Adaptive walks on changing landscapes: Levins' approach extended

The assumption that trade-offs exist is fundamental in evolutionary theory. Levins (Am. Nat. 96 (1962) 361-372) introduced a widely adopted graphical method for analyzing evolution towards an optimal combination of two quantitative traits, which are traded off. His approach explicitly excluded the possibility of density- and frequency-dependent selection. Here we extend Levins method towards models, which include these selection regimes and where therefore fitness landscapes change with population state. We employ the same kind of curves Levins used: trade-off curves and fitness contours. However, fitness contours are not fixed but a function of the resident traits and we only consider those that divide the trait space into potentially successful mutants and mutants which are not able to invade ('invasion boundaries'). The developed approach allows to make a priori predictions about evolutionary endpoints and about their bifurcations. This is illustrated by applying the approach to several examples from the recent literature.     

Physiological correlates of the morphology of early vascular plants

RAVEN, J. A., 1984. Physiological correlates of the morphology of early vascular plants. The early evolution of vascular land plants is considered in relation to the physiological problems of life on land. The universal characteristics of vascular plants (xylem, cuticle, stomata, intercellular air spaces, long-distance symplastic transport and alternation of generations) are discussed in terms of the essential properties of a homoiohydric phototroph. Likely precursors of vascular plants, and the physico-chemical and biotic environment in which they occurred, are outlined prior to a discussion of the selective forces acting on the evolution of vascular plants in the Upper Silurian and Lower Devonian. Emphasis is placed on biochemical and structural 'pre-adaptations' which may have occurred in the precursors of vascular plants and on which natural selection could have acted with lignified xylem, stomata, etc., as the end-products. Guiding principles in the analysis include the physiology of extant plants, physico-chemical constraints, and compatibility with the fossil record. It is concluded that the likely sequence of acquisition of vascular plant characteristics was: heteromorphic alternation of generations with an erect sporophyte; cuticularization of sporophyte; evolution of xylem; occurrence of intercellular air spaces with pores in the epidermis; stomatal activity of the pores. Endodermis and phloem-type long-distance transport probably originated around stages (3)-(5).     

Error thresholds for quasispecies on single peak Gaussian-distributed fitness landscapes

Based on the Eigen and Crow-Kimura models with a single peak fitness landscape, we propose that the fitness values of all molecules be Gaussian distributed random variables to incorporate the fluctuation effects of the fitness landscapes (noise of environments). And we investigate the quasispecies distribution and error threshold using ensemble average method within this theoretical framework. Numerical results show that a small fluctuation of the fitness landscape causes only a slight change in the concentration distribution and error threshold, which implies that the error threshold is stable against small perturbations. However, for a sizable fluctuation, quite different from the previous deterministic models, our statistical results reveal that the transition from quasi-species to error catastrophe is no longer so sharp, indicating the error threshold is located within a certain range and shifts toward a larger value.     

Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here we explore a promising new method, parsimony jackknifing, by analyzing a matrix comprising 2538 sequences of the chloroplast generbcL. The sequences included cover a broad taxonomic range, from cyanobacteria to flowering plants. Several parsimony jackknife analyses were performed, both with and without branch-swapping and multiple random addition sequences: 1) including all positions; 2) including only first and second codon positions; 3) including only third positions; and 4) using only transversions. The best resolution was obtained using all positions. Removal of third positions or transitions led to massive loss of resolution, although using only transversions somewhat improved basal resolution. While branch-swapping improved both resolution and the support found for several groups, most of the groups could be recovered by faster simple analyses. Designed to eliminate groups poorly supported by the data, parsimony jackknifing recognizes 1400 groups on the basis of allrbcL positions. These include major taxa such as green plants, land plants, flowering plants, monocots and eudicots. We include appendices of supported angiosperm families, as well as larger groups.     

Horizontal gene transfer in the innovation and adaptation of land plants

Horizontal gene transfer (HGT) has been well documented in prokaryotes and unicellular eukaryotes, but its role in plants and animals remains elusive. In a recent study, we showed that at least 57 families of nuclear genes in the moss Physcomitrella patens were acquired from prokaryotes, fungi or viruses and that HGT played a critical role in plant colonization of land. In this paper, we categorize all acquired genes based on their putative functions and biological processes, and further address the importance of HGT in plant innovation and evolution.     

The phylogeny of land plants: A cladistic analysis based on male gametogenesis

A cladistic analysis was carried out to resolve phylogenetic pattern among bryophytes and other land plants. The analysis used 22 taxa of land plants and 90 characters relating to male gametogenesis.Coleochaete orChara/Nitella were the outgroups in various analyses using HENNIG86, PAUP, and MacClade, and the land plant phylogeny was unchanged regardless of outgroup utilized. The most parsimonious cladograms from HENNIG86 (7 trees) have treelengths of 243 (C.I. = 0.58, R.I. = 0.82). Bryophytes are monophyletic as are hornworts, liverworts, and mosses, with hornworts identified as the sister group of a liverwort/moss assemblage. In vascular plants, lycophytes are polyphyletic andSelaginella is close to the bryophytes.Lycopodium is the sister group of the remaining vascular plants (minusSelaginella). Longer treelengths (over 250) are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors. This analysis challenges existing concepts of bryophyte phylogeny based on more classical data and interpretations, and provides new insight into land plant evolution.     

