Influence of hydrology and seasonality on DOC exports from three contrasting upland catchments

Variation in dissolved organic carbon (DOC) concentrations of surface waters is a consequence of process changes in the surrounding terrestrial environment, both within annual cycles and over the longer term. Long-term records (1987–2006) of DOC concentrations at six catchments (0.44–10.0 km²) across a climatic transect in Scotland were investigated for intra-annual relationships to evaluate potential long-term seasonal patterns. The intra-annual mode of DOC export contrasted markedly between catchments and appeared dependent on their hydrological characteristics. Catchments in wetter Central Scotland with high rainfall–runoff ratios, short transit times and well-connected responsive soils show a distinct annual periodicity in DOC concentrations throughout the long-term datasets. Increased DOC concentrations occurred between June and November with correspondingly lower DOC concentrations from December to May. This appears unrelated to discharge, and is dependent mainly on higher temperatures driving biological activity, increasing decomposition of available organic matter and solubility of DOC. The drier eastern catchments have lower rainfall–runoff ratios, longer transit times and annual drying–wetting regimes linked to changing connectivity of soils. These are characterised by seasonal DOC concentration–discharge relationships with an autumnal flush of DOC. Temperature influences the availability of organic matter for DOC transport producing a high DOC concentration–discharge relationship in summer/autumn and low DOC concentration–discharge relationship in winter/spring. These two distinct modes of seasonal DOC transport have important implications for understanding changes in DOC concentrations and export brought about by climate change (temperature and precipitation) and modelling of aquatic carbon losses from soil-types under different hydrological regimes.     

Genetic Structure of the Ancestral Population of Modern Humans

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n= 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The ``age before fixation' of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n= 860 chromosomes in total). Seventeen polymorphisms older tan 100,000–200,000 years, which contributed ∼90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000–200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period. Received: 3 February 1998 / Accepted: 9 February 1998     

The influence of predation risk on diet selectivity: A theoretical analysis

Studies that have examined the effect of experimental increases in predation risk on diet selectivity have shown both decreased and increased diet selectivity. A possible explanation for these disparate results emerges from an examination of the prey sets used in these studies, which differed in the relationship between the values of risk components associated with the capture of different prey types (‘danger’) and their profitabilities. When less profitable prey were more dangerous, selectivity increased with predation risk. When prey were equally dangerous, selectivity did not change. Finally, when the more profitable prey were also more dangerous, selectivity decreased with risk. Here, we examine theoretically the influence of a forager's estimate of the probability that a predator is present (φ) on the selection of diets from prey sets with varying danger–profitability relationships. A dynamic programming model is used to determine the maximum attack time (or distance) for each of two types of prey, differing in their energetic content, for a range of forager energy state and φ levels. The diets which would result if foragers attacked prey according to the rules provided by the dynamic model are then determined. The model results indicate that the prey danger–profitability relationship determines the diet selectivity response to φ, confirming that variation in this relationship could be responsible for the range of experimental results. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ontogeny of respiratory area of a marine teleost, porgy,pagrus major

Relationships of respiratory areas (gill, body surface and fin areas) (A) to body mass (W) were determined with a marine teleost, the porgyPagrus major of 0.0002–1230 g (just after hatch to 3+ years old), based on the allometric formula A=αW^β. (1) Early larvae (0.0002–0.0003 g) did not have the secondary lamellae that were responsible for gas exchange at the gills. After this stage, a tetraphasic relationship was observed between lamellar area (total area of secondary lamellae, often called gill area) (GA_L) and boby mass. During the late larval and early juvenile stages, the GA_L-W relationship showed a triphasic positive allometry with β-values of 3.773, 1.561 and 1.111 corresponding to the first half of the late larval stage (0.00034–0.001g), the second half of the stage (0.001–0.01 g) and the early juvenile stage (0.02–0.1 g), respectively, During the squamated juvenile and later stages (0.1–1080g), there was a negative allometry with a β-value of 0.813. (2) A triphasic relationship was observed between the total cutaneous surface area (body surface area and fin area) (CA_b+f) and body mass. During the early larval stage, in which an increase of body mass was very small. from 0.0002 to 0.00025 g, CA_b+p/W increased with growth with a β-value of 3.986. After this stage, the CA_b+t W relationship showed a diphasic negative allometry with β-values of 0.562, during the late larval stage (0.00028–0.0045 g) and 0.652 during the early juvenile and later stages (0.0045–1230 g). (3) Based on these results, factors controlling the metabolism-size relationship are discussed.     

