Incorporating functional dissimilarities into sample‐based rarefaction curves: from taxon resampling to functional resampling

Question: Indices of functional diversity have been seen as the key for integrating information on species richness with measures that focus on those components of community composition related to ecosystem functioning. For comparing species richness among habitats on an equal‐effort basis, so‐called sample‐based rarefaction curves may be used. Given a study area that is sampled for species presence and absence in N plots, sample‐based rarefaction generates the expected number of accumulated species as the number of sampled plots increases from 1 to N. Accordingly, the question for this study is: can we construct a ‘functional rarefaction curve’ that summarizes the expected functional dissimilarity between species when n plots are drawn at random from a larger pool of N plots? Methods: In this paper, we propose a parametric measure of functional diversity that is obtained by combining sample‐based rarefaction techniques that are usually applied to species richness with Rao's quadratic diversity. For a given set of N presence/absence plots, the resulting measure summarizes the expected functional dissimilarity at an increasingly larger cumulative number of plots n (n≤N). Results and Conclusions: Due to its parametric nature, the proposed measure is progressively more sensitive to rare species with increasing plot number, thus rendering this measure adequate for comparing the functional diversity of species assemblages that have been sampled with variable effort.     

An improved method to set significance thresholds for β diversity testing in microbial community comparisons

Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta‐community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full‐scale waterworks. We observe that β diversity, after subsampling, is inflated by intra‐sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta‐community‐based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters.     

Comparison of Fish Assemblage Diversity in Natural and Artificial Rip‐Rap Habitats in the Littoral Zone of a Large River (River Danube,Hungary)

We studied day‐night patterns in fish diversity in natural, gravel‐sand stretches and boulder covered rip‐rap habitats in the littoral zone of the River Danube. Sample‐based rarefaction indicated marked differences in species richness between day and night, and smaller differences between habitats for both day and night. Whereas, individual‐based rarefaction indicated no such substantial differences in species richness. However, distinct fish assemblages were found based on relative abundance data, and species of great conservation concern tended to link to natural habitats. The diversity of biological traits/attributes were generally higher in rip‐rap habitats. The differences in fish assemblage characteristics between habitats revealed the importance of gravel‐sand habitats in maintaining natural assemblages and that rip‐rap sections increase compositional beta diversity at the mesohabitat scale. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The role of environment and mid-domain effect on moth species richness along a tropical elevational gradient

Aim The biodiversity of geometrid moths (Lepidoptera) along a complete tropical elevational gradient was studied for the first time. The patterns are described, and the role of geometric constraints and environmental factors is explored. Location The study was carried out along the Barva Transect (10° N, 84° W), a complete elevational gradient ranging from 40 to 2730 m a.s.l. in Braulio Carrillo National Park, Costa Rica, and adjacent areas. Methods Moths were sampled manually in 2003 and 2004 at 12 rain forest sites using light ‘towers’, each with two 15 W ultraviolet fluorescent tubes. We used abundance‐based rarefaction, statistical estimation of true richness (Chao 1), geographically interpolated observed richness and Fisher's alpha as measures of local diversity. Results A total of 13,765 specimens representing 739 species were analysed. All four measures showed a hump‐shaped pattern with maxima between 500 and 2100 m elevation. The two subfamilies showed richness and diversity maxima at either lower (Ennominae) or higher (Larentiinae) elevation than Geometridae as a whole. Among the four environmental factors tested, relative humidity yielded the highest correlation over the transect with the rarefaction‐based richness estimates as well as with estimated true species richness of Geometridae as a whole and of Larentiinae, while rainfall explained the greatest variation of Ennominae richness. The elevational pattern of moth richness was discordant with both temperature and with tree species richness. A combination of all environmental factors in a stepwise multiple regression produced high values of r² in Geometridae. The potential effects of geometric constraints (mid‐domain effect, MDE) were investigated by comparing them with observed, interpolated richness. Overall, models fitted very well for Geometridae as a whole and for Ennominae, but less well for Larentiinae. Small‐ranged species showed stronger deviations from model predictions than large‐ranged species, and differed strikingly between the two subfamilies, suggesting that environmental factors play a more pronounced role for small‐ranged species. We hypothesize that small‐ranged species (at least of the Ennominae) may tend to be host specialists, whereas large‐ranged species tend to be polyphagous. Based on interpolated ranges, mean elevational range for these moths was larger with increasing elevation, in accordance with Rapoport's elevational rule, although sampling effects may have exaggerated this pattern. The underlying mechanism remains unknown because Rapoport's ‘rescue’ hypothesis could not explain the observed pattern. Conclusions The results clearly show that moth diversity shows a hump‐shaped pattern. However, remarkable variation exists with regard to taxon and range size. Both environmental and geometric factors are likely to contribute to the observed patterns.     

