for ex situ conservation. An extensive living collection derived from one population of Leucothrinax morrisii (Arecaceae) provided a model system. We compared 58 specimens from the ex situ collection with 100 individuals from throughout the parent population via 6 ISSR loci. Random bootstrapped resamples of the data were made to model differently structured ex situ collections. Mean diversity (He) differed little between the collection (0.204) and the population (0.216), and genetic distance (D) was very close (0.036). Very few private alleles were found between the collection and the population. Allelic capture, as measured by percent of private alleles, was greater than 94%. Resampled collections of different sizes captured from 48% to 94% of alleles. Pairwise comparison of bootstrapped resamples suggests that increasing the representation of half-sibling groups does not significantly increase allele capture. Increase in allele capture with increasing sample size is greatest at low resample sizes, and showed diminishing returns as resample size increased. No appreciable increase in allele capture was gained through maintaining different half-sibling groups. These data inform sampling for ex situ conservation purposes, and recommend sample sizes of at least 15 individuals, with the upper limit based on resources.     

Modelling bryophyte distribution based on ecological information for extent of occurrence assessment

For some groups such as bryophytes, the IUCN distribution criteria are of critical importance to evaluate threat status, since other parameters cannot be determined readily. In this study, we propose the use of ecological niche modelling methods to estimate the extent of occurrence (EOO) of species. Herbarium (LISU) collection data are used to estimate the potential distribution of bryophytes based on three different methods: GARP, MAXENT and ENFA. The records of bibliographic references were projected against model predictions, and used for validation purposes using the receiver operating characteristic (ROC) method, as well as knowledge about ecological and geographic affinities.Four species (Antitrichia californica, Riccia sommieri, Cryphaea heteromalla and Racomitrium hespericum) were chosen as case studies; they were selected to represent taxa with contrasting ecological requirements, biogeographic importance and conservation value. The main difference between the two approaches (topological and ecological) for determining EOO is that the former only consider species distribution in space, whereas ecological methods may include both spatial distribution as well as environmental ranges. The methodological advance presented here explores the links between population distribution and environmental data, filling the gaps between distribution and administrative borders.     

Threatened deer of the world: Research programmes for conservation

This paper is the sequel to an earlier publication (see Biological Conservation, Vol. 5, No. 4 pp. 243–250, October 1973) on the conservation status of deer and describes an IUCN programme for the conservation of world-threatened deer. Research requirements for conservation of deer that are currently threatened with extinction are discussed. The immediate conservation objective is to ensure the species' or subspecies' survival, and the long-term objective is to restore their productive status in the wild. A framework for research to provide data to guide conservation practices is outlined. It comprises a set of research questions, to aid the planning of studies, and statements of the conservation action potential of the results of these investigations. The proposed organization of the IUCN programme and its current status is described. University and other research institutions that would be interested in participating or co-operating in the programme are invited to write to IUCN.     

Towards an ecologically-sustainable forestry in the Atlantic Forest

Since pristine Atlantic Forest remnants are vanishing, and biological reserves are in short, conservation of biodiversity will largely depend on proper management of the anthropogenic matrix. Here, we test (1) the effectiveness of ecologically-managed tree monocultures in maintaining Araucaria Forest biodiversity, (2) how this effectiveness change among taxa, and (3) we discuss management principles that can be used by the forestry industry in order to contribute positively to biodiversity conservation. The study was conducted in the São Francisco de Paula National Forest, southern Brazil, an environmental mosaic composed mostly of patches of Araucaria Forest and ecologically-managed monocultures of Araucaria, Pinus and Eucalyptus. Using standardized sampling methods in these four main habitats, we have recorded the richness and species composition of small mammals, birds, leaf-litter frogs, butterflies, galling insects, spiders, opiliones, flatworms, woody plants, epiphytic angiosperms, epiphytic ferns, lichens, and fruit-body producing fungi. Overall, we recorded 506 species in Araucaria Forest, 181 (36%) of which were exclusive of this habitat while 325 (64%) could be found in at least one monoculture. Distribution patterns of species richness and number of records across taxonomic groups showed that a large biodiversity can be found inside ecologically-managed plantations of Araucaria, Pinus, and Eucalyptus. For all studied taxa, except for epiphytic angiosperms and fruit-body producing fungi, more than half of the Araucaria Forest species could be found living on monocultures. We discuss how the actual management practices of the forest industry can be improved to contribute positively to the conservation of the Atlantic Forest biodiversity.     