Evolutionary origins of two tightly linked mutations in arylsulfatase-A pseudodeficiency

Deficient arylsulfatase A activity causes the neurodegenerative disease metachromatic leukodystrophy. However, some individuals with deficient enzyme activity appear clinically normal. This “pseudodeficiency” allele commonly found among many reported populations (frequency ∼ 0.10) is associated with two A→G transitions in cis in the arylsulfatase A gene causing the simultaneous loss of an N-glycosylation and a polyadenylation signal. To understand the evolutionary relationship between such common and tightly linked mutations, we studied 400 individuals in the African, European, Indian and East Asian populations and found none carrying the polyadenylation mutation alone. However, the N-glycosylation mutation could occur independently. Its frequency varied from 0.01 in Indians, 0.06 in Europeans, 0.21 in East Asians to 0.32 in Africans. The frequencies of both mutations occurring together ranged from almost non-existent in the Africans and East Asians, to 0.075 in the Europeans and 0.125 in the Indians. These frequencies were significantly different among populations. Haplotype analysis among homozygous pseudodeficiency individuals and eight multi-generation families with six polymorphic enzymes showed that, of the five haplotypes found in the general population, only one was linked to the double mutations. Alleles among the four populations with only the N-glycosylation mutation also supported linkage to the same haplotype except in some Europeans whose alleles were discordant. These results are consistent with the hypothesis that the N-glycosylation mutation may be a recurrent event among the Europeans but first occurred in an ancestral allele before the emergence of modern Homo sapiens from Africa at ∼100 000–200 000 years ago. Subsequently, the polyadenylation mutation occurred in this ancient allele with the N-glycosylation mutation, an event that likely took place after the divergence between the European and East Asian lineages. Received: 23 December 1996 / Accepted: 21 July 1997     

Evolutionary Developmental Biology (Evo-Devo): Past, Present, and Future

Evolutionary developmental biology (evo–devo) is that part of biology concerned with how changes in embryonic development during single generations relate to the evolutionary changes that occur between generations. Charles Darwin argued for the importance of development (embryology) in understanding evolution. After the discovery in 1900 of Mendel’s research on genetics, however, any relationship between development and evolution was either regarded as unimportant for understanding the process(es) of evolution or as a black box into which it was hard to see. Research over the past two decades has opened that black box, revealing how studies in evo–devo highlight the mechanisms that link genes (the genotype) with structures (the phenotype). This is vitally important because genes do not make structures. Developmental processes make structures using road maps provided by genes, but using many other signals as well—physical forces such as mechanical stimulation, temperature of the environment, and interaction with chemical products produced by other species—often species in entirely different kingdoms as in interactions between bacteria and squid or between leaves and larvae (Greene Science 243:643–666, 1989). Not only do genes not make structures (the phenotype), but new properties and mechanisms emerge during embryonic development: genes are regulated differentially in different cells and places; aggregations of similar cells provide the cellular resources (modules) from which tissues and organs arise; modules and populations of differently differentiated cells interact to set development along particular tracks; and organisms interact with their environment and create their niche in that environment. Such interactions are often termed “epigenetic,” meaning that they direct gene activity using mechanisms that are not encoded in the DNA of the genes. This paper reviews the origins of evo–devo, how the field has changed over the past 30 years, evaluates the recognition of the importance for development and evolution of mechanisms that are not encoded in DNA, and evaluates what the future might bring for evo–devo. Although impossible to know, history tells us that we might expect more of the same; expansion of evo–devo into other areas of biology (ecology, physiology, behavior); absorption of evo–devo by evolution or a unification of biology in which evo–devo plays a major role.     

