DNA barcoding as a complementary tool for conservation and valorisation of forest resources

Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources.The “core barcode” for land plants (rbcL, matK, and trnH-psbA) was tested on 68 tree specimens (24 taxa). Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intraspecific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%.This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.     

Habitat preferences of oak-feeding xylophagous beetles in a temperate woodland: implications for forest history and management

Oaks host the richest fauna of saproxylic insect in Europe. We studied habitat preferences of two beetle families, Buprestidae and Cerambycidae, by rearing the beetles from standardised oak timber baits. Species density was higher in the understorey than in the canopy; and in sun-exposed baits if within the understorey. Insolation was the most important factor affecting the composition of reared assemblages (explaining ca. 30% of variation in the data), followed by vertical stratum (ca. 10%). Local dead wood volume had no effect. The high preference for sun-exposed wood located near the ground suggests that: (i) open-canopy woodlands had to be rather common in temperate Europe; (ii) oak-utilising xylophages would benefit from restoration of management practices such as coppicing or woodland pasture; (iii) the policy of increasing dead wood volume in commercial forests is principally correct, but its success will depend on dead wood location within the forests.     

Distribution and conservation status of forest bamboo biodiversity in the Asia-Pacific Region

Although Asian bamboo species constitute a non-timber forest product of major cultural and economic importance, no detailed regional assessment of their distribution patterns has previously been made. To assess the potential of the existing bamboo species distribution data for production of regional mapping tools for planning the conservation of forest-based biodiversity, data on bamboo distribution and forest cover were combined. Over 1000 bamboo species from 60 genera of woody bamboos were incorporated, allowing the mapping of individual species or groups of species and genera, along with potential species richness and biodiversity hotspots. Over 6.3 million km² of Asian forest potentially contains bamboo, with highest densities indicated from northeastern India through Burma to southern China, and through Sumatra to Borneo. The highest figures for potential species richness (144 spp per square km) were recorded in forests of south China, including Hainan Island. Despite substantial inadequacies and inconsistencies in knowledge of the taxonomy and distribution of bamboo species, this approach may provide a valuable tool for planning in situ conservation of forest biodiversity.     

Habitat fragmentation and biodiversity: testing for the evolutionary effects of refugia

Concordant areas of endemism among taxa have important implications both for understanding mechanisms of speciation and for framing conservation priorities. Here we discuss the need for careful testing of phylogeographic data for evidence of such concordance, with particular reference to the Indonesian island of Sulawesi. This is because there are good reasons to question whether concordance between taxa is likely to be a common pattern, and because of the serious implications of incorrectly concluding that the biodiversity of a given area can be partitioned in this way.     

Using a goal programming approach to design and evaluate protected areas for the conservation of multiple dimensions of biodiversity

The decline and loss of biodiversity provoked by human activities have caused ecologists and conservationists to center their attention on the design of conservation priority areas (PAs), focusing mainly on species conservation in terms of richness, rarity and/or vulnerability. However, biodiversity has multiple dimensions, evolutionary processes have recently been labeled the ‘missing component’ of conservation strategies, and increasingly more authors are suggesting that the ecological, evolutionary and historical aspects of biodiversity are key components of conservation planning. In this study we develop a prioritization system to design conservation PAs using the wild terrestrial mammals of the Iberian Peninsula as an example. We aim to contribute to the design of more suitable PAs by integrating ecological components of biodiversity (species richness, vulnerability and rarity), evolutionary aspects (accumulated genetic diversification) and historical information relevant to the study area. After selecting a set of biodiversity indicators, we applied a multi-objective technique (extended goal programming) to construct a combined index, where values in the top 90th percentile were then used to select the PAs. According to our most efficient and satisfactory results, some areas highlighted for their conservation are currently categorized as PAs, however, we found that it would be necessary to reconsider their extent, especially in northern Spain, where the historical aspects of biodiversity (the missing component) are more widely present. The need to determine PAs is unquestionable. However, it should also be a priority to move towards a model of sustainable and fair development.     