Potential distribution modelling, niche characterization and conservation status assessment using GIS tools: a case study of Iberian Copris species

Dung beetle populations, in decline, play a critical ecological role in extensive pasture ecosystems by recycling organic matter; thus the importance of their conservation status. Presence data available for Copris hispanus (L.) and Copris lunaris (L.) (Coleoptera, Scarabaeidae) in Comunidad de Madrid (CM), and BIOMAPPER, a GIS-based tool, was used to model their environmental niches. The so derived potential distributions of both species were used to exemplify the utility of this kind of methodologies in conservation assessment, as well as its capacity to describe the potential sympatry between two or more species. Both species, distributed along a Dry-Mediterranean to Wet-Alpine environmental conditions gradient, overlap in areas of moderate temperatures and mean annual precipitations in the north of CM. Copris are poorly conserved in the existing protected sites network, but protection provided by new sites included in the future Natura 2000 Network will improve the general conservation status of these species in CM.     

Contrasting levels of mitochondrial DNA variability between mites (Penthalodidae) and springtails (Hypogastruridae) from the Trans-Antarctic Mountains suggest long-term effects of glaciation and life history on substitution rates, and speciation processes

We carried out a comparative study using mtDNA (COI) for two free-living, endemic, terrestrial invertebrate taxa—the springtail Gomphiocephalus hodgsoni (Hypogastruridae) and the mite Stereotydeus mollis (Penthalodidae) collected from sites throughout Victoria Land and the Queen Maud Mountains, Antarctica. Maximum likelihood (ML) analyses revealed low levels of intraspecific substructuring for G. hodgsoni (?2% sequence divergence) with groups mostly corresponding to geographic location. Other well-defined (morphological) species within the Hypogastruridae ranged from 15% to 22% sequence divergence relative to G. hodgsoni. In contrast, ML analyses for S. mollis showed considerably higher levels of intraspecific divergence (up to 18% sequence divergence), suggesting the presence of morphologically cryptic species. Other presently described mite species were also readily discernible (14-18% sequence divergence). Within both G. hodgsoni and S. mollis there were three main groups corresponding to: (1) Taylor Valley; (2) Beaufort Island; and (3) Ross Island together with the adjacent continental sites. We suggest that a common pattern of climatic and geological history over long-term glacial habitat fragmentation have determined the similar geographic and haplotype distributions found for both species. However, a large variation in substitution rate, around eight times slower for G. hodgsoni, compared to S. mollis, may be due to their different life history strategies on the Antarctic continent.     

Coppice management effects on experimentally established populations of three herbaceous layer woodland species

Traditional coppice management creates a temporal release of resources. We determined how this affected three herbaceous species (Cardamine pratensis, Primula elatior and Geum urbanum) and if it was suitable for their conservation within woodland given their differing phenologies and habitat affinities for woodland.Reproductive adults were transplanted and their fate, i.e. survival and counts of leafs and flowers, plus the fate of their progeny, were monitored for three years following cutting of coppice shoots (three light levels) or yearly autumn mowing.Cardamine pratensis and P. elatior produced more flowers with increasing light availability. Mowing increased flower and leaf production with time for P. elatior. Seedling numbers followed a similar trend. Geum urbanum initially produced more flowers with increasing light and when mown, but the effect disappeared and did not increase seedling numbers. Its basal leaves showed the opposite pattern. Population growth rates (λ), calculated for P. elatior and G. urbanum, confirmed the strong treatment effects on the former and the absence of effects on the latter. Yet, decomposition of treatment effects, showed considerable flexibility in life history of G. urbanum, except for contributions of fecundity. The latter, however, contributed most to positive effects on λ for P. elatior.Early flowering species with an affinity for open habitats (C. pratensis > P. elatior) benefited more from temporal resource release than the later flowering, typical woodland species. Coppice management thereby maintains both typical forest herbs and herbs with affinity for more open habitats. This is an important conservation tool especially in intensively managed landscapes.     