Subsampling Herbarium Collections to Assess Geographic Diversity Gradients: A Case Study with Endemic Orchidaceae and Rubiaceae in Cameroon

We compiled herbarium specimen data to provide an improved characterization of geographic patterns of diversity using indices of species diversity and floristic similarity based on rarefaction principles. A dataset of 3650 georeferenced plant specimens belonging to Orchidaceae and Rubiaceae endemic to Atlantic Central Africa was assembled to assess species composition per half‐degree or one‐degree grid cells. Local diversity was measured by the expected number of species (S_k) per grid cell found in subsamples of increasing size and compared with raw species richness (S_R). A nearly unbiased estimator of the effective number of species per grid cell was also used, allowing quantification of ratios of ‘true diversity’ between grid cells. Species turnover was measured using a presence/absence‐based similarity index (Sørensen) and an abundance‐based index that corrects for sampling bias (NNESS). Our results confirm that the coastal region of Cameroon is more diverse in endemic species than those more inland. The southern part of this coastal forest is, however, as diverse as the more intensively inventoried northern part, and should also be recognized as an important center of endemism. A strong congruence between Sørensen and NNESS similarity matrices lead to similar delimitations of floristic units. Hence, heterogeneous sampling seems to confer more bias when measuring patterns of local diversity using raw species richness than species turnover using Sørensen index. Overall, we argue that subsampling methods represent a useful way to assess diversity gradients using herbarium specimens while correcting for heterogeneous sampling effort. Abstract in French is available in the online version of this article.     

CALIBRATED DIVERSITY,TREE TOPOLOGY AND THE MOTHER OF MASS EXTINCTIONS: THE LESSON OF TEMNOSPONDYLS

Abstract: Three family‐level cladistic analyses of temnospondyl amphibians are used to evaluate the impact of taxonomic rank, tree topology, and sample size on diversity profiles, origination and extinction rates, and faunal turnover. Temnospondyls are used as a case study for investigating replacement of families across the Permo‐Triassic boundary and modality of recovery in the aftermath of the end‐Permian mass extinction. Both observed and inferred (i.e. tree topology‐dependent) values of family diversity have a negligible effect on the shape of the diversity curve. However, inferred values produce both a flattening of the curve throughout the Cisuralian and a less pronounced increase in family diversity from Tatarian through to Induan than do observed values. Diversity curves based upon counts of genera and species display a clearer distinction between peaks and troughs. We use rarefaction techniques (specifically, rarefaction of the number of genera and species within families) to evaluate the effect of sampling size on the curve of estimated family‐level diversity during five time bins (Carboniferous; Cisuralian; Guadalupian–Lopingian; Early Triassic; Middle Triassic–Cretaceous). After applying rarefaction, we note that Cisuralian and Early Triassic diversity values are closer to one another than they are when the observed number of families is used; both values are also slightly higher than the Carboniferous estimated diversity. The Guadalupian–Lopingian value is lower than raw data indicate, reflecting in part the depauperate land vertebrate diversity from the late Cisuralian to the middle Guadalupian (Olson’s gap). The time‐calibrated origination and extinction rate trajectories plot out close to one another and show a peak in the Induan, regardless of the tree used to construct them. Origination and extinction trajectories are disjunct in at least some Palaeozoic intervals, and background extinctions exert a significant role in shaping temnospondyl diversity in the lowermost Triassic. Finally, species‐, genus‐, and family trajectories consistently reveal a rapid increase in temnospondyl diversity from latest Permian to earliest Triassic as well as a decline near the end of the Cisuralian. However, during the rest of the Cisuralian family diversity increases slightly and there is no evidence for a steady decline, contrary to previous reports.     

