A multi-taxa assessment of nestedness patterns across a multiple-use Amazonian forest landscape

Understanding how biodiversity is partitioned among alternative land-uses is an important first step for developing effective conservation plans in multiple-use landscapes. Here, we analysed nestedness patterns of species composition for nine different taxonomic groups [dung beetles, fruit-feeding butterflies, orchid bees, scavenger flies, leaf-litter amphibians, lizards, bats, birds and woody plants (trees and lianas)] in a multiple-use forestry landscape in the Brazilian Amazon containing primary, secondary and Eucalyptus plantation forests. A formal nestedness analysis was performed to investigate whether species-poor land-uses were comprised of a subset of species from more diverse forests, and the extent to which this pattern varied among taxa. At the landscape-scale the species-by-sites matrices were significantly nested for all nine taxonomic groups when both sites and species were sorted to maximally pack the species/occurrence matrix and, except for orchid bees when sorted by land-use intensity (primary forest to Eucalyptus plantation). Different patterns emerged when we conducted pairwise analyses of nestedness between the three forest types: (a) most of the taxonomic groups were nested in accordance with increased land-use intensity; (b) neither orchid bees nor leaf-litter amphibians from secondary forest made up a significant nested subset of primary forest species, although species found in Eucalyptus plantation sites were nested within secondary forest communities; and (c) lizards from Eucalyptus plantations were not a nested subset of either primary or secondary forest. Our findings emphasize the complex nature of patterns of species occupancy in tropical multiple-use forestry landscapes, and illustrate that there may be no easy solutions to questions regarding the conservation value of secondary and exotic plantation forests.     

Prospects for biodiversity conservation in the Atlantic Forest: Lessons from aging human-modified landscapes

Recent global assessments have shown the limited coverage of protected areas across tropical biotas, fuelling a growing interest in the potential conservation services provided by anthropogenic landscapes. Here we examine the geographic distribution of biological diversity in the Atlantic Forest of South America, synthesize the most conspicuous forest biodiversity responses to human disturbances, propose further conservation initiatives for this biota, and offer a range of general insights into the prospects of forest species persistence in human-modified tropical forest landscapes worldwide. At the biome scale, the most extensive pre-Columbian habitats across the Atlantic Forest ranged across elevations below 800 masl, which still concentrate most areas within the major centers of species endemism. Unfortunately, up to 88% of the original forest habitat has been lost, mainly across these low to intermediate elevations, whereas protected areas are clearly skewed towards high elevations above 1200 masl. At the landscape scale, most remaining Atlantic Forest cover is embedded within dynamic agro-mosaics including elements such as small forest fragments, early-to-late secondary forest patches and exotic tree monocultures. In this sort of aging or long-term modified landscapes, habitat fragmentation appears to effectively drive edge-dominated portions of forest fragments towards an early-successional system, greatly limiting the long-term persistence of forest-obligate and forest-dependent species. However, the extent to which forest habitats approach early-successional systems, thereby threatening the bulk of the Atlantic Forest biodiversity, depends on both past and present landscape configuration. Many elements of human-modified landscapes (e.g. patches of early-secondary forests and tree monocultures) may offer excellent conservation opportunities, but they cannot replace the conservation value of protected areas and hitherto unprotected large patches of old-growth forests. Finally, the biodiversity conservation services provided by anthropogenic landscapes across Atlantic Forest and other tropical forest regions can be significantly augmented by coupling biodiversity corridor initiatives with biota-scale attempts to plug existing gaps in the representativeness of protected areas.     