A chip for catching, separating, and transporting bio-particles with dielectrophoresis

This study aims at developing a 3D device for catching, separating, and transporting bio-particles based on dielectrophoresis (DEP). Target particles can be simultaneously caught and transported using the negative DEP method. In non-uniform electric fields, the levitation height or complex permittivity of certain particle may be different from that of another and this property can facilitate separation of particles. We have designed and constructed a 3D device consisting of two layers of electrodes separated by a channel formed by 50 μm thick photoresist. The electrodes can operate effectively with 10–15 V and 5–7 MHz to catch all particles in the channel, and can move particles after switching the electric field to 5–15 V and 500–1,000 KHz. Hence, particles experienced coupling force of two different directional twDEP forces, and tallied with our estimation to move along the coupling direction.     

Field ecology and behaviour of the rhesus macaque (Macaca mulatta): I. Group composition,home range,roosting sites,and foraging routes in the Asarori Forest

The data presented here resulted from about 1,100 observation hours in a nine-month field study of rhesus monkey from January to October 1976 in the Asarori Forest, Dheradun. Six groups were studied, the group size varied from 6–90 individuals. With the exception of one group, all were of the bisexual multimale type. The number of adult males per group varied from two to seven, and of adult females from 4 to 27. The adult sex ratio was male 1 to females 2.2–3.7 (mean 1:2.7). The exceptional group originally consisted of five juveniles only (3 ♂, 2 ♀); later on an adult male joined the group. Home ranges varied from 1.3–13.4 km² and overlapped extensively with another. The area of home range showed straight line relationship with group size. Roosting sites were not fixed but changed from night to night. The straight line distance between one night to the next varied from 75–2,500 m. Foraging routes per day ranged from 1,050–3,500 m (mean 1,803.3±160.2). There is a significant relationship between the foraging route (L) and the straight line distance between roosting sites (D). The ratio D/L varies from 0.14–0.87.     

Comparison of the Predicted Structures of Loops in the ras–SOS Protein Bound to a Single ras-p21 Protein with the Crystallographically Determined Structures in SOS Bound to Two ras-p21 Proteins

We have previously computed the structures of three loops, residues 591–596, 654–675 and 742–751, in the ras-p21 protein-binding domain (residues 568–1044) of the guanine nucleotide-exchange-promoting SOS protein that were crystallographically undefined when one molecule of ras-p21 (unbound to nucleotide) binds to SOS. Based on our computational results, we synthesized three peptides corresponding to sequences of each of these three loops and found that all three peptides strongly inhibit ras-p21 signaling. More recently, a new crystal structure of SOS has been determined in which this protein binds to two molecules of ras-p21, one unbound to GTP and one bound to GTP. In this structure, the 654–675 loop and residues 742–743 and 750–751 are now crystallographically defined. We have superimposed our energy-minimized structure of the ras-binding domain of SOS bound to one molecule of ras-p21 on the X-ray structure for SOS bound to two molecules of ras-p21. We find that, while the two structures are superimposable, there are large deviations of the residues 673 and 676 and 741 and 752, flanking the two loop segments. This suggests that the binding of the extra ras-p21 molecule, which is far from each of the three loops, induces conformational changes in these domains and further supports their role in signal transduction. In spite of these differences, we have superimposed our computed structures for the loop residues on those from the more recent X-ray structure. Our structure for the 654–675 segment is an anti-parallel beta-sheet with a reverse turn at residues 663–665; in the X-ray structure residues 655–662 adopt an alpha-helical conformation; on the other hand, our computed structure for residues 663–675 superimpose on the X-ray structure for these residues. We further find that our computed structures for residues 742–743 and 750–751 are superimposable on the X-ray structure for these residues.     

