Hidden treatments in ecological experiments: re-evaluating the ecosystem function of biodiversity

Interactions between biotic and abiotic processes complicate the design and interpretation of ecological experiments. Separating causality from simple correlation requires distinguishing among experimental treatments, experimental responses, and the many processes and properties that are correlated with either the treatments or the responses, or both. When an experimental manipulation has multiple components, but only one of them is identified as the experimental treatment, erroneous conclusions about cause and effect relationships are likely because the actual cause of any observed response may be ignored in the interpretation of the experimental results. This unrecognized cause of an observed response can be considered a “hidden treatment.” Three types of hidden treatments are potential problems in biodiversity experiments: (1) abiotic conditions, such as resource levels, or biotic conditions, such as predation, which are intentionally or unintentionally altered in order to create differences in species numbers for “diversity” treatments; (2) non-random selection of species with particular attributes that produce treatment differences that exceed those due to “diversity” alone; and (3) the increased statistical probability of including a species with a dominant negative or positive effect (e.g., dense shade, or nitrogen fixation) in randomly selected groups of species of increasing number or “diversity.” In each of these cases, treatment responses that are actually the result of the “hidden treatment” may be inadvertently attributed to variation in species diversity. Case studies re-evaluating three different types of biodiversity experiments demonstrate that the increases found in such ecosystem properties as productivity, nutrient use efficiency, and stability (all of which were attributed to higher levels of species diversity) were actually caused by “hidden treatments” that altered plant biomass and productivity. Received: 16 December 1996 / Accepted: 2 March 1997     

On the adsorption of ions at charged sites in an electric field: II

A study is made of the adsorption of one kind of monovalent positive ion at a long chain of alternating monovalent negative fixed charged (“lattice”) and uncharged (“interstitial”) sites both of one type in an electric field. Considering only nearest neighbor interactions an expression is obtained for the grand partition function. The fractions of sites of both types which are occupied and unoccupied are determined. It is shown that an equilibrium constant can be defined for the adsorption of ions at oppositely charged sites.     

Voiceprint identification and its application to sociological studies of wild Japanese monkeys (Macaca fuscata yakui)

Japanese monkeys often exchange the particular vocal sound, “coo,” especially when they feed or move as a group. It was considered that the “coo” sound had no positive social meaning, perhaps because the “coo” sound network and its function were hidden behind other behavioral observations. For identification of the vocalizer only from hearing the “coo” sound, three phonetic values, i.e., the “fundamental,” “duration,” and “formants,” plus other characteristics were used as indices of voiceprints. The results indicated that these were effective for identifying the vocalizer in two-thirds of the adults in the study troop which was composed of 12 adults and 16 immature members. The “coo” sound exchange network among the troop members (adults) was drawn on the basis of the voiceprint identification. The network showed three characteristics as follows: (1) matriarchs of the kin-groups frequently exchanged “coo” sounds with each other; (2) the other females exchanged “coo” sounds mostly within their own kin-groups; and (3) males seldom participated in the “coo” sound exchange. This suggests that “coo” sound exchange plays a central role for the matriarch of kin-groups in binding each kin-group and, ultimately, in binding all members together into an organized troop.     

An anatomical study of anther development in Acorus L.: Phylogenetic implications

 Critical morphological synapomorphies have not been found in support of the Acoranan hypothesis, the molecular phylogenetic discovery that Acoranae are the basal monocots. The previously undetermined pattern of anther wall development in Acorus has been suggested to be one such character. Two main types of anther wall development have been recognized: 1) the “monocotyledonous” type, which characterizes both monocots and dicots, and 2) the “dicotyledonous” type, which is almost exclusively found among dicots. An anatomical study of anther wall development in Acorus was here undertaken using the electron microscope. Development of the anther wall in Acorus was found to be somewhat irregular or perhaps even intermediate between the two types although largely consistent with the “monocotyledonous” type. The presumed significance of anther wall development and other critical morphological characters to the Acoranan hypothesis in the absence of knowledge about the sister group to the monocots is evaluated. Received August 28, 2000 Accepted February 19, 2001     

Recognition of sex in the acoustic communication of the grasshopper Chorthippus biguttulus (Orthoptera, Acrididae)