Options for biodiversity conservation in managed forest landscapes of multiple ownerships in Oregon and Washington,USA

We examine existing and developing approaches to balance biodiversity conservation and timber production with the changing conservation roles of federal and nonfederal forest land ownerships in the US Pacific Northwest. At landscape scales, implementation of the reserve-matrix approach of the federal Northwest Forest Plan in 1994 was followed by proposals of alternative designs to better integrate disturbance regimes or to conserve biodiversity in landscapes of predominantly young forests through active management without reserves. At stand scales, landowners can improve habitat heterogeneity through a host of conventional and alternative silvicultural techniques. There are no state rules that explicitly require biodiversity conservation on nonfederal lands in the region. However, state forest practices rules require retention of structural legacies to enhance habitat complexity and establishment of riparian management areas to conserve aquatic ecosystems. Habitat Conservation Plans (HCPs) under the US Endangered Species Act provide regulatory incentives for nonfederal landowners to protect threatened and endangered species. A state-wide programmatic HCP has recently emerged as a multi-species conservation approach on nonfederal lands. Among voluntary incentives, the Forest Stewardship Council certification comprehensively addresses fundamental elements of biodiversity conservation; however, its tough conservation requirements may limit its coverage to relatively small land areas. Future changes in landscape management strategies on federal lands may occur without coordination with nonfederal landowners because of the differences in regulatory and voluntary incentives between ownerships. This raises concerns when potentially reduced protections on federal lands are proposed, and the capacity of the remaining landscape to compensate has been degraded.     

Options for biodiversity conservation in managed forest landscapes of multiple ownerships in Oregon and Washington,USA

We examine existing and developing approaches to balance biodiversity conservation and timber production with the changing conservation roles of federal and nonfederal forest land ownerships in the US Pacific Northwest. At landscape scales, implementation of the reserve-matrix approach of the federal Northwest Forest Plan in 1994 was followed by proposals of alternative designs to better integrate disturbance regimes or to conserve biodiversity in landscapes of predominantly young forests through active management without reserves. At stand scales, landowners can improve habitat heterogeneity through a host of conventional and alternative silvicultural techniques. There are no state rules that explicitly require biodiversity conservation on nonfederal lands in the region. However, state forest practices rules require retention of structural legacies to enhance habitat complexity and establishment of riparian management areas to conserve aquatic ecosystems. Habitat Conservation Plans (HCPs) under the US Endangered Species Act provide regulatory incentives for nonfederal landowners to protect threatened and endangered species. A state-wide programmatic HCP has recently emerged as a multi-species conservation approach on nonfederal lands. Among voluntary incentives, the Forest Stewardship Council certification comprehensively addresses fundamental elements of biodiversity conservation; however, its tough conservation requirements may limit its coverage to relatively small land areas. Future changes in landscape management strategies on federal lands may occur without coordination with nonfederal landowners because of the differences in regulatory and voluntary incentives between ownerships. This raises concerns when potentially reduced protections on federal lands are proposed, and the capacity of the remaining landscape to compensate has been degraded. This paper was previously published in Biodiversity and Conservation, Volume 16(13) under doi:     

Characterization and ranking of biodiversity hotspots: centres of species richness and endemism

On the basis of 121 areas worldwide, the regressions of plantspecies–area relationships and of endemism–area relationships inlog–log space are calculated. These formulae form the basis forcalculating -values. -Valuesdetermine the ranking of biodiversity hotspots. In most cases, areas which havebeen published as biodiversity hotspots are characterized by high values of, i.e. by rich compositions of vascularplant species and high rates of endemism.     

Legacies of the past in the present-day forest biodiversity: a review of past land-use effects on forest plant species composition and diversity

Particularly in the temperate climate zone many forests have, at some moment in their history, been used as agriculture land. Forest cover is therefore often not as stable as it might look. How forest plant communities recovered after agriculture was abandoned allows us to explore some universal questions on how dispersal and environment limit plant species abundance and distribution. All studies looking at the effects of historical land use rely on adequate land use reconstruction. A variety of tools from maps, archival studies, and interviews to field evidence and soil analyses contribute to that. They allow us to distinguish ancient from recent forests and many studies found pronounced differences in forest plant species composition between them. A considerable percentage of our forest flora is associated with ancient forests. These ancient forest plant species (AFS) all have a low colonization capacity, suggesting that dispersal in space (distance related) and time (seed bank related) limit their distribution and abundance. However recent forests generally are suitable for the recruitment of AFS. There is clear evidence that dispersal limitation is more important than recruitment limitation in the distribution of AFS. Dispersal in time, through persistent seed banks, does not play a significant role. Ancient forests are not necessary more species-rich than recent forest, but if diversity is limited to typical forest plant species then ancient forests do have the highest number of plant species, making them highly important for nature conservation. The use of molecular markers, integrated approaches and modelling are all part of the way forward in this field of historical ecology.     