Reproductive biology and conservation implications of three endangered snapdragon species (Antirrhinum, Plantaginaceae)

About 32% of Antirrhinum species are considered to be endangered; however, no field studies have focused on their reproductive biology. In this work, several aspects of the reproductive biology (flowering phenology, floral biology, breeding system) and potential limits on seed quantity and quality (pollen limitation, inbreeding depression) were studied in natural populations of three endangered species of the genus (Antirrhinum charidemi, Antirrhinum subbaeticum, Antirrhinum valentinum). Results disclose that all three species need insect visitors for seed production since fruit set after autonomous self-pollination was lower than under hand cross-pollination. A. charidemi and A. valentinum were mainly self-incompatible, whereas A. subbaeticum was self-compatible but herkogamous. Supplementary pollination in open-pollinated flowers only increased fruit set and seed set relative to controls in a given population of A. valentinum. Preliminary data on inbreeding depression at early life-cycle stages of the self-compatible A. subbaeticum revealed that the cumulative level was low. Despite the three species being closely related and sharing many ecological characteristics, they show different mating systems, and different factors limit seed quantity and quality. Thus, caution should be taken when making a common conservation plan for a group of closely related taxa.     

Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest

Tropical rainforests are becoming increasingly fragmented and understanding the genetic consequences of fragmentation is crucial for conservation of their flora and fauna. We examined populations of the toad Rhinella ornata, a species endemic to Atlantic Coastal Forest in Brazil, and compared genetic diversity among small and medium forest fragments that were either isolated or connected to large forest areas by corridors. Genetic differentiation, as measured by F_ST, was not related to geographic distance among study sites and the size of the fragments did not significantly alter patterns of genetic connectivity. However, population genetic diversity was positively related to fragment size, thus haplotype diversity was lowest in the smallest fragments, likely due to decreases in population sizes. Spatial analyses of genetic discontinuities among groups of populations showed a higher proportion of barriers to gene flow among small and medium fragments than between populations in continuous forest. Our results underscore that even species with relatively high dispersal capacities may, over time, suffer the negative genetic effects of fragmentation, possibly leading to reduced fitness of population and cases of localized extinction.     

Efficiency of conservation shortcuts: an investigation with otters as umbrella species

The use of shortcuts is widespread in conservation practices to help ensure biodiversity conservation with minimal expenditures. An umbrella species is a species whose conservation confers protection to a large number of naturally co-occurring species. The aim of this study is to test the usefulness of the umbrella species concept for conservation management. As our umbrella, we chose a wide-ranging and flagship species, the European otter (Lutra lutra). Otters are widely distributed predators with numerous genera and species, so otter occurrence could virtually be used as “umbrella” in every freshwater habitat. To test the usefulness of the concept, we investigated whether an umbrella species might protect other species in the long term. We compared (1) bird and amphibian species richness in 1993 and in 2003 on nine sites where otters were monitored for 20 years, and (2) bird, amphibian and mollusc species richness between the previous sites and nine bio-equivalent sites where no otter occurrence has been detected for 20 years. The study was carried out for two spatial scales: total otter home range and core areas (most intensely exploited areas). Our results show that species richness was significantly different between years on sites inhabited by otters. However, we showed that biodiversity did not differ between pairs of bio-equivalent sites inhabited or deserted by otters, whatever the estimation method. Our results cast doubt on the validity of umbrella species use as an objective tool for conservation. However, the keystone functional role that otters could play in ecosystems might be an interesting way to reconsider the purpose of the umbrella species concept.     

Feral pigs in Namadgi National Park, Australia: dynamics, impacts and management

Feral pigs (Sus scrofa) have spread through Namadgi National Park (NNP) in south-eastern Australia since the early 1960s at a mean rate of 4 km/year. Pigs were abundant (approximately 1-2 pigs km⁻²) during the mid-1980s. Research from 1985 to 2000 inclusive has demonstrated a positive curved relationship across years between the frequency of occurrence of pig rooting and pig abundance (R²=0.48; P<0.001) and the extent of ground rooting; more pigs, more rooting. The ground rooting decreased plant species richness. There was a negative curved relationship between plant species richness and the extent of pig rooting at two sites (R²=0.81; P<0.0001 and R²=0.67; P<0.0001), with plant richness declining to zero with intensive pig rooting. Since the mid 1980s intensive pig control work has resulted in a significant (R²=0.39; P<0.001) decline in pig abundance with an annual instantaneous rate of change (r) of −0.15 between 1985 and 2000 inclusive. The results and their implications for biodiversity conservation and feral pig management are discussed.     