Comparison of Bacterial and Fungal Communities Between Natural and Planted Pine Forests in Subtropical China

To improve our understanding of the changes in bacterial and fungal diversity in natural pine and planted forests in subtropical region of China, we examined bacterial and fungal communities from a native and a nearby planted pine forest of the Mt. Lushan by constructing clone libraries of 16S and 18S rRNA genes. For bacterial communities, Proteobacteria and Acidobacteria were dominant bacterial taxa in both two types of forest soils. The Shannon–Wiener diversity index, rarefaction curve analysis, and LibShuff analysis suggest that these two forests contained similar diversity of bacterial communities. Low soil acidity (pH ≈ 4) of our study forests might be one of the most important selection factors determining growth of acidophilic Acidobacteria and Proteobacteria. However, the natural forest harbored greater level of fungal diversity than the planted forest according to the Shannon–Wiener diversity index and rarefaction curve analysis. Basidiomycota and Ascomycota were dominant fungal taxa in the soils of natural and planted forests, respectively. Our results suggest that fungal community was more sensitive than the bacterial community in characterizing the differences in plant cover impacts on the microbial flora in the natural and planted forests. The natural and planted forests may function differently due to the differences in soil fungal diversity and relative abundance.     

Low genetic diversity and small population size of Takahe Porphyrio hochstetteri on European arrival in New Zealand

The rediscovery of the Takahe Porphyrio hochstetteri in 1948 in the remote mountains of Fiordland, New Zealand, has been described as one of the greatest moments in ornithological history. The subsequent management of the population has become a model for avian recovery programmes, yet questions still remain regarding the population size at the time of, and prior to, its rediscovery. We used 20 microsatellite markers to genotype samples of the three surviving museum specimens (1849–1898) collected prior to the initial declaration of extinction to estimate levels of genetic diversity and effective population size. These estimates were compared with equivalent estimates from DNA samples of three specimens preserved at the time of rediscovery (1949) and with 20 contemporary samples. Using rarefaction simulations to account for the limited sample sizes, the results suggest that only slightly more genetic diversity (allelic diversity and numbers of polymorphic loci) existed in the earliest Takahe sampled and that levels of genetic diversity at the time of rediscovery were very similar to those today. Effective population size estimates showed a similar pattern. Contemporary samples from a widespread congener to Takahe, the Pukeko Porphyrio porphyrio, showed consistently higher levels of genetic diversity and greater effective population size, even after equivalent rarefaction to the same small sample sizes available for Takahe. It is likely that the population size of Takahe in Fiordland at the time of European arrivals in the 1800s was similar to its current size. These results provide molecular support for the hypothesis that Takahe were common throughout most coastal and eastern parts of the South Island of New Zealand before being hunted to extinction in these regions by early Maori, and persisted as a relatively small and isolated population in Fiordland where they may never have been very common. This is in marked contrast to other New Zealand endemic birds found in Fiordland, such as the Kakapo Strigops habroptilus and several forest passerines, which remained relatively numerous until the time of European arrival before undergoing rapid declines thereafter.     

A sampling optimization analysis of soil‐bugs diversity (Crustacea,Isopoda, Oniscidea)