Many gomphocerine grasshoppers communicate acoustically: a male's calling song is answered by a female which is approached phonotactically by the male. Signals and recognition mechanisms were investigated in Chorthippus biguttulus with regard to the cues which allow sex discrimination. (1) The stridulatory files on the hindfemur of both sexes are homologous in that they are derived from the same row of bristles, but convergent with respect to the “pegs”. In males the pegs are derived from the bristles, and in females from the wall of the bristle's cup. (2) Male and female songs are generated by similar, probably homologous motor programs, but differ in the duration, intensity, “gappyness” of syllables, risetime of pulses, and the frequency spectra. The hindleg co-ordination during stridulation and the resulting temporal song patterns are less variable in males than in females. (3) For both sexes, recognition of a mate's signal depends on species-specific syllable structure. For males it is essential that the female syllables consist of distinct short pulses, whereas females reject “gappy” syllables. Males strongly prefer “ramped” pulses, females respond to syllables irrespective of steeply or slowly rising ramps. Males react only to the low-frequency component, whereas females prefer spectra containing both, low and high frequency components. Accepted: 20 November 1996     

Relationships among three Japanese <Emphasis Type="Italic">Laetiporus</Emphasis> taxa based on phylogenetic analysis and incompatibility tests

Relationships among three Japanese Laetiporus taxa (“L. sulphureus var. sulphureus” auct. jap., L. sulphureus var. miniatus, and L. versisporus) were assessed with phylogenetic analysis and incompatibility tests. Gene phylogenies inferred from the internal transcribed spacer region of nuclear ribosomal DNA, elongation factor 1α, and β-tubulin gene regions suggested that Japanese Laetiporus was divided into four groups: the yellow pore form of L. sulphureus var. miniatus, the white pore form of L. sulphureus var. miniatus, and two “L. sulphureus var. sulphureus”/ L. versisporus groups. A morphologically distinct species, Laetiporus versisporus, sharing a clade with “L. sulphureus var. sulphureus” auct. jap., was proved to be an anamorphic form of “L. sulphureus var. sulphureus” auct. jap. The “sulphureus/versisporus” isolates showed two divergent sequence types in each region. Some isolates had intraindividual polymorphism assigned to both sequence types. This finding suggests that speciation via hybridization is ongoing in the “sulphureus/versisporus” group. Single spore isolates from the “sulphureus/versisporus” group, white pore group, and yellow pore group were incompatible with each other. Our results provided strong support for the new recognition of three Laetiporus taxa in Japan.     

Transport of receptors

The axonal transport of neurotransmitter receptors is thought to be a common phenomenon in many neuronal systems. The “machinery” for receptor (protein) “assembly” is found in the cell bodies of neurons and the “manufacture” of receptors takes place there. These receptors are then “shipped” to their ultimate destinations by a transport process. This is an axonal transport mechanism in the case of presynaptic receptors. Some form of transport process may also exist to send receptors out into the dendritic arborizations of neurons, although the latter is more difficult to verify. Axonal transport has been demonstrated, in the peripheral nervous systems, for many different neurotransmitter receptors. In the central nervous system, the results are less clear, but indicate the presence of a transport mechanism for catecholamine, acetylcholine, and opiate sites. One important component then, in the development of receptors, is the transportation to terminal membrane sites where they are ultimately incorporated and available for interaction with neurotransmitters and drugs.     

Amerindian cannibalism: practice and discursive strategy

This paper examines certain colonial and contemporary texts for their representations of Amerindian cannibalism during the Columbian period. Colonial texts from this period describe cannibalism as one of the Amerindians’ major “offences” against humanity. Some contemporary studies criticize this depiction of Amerindian cannibalism as a “myth” perpetrated by colonizers and their apologists to justify the enslavement and genocide of Amerindians. On the one hand colonial texts fall prey to an ethnocentric view of cannibalism; on the other hand contemporary texts explain away this amply documented cultural phenomenon. While the two positions appear to be at variance with each other, it is suggested that what they hold in common is a schema of analyzing culture that does not easily admit the existence of a phenomenon that is “Other” without explaining it as a totalized alterity or without explaining it away. Both positions thus help reinscribe the Wild Savage-Noble Savage stereotypes. ...each man calls barbarism, whatever is not his own practice ... Michel De Montaigne     

Use of microsatellite DNA and otolith Sr:Ca ratios to infer genetic relationships and migration history of four morphotypes of <Emphasis Type="Italic">Rhinogobius</Emphasis> sp. OR