Status, distribution and definition of mycologically important grasslands in Scotland

In northern Europe, unimproved grasslands provide the habitat for a diverse group of fungi, including members of the genera Camarophyllopsis, Hygrocybe, Entoloma and Dermoloma, and the families Clavariaceae and Geoglossaceae. These fungi are currently the focus of international conservation concern, owing to rapid declines in the availability of suitable habitat. To assess their status in Scotland, 621 field surveys were undertaken on a total of 511 sites, distributed throughout the country. Taxa were found to differ substantially in abundance; for example, whereas five Hygrocybe taxa were recorded at a single site, seven taxa were recorded on more than 200 sites. The number of Hygrocybe taxa per site was found to be positively correlated with number of Clavariaceae taxa (r=0.60); however, the total number of Entoloma taxa was poorly correlated with diversity of other groups (r<0.35). Detrended correspondence analysis (DCA) of field data highlighted variation in composition of fungal communities; in particular, Entoloma taxa were found to cluster together, and were rarely found in association with Geoglossaceae. The data were used to critically examine current approaches to defining the conservation importance of grassland sites on the basis of their mycota. Species accumulation curves indicated that more than 16 visits may be required to fully characterize the fungal diversity of a site. Different groups of fungi also displayed constrasting patterns of seasonal variation in sporome production; peak diversity values for Geoglossaceae and Clavariaceae tended to occur later in the year than for Hygrocybe and Entoloma. Such results indicate that intensive, multiple surveys over prolonged periods are required to accurately define the conservation value of grassland sites. However, these preliminary data suggest that the unimproved grasslands of Scotland are of exceptional importance for fungal conservation, compared with other countries of northern Europe.     

Hybridization and conservation of Mediterranean orchids: Should we protect the orchid hybrids or the orchid hybrid zones?

Natural hybridization between plant species often occurs in disturbed habitats and it is generally considered a threat for rare and endangered species. A different situation occurs in Mediterranean food deceptive orchids, where hybridization is a common phenomenon, as a natural consequence of their unspecific pollination system.Here, we present molecular and ecological evidence from a hybrid zone between Orchis mascula and O. pauciflora in order to address the consequences of hybridization on local orchid evolution and to assess conservation priorities for hybrids and hybrid zones in orchid conservation programs.We find that, although hybrids among the two target taxa are formed relatively frequently, hybrid zones often consist of F1 individuals, whereas backcrosses and later generation hybrids appear to be either rare or absent, presumably as a consequence of post-zygotic reproductive barriers acting in these food-deceptive orchids. Experimental evidence further indicates that hybrids are less fit than the parental species in attracting pollinators and that parental taxa exhibit higher or similar fitness in sympatry compared to allopatric populations. Since introgression is not frequent as indicated by molecular analyses, fitness and phenotypic trait differences observed among sympatric and allopatric populations of the parental taxa may be a consequence of pollinator-mediated selection.Our experimental data confirm that hybridization is a natural phenomenon in food-deceptive orchids and that it does not pose a threat to their survival. Furthermore, sympatric zones provide the stage for evolutionary processes in orchids, and this peculiarity should be taken into account when devising orchid conservation strategies.     

Conservation of isolated Atlantic heathlands in the Mediterranean region: effects of land-use changes in the Montseny biosphere reserve (Spain)

