Commentary: do we have a consistent terminology for species diversity? We are on the way

A consistent terminology for species diversity is subject of an ongoing debate. Recently Tuomisto (Oecologia 164:853–860, 2010) stated that a consistent terminology for diversity already exists. The paper comments on recent papers by ourselves (Jurasinski et al. Oecologia 159:15–26, 2009) and by Moreno and Rodriguez (Oecologia 163:279–282, 2010). Both started from Whittaker’s diversity concept to discuss the ambiguities of the terminology and propose a new, more consistent terminology that is based on the different approaches to diversity analysis. In contrast, Tuomisto adheres to a strict school of thinking and derives a diversity framework in the sense of Whittaker (alpha, beta, gamma) from the conceptual definition of diversity itself. A third group of papers discusses appropriate methods for the analysis of the variation in species composition. Here, we support the idea that alpha, beta and gamma diversity should be used in a strict sense that is based only on the conceptual definition of diversity. We accordingly extend and modify our terminological concept for species diversity. All approaches to the analysis and quantification of species composition and diversity can be assigned to three abstraction levels (species composition, variation in species composition,and variation in variation in species composition) and two scale levels (sample scale, aggregation scale). All methods that investigate the variation in species composition across scale levels evaluate beta relation with beta diversity being just one form of beta relation, which is calculated by dividing gamma diversity of order q by the appropriate alpha diversity of the same order. In contrast, differentiation refers to a pairwise calculation of resemblance in species composition. It is restricted to sample scale and is therefore most often only an intermediate step of analysis. Many ecological questions can be addressed either by direct analysis of the variation in species composition using raw data approaches or by further analysis of differentiation datasets on aggregation scale with or without respect to an external gradient.     

Additive partition of parametric information and its associated beta-diversity measure

A desirable property of a diversity index is strict concavity. This implies that the pooled diversity of a given community sample is greater than or equal to but not less than the weighted mean of the diversity values of the constituting plots. For a strict concave diversity index, such as species richness S, Shannon's entropy H or Simpson's index 1-D, the pooled diversity of a given community sample can be partitioned into two non-negative, additive components: average within-plot diversity and between-plot diversity. As a result, species diversity can be summarized at various scales measuring all diversity components in the same units. Conversely, violation of strict concavity would imply the non-interpretable result of a negative diversity among community plots. In this paper, I apply this additive partition model generally adopted for traditional diversity measures to Aczél and Daróczy's generalized entropy of type . In this way, a parametric measure of -diversity is derived as the ratio between the pooled sample diversity and the average within-plot diversity that represents the parametric analogue of Whittaker's -diversity for data on species relative abundances.     

A comparative study of Odonata (Insecta) assemblages along an altitudinal gradient in the sierra de Coalcomán Mountains, Michoacán, Mexico

Odonate diversity in the Coalcomán Mountain Range (CMR), Michoacán State, Mexico, was surveyed, and samplings were made during 2 years in eight streams along an altitudinal gradient. Presence–absence data were analyzed using non-parametric and parametric methods. Beta and gamma diversities were estimated using Whittaker’s and Lande’s formulae, respectively. A total of 2,526 adults and 489 larvae were captured, yielding 116 species (γ diversity), 44 genera and 9 families. Five new species were discovered. The genus Argia was the most important contributor to Zygoptera diversity and total richness (γ diversity), yielding 40.4 and 14.7%, respectively. The non-parametric estimator Chao2 provided the closest theoretical estimate of species richness, and Clench’s model fit the data well (R ² ranged from 99.44 to 99.99) to explain a high proportion of the variance (98.8). We conclude that beta diversity is important at the landscape scale, supporting the hypothesis that Mexico is a beta diverse country. Our results triple the number of known species of Odonata for Michoacán. Given the considerable richness of odonates at local and landscape scales, our results support the proposal of the Coalcomán Mountain Range as a priority area for conservation and related research.     