The genetic diversity and relationship among four morphotypes of Rhinogobius sp. OR, Gobiidae (“Tōshoku,” “Shinjiko,” “Gi-tōshoku,” and “Shimahire”) were investigated with seven microsatellite DNA loci, and amphidromy of these morphotypes was verified by strontium (Sr) and calcium (Ca) deposition in the otolith. Samples of “Tōshoku,” “Shinjiko,” “Gi-tōshoku,” and “Shimahire” were collected from, respectively, three, three, two, and four locations in Japan. Microsatellite analysis detected high genetic diversity (based on the number of alleles, allelic richness, and average observed heterozygosity) in the “Tōshoku” and “Shinjiko” morphotypes relative to the “Shimahire” morphotype; the “Gi-tōshoku” morphotype had an intermediate level of variation. Almost all pairwise F _ST values were significantly different from zero (P < 0.001), except between two populations of “Tōshoku.” Clear genetic independence was observed between the “Shinjiko” and “Shimahire” morphotypes in the Maruyama River. A principle component analysis based on microsatellite data indicated that the “Tōshoku,” “Shinjiko,” and “Gi-tōshoku” morphotypes were genetically similar. Furthermore, the three populations of “Tōshoku” were closely related each other, and two of those collected from the Lake Biwa system were a single population. There was, however, a high degree of genetic differentiation between “Shimahire” and the other morphotypes; moreover, there was high genetic divergence among four populations of the “Shimahire” morphotype. Amphidromous migratory histories were indicated by Sr:Ca ratios in two of three populations of the “Shinjiko” morphotype and in one of two “Gi-tōshoku” morphotypes, whereas all populations of the “Shimahire” morphotype were freshwater residents. The large genetic divergence and low genetic diversity in “Shimahire” are likely related to migration history.     

Source-sink landscape theory and its ecological significance

Exploring the relationships between landscape pattern and ecological processes is the key topic of landscape ecology, for which, a large number of indices as well as landscape pattern analysis model were developed. However, one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process. Linking landscape pattern and ecological processes has become a challenge for landscape ecologists. “Source” and “sink” are common concepts used in air pollution research, by which the movement direction and pattern of different pollutants in air can be clearly identified. In fact, for any ecological process, the research can be considered as a balance between the source and the sink in space. Thus, the concepts of “source” and “sink” could be implemented to the research of landscape pattern and ecological processes. In this paper, a theory of sourcesink landscape was proposed, which include: (1) In the research of landscape pattern and ecological process, all landscape types can be divided into two groups, “source” landscape and “sink” landscape. “Source” landscape contributes positively to the ecological process, while “sink” landscape is unhelpful to the ecological process. (2) Both landscapes are recognized with regard to the specific ecological process. “Source” landscape in a target ecological process may change into a “sink” landscape as in another ecological process. Therefore, the ecological process should be determined before “source” or “sink” landscape were defined. (3) The key point to distinguish “source” landscape from “sink” landscape is to quantify the effect of landscape on ecological process. The positive effect is made by “source” landscape, and the negative effect by “sink” landscape. (4) For the same ecological process, the contribution of “source” landscapes may vary, and it is the same to the “sink” landscapes. It is required to determine the weight of each landscape type on ecological processes. (5) The sourcesink principle can be applied to non-point source pollution control, biologic diversity protection, urban heat island effect mitigation, etc. However, the landscape evaluation models need to be calibrated respectively, because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas. This theory is helpful to further study landscape pattern and ecological process, and offers a basis for new landscape index design. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1444–1449 [译自: 生态学报]     

Dynamic role of “illite-like” clay minerals in temperate soils: facts and hypotheses

Analysis of new data and reinterpretation of published information for clay minerals found in temperate climate soil profiles indicates that there is often a gradient of “illite-like” clay minerals with depth. We used the term “illite-like” because these observations are based on X-Ray Diffractogram patterns and not on layer charge measurements which allow to define properly illite. It appears that “illite-like” layers are concentrated in the upper, organic - rich portion of the soil profile both under grassland and forest vegetation. “Illite-like” layer quantity seems directly related to soil potassium status. Indeed, intensive agriculture practises without potassium fertilization reduce “illite-like” content in surface soils, whereas several years of potassic fertilization without plant growth can increase “illite-like” content. The potassic soil clay mineral, illite, is particularly important in that it can be the major source of readily available potassium for plants. Spatial and temporal dynamics of clay minerals should be related to the potassium cycle. We propose that the frequently observed general trend of increasing exchangeable potassium in the top soil can be correlated with an increase in “illite-like” in the clays and that the decrease of potassium caused by intensive agricultural practices leads to “illite-like” layer destabilization. This vision of “illite-like” layer as a potassium reservoir refueled by plants and emptied by intensive cropping renews the concept of potassium availability and indicates a need to be discussed as well in natural ecosystems as in cultivated ecosystems.     