In the Mediterranean region, cycles of controlled burning combined with continuous grazing appear to have been an effective tool for maintaining isolated Calluna vulgaris heathlands in the form in which they occur in many places in the Atlantic region. Changes in land use and management of the mosaic of extensively exploited heathland and associated grassland over recent decades, such as bringing land into cultivation followed by its abandonment and the prohibition of fires has resulted in a process of transformation into new shrub communities with lower biodiversity. In the Mediterranean region, these changes are similar to those described in the Atlantic area, but encroachment occurs faster and could lead ultimately to afforestation by Mediterranean woodland.In a study area of 300 ha of heathland in the Spanish Mediterranean basin (specifically, in the Montseny Natural Park and Biosphere Reserve), comparison of present and former vegetation showed that shrub cover increased from 15% in 1967 to 32% in 2000. Broom (Cytisus scoparius) was the main invasive species in abandoned crop fields, whereas Mediterranean holm oak forest (Quercus ilex) increased by 18%. The surface area of fernlands doubled and C. vulgaris heathlands decreased from 35% to just 9% during the same period. Intermixed grasslands also decreased moderately and progressively from 4% to 3%.It seems probable that cycles of fires are more important in terms of shrub control and biodiversity conservation than continuous grazing alone, even at a high rate of stocking (four small ruminants per hectare per year). This encroachment process throws into relief the role that isolated habitats can play as a monitor of land use changes.     

Minimum viable population and conservation status of the Atlantic Forest spiny rat Trinomys eliasi

A population viability analysis (PVA) was conducted to assess the minimum viable population (MVP) of the Atlantic Forest spiny rat Trinomys eliasi, a species threatened by habitat loss and restricted geographical distribution. Objectives were to suggest quasi-extinction thresholds, estimate minimum areas of suitable habitat (MASH) and MVPs, and compare results with the species’ current status. The computer package VORTEX was used. The model predicted sizes of 200 animals to achieve demographic stability, but buffering declines in genetic variability required populations of 2000 animals. Estimated MASHs were approximately 250 and 2500 ha for demographic and genetic stability, respectively. Mortality rate and mean litter size were the most sensitive parameters to changes in model assumptions. The protection of known populations and the search for extant populations are the first steps in conservation. T. eliasi's issue could help protecting the coastal shrubland ecosystem of Rio de Janeiro state. Observing IUCN's criteria for listing threatened species, it is suggested that T. eliasi should be ranked as vulnerable in red lists.     

Artificial dispersal of endangered epiphytic lichens: a tool for conservation in boreal forest landscapes

Due to increasing fragmentation of the boreal forests of Fennoscandia, a number of epiphytic lichens are now becoming threatened. Since these species typically are limited by a poor ability of dispersal, one possible but largely unexplored strategy for conservation is to disperse lichen material artificially into suitable habitats. Therefore, the objective of this study was to evaluate survival and vitality in lichen fragments from Evernia divaricata (L.) Ach. and Ramalina dilacerata (Hoffm.) Hoffm. after transplantation into three different stand types situated in northern Sweden, using different fragment sizes and modes of transplantation. After one year, survival ranged between 85% and 97.5%, and new growth occurred at all transplantation sites. The study has shown that transplantations of small fragments might constitute a resource-efficient option for establishment of new populations of endangered lichen species, or for enlarging their populations at the present sites of occurrence. In addition, the mode of transplantation was of importance for fragment vitality.     

Microbial communities in forest floors under four tree species in coastal British Columbia

We compare forest floor microbial communities in pure plots of four tree species (Thuja plicata, Tsuga heterophylla, Pseudotsuga menziesii, and Picea sitchensis) replicated at three sites on Vancouver Island. Microbial communities were characterised through community level physiological profiles (CLPP), and profiling of phospholipid fatty acids (PLFA).Microbial communities from cedar forest floors had higher potential C utilisation than the other species. The F layer of the forest floor under cedar contained significantly higher bacterial biomass (PLFA) than the F layer under the other three tree species. There were differences in microbial communities among the three sites: Upper Klanawa had the highest bacterial biomass and potential C utilisation; this site also had the highest N availability in the forest floors. Forest floor H layers under hemlock and Douglas-fir contained greater biomass of Gram positive, Gram negative bacteria and actinomycetes than F layers based on PLFA, and H layers under spruce contained greater biomass of Gram negative bacteria than F layers. There were no significant differences in bacterial biomass between forest floor layers under cedar. Fungal biomass displayed opposite trends to bacteria and actinomycetes, being lowest in cedar forest floors, and highest in the F layer and at the site with lowest N availability. There were also differences in community composition among species and sites, with cedar forest floors having a much lower fungal:bacterial ratio than spruce, hemlock and Douglas-fir. The least fertile Sarita Lake site had a much greater fungal:bacterial ratio than the more fertile San Juan and Upper Klanawa sites. Forest floor layer had the greatest effect on microbial community structure and potential function, followed by site, and tree species. The similarity in trends among measures of N availability and microbial communities is further evidence that these techniques provide information on microbial communities that is relevant to N cycling processes in the forest floor.     

