Effects of landscape structure and land-use intensity on similarity of plant and animal communities

Aim Species richness in itself is not always sufficient to evaluate land management strategies for nature conservation. The exchange of species between local communities may be affected by landscape structure and land‐use intensity. Thus, species turnover, and its inverse, community similarity, may be useful measures of landscape integrity from a diversity perspective. Location A European transect from France to Estonia. Methods We measured the similarity of plant, bird, wild bee, true bug, carabid beetle, hoverfly and spider communities sampled along gradients in landscape composition (e.g. total availability of semi‐natural habitat), landscape configuration (e.g. fragmentation) and land‐use intensity (e.g. pesticide loads). Results Total availability of semi‐natural habitats had little effect on community similarity, except for bird communities, which were more homogeneous in more natural landscapes. Bee communities, in contrast, were less similar in landscapes with higher percentages of semi‐natural habitats. Increased landscape fragmentation decreased similarity of true bug communities, while plant communities showed a nonlinear, U‐shaped response. More intense land use, specifically increased pesticide burden, led to a homogenization of bee, bug and spider communities within sites. In these cases, habitat fragmentation interacted with pesticide load. Hoverfly and carabid beetle community similarity was differentially affected by higher pesticide levels: for carabid beetles similarity decreased, while for hoverflies we observed a U‐shaped relationship. Main conclusions Our study demonstrates the effects of landscape composition, configuration and land‐use intensity on the similarity of communities. It indicates reduced exchange of species between communities in landscapes dominated by agricultural activities. Taxonomic groups differed in their responses to environmental drivers and using but one group as an indicator for ‘biodiversity’ as such would thus not be advisable.     

Electrophoretic study of plant histones: Comparison with vertebrate histones

The histones of seven plant species (barley, leek, onion, pea, radish, rye, and wheat) were isolated and compared to the histones of calf thymus and rat liver using electrophoresis on polyacrylamide-urea and polyacrylamide-SDS gels. It was found that the F1 histone of plants contains more subspecies and has generally higher molecular weights than their animal histone counterparts. Histones F3 of plants and animals have identical molecular weights and similar but not identical mobilities on polyacrylamide-urea gels. No histones were found in plants which have molecular weights and mobilities on polyacrylamide-urea gels which resemble the values for histones F2a2 and F2b of animals, but instead the series of histones observed differ from any of the animal histones. These plant histones may represent either substantially modified forms of F2a2 and F2b, or else may be a different class of histone molecules unique to plants. Fractions F2al in plants and animals are identical in electrophoretic behavior, but seem to differ in degree of acetylation.     

Plant and animal histones are completely interchangeable in the nucleosome core

Nucleosome core particles were reconstituted using mixtures of plant (corn or tobacco) and animal (chicken erythrocytes) histones. We show by electron microscopy and sucrose gradient sedimentation that H3 and H4 from tobacco and chicken erythrocytes can be interchanged in the nucleosome kernel. Cross-linking experiments with the protein cross-linking reagent dimethylsuberimidate reveal that, despite structural differences between the histones of the two species, H2A and H2B can be interchanged provided the homologous H2A-H2B dimers are dissociated prior to the annealing.     

An evolutionary comparison of plant histones.

Histones were extracted from chromatin of the following: a moss (Polytrichum juniperinum); the primitive vascular plants Psilotum nudum and Equisetum arvense; a fern (Polypodium vulgare); the gymnosperms fir (Abies concolor), yew (Taxus canadensis) and Gingko biloba; the dicotyledonous angiosperms tobacco (Nicotiana tabacum) and maple (Acer saccharinum); and the monocotyledonous angiosperms corn (Zea mays) and lily (Lilium longiflorum). The histones were subjected to polyacrylamide gel electrophoresis and compared to standard histones of pea (Pisum sativum) and cow (Bos taurus). All species have histones of the exact electrophoretic mobility of histones F2a1 and F3 of cow and pea. All species have histones of low electrophoretic mobility assumed to be F1 histones. None of the plant histones displayed electrophoretic mobility between F3 and F2a1 while animal histone fractions F2b and F2a2 do migrate to this position. No animal histone fraction was found to migrate between F3 and F1 while a major plant fraction, designated "F2b-like" was found to migrate to this position in all plant species studied except for the moss and Psilotum. A band of similar mobility was strikingly absent from the histones of these two species.     

On the similarity of dendrograms

A metric on binary trees is defined to give the similarity of two dendrograms. One of the major desirable properties of the proposed tree similarity measure is to clarify the decision ordering nature of biological trees. This metric is applied to evolutionary tree reconstructions and comparative embryogenesis. The mathematical properties of this metric are discussed, and an algorithm is proposed to compute the metric.“ …. our essential task lies in the comparison of related forms rather than in the precise definition of each; and the deformation of a complicated figure may be a phenomenon easy of comprehension, though the figure itself have to be left unanalysed ….”     

On the arrangement of histones in chromatin.

It was found that nucleoprotein particles formed after DNase I action on calf thymus chromatin contain single-stranded DNA fragments, associated with histones only by ionic linkages. These results suggest that histones in chromatin are bound ionically only to one polynucleotide strand of double-helical DNA, protecting it against nucleolytic attack.     