Sangiran 5,(“Pithecanthropus dubius”), homo erectus, “Meganthropus,” orPongo?

There are now eleven known mandibular remains from the Lower and Middle Pleistocene of Java, all but one being from the Sangiran site. All of these have been assigned toHomo erectus by most workers, while others have suggested as many as four different hominoid taxa. The author finds that the jaws cannot be a homogeneous sample. Morphologically, they are a mixture of undoubtedH. erectus, “H. meganthropus,” and possibly a pongid. If the jaws are allH. erectus then they have a sexual dimorphism exceeding that of modern gorillas. The case of“Pithecanthropus dubius” (Sangiran 5) is even less certain; even its hominid status is disputed. If it is indeedHomo it must be placed with the other“H. meganthropus” specimens. Its size and morphology are well beyond the known range anyH. erectus.     

Two new motile phototrophic consortia: “Chlorochromatium lunatum” and “Pelochromatium selenoides”

Two new phototrophic consortia, “Chlorochromatium lunatum” and “Pelochromatium selenoides”, were observed and collected in the hypolimnion of several dimictic lakes in Wisconsin and Michigan (USA). The two consortia had the same morphology but different pigment composition. The cells of the photosynthetic components of the consortia were half-moon-shaped. This morphology was used to differentiate them from the previously described motile phototrophic consortia “Chlorochromatium aggregatum” and “Pelochromatium roseum”. These phototrophic cells did not resemble any described unicellular green sulfur bacteria. The predominant pigments detected were bacteriochlorophyll d and chlorobactene for the green-colored “Clc. lunatum”, and bacteriochlorophyll e and isorenieratene for the brown-colored “Plc. selenoides”. Their pigment compositions and the presence of chlorosomes attached to the inner face of the cytoplasmic membrane in both kinds of photosynthetic cells confirmed this new half-moon-shaped morphotype as a green sulfur bacterium. Both consortia were found thriving in lakes with low concentrations of sulfide (< 60 μM), below the layers of “Clc. aggregatum” and “Plc. roseum”. The green consortia were observed in lakes where the oxic-anoxic interface was located at shallow depths (2–7 m), while the brown consortia were found at greater depths (8–16 m). The two newly described consortia were never detected together at the same depth in any lake. Received: 30 April 1997 / Accepted: 17 January 1998     

Using sensory weighting to model the influence of canal,otolith and visual cues on spatial orientation and eye movements

 The sensory weighting model is a general model of sensory integration that consists of three processing layers. First, each sensor provides the central nervous system (CNS) with information regarding a specific physical variable. Due to sensor dynamics, this measure is only reliable for the frequency range over which the sensor is accurate. Therefore, we hypothesize that the CNS improves on the reliability of the individual sensor outside this frequency range by using information from other sensors, a process referred to as “frequency completion.” Frequency completion uses internal models of sensory dynamics. This “improved” sensory signal is designated as the “sensory estimate” of the physical variable. Second, before being combined, information with different physical meanings is first transformed into a common representation; sensory estimates are converted to intermediate estimates. This conversion uses internal models of body dynamics and physical relationships. Third, several sensory systems may provide information about the same physical variable (e.g., semicircular canals and vision both measure self-rotation). Therefore, we hypothesize that the “central estimate” of a physical variable is computed as a weighted sum of all available intermediate estimates of this physical variable, a process referred to as “multicue weighted averaging.” The resulting central estimate is fed back to the first two layers. The sensory weighting model is applied to three-dimensional (3D) visual–vestibular interactions and their associated eye movements and perceptual responses. The model inputs are 3D angular and translational stimuli. The sensory inputs are the 3D sensory signals coming from the semicircular canals, otolith organs, and the visual system. The angular and translational components of visual movement are assumed to be available as separate stimuli measured by the visual system using retinal slip and image deformation. In addition, both tonic (“regular”) and phasic (“irregular”) otolithic afferents are implemented. Whereas neither tonic nor phasic otolithic afferents distinguish gravity from linear acceleration, the model uses tonic afferents to estimate gravity and phasic afferents to estimate linear acceleration. The model outputs are the internal estimates of physical motion variables and 3D slow-phase eye movements. The model also includes a smooth pursuit module. The model matches eye responses and perceptual effects measured during various motion paradigms in darkness (e.g., centered and eccentric yaw rotation about an earth-vertical axis, yaw rotation about an earth-horizontal axis) and with visual cues (e.g., stabilized visual stimulation or optokinetic stimulation). Received: 20 September 2000 / Accepted in revised form: 28 September 2001     