Brocchi,Darwin, and Transmutation: Phylogenetics and Paleontology at the Dawn of Evolutionary Biology

Giambattista Brocchi’s (1814) monograph (see Dominici, Evo Edu Outreach, this issue, 2010) on the Tertiary fossils of the Subappenines in Italy—and their relation to the living molluscan fauna—contains a theoretical, transmutational perspective (“Brocchian transmutation”). Unlike Lamarck (1809), Brocchi saw species as discrete and fundamentally stable entities. Explicitly analogizing the births and deaths of species with those of individual organisms (“Brocchi’s analogy”), Brocchi proposed that species have inherent longevities, eventually dying of old age unless driven to extinction by external forces. As for individuals, births and deaths of species are understood to have natural causes; sequences of births and deaths of species produce genealogical lineages of descent, and faunas become increasingly modernized through time. Brocchi calculated that over 50% of his fossil species are still alive in the modern fauna. Brocchi’s work was reviewed by Horner (1816) in Edinburgh. Brocchi’s influence as a transmutational thinker is clear in Jameson’s (1827) “geological illustrations” in his fifth edition of his translation of Cuvier’s Theory of the Earth (read by his student Charles Darwin) and in the anonymous essays of 1826 and 1827 published in the Edinburgh New Philosophical Journal—which also carried a notice of Brocchi’s death in 1827. The notion that new species replace older, extinct ones—in what today would be called an explicitly phylogenetic context—permeates these essays. Herschel’s (1830) discussion of temporal replacement of species and the modernization of faunas closely mirrors these prior discussions. His book, dedicated to the search for natural causes of natural phenomena, was read by Charles Darwin while a student at Cambridge. Darwin’s work on HMS Beagle was in large measure an exploration of replacement patterns of “allied forms” of endemic species in time and in space. His earliest discussions of transmutation, in his essay February 1835, as well as the Red Notebook and the early pages of Notebook B (the latter two written in 1837 back in England), contain Brocchi’s analogy, including the idea of inherent species longevities. Darwin’s first theory of the origin of species was explicitly saltational, invoking geographic isolation as the main cause of the abrupt appearance of new species. We conclude that Darwin was testing the predicted patterns of both Brocchian and Lamarckian transmutation as early as 1832 at the outset of his work on the Beagle.     

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.     

Commentary: Do we have a consistent terminology for species diversity? The fallacy of true diversity

There is no single best index that can be used to answer all questions about species diversity. Entropy-based diversity indices, including Hill’s indices, cannot account for geographical and phylogenetic structure. While a single diversity index arises if we impose several constraints—most notably that gamma diversity be completely decomposed into alpha and beta diversity—there are many ecological questions regarding species diversity for which it is counterproductive, requiring decomposability. Non-decomposable components of gamma diversity may quantify important intrinsic ecological properties, such as resilience or nestedness.     

Do tree-level monocultures develop following Canadian boreal silviculture? Tree-level diversity tested using a new method

Concern about forestry practices creating tree-level monoculture plantations exists. Our study investigates tree diversity responses for six early seral boreal forest plantations in Ontario, Canada, representing three conifer species; black spruce (Picea mariana), white spruce (P. glauca), and jack pine (Pinus banksiana), 14 release treatments, and 94 experimental units. Dominance-diversity curves and Simpson’s indices of diversity and evenness indicate tree alpha diversity. We propose a new method for assessing diversity, using percentage of theoretical species maximum (%TSM) which is determined by comparing post-disturbance richness (S) with a theoretical species maximum (TSM). Our results support the hypothesis that alternative vegetation release treatments generally do not reduce tree species diversity levels (%TSM) relative to untreated plots. The only %TSM (P ≤ 0.05) comparison that produced less diversity than in control plots was repeated annual treatments of Vision herbicide at one of the black spruce study sites. Our results generally support the hypothesis that tree monocultures do not develop after vegetation release. Only one out of 94 experimental units developed into a tree layer monoculture (Simpson’s reciprocal diversity index = 1). Again this was one of the repeated annual treatments of Vision herbicide at one of the black spruce study sites—a treatment which is atypical of Canadian forest management.

