A quantitative method of palaeolake-level reconstruction using ostracod assemblages: an example from the Bolivian Altiplano

This paper provides quantitative information concerning the response of ostracods to environmental variability in order to reconstruct past environments. Ostracod faunas from modern sediments of Bolivian lakes and swamps were studied. Ostracod distribution is controlled by several ecological characteristics such as lake-level and water chemistry. Statistical results indicate that three transfer functions (on water depth, Total dissolved Salts and water in Mg/Ca ratio) can be developed, from ostracod species frequencies in lacustrine sediments, with some restrictions for the two last ones.     

Diversification of ectoparasite assemblages and climate: an example with fleas parasitic on small mammals

Aim We studied the relationships between the numbers of species and numbers of higher taxa (genera, tribes, subfamilies and families) in flea assemblages of small mammalian hosts with the aims of: (a) comparing these relationships across different regions, and (b) testing the hypothesis that flea assemblages in warmer regions diversify mainly via intrahost speciation, whereas those in colder regions diversify mainly via host switching. Location The study used previously published data on flea assemblages on small mammalian hosts from 25 different regions of the Holarctic. Methods The number of flea genera, tribes, subfamilies or families in an assemblage (host species) was plotted against the number of flea species in this assemblage for each region separately, and a power function was fitted to the resulting relationships. Then, the values of the exponent of the power function for a region were regressed against the mean annual temperature in this region, across all regions. Results The relationships between the number of flea species and the numbers of flea genera, tribes, subfamilies or families on a host species in each region were found to be well described by simple power functions. The exponent of the power function of the relationship between the number of flea species and the number of flea genera per host tended to decrease with increasing local mean annual temperature. When two apparent outliers from the trend (corresponding to regions where sampling was not performed as in other regions) were omitted from the analysis, the negative relationship between temperature and the exponent of the power function between the number of flea species and number of flea genera per host became highly significant. No relationship was found between the values of the exponents of the power functions between the number of flea species and the number of flea tribes, subfamilies or families per host, and the mean local annual temperature. Main conclusions The results suggest that the diversification of flea assemblages is associated with climatic variables. In warm regions, the greater number of congeneric species per flea assemblage, reflected by the lower exponent of the power function, may well be the outcome of intrahost speciation. This indicates that, as regional temperature increases, intrahost speciation becomes a relatively more important mode of diversification than acquisition of fleas via host switching.     

Assessing tillage disturbance on assemblages of ground beetles (Coleoptera: Carabidae) by using a range of ecological indices

Many ecological studies have used diversity indices to assess the impact of environmental disturbance. In particular, ground beetles have been advocated as a good group for assessing disturbance. Most studies on various organisms have used only one or two indices. For our study of the impact of tillage disturbance on carabid beetles in farm fields in southern Ontario, Canada, we used seven different diversity indices (richness, Shannon–Wiener, Berger–Parker, Q-statistic, Margalef, and evenness). Few studies have used deviation from diversity abundance models as a measure of disturbance; however, we use three that are applicable to our data (geometric, log-normal and log-series). The indices and models were used to test the null hypothesis that there is no change in diversity with increasing tillage disturbance, and that there is no difference in diversity with different crops or years. We were not able to reject the null hypothesis that there is any diversity difference among farms. We also found that there was no single diversity index or model that was better than any other at detecting disturbance. These results are supplemented by a meta-analysis of 45 published data sets for the same taxon but in different habitats. The meta-analysis supports the conclusions from our field research that diversity indices and models are not useful for detecting the possible effect of disturbance on assemblages of carabid beetles.     

Hurricane-induced modification of nitrogen and phosphorus resorption in an aspen clone: an example of diffuse disturbance

Summary On 27 September 1985, Hurricane Gloria intersected the Rhode Island land mass and disrupted normal autumnal element resorption in 20 ramets of a trembling aspen clone (Populus tremuloides). No mechanical injury to the plants was observed, but in contrast to undamaged aspens, the wind/salt-damaged aspens did not withdraw nitrogen (N) or phosphorus (P) from senescing leaves. There was actually 17% more N in abscising leaves than in presenescent, pre-hurricane leaves.     