The effect of stand structure and tree species composition on epiphytic bryophytes in mixed deciduous-coniferous forests of Western Hungary

The effect of tree species, stand structure, landscape and historical variables was studied on the species composition, species richness and cover of epiphytic bryophyte assemblages in mixed deciduous-coniferous forests of Western Hungary. Stand and tree level assemblages were analyzed by ordinations and generalized linear modeling in 35 70-110 year old stands of different management regimes.Bryophytes showed a considerable preference to different host trees, so that stand level diversity of bryophyte assemblages was determined mainly by tree species diversity, and their composition by tree species composition. Cover and diversity of epiphytic bryophytes were the highest on oaks (Quercus petraea and Quercus robur), and the lowest on Scotch pine (Pinus sylvestris). The presence of sapling (shrub) layer increased, whereas a large number of medium sized trees decreased bryophyte species richness in this study. Tree size was much less influential which is explained by the lack of large, veteran trees. Forest management maintaining tree species diversity, structural heterogeneity and temporal continuity of the stands could considerably contribute to the conservation of this organism group. Selective cutting is more appropriate for these conservational purposes than shelterwood management system.     

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.     

Restoring forest herb communities through landscape-level deer herd reductions: Is recovery limited by legacy effects?

White-tailed deer (Odocoileus virginianus) overbrowsing has altered plant species diversity throughout deciduous forest understories in eastern North America. Here we report on a landscape-level (306 km²) project in Pennsylvania, USA that tracked the herbaceous community response to deer herd reductions. From 2001 to 2007, we estimated deer densities, browse impact on woody seedlings, and censused the herbaceous flora in permanent plots throughout the area. We assessed herb layer species richness, abundance, and dominance and measured three known phytoindicators of deer impact: Trillium spp., Maianthemum canadense, and Medeola virginiana. We predicted that browse-sensitive taxa would increase in abundance, size, and flowering as would overall species diversity following deer culls and browse impact that declined by an order of magnitude by 2007. Following intensified deer harvests, we observed a limited recovery of the herbaceous community. Trillium spp. abundance, height, and flowering; M. canadense cover; and M. virginiana height all increased following herd reductions. Similarly, forb and shrub cover increased by 130% and 300%, respectively. Nevertheless, species diversity (i.e., richness and dominance) did not vary. Our work demonstrates that reducing deer densities can provide rapid morphological and population-level benefits to palatable species without a concomitant recovery in diversity. We suggest that decreasing deer populations alone may not promote plant diversity in overbrowsed, depauperate forests without additional restoration strategies to mitigate a browse-legacy layer dominated by browse-resistant species.     

Niche differentiation among neotropical soldierless soil-feeding termites revealed by stable isotope ratios

Termites represent one of the most abundant belowground animal taxa in tropical rainforests, where their species richness is much higher than in any other ecosystem. This high diversity in soil ecosystems is however difficult to explain by classical Hutchinsonian niche theory, as there is little evidence for spatial or temporal separation between species. Using δ¹³C and δ¹⁵N isotopic ratios, we tested if resource partitioning along the humification gradient occurs in neotropical soldierless termites of the Anoplotermes-group. Two distinct sites were investigated to check if interspecific differences are transposable between sites. Significant differences in δ¹⁵N were found between species of the Anoplotermes-group. Although some species displayed higher intersite δ¹⁵N variation than others, species-average δ¹⁵N values for both sites were highly correlated, showing that sympatric soldierless soil-feeding termites feed on distinct components of the soil. Our data also suggest that some species are more likely to shift along this gradient than others, in response to overall habitat conditions or to the presence of competitors. Feeding niche differentiation can therefore account for the high species richness and diversity of soldierless soil-feeding termites in neotropical rainforests.     