An assessment of orchids’ diversity in Penang Hill,Penang, Malaysia after 115 years

A comprehensive study on the orchid diversity in Penang Hill, Penang, Malaysia was conducted from 2004 to 2008 with the objective to evaluate the presence of orchid species listed by Curtis (J Strait Br R Asiat Soc 25:67–173, 1894) after more than 100 years. A total of 85 species were identified during this study, of which 52 are epiphytic or lithophytic and 33 are terrestrial orchids. This study identified 57 species or 64.8% were the same as those recorded by Curtis (1894), and 78 species or 66.1% of Turner’s (Gardens’ Bull Singap 47(2):599–620, 1995) checklist of 118 species for the state of Penang including 18 species which were not recorded by Curtis (1894) and the current study but are actually collected from Penang Hill. A comparison table of the current findings against Curtis (1894) and Turner (1995) is provided which shows only 56 species were the same in all three studies. The preferred account for comparison was Curtis’ (1894) list as his report was specifically for the areas around Penang Island especially Penang Hill, Georgetown and Ayer Itam areas. Our study reveals that about 50% of Curtis’ collection localities have been converted to residential areas and agricultural land, and this probably explains the decreasing numbers of species found in the current study especially for the terrestrial species as epiphytic species have better adaptation capabilities towards environmental changes. Seven species were identified as new records to Penang Hill as they were not recorded by Curtis (1894). None of the three species recorded as endemic to Penang by Turner (1995) was recollected during the current study, of which only Zeuxine rupestris was in Curtis’ (1894) list. Overall, we concluded that Penang hill harbours at least 136 species of orchids of which 78 species or 57.4% were recollected in this study. This also indicates that this area is still suitable for orchid growth even though it is surrounded by rapid development and mass conversion of forested land into fruit orchards and residential area. The designation of Penang Hill as a Permanent Forest Reserve would better guarantee the survival of some orchid species unless human interventions and climatic changes occur.     

From plots to islands: species diversity at different scales

Aim To investigate how plant diversity of whole islands (‘gamma’) is related to alpha and beta diversity patterns among sampling plots within each island, thus exploring aspects of diversity patterns across scales. Location Nineteen islands of the Aegean Sea, Greece. Methods Plant species were recorded at both the whole‐island scale and in small 100 m² plots on each island. Mean plot species richness was considered as a measure of alpha diversity, and six indices of the ‘variation’‐type beta diversity were also applied. In addition, we partitioned beta diversity into a ‘nestedness’ and a ‘replacement’ component, using the total species richness recorded in all plots of each island as a measure of ‘gamma’ diversity. We also applied 10 species–area models to predict the total observed richness of each island from accumulated plot species richness. Results Mean alpha diversity was not significantly correlated with the overall island species richness or island area. The range of plot species richness for each island was significantly correlated with both overall species richness and area. Alpha diversity was not correlated with most indices of beta diversity. The majority of beta diversity indices were correlated with whole‐island species richness, and this was also true for the ‘replacement’ component of beta diversity. The rational function model provided the best prediction of observed island species richness, with Monod’s and the exponential models following closely. Inaccuracy of predictions was positively correlated with the number of plots and with most indices of beta diversity. Main conclusions Diversity at the broader scale (whole islands) is shaped mainly by variation among small local samples (beta diversity), while local alpha diversity is not a good predictor of species diversity at broader scales. In this system, all results support the crucial role of habitat diversity in determining the species–area relationship.     

Recommendations for the use of species diversity indices with reference to a recently published article as an example

There are some recommendations for the use of species diversity indices in a paper recently published in this journal by M. Ohsawa on the species richness and composition of weevils in five forest types in the middle region of Japan. Because several factors, such as small sample size, calculation of Simpson’s diversity index by the use of the original equation of Simpson’s measure of concentration D, and a weak point in the Shannon–Wiener diversity index H′, may have led to biased estimates, I recalculated these indices using combined species diversity values of the five forest types. As the general tendencies of 1−D and H′ values calculated here were similar to those in Ohsawa’s paper, there is no need to propose any change to his view. However, these recalculated diversity indices indicated that they are values which are more suitable for use. It should be noted that the characteristics and weak point associated with the diversity indices need to be taken into account in future studies.     