On estimating diversity in species-rich fish assemblages: an example with coral-reef fishes of eastern Indonesia

A new procedure for estimating fish species richness in open or semi-open habitats is presented with unpublished data on the coral-reef fish assemblages of Raja Ampat, eastern Indonesia, known as the centre of marine biodiversity in the western Pacific.     

Does disturbance affect the structure of tropical fish assemblages? A test using null models

Null model analyses on fish presence-absence data from tropical river assemblages of the Western Ghats, India, revealed a difference in the extent of randomness in species assemblage structure among impacted and unimpacted rivers in the region.     

Legacy effects of canopy disturbance on ecosystem functioning in macroalgal assemblages

Macroalgal assemblages are some of the most productive systems on earth and they contribute significantly to nearshore ecosystems. Globally, macroalgal assemblages are increasingly threatened by anthropogenic activities such as sedimentation, eutrophication and climate change. Despite this, very little research has considered the potential effects of canopy loss on primary productivity, although the literature is rich with evidence showing the ecological effects of canopy disturbance. In this study we used experimental removal plots of habitat-dominating algae (Order Fucales) that had been initiated several years previously to construct a chronosequence of disturbed macroalgal communities and to test if there were legacy effects of canopy loss on primary productivity. We used in situ photo-respirometry to test the primary productivity of algal assemblages in control and removal plots at two intertidal elevations. In the mid tidal zone assemblage, the removal plots at two sites had average primary productivity values of only 40% and 60% that of control areas after 90 months. Differences in productivity were associated with lower biomass and density of the fucoid algal canopy and lower taxa richness in the removal plots after 90 months. Low-shore plots, established three years earlier, showed that the loss of the large, dominant fucoid resulted in at least 50% less primary productivity of the algal assemblage than controls, which lasted for 90 months; other smaller fucoid species had recruited but they were far less productive. The long term reduction in primary productivity following a single episode of canopy loss of a dominant species in two tidal zones suggests that these assemblages are not very resilient to large perturbations. Decreased production output may have severe and long-lasting consequences on the surrounding communities and has the potential to alter nutrient cycling in the wider nearshore environment.     

Small-sample reproducibility estimates: an example using rebreathing measurements

We developed a statistical technique to estimate the reproducibility of a parameter from a population in which only two repeated measurements can be made in a single individual. The following data were analyzed: acetylene cardiac output (Qc), lung tissue volume (Vti), and carbon monoxide diffusing capacity (DLCO) measured by rebreathing techniques in a population of 86 healthy subjects (51 men and 35 women). Each subject was measured twice with a computerized rebreathing system using a test gas of 10% He-0.3% C18O-0.7% C2H2-25% O2-balance N2 while sitting at rest. The estimated coefficients of variation for repeated measurements were 6.8, 10.3, and 5.7% for Qc, Vti, and DLCO, respectively. Chebyshev's inequality was used to estimate the imprecision for a single measurement of these parameters and for averages of two or more repeated values. A single measurement of Qc would be within 14.2% of a "true" mean 90% of the time, whereas an average of three consecutive measurements would be within 8.2% of the true mean 90% of the time. Single measurements of Vti and DLCO were found to be within 21.7 and 12.0%, respectively, of the true mean 90% of the time. When three consecutive measurements are averaged, Vti is within 12.6% and DLCO is within 6.9% of the true mean 90% of the time. We conclude that 1) rebreathing Qc is as reproducible as other measurements of cardiac output, 2) rebreathing measurements of DLCO are as reproducible as those made by the single-breath technique, and 3) an average of two to three measurements of Vti should be made to obtain values with a reasonable degree of precision.     