The relationship between biodiversity and population centres: the high Andes region as an example

Several coarse-scale studies have demonstrated a positive correlation between biodiversity and human population density. In this paper this relationship is studied for part of the Andean highland, on a finer spatial scale than in earlier studies, and comparing bird distribution data with pre-Columbian as well as contemporary population centres. A particularly close correspondence was found between ancient population centres and high numbers of species with small distributions. This suggests that the growth of resident human cultures was related, in some way, to local factors which—over a much longer time-scale—stimulated the process of evolution of new species. This correspondence may be a consequence of climate moderation in the mountain areas leading to local persistence, of wild species as well as human communities. However, the result also suggests that we need to study to what extent high biodiversity as such, under certain conditions, yields environmental services which were important for people. It also suggests that traditional efforts to preserve biodiversity in wilderness areas with few people should be supplemented with efforts to promote a more sustainable development in the populated areas, allowing cloud forest and other biologically rich habitats to persist in suitable places near population centres.     

Shrew species diversity and abundance in Ziama Biosphere Reserve, Guinea: comparison among primary forest, degraded forest and restoration plots

The aim of our study was to compare the shrew community diversity and structure in gradients of tropical forest degradation and restoration. Four plots within each of six habitats of the Ziama Biosphere Reserve were surveyed, including primary forest, secondary forest, cultivated fields, recently (less than 3 years) abandoned fields, young (10–12 years) forest restoration plots, and old (34 years) restoration plots. From August to November 2003, we pitfall-trapped 2,509 shrews representing 11 species. Shrew species richness and composition was similar in the six habitat surveyed, while shrew species abundance varied between habitats. Canopy height and cover, density of stems and trees and understorey density were shown to constitute important parameters influencing the abundance of several shrew species. After clear-cutting, restoration of key attributes of the forest vegetation structure was possible in 10–34 years, either by natural regeneration or by planting of seedlings. The relative abundance of most shrew species was similar between restoring forest (i.e., young restoration plots or fallows) and primary forest. Considering the advantages and disadvantages of these two methods of forest restoration, one of the most suitable management practices to restore forest while preserving shrew biodiversity could be to perform an alternation of native seedling plantation lines and fallows.     

Indicator species for avian biodiversity hotspots: Combination of specialists and generalists is necessary in less natural environments

In this work, I tested the premise that the distribution of a group of few common bird species can be used to predict bird species hotspots in Central Italy. The data on bird observations were collected on 530 sampled sites (150 in cultivated, 150 in forest, 150 in grassland and 80 in urban and peri-urban environments). In each environment, sampled sites with values of bird species richness in the upper than third quartile were classified as high species richness spots (HSRS), while sites with lower bird species richness were classified as non-HSRS (binary classification system).Generalized Linear Models (GLM) were applied using HSRS or non-HSRS as binomial response variable and bird species occurrence was used as the predictor variable. All selected models showed “fair” or “good” capacities to predict the avian hotspots, using only few common birds (4–6) species. However, bird species selected as predictors were different on each environment. In more natural environments (grassland, forest), specialist species were selected, while in most disturbed environments (cultivated and urban) both generalist and specialist species were selected. The results are in agreement with other studies which show how homogenization of bird communities is strongly correlated to landscape disturbance. The findings supports the hypothesis that indicators have to incorporate both specialists and generalist’s species simultaneously. Furthermore, the groups of birds selected as surrogates are easy to detect and this makes it possible to involve citizen-science programmes in obtain data. This approach can be a cheap and efficient and can help to significantly speed up the process of assessing ecosystems that might be under threat.     

Land use and biodiversity indicators for life cycle impact assessment

Background  The primary purpose of environmental assessment is to protect biological systems. Data collected over the last several decades indicates that the greatest impacts on biological resources derive from physical changes in land use. However, to date there is no consensus on indicators of land use that could be applicable worldwide at all scales. This has hampered the assessment of land use in the context of LCA. Objectives  The Institute for Environmental Research and Education and its partner Defenders of Wildlife have begun an effort to develop the necessary consensus. Methods  In July 2000, they held a workshop attended by a diverse group of interested parties and experts to develop a preliminary list of life cycle indicators for land use impacts. Results  Their preliminary list of impact indicators includes: protection of priority habitats/species; soil characteristics: soil health; proximity to & protection of high priority vegetative communities; interface between water and terrestrial habitats/buffer zones; assimilative capacity of water and land; hydrological function; percent coverage of invasive species within protected areas; road density; percent native-dominated vegetation; restoration of native vegetation; adoption of Best Management Practices linked to biodiversity objectives; distribution (patchiness; evenness, etc.); and connectivity of native habitat. Conclusion  The list of indicators conforms well to other efforts in developing indicators. There appears to be convergence among experts in the field and in related fields on the appropriate things to measure. Future Prospects  These indicators are currently being tested in the United States. Further workshops and testing is planned towards developing internationally recognized indicators for land use.     