The importance of secondary forest blocks for terrestrial mammals within an Acacia/secondary forest matrix in Sarawak, Malaysia

With the rapid conversion of tropical forests in Asia to plantation forests for timber or biofuel production there is a need to determine if these forests serve any viable role in wildlife conservation. We used infra-red trip cameras to survey for large terrestrial mammals within an Acacia/secondary forest matrix being created for pulpwood production in Sarawak, Malaysia. We detected at least 27 species of mammals within the matrix and 18 species were detected in both Acacia and secondary forest. Using occupancy modeling to determine important covariates for seven mammal species within the project area, six of these species were sensitive to forest type, and most were sensitive to the amount of secondary forest within 1 km of the sample point. For four species (sun bear, Helarctos melayanus; common porcupine, Hystrix brachyura; mousedeer, Tragulus spp.; and pig-tailed macaque, Macaca nemestrina), the mean distance of detection from large secondary forest blocks was significantly closer than expected from the distribution of sample points. Most species used Acacia forest less frequently than secondary forest, possibly for transit or foraging, with the exception of bearded pigs (Sus barbatus), sambar (Rucervus unicolor), and civets which were more common in Acacia stands. The amount of secondary forest preserved within forest plantations seems to be the best measure of conservation potential for these industrial forests. Forest plantations can provide a conservation value if managed properly and those retaining significant amounts of secondary forest should be eligible for a base level of certification as they comprise a significant portion of the landscape in this region.     

Does forest continuity matter in conservation? - A study of epiphytic lichens and bryophytes in beech forests of southern Sweden

The effects of forest continuity at local scale for red-listed and indicator species of epiphytic lichens and bryophytes were investigated in 150 Fagus sylvatica stands in southern Sweden. Stands having forest continuity (n = 106) had continuous forest cover more than 350 years, whereas stands lacking continuity (n = 44) had forest cover less than 160 years. Forest continuity was identified by comparing a sequence of historical maps with a modern survey of beech forests. In the field woody beech substrates were searched for the epiphytes of interest. A number of environmental and spatial variables were inventoried and compiled for each stand. In all 64 species (51 lichens, 13 bryophytes) were found in the stands having continuity, and 21 (14 lichens, 7 bryophytes) in the stands lacking continuity. Controlling for the different number of surveyed stands, stands having continuity had significantly more species of lichens, but not of bryophytes. In the stands lacking continuity we did not find lichens associated with the very late succession stage. The quantity of substrates, stand age and forest continuity were the three most important factors explaining species richness as well as composition of studied epiphytes. The effect of continuity was probably due to a combination of a higher substrate quality, mainly old beeches, and a longer time available for colonization. Also, we found strong positive correlations between number of indicator and red-listed epiphyte species. In short-term conservation old stands having continuity, containing suitable substrates and indicator species are target areas.     

Neutral DNA markers fail to detect genetic divergence in an ecologically important trait

The development of strategies for in situ, ex situ conservation and reforestation of the monkey puzzle tree (Araucaria araucana), a vulnerable tree endemic to southern South America, has led to an interest in the level and distribution of the genetic diversity of the species. Neutral DNA markers (RAPDs) and quantitative genetic techniques were used to characterise genetic heterogeneity within and among populations from throughout the natural range of the species. Both the level and pattern of genetic variation estimated using the different techniques were essentially uncorrelated. An important discrepancy was found with the neutral markers failing to detect an important quantitative genetic divergence across the Andean Range relating to drought tolerance. This study clearly demonstrates the potential problems associated with making recommendations for conserving the genetic resource of threatened species based solely on neutral marker studies. Alternative approaches are discussed, including a stronger focus on ecologically important traits and the potential use of surrogate measures of genetic variability.