“Meganthropus” cranial fossils from Java

There are now twelve significant hominid cranial fossils from the Lower and Middle Pleistocene of Java, all but two being from the Sangiran site. Most of this material is well-known in the literature, but three skulls, possibly representing “Meganthropus” are here described in detail for the first time. Most scholars have assigned them all toHomo erectus, while others have suggested that they represent as many as four different hominoid taxa. The author argues that they represent two possible species of hominids. “Meganthropus” I, II, and III are more massive than any of the knownH. erectus specimens. They are also relatively higher vaulted, apparently smaller brained, and have unusually thick lower occipital planes. “Meganthropus” may represent a species that separated fromH. erectus upon its arrival to Java.     

Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances

Suppose G is a phylogenetic network given as a rooted acyclic directed graph. Let X be a subset of the vertex set containing the root, all leaves, and all vertices of outdegree 1. A vertex is “regular” if it has a unique parent, and “hybrid” if it has two parents. Consider the case where each gene is binary. Assume an idealized system of inheritance in which no homoplasies occur at regular vertices, but homoplasies can occur at hybrid vertices. Under our model, the distances between taxa are shown to be described using a system of numbers called “originating weights” and “homoplasy weights.” Assume that the distances are known between all members of X. Sufficient conditions are given such that the graph G and all the originating and homoplasy weights can be reconstructed from the given distances.     

Chain processes and their biophysical applications: Part I. General theory

A mathematical theory applicable to the biological effects of radiations as chain processes is developed. The theory may be interpreted substantially as a “hit theory” involving the concepts of “sensitive volume” or “target area”. The variability of the sensitivity of the organism to the radiation and its capacity of recovery between single hits is taken into account. It is shown that in a continuous irradiation of a biological aggregate in which the effect of each single hit cannot be observed, recovery and variation of sensitivity are formally equivalent to each other so that a discrimination between these two phenomena is possible only by discontinuous irradiation or by using different radiation intensities. Methods for the calculation of the “number of hits” and for the determination of the kinetics of the processes from “survival curves” or similar experimental data are given. The relation between the recovery and the Bunsen-Roscoe law is discussed. The case in which the injury of the organism is dependent on the destruction of more than one “sensitive volume” is also considered.     

Stereotyped sequence of mating behavior in the Far Eastern catfish, Silurus asotus, from Lake Biwa

 Mating behavior of the Far Eastern catfish, Silurus asotus (Siluriformes: Siluridae), was observed in a ricefield system facing the shore of Lake Biwa in mid-May to early June in 1990–1997. A set behavioral sequence similar to those of two other silurid fishes, S. biwaensis and S. lithophilus, both endemic to the Lake Biwa system, was observed: “chasing,”“clinging,”“enfolding” while “squeezing” by the male, and “circling” by the spawning pair. This form of mating behavior is quite different from that of S. asotus reported from the Ooi River system in Kyoto Prefecture, which mainly spawns in running water in ditches. Received: April 10, 2001 / Revised: November 5, 2001 / Accetped: November 20, 2001     

The infinitesimal, the deterministic, and the probabilistic: Alternate container inspection policies in invasive species management

Recently, Batabyal and Nijkamp (2005, Stochastic Environmental Research and Risk Assessment 19: 340–347) have shown that in an inspection cycle, regardless of whether the inspection policy choice is made on the basis of an optimization exercise or on the basis of a rule of thumb, the “container policy” dominates the “temporal policy” because the former results in lower long run expected net cost (LRENC) from inspections. In this paper, we continue this line of inquiry and analyze container policies in three scenarios. In the first scenario the time taken to conduct inspections is negligible. In the second scenario, this inspection time is deterministic and in the third scenario this inspection time is stochastic. Specifically, we compare and contrast the LRENC and the optimal container policy in each of these three scenarios.      

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.