Comparison of the developmental stages of some European allocreadiid trematode species and a clarification of their life-cycles based on ITS2 and 28S sequences

Genetic data were used to examine the diversity in some allocreadiid trematodes. Nuclear ribosomal DNA (ITS2 and partial sequences of 5.8S and 28S) was sampled from sexual adult and ‘larval’ stages. From these and previous reference datasets phylogenetic trees were constructed. The results uncovered genetically distinct lineages within Bunodera luciopercae (Müller, 1776), suggesting that the two Palaearctic subspecies, B. l. luciopercae and B. l. acerinae Roitman & Sokolov, 1999, and Nearctic B. luciopercae from Perca flavescens may represent distinct species with a restricted host-specificity. Identical rDNA was revealed for the sexual adult of B. l. acerinae and ‘larval’ B. luciopercae described by Wiśniewski (1958). An unexpected match between the rDNA sequences of adult B. l. luciopercae and ‘larval’ Allocreadium isoporum (sensu Wiśniewski, 1958) was also detected. The adult A. isoporum (Looss, 1894) differs significantly from the ‘larval’ A. isoporum, the level of rDNA sequence divergence between them (8.6 % for 5.8S-ITS2-28S sequences and 6.26% for 28S) being consistent with the level expected for intergeneric variation. These results revealed the possible existence of a cryptic species complex within the nominal species B. luciopercae and a clear need for reconsideration of some of the accepted, but largely untested, tenets regarding allocreadiid life-cycles.     

Phylogeography of the endemic St. Lucia whiptail lizard Cnemidophorus vanzoi: Conservation genetics at the species boundary

Vicariance and isolation leading to speciation of reptiles on islands is well exemplified in a number of taxa in the Caribbean. The St. Lucia whiptail (Cnemidophorus vanzoi), considered a single species, is found on two small islets (Maria Major and Maria Minor) off the main island of St. Lucia. From lizards collected from both localities, we gathered morphological measurements and analysed the genetic divergence between populations, using a molecular survey of ∼ ∼2800 mtDNA base pairs and 8 microsatellites. There are significant differences in body size and general form and fixed but small mtDNA differences between island populations. Microsatellites reveal low diversity within populations but very high differentiation between islands with non-overlapping allele size ranges at all except one microsatellite and two loci exhibiting single-base polymorphism, fixed between islands. Based on these results, we examine published criteria to determine whether the studied island forms could be considered true species. According to the phylogenetic species concept and Moritz’s evolutionary significant unit (ESU) criteria, the two lizard populations can be considered separate entities. Crandall et al.’s (2000, Trends Ecol. Evol., 15, 290–295) broader categorization of population distinctiveness, based on concepts of ecological and genetic exchangeability, produces conflicting results depending on the interpretation of the observed ecological data. Following Fraser and Bernatchez’s (2001, Mol. Ecol., 10, 2741–2752) framework for management decisions when ecological data are not sufficient we propose that the lizard populations on the Maria islands are on differing evolutionary trajectories and thus at the species boundary. The populations are of high priority to conservation, thus meriting separate management.     

The variation of tree beta diversity across a global network of forest plots

Aims With the aim of understanding why some of the world's forests exhibit higher tree beta diversity values than others, we asked: (1) what is the contribution of environmentally related variation versus pure spatial and local stochastic variation to tree beta diversity assessed at the forest plot scale; (2) at what resolution are these beta‐diversity components more apparent; and (3) what determines the variation in tree beta diversity observed across regions/continents? Location World‐wide. Methods We compiled an unprecedented data set of 10 large‐scale stem‐mapping forest plots differing in latitude, tree species richness and topographic variability. We assessed the tree beta diversity found within each forest plot separately. The non‐directional variation in tree species composition among cells of the plot was our measure of beta diversity. We compared the beta diversity of each plot with the value expected under a null model. We also apportioned the beta diversity into four components: pure topographic, spatially structured topographic, pure spatial and unexplained. We used linear mixed models to interpret the variation of beta diversity values across the plots. Results Total tree beta diversity within a forest plot decreased with increasing cell size, and increased with tree species richness and the amount of topographic variability of the plot. The topography‐related component of beta diversity was correlated with the amount of topographic variability but was unrelated to its species richness. The unexplained variation was correlated with the beta diversity expected under the null model and with species richness. Main conclusions Because different components of beta diversity have different determinants, comparisons of tree beta diversity across regions should quantify not only overall variation in species composition but also its components. Global‐scale patterns in tree beta diversity are largely coupled with changes in gamma richness due to the relationship between the latter and the variation generated by local stochastic assembly processes.     