Sacred groves of Manipur,northeast India:biodiversity value,status and strategies for their conservation

The people of Manipur, a state in northeast India, follow ancestral worship and animism in the form of deity worship, with the central focus on worship in forest patches. The beliefs and taboos associated with the Sylvan deities (Umanglais) in the forest patches are restricted to any sort of disturbance of flora and fauna. These social boundaries help to conserve the entire organism as a whole, which stand the concept of sacred groves. The pleasing of deities is performed every year by the Meiteis, a dominant community of Manipur, in honour of the deities and to gain their favour. Indigenous cultural and rituals practices of the local people in sacred groves serve as a tool for conserving biodiversity. Sacred groves are distributed over a wide ecosystem and help in conservation of rare and endemic species. Well-preserved sacred groves are store houses of valuable medicinal and other plants having high economic value, and serve as a refuge to threatened species. One hundred and sixty-six sacred groves were inventoried in Manipur valley that comprises Imphal east, Imphal west, Thoubal and Bishnupur districts of the state. Detailed studies were carried out in four selected sacred groves, to know the importance of biodiversity status and vegetation characteristics. A total of 173 plant species representing 145 genera under 70 families were recorded through baseline floristic survey. The species diversity indices were compared among the four studied groves. The vegetation composition and community characteristics were recorded. Ethnobotanical uses of species were examined, which reveal that 96% of the species were used as medicine for the treatment of various ailments. Utilization of herbal medicine by the Meiteis is closely related to the cultural and ritual practices. A few of the medicinal plants which have disappeared from the locality are now confined only to the groves. Socio-cultural aspects were investigated taking into account the attitudes of local people, which indicate social beliefs and taboo are eroding, simultaneously degrading the degree of protection of sacred groves. Therefore, conservation measures of sacred groves need to be formulated considering the factor of degradation and the basic necessities of the local people. Until and unless a viable option is provided to the local people (especially those who habitat nearby the adjoining areas) for sustaining their economic condition, no step for conservation of biodiversity will be successful.     

A comparison of some population density sampling techniques for biodiversity, conservation, and environmental impact studies

Twelve terrestrial and marine studies were conducted at various sites in Malaysia, Brazil, and the United States between April 1999 and February 2004. These data were analyzed using five density estimate techniques for stationary (non-motile) organisms including Stratified Random Sampling, Point-Center Quarter, Third Nearest Object, Weinberg, and Strong. The Strong method gave the most accurate density estimates of stationary animals and plants. Stratified Random Sampling ranked second best and the Third Nearest Object the third best. Belt or strip transects may be preferable but can be restrictive in some situations because of logistics and associated time constraints. Straight line measurements on reefs were 3–27% more accurate than reef slack line and reef contour measurements. Most study areas measured with the standardized Morisita index of dispersion were moderately aggregated. Results from the Third Nearest Object and Point-Center Quarter techniques indicate that the addition of more data to establish a density correction factor does not necessarily give more accurate estimates of density.     

Bird community variation across <Emphasis Type="Italic">Polylepis</Emphasis> woodland fragments and matrix habitats: implications for biodiversity conservation within a high Andean landscape