Effect of an abiotic disturbance on a lotic predator-prey interaction

Summary A model derived from marine research, and recently applied to stream communities, suggests that community structure is more likely to be influenced by predators in benign versus harsh abiotic regimes. Experiments were conducted to determine if increasing the harshness of a particular regime would alter the impact of a stream invertebrate predator on prey densities in field enclosures. Density of a stonefly predator, Kogotus nonus, was varied in containers exposed to low (benign) and high (harsh) levels of fine sediment. As predicted by the model, the harsher regime eliminated predator effects in two of three experiments. In the third experiment, however, high levels of sediment actually enhanced the impact of the predator on the prey community. A consideration of the possible mechanisms underlying this model led to the conclusion that increasing the harshness of a regime can be expected to produce outcomes ranging from elimination to enhancement of predator effects, depending on how the regime is perceived by the predator versus the prey.     

Typification of urban habitats,with ant assemblages of Moscow city taken as an example

A typification of Moscow city habitats is undertaken, based on their consideration as mosaic of patches and using such fundamental parameters as habitat origin (soil type), floristic composition, vegetation structure, and area of the biotopes. Altogether, 11 habitat types are distinguished: lawns, agrocenoses, xerophytic and mesophytic meadows, tall weeds, boulevards, small degenerative parks, small oppressed artificial parks, landscape parks, forest parks, and technocenoses. Such a classification is primarily useful for studying ants. The present paper describes the basic structure of ant assemblages in most types of urban biocenoses. The main pool of Moscow’s ant species ranked by their occurrence is as follows: Lasius niger (87%), Myrmica rugulosa (44%), Myrmica rubra (33%), Formica cunicularia (11%), Myrmica ruginodis (10%), etc. Leaf litter removal with a rake was shown to negatively affect the numbers, biomass, and species diversity of ant communities in urban areas with trees. The most stable two-species ant community revealed in Moscow City, termed an “elementary urban community,” consists of L. niger and M. rugulosa, with the former always outnumbering the latter.     

The origin of metazoan complexity: porifera as integrated animals

Sponges [Porifera] are the phylogenetically oldest metazoanphylum still extant today; they share the closest relationshipwith the hypothetical common metazoan ancestor, the Urmetazoa.During the past 8 years cDNAs coding for proteins involved incell-cell- and cell-tissue interaction have been cloned fromsponges, primarily from Suberites domuncula and Geodia cydoniumand their functions have been studied in vivo as well as invitro. Also, characteristic elements of the extracellular matrixhave been identified and cloned. Those data confirmed that allmetazoan phyla originate from one ancestor, the Urmetazoa. Theexistence of cell adhesion molecules allowed the emergence ofa colonial organism. However, for the next higher stage in evolution,individuation, two further innovations had to be formed: theimmune- and the apoptotic system. Major defense pathways/moleculesto prevent adverse effects against microbes/parasites have beenidentified in sponges. Furthermore, key molecules of the apoptoticpathway(s), e.g., the pro-apoptotic molecule comprising twodeath domains, the executing enzyme caspases, as well as theanti-apoptotic/cell survival proteins belonging to the Bcl-2family have been identified and cloned from sponges. Based onthese results—primarily obtained through a molecular biologicalapproach—it is concluded that cell-cell- and cell-matrixadhesion systems were required for the transition to a colonialstage of organization, while the development of an immune systemas well as of apoptotic processes were prerequisites for reachingthe integrated stage. As the latter stage already exists insponges, it is therefore likely that the hypothetical ancestor,the Urmetazoa, was also an "integrated colony."     

Evaluating trans-tethys migration: an example using acrodont lizard phylogenetics