Biological diversity analysis is among the most informative approaches to describe communities and regional species compositions. Soil ecosystems include large numbers of invertebrates, among which soil bugs (Crustacea, Isopoda, Oniscidea) play significant ecological roles. The aim of this study was to provide advices to optimize the sampling effort, to efficiently monitor the diversity of this taxon, to analyze its seasonal patterns of species composition, and ultimately to understand better the coexistence of so many species over a relatively small area. Terrestrial isopods were collected at the Natural Reserve “Saline di Trapani e Paceco” (Italy), using pitfall traps monthly monitored over 2 years. We analyzed parameters of α‐ and β‐diversity and calculated a number of indexes and measures to disentangle diversity patterns. We also used various approaches to analyze changes in biodiversity over time, such as distributions of species abundances and accumulation and rarefaction curves. As concerns species richness and total abundance of individuals, spring resulted the best season to monitor Isopoda, to reduce sampling efforts, and to save resources without losing information, while in both years abundances were maximum between summer and autumn. This suggests that evaluations of β‐diversity are maximized if samples are first collected during the spring and then between summer and autumn. Sampling during these coupled seasons allows to collect a number of species close to the γ‐diversity (24 species) of the area. Finally, our results show that seasonal shifts in community composition (i.e., dynamic fluctuations in species abundances during the four seasons) may minimize competitive interactions, contribute to stabilize total abundances, and allow the coexistence of phylogenetically close species within the ecosystem.     

Heterogeneity, speciation/extinction history and climate: explaining regional plant diversity patterns in the Cape Floristic Region

This paper investigates the role of heterogeneity and speciation/extinction history in explaining variation in regional scale (c. 0.1–3000 km²) plant diversity in the Cape Floristic Region of south‐western Africa, a species‐ and endemic‐rich biogeographical region. We used species‐area analysis and analysis of covariance to investigate geographical (east vs. west) and topographic (lowland vs. montane) patterns of diversity. We used community diversity as a surrogate for biological heterogeneity, and the diversity of naturally rare species in quarter degree squares as an indicator of differences in speciation/extinction histories across the study region. We then used standard statistical methods to analyse geographical and topographic patterns of these two measures. There was a clear geographical diversity pattern (richer in the west), while a topographic pattern (richer in mountains) was evident only in the west. The geographical boundary coincided with a transition from the reliable winter‐rainfall zone (west) to the less reliable non‐seasonal rainfall zone (east). Community diversity, or biological heterogeneity, showed no significant variation in relation to geography and topography. Diversity patterns of rare species mirrored the diversity pattern for all species. We hypothesize that regional diversity patterns are the product of different speciation and extinction histories, leading to different steady‐state diversities. Greater Pleistocene climatic stability in the west would have resulted in higher rates of speciation and lower rates of extinction than in the east, where for the most, Pleistocene climates would not have favoured Cape lineages. A more parsimonious hypothesis is that the more predictable seasonal rainfall of the west would have favoured non‐sprouting plants and that this, in turn, resulted in higher speciation and lower extinction rates. Both hypotheses are consistent with the higher incidence of rare species in the west, and higher levels of beta and gamma diversity there, associated with the turnover of species along environmental and geographical gradients, respectively. These rare species do not contribute to community patterns; hence, biological heterogeneity is uniform across the region. The weak topography pattern of diversity in the west arises from higher speciation rates and lower extinction rates in the topographically complex mountains, rather than from the influence of environmental heterogeneity on diversity.     

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.     

Elevational variation in regional vegetation responses to late‐glacial climate changes in the Carpathians

Aim We used fossil records to explore patterns of change in vegetation composition, turnover and diversity along an elevational gradient during the late‐glacial to early Holocene, and to locate the elevations most sensitive to past climate changes. Location Romania. Methods Changes in the late‐glacial vegetation communities were inferred from seven published pollen records distributed within the main vegetation belts of the Romanian Carpathians, at elevations from 275 to 1840 m. Principal components analysis, detrended canonical correspondence analysis (DCCA) and rarefaction analysis were undertaken on these data. Results DCCA indicates that compositional change is strongest (SD 1.2, c. 70%) at the late‐glacial/Holocene transition (c. 11,500 cal. yr bp ), but significant shifts also occur at c. 14,700, c. 13,800 and c. 12,700 cal. yr bp (SD 0.4–0.8, 25–50%). Palynological turnover is greater for mid‐elevation records (730–1100 m) than at low and high elevations. Intervals of greater palynological richness occur between c. 13,800 and 12,500 cal. yr bp and after 11,500 cal. yr bp , and intervals of lower richness occur before c. 14,000 cal. yr bp and between c. 12,900 and 11,500 cal. yr bp . Main conclusions Variations in species composition during repeated climate changes of the late‐glacial suggest that community composition at a given time was not only a result of the environmental conditions of that period, but also the legacy of previous cumulative recruitment and extirpation events. Turnover estimates suggest that mid‐elevations have been the most sensitive to climate change during the late‐glacial and early Holocene. Palynological richness estimates show a less clear elevational pattern and no evidence for a greater sensitivity of this measure of biodiversity at high elevations to past climate change. However, results may have been affected by taxa with high pollen productivity and distance dispersability. Our finding concurs with other palaeoecological and local‐scale modelling studies in suggesting that small populations have survived in favourable microhabitats embedded within larger unsuitable areas during the late‐glacial, features not captured by broad‐scale model predictions.     