小兴安岭阔叶红松林地表甲虫Beta多样性

Beta多样性用来衡量集群内物种组成的变异性,可以被分解为空间物种转换和物种集群镶嵌两个组分,是揭示群落构建机制的重要基础。目前开展了较多的地上生态系统beta多样性研究,然而地下生态系统beta多样性进展缓慢。以小兴安岭凉水和丰林自然保护区为研究地区,于2015年8、10月采用陷阱法对阔叶红松林进行调查,揭示地表甲虫(步甲科、隐翅虫科、葬甲科)的beta多样性。结果表明:(1)凉水共发现39种、856只地表甲虫,丰林共发现43种、1182只地表甲虫。8月凉水明显具有较高的全部甲虫(三个科的总和)物种多样性和丰富度,10月正好相反。(2)凉水和丰林之间地表甲虫beta多样性的差异仅发现于8月的步甲科和葬甲科之间。(3)凉水和丰林地表甲虫的beta多样性主要由空间物种转换组成,物种集群镶嵌对beta多样性的贡献很小,说明地表甲虫物种组成变异主要由本地物种之间较高的转换引起。研究表明小兴安岭阔叶红松林地表甲虫的beta多样性主要由空间物种转换组成,在揭示群落构建机制过程中,其内部物种交换和环境调控不容忽视。     

Traveller or tourist? Jack Kerouac and the commodification of culture

Jack Kerouac, the author of On The Road, was a central figure of the Beat Generation, a generation which rebelled against middle-class conformity in post–World War II America. Kerouac described himself as “a religious wanderer” (Kerouac 2006: 2), but an examination of his texts and life suggest his travels may also be understood as tourism. Viewed through the prism of tourism, this study will argue, for example, that MacCannell’s notion of the tourist’s quest for reality and authenticity (MacCannell 1989: 3) provides some insight into why Kerouac wrote that just south of Macon, Georgia, he and his travelling companion Neal Cassady stopped and got out of the car, “and suddenly both of us were stoned with joy to realize that in the darkness all around us was fragrant green grass and the smell of fresh manure and warm waters” (Kerouac 1957: 115). As Kerouac rebelled against being, as one of his protagonists in The Dharma Bums put it, “imprisoned in a system of work, produce, consume, work, produce, consume” (Kerouac 2006: 73) he travelled across America on a rapidly improving network of highways, turning “mobility into a retreat” (Holladay and Holton 2009: 42). Kerouac alternately identified himself as a hobo (Kerouac 1973: 181) and “not a real hobo” (Kerouac 1973: 173), but this article asks whether Kerouac’s travels were those of the last in a line of wanderers rebelling against conformity and modernization or a precursor of mobile mass tourism in America.     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers

Hill numbers (or the “effective number of species”) are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify “the effective number of equally abundant and (functionally) equally distinct species” in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration.     

A consistent terminology for quantifying species diversity? Yes, it does exist

The prevailing terminological confusion around the concept ‘diversity’ has hampered accurate communication and caused diversity issues to appear unnecessarily complicated. In fact, a consistent terminology for phenomena related to (species) diversity is already available. When this terminology is adhered to, diversity emerges as an easily understood concept. It is important to differentiate between diversity itself and a diversity index: an index of something is just a surrogate for the thing itself. The conceptual problem of defining diversity also has to be separated from the practical problem of deciding how to adequately quantify diversity for a community of interest. In practice, diversity can be quantified for any dataset where units of observation (such as individuals) have been classified into types (such as species). All that needs to be known is what proportion of the observed units belong to a type of mean abundance. Diversity equals the inverse of this mean, and it quantifies the effective number of the types of interest. In ecology, interest often (but not always) focuses on species diversity. If the dataset consists of (or gets divided into) subunits, then the total effective number of species (gamma diversity) can be partitioned into the effective number of compositionally distinct subunits (beta diversity) and the mean effective number of species per such subunit (alpha diversity). Species richness is related to species diversity, but they are not the same thing; richness does not take the proportional abundances into account and is therefore the actual—rather than the effective—number of types. Most of the phenomena that have been called ‘beta diversity’ in the past do not quantify an effective number of types, so they should be referred to by names other than ‘diversity’ (for example, species turnover or differentiation).