The scattered and dwindling Polylepis woodlands of the high Andean global hotspot have been identified as being of particular importance to biodiversity conservation, and yet little is known of the make-up of their faunal communities, how these vary across landscapes, and how well species might tolerate matrix/edge habitats. We examined the bird communities and vegetation characteristics of Polylepis woodlands and the surrounding matrix habitats at three sites in the Cordillera Vilcanota, southern Perú (3,400–4,500 m). The vegetation structure of woodlands varied significantly across the three sites but all were dominated by two Polylepis tree species, with mossy ground cover. Matrix habitats were treeless and dominated by ground-level puna grass-steppe or boulder scree vegetation. Bird species richness and diversity, encounter rates and the number of globally-threatened and restricted-range bird species were consistently higher in the Polylepis forests, than in matrix habitat. We used canonical correspondence analysis (CCA) to identify habitat gradients across the landscape, and to classify bird species according to their association with Polylepis, the matrix or Polylepis-matrix interface. There were few matrix-restricted bird species, but around half the bird community, including fourteen threatened or restricted-range species, were Polylepis-dependant. Many of these species had very narrow niches. The Polylepis-matrix interface was dominated by species traditionally considered invasive ecological generalists. Our study illustrates the overriding importance of Polylepis interior habitats, indicating that conservation strategies for high Andean birds must focus on patch size maintenance/enlargement, enhancement of within-patch habitat quality, and efforts to safeguard connectivity of suitable habitat across what is essentially an inhospitable puna/scree matrix.     

The development and demise of a Medieval forest-meadow system at Linnaeus' birthplace in southern Sweden: implications for conservation and forest history

The rapid industrialisation of agriculture and forestry during the last century has contributed to a transformation of the forested landscape in southern Sweden. Palaeoecological investigation revealed how the Medieval forest-meadow system was created about 900 years ago from a deciduous forest type that had been rather stable for the previous 3000 years. The study site was a forest hollow close to where Linnaeus was born and brought up. The species-rich forest-meadow system suffered from over-grazing during the human-population peak of the nineteenth century, and was abandoned about one hundred years ago. The recent forest succession in southern Sweden has led to reduced floristic biodiversity and created conservation problems related to disappearance of open landscape, even though the remnant vegetation is moving towards the near-natural forest type. Spatially detailed palaeoecology permits documentation of baseline conditions, and places conservation debates in a valuable temporal perspective.     

Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation

Forest musk deer (Moschus berezovskii) are rare as a result of poaching for musk and habitat loss. Some captive populations of forest musk deer have been established for decades in China. However, little genetic information is available for conservation management. In this paper, genetic variations, population structures, and the genetic bottleneck hypothesis were examined using 11 microsatellite loci from captive populations in Miyalo, Jinfeng and Maerkang in Sichuan Province, China. Estimates of genetic variability revealed substantial genetic variation in the three populations. A total of 142 different alleles were observed in 121 forest musk deer and the effective number of alleles per locus varied from 6.76 to 12.95. The average values of observed heterozygosity, expected heterozygosity, and Nei's expected heterozygosity were 0.552, 0.899 and 0.894 respectively. The overall significant (P < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 34.5%. The mean F_ST (P < 0.001) showed that approximately 90.2% of the genetic variation was within populations and 9.8% was across populations. The UPGMA diagram, based on Nei's unbiased genetic distance, indicated that the three populations were differentiated into two different groups and it agreed with their origin and history. Bottleneck tests indicated that all three populations have undergone a population bottleneck, suggesting a small effective population size. Acknowledging that the genetic structure of populations has crucial conservation implications, the present genetic information should be taken into account in management plans for the conservation of captive forest musk deer.     

Geographic patterns of genetic diversity in Poulsenia armata (Moraceae): implications for the theory of Pleistocene refugia and the importance of riparian forest

Abstract. Tropical forests are species-diverse communities, but we know very little about the geographical distribution of genetic diversity within a species. During the late Pleistocene, lower temperatures and rainfall reduced the distribution of tropical wet forests, and in Central America lowland species may have been limited to riparian habitats. Approximately 12,000 years bp , temperature and rainfall increased in Central America, the distribution of wet forest species expanded, and today the distribution of some species extends into southern Mexico. The distribution of genetic diversity, based on RAPD markers, among ten populations of Poulsenia armata (Miq.) Standl. (Moraceae) suggests that these populations did not originate from a single refugium or region in the late Pleistocene. The Central American populations had high genetic diversity and unique bands giving support to the hypothesis that populations of P. armata occurred in Central American during the late Pleistocene. The majority of genetic diversity was partitioned among populations and there was no geographical relationship among populations, suggesting that these populations were isolated for a long period and there has been little gene flow. Populations of P. armata may have persisted in riparian zones along the Caribbean coast during the late Pleistocene. Given that riparian forest can support high levels of biodiversity in ecological time, and they have played an important role during periods of climate change over geological time, their conservation is of utmost importance particularly with the threat of a rapid shift in climatic patterns.