Direct and indirect effects of glaciers on aquatic biodiversity in high Andean peatlands

The rapid melting of glacier cover is one of the most obvious impacts of climate change on alpine ecosystems and biodiversity. Our understanding of the impact of a decrease in glacier runoff on aquatic biodiversity is currently based on the ‘glacier‐heterogeneity‐diversity’ paradigm, according to which there is high α‐diversity at intermediate levels of glacial influence due to the high degree of environmental heterogeneity caused by glacier water. This α‐diversity pattern generates high levels of between‐site aquatic community variation (high β diversity) and increases regional diversity (γ‐diversity). There is a rich conceptual background in favor of this paradigm, but empirical data supporting it are scarce. We investigated this paradigm by analyzing the different diversity patterns (α, β and γ‐diversity) of four aquatic groups (zooplankton, macroinvertebrates, algae and macrophytes) living in high‐elevation peatlands (>4500 m above sea level). We sampled 200 pools from 20 peatlands along a glacier gradient in the Cordillera Real of Bolivia. We performed structural equation modeling (SEM) to analyze the potential mechanisms underlying the observed diversity patterns. Intermediate levels of glacial influence (15–20% cover) resulted in high heterogeneity, but α‐diversity responded to glacial influence only for the zooplankton group (Cladocera). Our SEM analysis did not identify environmental heterogeneity as a significant variable explaining the relationship between glacier and α‐diversity. Peatland area had a strong positive effect on heterogeneity and diversity. β‐diversity was significantly associated with glacier gradient, and 12.9% of the total regional diversity (γ‐diversity) was restricted to peatlands with a high degree of glacial influence. These species might be lost in a context of glacial retreat. These findings provide new insight into the potential effects of glacial retreat on the aquatic environment and biodiversity in the peatlands of the tropical Andes.     

Small‐scale patterns of genetic variation in a headwater specialist mayfly: No influence of selective forest harvesting on diversity

Terrestrial environments allow the adults of some aquatic insects to disperse between headwater streams, which may be important for maintaining population connectivity and persistence. Winged adult stages of aquatic insects are particularly sensitive to degradation of terrestrial habitat, relying on it for food, reproduction and dispersal. In this study we examined the genetic pattern of the Australian mayfly Ulmerophlebia sp. AV2, in north‐eastern New South Wales, and compared the genetic diversity in forested and partially deforested sub‐catchments. Our hypotheses were (i) patterns of mitochondrial DNA (mtDNA) variation in the Leptophlebiidae mayfly Ulmerophlebia sp. AV2 show a pattern of structuring that reflects low or widespread dispersal along the stream network and across catchments; and (ii) genetic diversity will be lower in partially deforested sub‐catchments compared to forested sub‐catchments. We found gene flow was not restricted among headwater streams within sub‐catchments but was restricted at distances >15 km. Genetic diversity was high (mean haplotype diversity >0.85) in both control and harvested sub‐catchments. Instead, a historical signature of population expansion was detected which is consistent with findings for other aquatic insect taxa of eastern Australia. Our results suggest that the selective harvesting management strategy, including the use of riparian buffer zones, within these sub‐catchments does not appear to restrict dispersal between streams or erode diversity within streams for Ulmerophlebia sp. AV2. Selective harvesting therefore appears to have minimal impacts on terrestrial/aquatic links in the life cycle of this insect.     