甜菜夜蛾虫酰肼抗性品系选育及相对适合度研究

本试验在室内对甜菜夜蛾Spodoptera exigua(Hübner)武汉敏感品系进行了8代群体汰选后分别于9、10、12代采用了单对汰选。结果表明虫酰肼处理后各单对品系后代幼虫存活率发生明显分离,F9(s1)、F10(s2)和F12(s3)代幼虫平均存活率分别为48.34%、11.72%和2.37%,筛选后分别为84.00%、83.33%和7.29%。经过12代汰选后,汰选品系抗性倍数为敏感品系的5.24倍,且单对汰选世代对虫酰肼的抗性发展较快,其抗性倍数分别是群体汰选的1.27、1.67和1.38倍。比较单对汰选世代与群体汰选世代某些生物学特性,显示单对汰选世代并不存在生长发育和生殖不利性,表明在虫酰肼群体汰选中穿插几代单对汰选可以加速抗性品系的选育。汰选品系相对于敏感品系具有0.31的适合度,表明甜菜夜蛾对虫酰肼产生抗性后存在适合度缺陷。     

Evolution of DNA amounts across land plants (embryophyta)

BACKGROUND AND AIMS: DNA C-values in land plants (comprising bryophytes, lycophytes, monilophytes, gymnosperms and angiosperms) vary approximately 1000-fold from approx. 0.11 to 127.4 pg. To understand the evolutionary significance of this huge variation it is essential to evaluate the phylogenetic component. Recent increases in C-value data (e.g. Plant DNA C-values database; release 2.0, January 2003; http://www.rbgkew.org.uk/cval/homepage.html) together with improved consensus of relationships between and within land plant groups makes such an analysis timely. METHODS: Insights into the distribution of C-values in each group of land plants were gained by superimposing available C-value data (4119 angiosperms, 181 gymnosperms, 63 monilophytes, 4 lycophytes and 171 bryophytes) onto phylogenetic trees. To enable ancestral C-values to be reconstructed for clades within land plants, character-state mapping with parsimony and MacClade was also applied. KEY RESULTS AND CONCLUSIONS: Different land plant groups are characterized by different C-value profiles, distribution of C-values and ancestral C-values. For example, the large ( approximately 1000-fold) range yet strongly skewed distribution of C-values in angiosperms contrasts with the very narrow 12-fold range in bryophytes. Further, character-state mapping showed that the ancestral genome sizes of both angiosperms and bryophytes were reconstructed as very small (i.e. < or =1.4 pg) whereas gymnosperms and most branches of monilophytes were reconstructed with intermediate C-values (i.e. >3.5, <14.0 pg). More in-depth analyses provided evidence for several independent increases and decreases in C-values; for example, decreases in Gnetaceae (Gymnosperms) and heterosperous water ferns (monilophytes); increases in Santalales and some monocots (both angiosperms), Pinaceae, Sciadopityaceae and Cephalotaxaceae (Gymnosperms) and possibly in the Psilotaceae + Ophioglossaceae clade (monilophytes). Thus, in agreement with several focused studies within angiosperm families and genera showing that C-values may both increase and decrease, it is apparent that this dynamic pattern of genome size evolution is repeated on a broad scale across land plants.     

The branching pattern of major groups of land plants inferred from parsimony analysis of ribosomal RNA sequences

The parsimony and bootstrap branching pattern of major groups of land plants derived from relevant 5S rRNA sequence trees have been discussed in the light of paleobotanical and morphological evidences. Although 5S rRNA sequence information is not useful for dileneating angiosperm relationships, it does capture the earlier phase of land plant evolution. The consensus branching pattern indicates an ancient split of bryophytes and vascular plants from the charophycean algal stem. Among the bryophytes,Marchantia andLophocolea appear to be phylogenetically close and together withPlagiomnium form a monophyletic group.Lycopodium andPsilotum arose early in vascular land plant evolution, independent of fem-sphenopsid branch. Gymnosperms are polyphyletic; conifers, Gnetales and cycads emerge in that order with ginkgo joiningCycas. Among the conifers,Metasequoia,Juniperus andTaxus emerge as a branch independent ofPinus which joins Gnetales. The phylogeny derived from the available ss-RNA sequences shows that angiosperms are monophyletic with monocots and dicots diverging from a common stem. The nucleotide replacements during angiosperm descent from the gymnosperm ancestor which presumably arose around 370 my ago indicates that monocots and dicots diverged around 180 my ago, which is compatible with the reported divergence estimate of around 200 my ago deduced from chloroplast DNA sequences. Since deceased.     