A phylogenetic tree for acrodont lizards (Chamaeleonidae and Agamidae) is established based on 1434 bases (1041 informative) of aligned DNA positions from a 1685-1778 base pair region of the mitochondrial genome. Sequences from three protein-coding genes (ND1, ND2, and COI) are combined with sequences from eight intervening tRNA genes for samples of 70 acrodont taxa and two outgroups. Parsimony analysis of nucleotide sequences identifies eight major clades in the Acrodonta. Most agamid lizards are placed into three distinct clades. One clade is composed of all taxa occurring in Australia and New Guinea; Physignathus cocincinus from Southeast Asia is the sister taxon to the Australia-New Guinea clade. A second clade is composed of taxa occurring from Tibet and the Indian Subcontinent east through South and East Asia. A third clade is composed of taxa occurring from Africa east through Arabia and West Asia to Tibet and the Indian Subcontinent. These three clades contain all agamid lizards except Uromastyx, Leiolepis, and Hydrosaurus, which represent three additional clades of the Agamidae. The Chamaeleonidae forms another clade weakly supported as the sister taxon to the Agamidae. All eight clades of the Acrodonta contain members occurring on land masses derived from Gondwanaland. A hypothesis of agamid lizards rafting with Gondwanan plates is examined statistically. This hypothesis suggests that the African/West Asian clade is of African or Indian origin, and the South Asian clade is either of Indian or Southeast Asian origin. The shortest tree suggests a possible African origin for the former and an Indian origin for the latter, but this result is not statistically robust. The Australia-New Guinea clade rafted with the Australia-New Guinea plate and forms the sister group to a Southeast Asian taxon that occurs on plates that broke from northern Australia-New Guinea. Other acrodont taxa are inferred to be associated with the plates of Afro-Arabia and Madagascar (Chameleonidae), India (Uromastyx), or southeast Asia (Hydrosaurus and Leiolepis). Introduction of different biotic elements to Asia by way of separate Gondwanan plates may be a major theme of Asian biogeography. Three historical events may be responsible for the sharp faunal barrier between Southeast Asia and Australia-New Guinea, known as Wallace's line: (1) primary vicariance caused by plate separations; (2) secondary contact of Southeast Asian plates with Eurasia, leading to dispersal from Eurasia into Southeast Asia, and (3) dispersal of the Indian fauna (after collision of that subcontinent) to Southeast Asia. Acrodont lizards show the first and third of these biogeographic patterns and anguid lizards exhibit the second pattern. Modern faunal diversity may be influenced primarily by historical events such as tectonic collisions and land bridge connections, which are expected to promote episodic turnover of continental faunas by introducing new faunal elements into an area. Repeated tectonic collisions may be one of the most important phenomena promoting continental biodiversity. Phylogenetics is a powerful method for investigating these processes.     

Quantifying income breeding: using geometrid moths as an example

Although the general concept of capital vs. income breeding has become widely used in insect ecology, finding easy‐to‐measure indices for quantifying the role of larval‐ vs. adult‐derived nutrients in egg production has remained a challenge. When searching for possible candidates for this task, we evaluated the applicability of three morphometric ratios to be measured on freshly eclosed adults: (1) relative size of female abdomen, (2) sexual size dimorphism, and (3) proportion of volume of mature eggs relative to total volume of female abdomen. We report the values of these indices in five species of geometrid moths [Hypomecis punctinalis Scopoli, Ematurga atomaria L., Selenia tetralunaria Hufnagel, Semiothisa clathrata L., and Epirrhoe alternata Müller (all Lepidoptera: Geometridae)] and compare them to the degrees of income breeding measured directly by oviposition experiments. As a comparison, we also recorded the ovigeny index and the effect of income on lifespan. All morphometric indices varied considerably between the species studied, and, as predicted, the values of all three proposed indices were higher in the more capital‐breeding species. The only exception to this pattern was a low proportion of mature eggs in abdomens in one primarily capital‐breeding species, S. tetralunaria. Unlike other capital breeders, this species also proved to be largely synovigenic, indicating that capital breeding and pro‐ovigeny are not strictly linked. The reproductive traits measured concord with ecological niches occupied by the species studied: the oligophagous meadow dwellers were largely income breeding and synovigenic, whereas the polyphagous forest dwellers were capital breeders. The high and predictable among‐species variation in egg‐production strategies suggests that geometrid moths form a promising target group for comparative studies on respective traits. Simple anatomical indices, in turn, appear to be applicable as easy‐to‐record proxies of egg production strategies.     