Natural selection at genomic regions associated with obesity and type-2 diabetes: East Asians and sub-Saharan Africans exhibit high levels of differentiation at type-2 diabetes regions

Different populations suffer from different rates of obesity and type-2 diabetes (T2D). Little is known about the genetic or adaptive component, if any, that underlies these differences. Given the cultural, geographic, and dietary variation that accumulated among humans over the last 60,000 years, we examined whether loci identified by genome-wide association studies for these traits have been subject to recent selection pressures. Using genome-wide SNP data on 938 individuals in 53 populations from the Human Genome Diversity Panel, we compare population differentiation and haplotype patterns at these loci to the rest of the genome. Using an “expanding window” approach (100–1,600 kb) for the individual loci as well as the loci as ensembles, we find a high degree of differentiation for the ensemble of T2D loci. This differentiation is most pronounced for East Asians and sub-Saharan Africans, suggesting that these groups experienced natural selection at loci associated with T2D. Haplotype analysis suggests an excess of obesity loci with evidence of recent positive selection among South Asians and Europeans, compared to sub-Saharan Africans and Native Americans. We also identify individual loci that may have been subjected to natural selection, such as the T2D locus, HHEX, which displays both elevated differentiation and extended haplotype homozygosity in comparisons of East Asians with other groups. Our findings suggest that there is an evolutionary genetic basis for population differences in these traits, and we have identified potential group-specific genetic risk factors.     

Isotopic insight into host–endosymbiont relationships in Liolaemid lizards

Nitrogen isotopes have been widely used to investigate trophic levels in ecological systems. Isotopic enrichment of 2–5‰ occurs with trophic level increases in food webs. Host–parasite relationships deviate from traditional food webs in that parasites are minimally enriched relative to their hosts. Although this host–parasite enrichment pattern has been shown in multiple systems, few studies have used isotopic relationships to examine other potential symbioses. We examined the relationship between two gut-nematodes and their lizard hosts. One species, Physaloptera retusa, is a documented parasite in the stomach, whereas the relationship of the other species, Parapharyngodon riojensis (pinworms), to the host is putatively commensalistic or mutualistic. Based on the established trophic enrichments, we predicted that, relative to host tissue, parasitic nematodes would be minimally enriched (0–1‰), whereas pinworms, either as commensals or mutualists, would be significantly enriched by 2–5‰. We measured the ¹⁵N values of food, digesta, gut tissue, and nematodes of eight lizard species in the family Liolaemidae. Parasitic worms were enriched 1±0.2‰ relative to host tissue, while the average enrichment value for pinworms relative to gut tissue was 6.7±0.2‰. The results support previous findings that isotopic fractionation in a host–parasite system is lower than traditional food webs. Additionally, the larger enrichment of pinworms relative to known parasites suggests that they are not parasitic and may be several trophic levels beyond the host.     

Origin of Life and Definition of Life,from Buffon to Oparin

Many theories on origin of life at the end of the XIXth century and the beginning of the XXth, generally use conceptions of life instead of explicit definitions of life. This paper presents ideas on the origin of life as studied by Buffon (1707–1788), Lamarck (1744–1829), Darwin (1809–1882), Huxley (1825–1895), Oparin (1894–1980) and Haldane (1892–1964). We show that their conceptions on the evolution of matter and life reveal their conceptions of life rather than their definitions of life.     

Subcellular distribution of aluminum, bismuth, cadmium, chromium, copper, iron, manganese, nickel, and lead in cultivated mushrooms (Agaricus bisporus and Pleurotus ostreatus)