Species diversity versus phylogenetic diversity: A practical study in the taxonomically difficult genus Dactylorhiza (Orchidaceae)

Setting conservation priorities in taxonomically complex groups such as the orchid genus Dactylorhiza is a difficult task. As an alternative to taxonomic diversity, we used here a molecular phylogenetic analysis and the results of a genetic investigation using plastid microsatellites with an extensive geographic sampling to assess in a more objective way the patterns of diversity within this genus. Although western Europe is thought to be the main diversity centre for the genus due to the large number of species found there, we found higher phylogenetic and genetic diversity as well as higher endemicity in the Caucasus and the Mediterranean Basin, two biodiversity hotspots. Species number seems to be correlated with taxonomic effort, tentatively estimated here by the number of herbaria, and is thus biased and not an appropriate measure of diversity. Our results show that phylogenetic analyses and genetic data obtained with molecular tools can offer an alternative measure of biodiversity that is not sensitive to taxonomic inflation. Conservation of allotetraploid taxa is also discussed, and it is recommended that sites in which polyploids are formed should be conserved rather than any specific allotetraploid taxon.     

Phylogenetic diversity of endangered and critically endangered southeast Asian softshell turtles (Trionychidae: Chitra)

The intense exploitation of turtles in Asian markets has contributed to declines in turtle populations across the continent. Three-quarters of Asia’s turtles are threatened and half are endangered. A recent workshop on the Asian turtle crisis identified taxonomic studies of widespread species as a priority for research because these low risk species may include unrecognized, narrowly distributed taxa of much higher concern. Chitra indica is a widely exploited softshell turtle (family Trionychidae) found across southern Asia. Individuals from Thailand have been described as a separate species, Chitra chitra, but this has not been universally accepted, and many sources consider Chitra monotypic. Phylogenetic analysis of sequence data from the mitochondrial ND4 gene revealed three deeply divergent, monophyletic lineages within Chitra: C. indica, C. chitra, and a third unnamed form from Myanmar. This new form is probably Critically Endangered, which highlights the importance of systematic studies in determining conservation priorities.     

Plant communities at the periphery of the Atlantic rain forest: Rare-species bias and its risks for conservation

Initiatives that establish species rarity as an indicator of conservation priority might be biased if they disregard important evolutionary and adaptive processes taking place in lower diversity communities and ecotones. Conservation policies regarding the Atlantic forest strongly emphasize the core formation (i.e. the rainforest stricto sensu) rather than the marginal habitats (e.g. restingas, swamps, and high altitude campos) and species that are rare/endemic. To discuss this issue I revisit a hypothesis I have forwarded in 2002 that postulates that plant colonization of habitats marginal to the Atlantic rain forests of the State of Rio de Janeiro was largely related to terrestrial nurse plants that originally, in the rainforest habitat, were canopy plants such as epiphytes or hemi-epiphytes. Adaptations to water and nutrient restrictions, typical of life in the canopy, granted success to such plants upon migration to sandy, swampy or rocky substrates in neighbouring areas. Many such species, then, behaved as nurse plants and favoured colonization of these more extreme habitats by a number of other rainforest species. I now review recent evidence that corroborate this hypothesis, while examining the nature of such nurse plants. In all marginal habitats, nurse plants are often highly abundant locally and have high ecophysiological vigour, while both widespread and endemic species are found among them. Thus, nursing effect, local abundance, and ecophysiological performance are not related to species geographic distribution or to their spectrum of habitat preference. Paradoxically, several abundant nurse plant species have low Darwinian fitness. These studies provoke two reflections. First, the Atlantic forest sensu lato, i.e. the core formation plus the peripheral ones, should be treated collectively as a biodiversity hotspot, rather than the core rainforest formation alone. Second, widespread or common species play important functional roles in such marginal habitats and, despite their ubiquity, ecologically they might be less fit than rare/endemic ones at the local level due, for instance, to current constraints to sexual reproduction. Thus, they should also be targeted as conservation priorities.     