Genetic population structure in horse chestnut (Aesculus hippocastanum L.): effects of human‐mediated expansion across Europe

The geographical distribution of existing populations of horse chestnut (Aesculus hippocastanum L.) in Europe is determined by past demographic events during the Quaternary. In the present study we evaluate the imprints that northward expansions originated from common ancestry at southern Europe may have left on the present patterns of genetic variation for horse chestnut across the continent. Genetic diversity and levels of population structure in a European south–north gradient, ranging from the Balkans to the Scandinavian Peninsula, were determined with Amplified Fragment Length Polymorphism (AFLP) markers in 159 loci. A family of rarefaction techniques for the estimation of gene diversity was used to exclude potential confounding effects as a result of the unequal sample sizes. The results indicate that northern populations are not more genetically depleted than southern populations, thus suggesting that diversity for this species is not correlated with latitudinal distribution. Detailed hypotheses based on prediction models for different historical events associated with human‐mediated spread of cultivation are examined for a better understanding of the current genetic patterns of regional differentiation.     

Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments

Chesapeake Bay, the largest estuary in North America, encompasses a wide range of nutrient loading and trophic levels from the rivers and upper Bay to the sea, providing an ideal natural environment in which to explore relationships between functional diversity, physical/chemical complexity and ecosystem function (e.g. nitrification). In this study, amoA gene fragments (encoding subunit A of the key nitrification enzyme, ammonia monooxygenase) were PCR‐amplified from DNA extracted from sediment cores collected at five stations spanning gradients of salinity, ammonium, nitrate, oxygen and organic carbon along the Bay and Choptank River, a subestuary of the Bay. Phylogenetic analysis of ～30 amoA clones from each station revealed extensive diversity within the β‐Proteobacteria group of ammonia‐oxidizing bacteria (AOB), with the vast majority of sequences falling into coherent phylogenetic clusters distinct from sequences of cultivated AOB. Over 70% of the clones fell into two major phylogenetic clusters that appear to represent novel groups of Nitrosomonas‐like and Nitrosospira‐like amoA sequences that may be specific to estuarine and marine environments. Rarefaction analysis, estimators of genetic variation and dissimilarity indices all revealed differences in the relative amoA‐based diversity and/or richness among most of the stations, with the highest diversity at the North Bay station and the lowest at the mesohaline stations. Although salinity appears to play a role, no single physical or chemical parameter entirely explains the pattern of diversity along the estuary, suggesting that a complex combination of environmental factors may shape the overall level of AOB diversity in this dynamic environment.     

Assessing the diversity pattern of cryophilous plant species in high elevation habitats

This study aimed to better document the diversity and distribution patterns of vascular cryophilous species across major habitat types in a high-elevation Mediterranean system in central Italy. The research addressed the following questions: (a) whether different habitats support similar levels of biodiversity in terms of total vascular plants richness and cryophilous species richness, and (b) how each habitat contributes to the total cryophilous species diversity. A random stratified sampling approach based on a habitat map was applied to construct rarefaction curves for overall cryophilous species richness and habitat type-specific cryophilous richness. Rarefaction curves were also constructed for all-species and exclusive species. To determine whether the targeted species represented a constant proportion of all species, the ratio between the rarefaction curves of the cryophilous species and all species was also calculated. The results highlight the importance of the different habitat types in overall and cryophilous species conservation because these different habitat types had progressively higher richness values. At the regional scale, steep slopes had the highest species diversity, the greatest exclusive species richness and a steep rarefaction curve. The diversity pattern of cryophilous taxa was not related to the general pattern of total species richness, with these species being more common in three habitat types with extreme environmental conditions: ridges, cliffs, and screes. For the establishment of successful biodiversity conservation programs, it is imperative to include species-poor habitats containing a high proportion of cryophilous species, which are considered to be threatened by climate warming.     