In this work, the distribution of nine metals in two types of cultivated mushroom had been investigated. For Agaricus bisporus, the biomass was separated into caps and stalks, and for Pleurotus ostreatus, the entire mushrooms were taken for analysis. Electrothermal atomic absorption spectrometry was used for total element determination in acid digests. For accuracy checking, the certified reference material (NIST 1571, citrus leaves) was analyzed. The results obtained for the two fungi species were within the ranges of concentration reported previously by other authors. Subcellular fractionation was accomplished by centrifugation of cell homogenates, which has been suspended in Tris-HCl buffer. In the first centrifugation (7300g, 4°C, 10 min), cell walls were separated (pellet I), and the second centrifugation (147,000g, 4°C, 60 min) yielded mixed membrane fraction (pellet II) and cytosol (supernatant II). Recoveries of the fractionation procedure were in the range 70–100% (with the exception of Fe). For all elements studied, the highest relative contributions were found in cytosol fractions of the fruiting bodies (63–72%, 49–76%, 44–93%, 26–87pc, 55–85%, 50–68%, 41–78%, 39–78%, 54–67% respectively for Al, Bi, Cd, Cr, Cu, Fe, Mn, Ni, and Pb. Lower contributions were found in cell walls (respectively 22–32%, 24–44%, 6.1–47%, 12–52%, 7.3–37%, 7.9–32%, 19–52%, 20–42%, and 25–38%) and only minute amounts in the mixed membrane fraction (3.0–5.8%, 0.7–7.0%, 0.7–8.3%, 1.0–22%, 7.5–14%, 16–24%, 1.1–19%, and 5.1–7.7%). The results obtained indicate that small water-soluble molecules were the primary forms of nine elements in two mushroom species studied. On the other hand, the evidence has been provided on elements binding to larger, water-insoluble molecules contained in the structures of cell wall and membranes. The relative distribution was both element and fungi dependent. Thus, in P. ostreatus, total element levels were higher than in A. bisporus, with the preference for their accumulation in cytosol. On the contrary, total element content in the latter fungi was lower; however, a clear tendency toward more efficient element incorporation to the water-insoluble structures was observed (no apparent differences between stalks and caps). These findings might contribute in a better understanding of the accumulation of metals in mushrooms.     

Effect of LEPR Gln223Arg polymorphism on breast cancer risk in different ethnic populations: a meta-analysis

Leptin and leptin receptor have been implicated in processes leading to breast cancer initiation and progression. An A to G transition mutation in codon 223, in exon 6 of the leptin receptor gene (LEPR) can result in glutamine to arginine substitution (Gln223Arg). A variety of case–control studies have been published evaluating the association between LEPR Gln223Arg polymorphism and breast cancer. However, published studies have yielded contradictory conclusions. This meta-analysis enrolled eight studies to estimate the overall risk of LEPR Gln223Arg polymorphism associated with breast cancer. The pooled ORs were performed for codominant model (Arg/Arg versus Gln/Gln; Arg/Gln versus Gln/Gln), dominant model (Arg/Arg + Arg/Gln versus Gln/Gln), recessive model (Arg/Arg versus Arg/Gln + Gln/Gln). Overall significantly elevated breast cancer risk was found for recessive model (OR 1.32, 95% CI 1.03–1.69) and for genotype Arg/Gln versus Gln/Gln (OR 1.16, 95% CI 1.01–1.34). In the stratified analysis by ethnicity, significantly increased risks were also found among Africans for genotype Arg/Arg versus Gln/Gln: OR 1.86, 95% CI 1.28–2.71, Arg/Gln versus Gln/Gln: OR 1.48, 95% CI 1.10–1.99, dominant model: OR 1.60, 95% CI 1.21–2.11 and recessive model: OR 1.48, 95% CI 1.07–2.05; for Asians, Arg/Arg versus Gln/Gln: OR 6.79, 95% CI 3.42–13.47 and dominant model: OR 2.03, 95% CI 1.42–2.90. However, no significantly increased risk was found among Europeans for all genetic models. In conclusion, the LEPR 223Arg is a low-penetrant risk for developing breast cancer, especially for black African women.     