以胶原蛋白为例浅述古蛋白质组学研究现状与未来*

蛋白质作为参与构建生物体的重要生物大分子,是生物功能与代谢的物质基础,同时蛋白质的序列信息又源自生物的遗传编码信息,因此是认识生物演化本质的重要研究对象。近年来,随着质谱技术的发展,获取生物化石中的古蛋白质序列信息不再遥不可及,这为在形态学与DNA序列信息缺乏的条件下对古生物的认识提供了一条新途径。胶原蛋白(Collagen)在动物骨骼中极为丰富,又因为其特殊的结构,易于在化石中保存,故已成为古蛋白质组学研究的重要对象。本文将以胶原蛋白为例,对古蛋白质组学现有的研究方法与已经取得的研究成果进行总结,并对古蛋白质组学目前面临的挑战与困难及未来研究趋势进行讨论,旨在展示古蛋白质组学的应用潜力,并探讨其在生物演化研究中的意义。     

A new methodology for reconstructing climate and vegetation from modern pollen assemblages: an example from British Columbia

Aim We used modern pollen assemblages to develop a method for climate reconstruction that reduces the spatial autocorrelation of residuals and accounts for the strong topographic and climatic variation that occurs in British Columbia, Canada. Location British Columbia, Canada, including sites both on the mainland and on adjacent islands (Queen Charlotte Islands and Vancouver Island). Methods New pollen assemblages from surface‐sediment samples collected in British Columbia were combined with other published and unpublished samples (n = 284). Multivariate rank‐distances between sample sites and a randomized set of sites within the province were calculated for climate parameters to determine whether gaps in the current network of present‐day pollen sample sites exist. Lacustrine surface‐sediment pollen assemblages (n = 145) were ordinated using non‐metric multidimensional scaling (NMDS), and a generalized additive model (GAM) was used to reconstruct modern mean warmest month temperature (MWMT) and mean annual precipitation (MAP) from the NMDS ordination. The results were compared with standard climate reconstruction techniques, including the modern analogue technique, partial least squares, weighted averaging, weighted averaging–partial least squares and factor analysis. Results Reconstructions of MWMT and MAP using NMDS and GAM were comparable to those of existing models. When reconstructing MWMT, the NMDS/GAM method had a lower root‐mean‐squared error of prediction (RMSEP), lower spatial autocorrelation and higher correlation with observed temperature values than the other methods tested. When reconstructing MAP, the partial least squares method performed better than the NMDS/GAM method for RMSEP and correlation with observed values; however, the NMDS/GAM method had a lower spatial autocorrelation of residuals. Main conclusions NMDS reveals strong relationships among modern pollen assemblages, vegetation and climate parameters. Climate models using NMDS and GAM are comparable to other palaeoecological reconstruction models, but provide lower spatial autocorrelation of residuals for both parameters tested. An inverse distance‐weighted surface of multivariate rank‐climate distances generated from the network of pollen sample sites indicates that greater sampling intensity in north‐western and central‐interior British Columbia is required in order to obtain an accurate representation of climatic and vegetation diversity in the province.     

Effect of the radiation factor on flavonoid content and morphometric indices using Pentaphylloides fruticosa as an example

An attempt is made to estimate the features of the influence of the chronic action of radiation on the variability of biochemical and morphometric parameters of Pentaphylloides fruticosa grown under the gradient of pollution with radionuclides ⁹⁰Sr and ¹⁸⁷Cs and to demonstrate, using the coefficient of variability (CV), an analysis of the variation curves of distribution, and a discriminant analysis, that the samples differ depending on the level of radiation.     

Predicting bacterial community assemblages using an artificial neural network approach

Understanding the interactions between the Earth's microbiome and the physical, chemical and biological environment is a fundamental goal of microbial ecology. We describe a bioclimatic modeling approach that leverages artificial neural networks to predict microbial community structure as a function of environmental parameters and microbial interactions. This method was better at predicting observed community structure than were any of several single-species models that do not incorporate biotic interactions. The model was used to interpolate and extrapolate community structure over time with an average Bray-Curtis similarity of 89.7. Additionally, community structure was extrapolated geographically to create the first microbial map derived from single-point observations. This method can be generalized to the many microbial ecosystems for which detailed taxonomic data are currently being generated, providing an observation-based modeling technique for predicting microbial taxonomic structure in ecological studies.