HS‐SPME/GC Analysis Reveals the Population Variability of Terpene Contents in Juniperus communis Needles

Juniperus communis var. communis L. is an aromatic plant – typical boreal element of flora. In the extensive literature concerning J. communis, there is much data on the composition and the content of essential oil of needles and coneberries, but a detailed analysis of terpene distribution within and between populations is missing. A representative pool of 74 J. communis individuals originating from ten populations of Northern Poland was investigated in order to evaluate the intra‐ and interpopulational variability of the terpene pattern. Headspace solid‐phase microextraction (HS‐SPME) coupled with GC/MS and GC/FID was applied in achiral and enantioselective analysis. The majority of the samples (85%), despite different origin, were similar in the terpene pattern. High diversity of terpenes was observed within the populations and low diversity between them. High variation of enantiomeric composition was in accordance with large variation of individual compounds in general (achiral analysis). J. communis samples from Northern Poland could be distinguished by the α‐pinene/sabinene ratio, and they were divided into three chemical races.     

Global patterns of Rhododendron diversity: The role of evolutionary time and diversification rates

Aim

Understanding the evolution of the latitudinal diversity gradient (i.e. increase in species diversity towards the tropics) is a prominent issue in ecology and biogeography. Disentangling the relative contributions of environment and evolutionary history in shaping this gradient remains a major challenge because their relative importance has been found to vary across regions and taxa. Here, using the global distributions and a molecular phylogeny of Rhododendron, one of the largest genera of flowering plants, we aim to compare the relative contributions of contemporary environment, evolutionary time and diversification rates in generating extant species diversity patterns.

Location

Global.

Time period

Undefined.

Major taxa studied

Rhododendron.

Methods

We compiled the global distributions of all Rhododendron species, and constructed a dated molecular phylogeny using nine chloroplast genes and seven nuclear regions. By integrating these two datasets, we estimated the temporal trends of Rhododendron diversification, and explored the global patterns of its species diversity, net diversification rates, and species ages. Next, we reconstructed the geographical ancestral area of the clade. Finally, we compared the relative contribution of contemporary environment, time‐for‐speciation, and diversification rates on the species diversity pattern of Rhododendron.

Results

In contrast to the predictions of the time‐for‐speciation hypothesis, we found that although Rhododendron originated at a temperate latitude, its contemporary species diversity is highest in the tropics/subtropics, suggesting an into‐the‐tropics colonization for this genus. We found that the elevated diversification induced by heterogeneous environmental conditions in the tropics/subtropics shapes the global pattern of Rhododendron diversity.

Main conclusions

Our findings support tropical and subtropical mountains as not only biodiversity and endemism hotspots, but also as cradles for the diversification of Rhododendron. Our study emphasizes the need of unifying ecological and evolutionary approaches in order to gain comprehensive understanding of the mechanisms underlying the global patterns of plant diversity.     

A unified mathematical framework for the measurement of richness and evenness within and among multiple communities

Biodiversity can be divided into two aspects: richness (the number of species or other taxa in a community or sample) and evenness (a measure of the distribution of relative abundances of different taxa in a community or sample). Sample richness is typically evaluated using rarefaction, which normalizes for sample size. Evenness is typically summarized in a single value. It is shown here that Hurlbert's probability of interspecific encounter (Δ₁), a commonly used sample-size independent measure of evenness, equals the slope of the steepest part of the rising limb of a rarefaction curve. This means that rarefaction curves provide information on both aspects of diversity. In addition, regional diversity (gamma) can be broken down into the diversity within local communities (alpha) and differences in taxonomic composition among local communities (beta). Beta richness is expressed by the difference between the composite rarefaction curve of all samples in a region with the collector's curve for the same samples. The differences of the initial slopes of these two curves reflect the beta evenness thanks to the relationship between rarefaction and Δ₁. This relationship can be further extended to help interpret species-area curves (SAC's). As previous authors have described, rarefaction provides the null hypothesis of passive sampling for SAC's, which can be interpreted as regional collector's curves. This allows evaluation of richness and evenness at local and regional scales using a single family of well-established, mathematically related techniques.