Association between α1-antichymotrypsin signal peptide −15A/T polymorphism and the risk of Alzheimer’s disease: a meta-analysis

No consensus has been recently reached at the relationship between the α1-antichymotrypsin (ACT) signal peptide −15A/T polymorphism and Alzheimer’s disease (AD) risk. Thus, our study aimed to better assess this association by performing a meta-analysis, including 4,212 cases and 4,039 controls from 29 studies. Odds ratios (ORs) with the 95% confidence interval (CI) were used to assess the strength of relationship between ACT −15A/T polymorphism and AD risk. Overall, a borderline statistically significant association was detected under recessive model comparison in all subjects (AA vs. AT+TT: OR 1.12, 95% CI 1.01–1.25, P = 0.04). But in subgroup analysis by ethnicity, no significant association was found in Caucasians, Asians, or Africans. Moreover, after exclusion of one study which affect the heterogeneity, the ACT A allele and AA genotype were statistically associated with late-onset AD (LOAD) risk (AA vs. TT: OR 1.25, 95% CI 1.06–1.48, P = 0.007, A vs. T: OR 1.12, 95% CI 1.03–1.21, P = 0.008), especially in Caucasians. In conclusion, our study suggests that the common α1-antichymotrypsin signal peptide −15A/T polymorphism may not be a major risk factor for AD. However, the polymorphism is capable of increasing LOAD risk.     

Four marine-derived fungi for bioremediation of raw textile mill effluents

Textile dye effluents pose environmental hazards because of color and toxicity. Bioremediation of these has been widely attempted. However, their widely differing characteristics and high salt contents have required application of different microorganisms and high dilutions. We report here decolorization and detoxification of two raw textile effluents, with extreme variations in their pH and dye composition, used at 20–90% concentrations by each of the four marine-derived fungi. Textile effluent A (TEA) contained an azo dye and had a pH of 8.9 and textile effluent B (TEB) with a pH of 2.5 contained a mixture of eight reactive dyes. The fungi isolated from mangroves and identified by 18S and ITS sequencing corresponded to two ascomycetes and two basidiomycetes. Each of these fungi decolorized TEA by 30–60% and TEB by 33–80% used at 20–90% concentrations and salinity of 15 ppt within 6 days. This was accompanied by two to threefold reduction in toxicity as measured by LC₅₀ values against Artemia larvae and 70–80% reduction in chemical oxygen demand and total phenolics. Mass spectrometric scan of effluents after fungal treatment revealed degradation of most of the components. The ascomycetes appeared to remove color primarily by adsorption, whereas laccase played a major role in decolorization by basidiomycetes. A process consisting of a combination of sorption by fungal biomass of an ascomycete and biodegradation by laccase from a basidiomycete was used in two separate steps or simultaneously for bioremediation of these two effluents.     

Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape

Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32–43%), Bantu-speaking Africans (20–36%), European (21–28%) and a smaller Asian contribution (9–11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.     

International radiobiology archives of long-term animal studies: structure, possible uses and potential extension

Animal experiments have contributed a great deal to our information on effects and risks arising from exposure to radionuclides. This applies, in particular, to alpha-emitting radionuclides where information from man is limited to thorotrast, ²²⁴Ra and ²²⁶Ra. The late C.W. Mays was the first to suggest that animal data in conjunction with epidemiological data could allow estimates of human risks for radionuclides – predominantly from actinides – where information in man is scarce. The ’International Radiobiology Archives of Long-term Animal Studies’ were created through the combined efforts of European, American and Japanese scientists and aim to safeguard the large amount of existing data on long-term animal experiments and make them available for, among others, an improved assessment of risks from alpha-emitting radionuclides. This paper summarizes the structure of the archives and reviews their present status and future plans. It also demonstrates the extensive information available in these archives on alpha-emitting radionuclides which is suitable for further analysis. Also, the structure of the animal archives could – in a slightly modified form – accommodate the epidemiological data available on ²²⁴Ra and thorotrast and, thus, facilitate a direct comparison of data from man, dogs and rodents. Received: 9 January 1999 / Accepted in revised form: 23 March 1999     

Causation in biology: stability,specificity, and the choice of levels of explanation

This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to David Lewis’ notion of “influence” and also with the extent to which a causal relation approximates to the ideal of one cause–one effect. Interrelations among these notions and their possible biological significance are also discussed.     

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.