The impact of clonality on an endangered tree (Elaeocarpus williamsianus) in a fragmented rainforest

The occurrence and distribution of clonality in the endangered rainforest tree Elaeocarpus williamsianus (Elaeocarpaceae) was investigated using SSR and RAPD analyses for 170 apparent individual trees found across seven sites. The results obtained with the two molecular techniques were in complete agreement in showing that single clones are present in most of the E. williamsianus sites with two genets occurring at the largest and most adequately protected site. In addition, seed production, viability and germinability were determined for four of these populations. Fruit were produced in all four populations tested although sterile fruit were very common. Only two E. williamsianus trees representing different genets within the same site produced viable seed. The overall genetic diversity within E. williamsianus is much lower than expected and thus the potential for sexual reproduction has been significantly diminished. It is concluded that habitat fragmentation removed an existing balance between vegetative and sexual reproduction in this species. Such findings have added urgency to the management of this species which could include a reintroduction program incorporating the collation of all clones within selected sites.     

Partitioning of molecular variation at local spatial scales in the vulnerable neotropical freshwater turtle, Hydromedusa maximiliani (Testudines, Chelidae): implications for the conservation of aquatic organisms in natural hierarchical systems

Hydromedusa maximiliani is a vulnerable freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD) were surveyed with the purpose of assessing the genetic structure and determining the partitioning of molecular variation in H. maximiliani across the natural spatial hierarchical scale of its habitat. The goal of the study was to integrate ecological data with estimates of molecular genetics diversity to develop strategies for the conservation of this freshwater turtle. Specimens were sampled from rivers and streams across three drainages. Nine of the 80 primers used generated 27 scoreable bands of which 10 (37%) were polymorphic and produced 16 RAPD phenotypes. Significant heterogeneity was found in the distribution of RAPD molecular phenotypes across the three drainages. Analysis of molecular variance for molecular phenotypes showed that the heterogeneity had a spatial structure since a significant amount (22%) of the total variance was attributable to variation among rivers and streams. Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, it is suggested that local populations should be considered as separate management units.     

Habitat selection by the pale-headed brush-finch (Atlapetes pallidiceps) in southern Ecuador: implications for conservation

The pale-headed brush-finch (Atlapetes pallidiceps) is threatened with extinction due to habitat loss, but very little is known about its ecological requirements. We used multiple logistic regression to study habitat selection of this species at landscape, territory, and nest site scales in order to make recommendations about effective management. Habitat selection by the sympatric stripe-headed brush-finch (Buarremon torquatus) was examined with the same methods in order to analyse interspecific resource partitioning and potential competition. The pale-headed brush-finch selected semi-open habitat types with intermediate scrub heights, and avoided forests. Nest sites depended on the presence of vines or bamboo. By contrast, the stripe-headed brush-finch chose dense habitat with low ground cover under tall vegetation and avoided semi-open habitat. The two species had overlapping territories but differed significantly in microhabitat use and the use of vegetation strata. We found no convincing evidence that the stripe-headed brush-finch displaces the pale-headed brush-finch from optimal habitat. The preservation of semi-open scrubland maintained by low-intensity grazing is suggested for future conservation of the pale-headed brush-finch.     

Ecological effects on estimates of effective population size in an annual plant

Effective population size (N_e) is a critical indicator of the vulnerability of a population to allele loss via genetic drift, and it can also be used to assess the evolutionary potential of a population. While some plant conservation plans have focused on outcrossing through cross-pollination as a way to increase estimated N_e, variance in reproductive output determined by ecological factors such as competition can also strongly affect estimated N_e. We examined the effects of intraspecific and interspecific competition, stressful soils, and local adaptation on estimates of N_e in an annual plant species. While ecological influences on plant growth rate variance have been predicted to influence estimates of N_e/N, we found a significant effect on the estimate of N_e/N, but no significant ecological effects on growth rate variance. Lower survivorship on stressful soil was the most important effect reducing estimates of N_e/N. If stochastic mortality is greater in environments that are abiotically stressful, then populations in these stressful environments may be slower to adapt because of lower census sizes and reduction of N_e/N. In populations of conservation concern, increasing survivorship may be of greater benefit for maximizing N_e than the reduction of variability in reproductive output among surviving adults.     