Analysis of non-coding small RNA similarity/sharing between plant and animal genomes

<正>Dear Editor,During the construction and analysis of the Bencao(herbal)small RNA(s RNA) Atlas, the fact that many s RNAs from the human genome are present in the Bencao(herbal) database attracted our attention(Cao et al., 2023). The Bencao Atlas contains millions of s RNAs from hundreds of plants used in traditional Chinese Medicines(TCMs). Therefore,     

On the origin of biological similarity

The principles of biological similarity have not been adequately defined. Previous studies have not been fully successful, mainly because the search for such principles centered around the idea that a few of them would apply to all animals, just as Newton's principles of mechanical similarity apply to all inanimate objects. However, this is not possible, so that the search has led up a number of blind alleys, ending with a failure to provide a fundamental and unified explanation—as contrasted with empirical justification—for the scaling of basal metabolic rate of many kinds of animals (e.g. mammals, birds, fish, certain small metazoa) according to a $\text{3}\text{4}\text{-}\text{power}$ of body mass, M, rather than as $\text{M}{}^{\mathrm{<mtext>2</mtext><mtext>3</mtext>}}$ (“surface law”) or M^1·0; moreover, none of the previous theories can account for the fact that other kinds of animals (e.g. insects, snakes, hibernating mammals) do not obey the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$. Two basic characteristics of all animals are that in the water they are on “the verge of floating” and that movement is interwoven with the nature of animal life itself. These observations lead to the principle of constancy of body density ($\text{ρ ? 1}$) and to the principle of similarity in some defined sense of the muscular apparatus—the universal generator of movement—across species, but only within classes of animals that have evolved similar methods of locomotion. Because muscle tissues are subject to elastic (“spring-type”) contraction forces, a general elastic similarity principle holds for muscle diameter, d, vs. a linear body dimension, L, i.e., d² ∝ L³ (Galileo-Rashevsky principle; this principle is valid also for the dimensions of the trunk of animals without exoskeleton subject to a gravitational load, e.g. for land mammals but not for sea mammals). A final principle which, combined with the above, leads to the $\text{M}\text{3}\text{4}\text{-}\text{rule}$ for muscle-power generation, is that time is scaled as the linear dimension, T ∝ L (in contrast to Newton's second principle of mechanical similarity for physical objects, $\text{T ∝ L}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$). This principle was introduced in the past either as an arbitrary assumption (Lambert & Teissier) or based on the empirical finding of constancy of muscle shortening velocity ($\text{∝}\text{L}\text{T}$ across mammalian species (Hill-McMahon). However, this principle cannot be valid for the classes of animals which do not obey the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$. This principle is derived here from the more fundamental principle of constancy, across similar species, of mechanical stress (force over cross-section) endured by contracting muscles. In species such as snakes, however, in which locomotion is generated in a different way, friction forces assume an important role and scaling of time as with mechanical similarity, $\text{T ∝ L}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$, is obtained by assuming a similar velocity of the animals along their axis as size increases; using this scaling, the deviation of snakes from the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$ is explained. Interestingly, though, such scaling may have limited the maximal body size of snakes. A yet different principle seems to be operating in insects, leading to the scaling: $\text{T ∝ L}{}^{\mathrm{<mtext>?</mtext><mtext>1</mtext><mtext>3</mtext>}}$ and a faster than body mass increase of basal metabolic rate. Finally, neither heat loss nor surface-related transport appear to be limiting and setting factors for metabolic rate—indeed “surface arguments” are entirely unbased. Only in some situations where the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$ is not obeyed because of heat loss considerations (e.g. dogs adapted to the tropics or to the arctic cold) is a surface argument relevant.     

Phospholipids in plant and animal chromatin

Isolated hepatic nuclei and hepatic chromatin have been analysed for their DNA, RNA, protein and phospholipid content. The protein/DNA ratio is 3 for nuclei and 1.95 for chromatin extracted from Triton X-100 treated nuclei. The phospholipids, (2.36 +/- 0.91 (S.D.) per cent of the total nuclear material), are lost during the chromatin preparation mainly during the Triton X-100 washings of the nuclei. Nevertheless, 10 per cent of the total nuclear phospholipids remain bound to the chromatin. The comparative analysis of both nuclei and chromatin shows a difference in phospholipids and fatty acid composition. Thus, the chromatin-associated phospholipid cannot be attributed simply to contaminating nuclear membrane. This is supported by the autoradiographic study of semi-thin sections of interphase nuclei from root apices of Vicia faba in which [3H] ethanolamine is clearly localized in the chromatin and nucleolar regions of the nuclei.     

Distinction and similarity in the structure of histones H1 and H5 as indicated by 13C nuclear-magnetic-resonance spectroscopy

The 13C nuclear magnetic resonance studies have been carried out on histones H1 and H5, by focusing our interest on possible formation of specific salt bridges between acidic and basic amino acid residues in the proteins and also on the structural difference between the two proteins. The 13C chemical shift and pKa values of the carboxyl group of glutamic acid residues in the histones coincided with those of free glutamic acid. Based on this result and another experiment using completely modified lysine residues in the histones, no evidence for a specific interaction between acidic and basic residues has been found. It has also been shown that the pH-effects of aliphatic and aromatic resonances are quite different between H1 and H5, suggesting that the globular domain of H5 is more stable than that of H1. The correlation time (1.5 ns) for the alpha-carbons of H5 estimated from 13C nuclear Overhauser enhancement was twice as long as that of H1 (0.9 ns), indicating that the backbone in the N-terminal and C-terminal domains of H5 is less mobile than that of H1.