Systematics and conservation of the swift fox,Vulpes velox,in North America

Two subspecies of swift fox have been described for North America, Vulpes velox velox and Vulpes velox hebes, but the latter northern subspecies is no longer recognised as endangered due to controversy over systematic status. We analyse morphological variation in these North American foxes, and conclude that subspecific status for northern populations is probably not justified, even though there is significant geographic variation. Because geographic variation may reflect genetic variation, we feel it should be the object of conservation effort. Although taxa may receive variable conservation attention due to the existence of arbitrary subspecies classifications, such preservation efforts may be desirable.The Canadian Wildlife Service has initiated a swift fox rehabilitation project in Alberta, Saskatchewan, and Manitoba, where foxes are re-introduced from Colorado stock. We urge extreme caution in such programmes because of risk of interbreeding with rare swift foxes known to exist in northern Great Plains states and potential loss of genetic adaption to the rigours of northern environments.     

Converting Australian tropical rainforest to native Araucariaceae plantations alters soil fungal communities

Native rainforest tree plantations are increasingly viewed as potentially important for high value timber production and provision of a range of ecological services in tropical and subtropical areas. In order to determine the extent to which conversion of rainforest to native Araucariaceae plantation influences soil fungi, we compared soil fungal communities under native rainforest and 73-74 year-old Araucaria bidwillii, Araucaria cunninghamii and Agathis robusta plantations at Gadgarra State Forest, Queensland, Australia. Following direct extraction of DNA from soil, terminal restriction fragment length polymorphism (T-RFLP) analysis of rDNA internal transcribed spacer (ITS) regions was conducted. Ordination analysis of the T-RFLP data revealed significant separation of the fungal communities according to forest type along the first canonical axis, with the native rainforest samples separating from the three Araucariaceae plantations along the second axis. Overall, the most abundant ITS sequences in clone assemblages from the four forest types were Ascomycota, followed by Basidiomycota, Zygomycota and Chitridomycota, however their relative importance varied in individual forest types. The results indicate that conversion of tropical rainforest to monoculture plantations of native trees can significantly alter soil fungal diversity.     

Genetic diversity among Elaeagnus compatible Frankia strains and sympatric-related nitrogen-fixing actinobacteria revealed by nifH sequence analysis

Elaeagnus compatible Frankia isolates from Tunisian soil have been previously clustered with Frankia, colonizing Elaeagnaceae and Rhamnaceae in two different phylogenetic subgroups, while strain BMG5.6 was described as a new lineage closely related to Frankia and Micromonospora genera. In this study we further assess the diversity of captured Frankia and the relationship with BMG5.6-like actinobacteria, by using nifH gene sequences. Using PCR-RFLP screening on DNA extracted from lobe nodules, additional microsymbionts sharing BMG5.6 features have been detected proving a widespread occurrence of these actinobacteria in Elaeagnus root nodules. Neighbour-Joining trees of Frankia nifH sequences were consistent with previously published 16S rRNA and GlnII phylogenetic trees. Although four main clades could be discerned, actinobacterial strain BMG5.6 was clustered with Frankia strains isolated from Elaeagnus. The present study underscored the emanation of new diazotrophic taxon isolated from actinorhizal nodules occupying intermediate taxonomic position between Frankia and Micromonospora. Moreover, its aberrant position in nifH phylogeny should open network investigations on the natural history of nitrogen-fixing gene among actinobacteria.     

Current status of two endangered Caribbean rodents

Living rodents of the genus Geocapromys of the hutia family have been known during this century on three Caribbean islands (Walker, 1968). Visits were made in 1974 to Jamaica and Little Swan Island to check the current status of two of these endangered populations. It appears from these field investigations that the Swan Island hutia, Geocapromys brownii thoracatus, has been exterminated from Little Swan Island. The main cause may have been predation by cats introduced in the late 1950s and after. The Jamaican hutia, G. b. brownii, remains in three remote areas of Jamaica. It exists at low population levels which have been much reduced from those occurring 30 years ago. The Jamaican hutias are shy and secretive in habits compared to the undisturbed Bahamian hutias, G. i. ingrahami, of East Plana Cay, Bahama Islands.