Constraining the role of early land plants in Palaeozoic weathering and global cooling

How the colonization of terrestrial environments by early land plants over 400 Ma influenced rock weathering, the biogeochemical cycling of carbon and phosphorus, and climate in the Palaeozoic is uncertain. Here we show experimentally that mineral weathering by liverworts—an extant lineage of early land plants—partnering arbuscular mycorrhizal (AM) fungi, like those in 410 Ma-old early land plant fossils, amplified calcium weathering from basalt grains threefold to sevenfold, relative to plant-free controls. Phosphate weathering by mycorrhizal liverworts was amplified 9–13-fold over plant-free controls, compared with fivefold to sevenfold amplification by liverworts lacking fungal symbionts. Etching and trenching of phyllosilicate minerals increased with AM fungal network size and atmospheric CO₂ concentration. Integration of grain-scale weathering rates over the depths of liverwort rhizoids and mycelia (0.1 m), or tree roots and mycelia (0.75 m), indicate early land plants with shallow anchorage systems were probably at least 10-fold less effective at enhancing the total weathering flux than later-evolving trees. This work challenges the suggestion that early land plants significantly enhanced total weathering and land-to-ocean fluxes of calcium and phosphorus, which have been proposed as a trigger for transient dramatic atmospheric CO₂ sequestration and glaciations in the Ordovician.     

Phytochrome-mediated development in land plants: red light sensing evolves to meet the challenges of changing light environments

Phytochromes are photoreceptors that provide plants with circadian, seasonal, and positional information critical for the control of germination, seedling development, shade avoidance, reproduction, dormancy, and sleep movements. Phytochromes are unique among photoreceptors in their capacity to interconvert between a red-absorbing form (absorption maximum of approximately 660 nm) and a far-red absorbing form (absorption maximum of approximately 730 nm), which occur in a dynamic equilibrium within plant cells, corresponding to the proportions of red and far-red energy in ambient light. Because pigments in stems and leaves absorb wavelengths below about 700 nm, this provides plants with an elegant system for detecting their position relative to other plants, with which the plants compete for light. Certain aspects of phytochrome-mediated development outside of flowering plants are strikingly similar to those that have been characterized in Arabidopsis thaliana and other angiosperms. However, early diverging land plants have fewer distinct phytochrome gene lineages, suggesting that both diversification and subfunctionalization have been important in the evolution of the phytochrome gene family. There is evidence that subfunctionalization proceeded by the partitioning among paralogues of photosensory specificity, physiological response modes, and light-regulated gene expression and protein stability. Parallel events of duplication and functional divergence may have coincided with the evolution of canopy shade and the increasing complexity of the light environment. Within angiosperms, patterns of functional divergence are clade-specific and the roles of phytochromes in A. thaliana change across environments, attesting to the evolutionary flexibility and contemporaneous plasticity of phytochrome signalling in the control of development.     

MPH1 is a thylakoid membrane protein involved in protecting photosystem II from photodamage in land plants

Photosystem II (PSII) is highly susceptible to photoinhibition caused by environmental stimuli such as high light; therefore plants have evolved multifaceted mechanisms to efficiently protect PSII from photodamage. We previously published data suggesting that Maintenance of PSII under High light 1 (MPH1, encoded by AT5G07020), a PSII-associated proline-rich protein found in land plants, participates in the maintenance of normal PSII activity under photoinhibitory stress. Here we provide additional evidence for the role of MPH1 in protecting PSII against photooxidative damage. Two Arabidopsis thaliana mutants lacking a functional MPH1 gene suffer from severe photoinhibition relative to the wild-type plants under high irradiance light. The mph1 mutants exhibit significantly decreased PSII quantum yield and electron transport rate after exposure to photoinhibitory light. The mutants also display drastically elevated photodamage to PSII reaction center proteins after high-light treatment. These data add further evidence that MPH1 is involved in PSII photoprotection in Arabidopsis. MPH1 homologs are found across phylogenetically diverse land plants but are not detected in algae or prokaryotes. Taken together, these results suggest that MPH1 protein began to play a role in protecting PSII against excess light following the transition from aquatic to terrestrial conditions.     

Dispersive and non-dispersive waves through plants: implications for arthropod vibratory communication

Vibratory communication in arthropods is a widespread phenomenon. Arthropods living on plants have been reported to use only dispersive bending waves in the context of prey-predator, competition, social and sexual interactions. Differences in signal structure have also been postulated to work as species recognition mechanisms and speciation agents. Using two identical laser Doppler vibrometers and a wavelet analysis, we quantified the wave propagation modes in rush stems (Juncus effusus) over the whole range of frequencies used by arthropods. A non-dimensionalized analysis shows that mechanical waves propagate not only as dispersive bending waves, but also as non-dispersive waves. Our analysis implies that an arthropod can communicate through non-dispersive bending waves by either producing signals of high frequencies or by choosing large stems, two widely different options tapping into the physiological and the behavioural repertoires, respectively. Non-dispersive waves, unreported so far in insect vibratory communication in plants, present serious advantages over dispersive bending waves in terms of signal integrity and may well be much more widely used than anticipated, in particular for species recognition.     

The influence of floating vascular plants on the diurnal fluctuations of temperature near the water surface in early spring

On clear days the temperature in a mat of floating Lemnaceae was 4° to 11° above that of the surface of the open water. The temperature of the environment 2 cm above or below the plant surface closely followed the surface temperature's quick response to changes in net radiation. The plant surface reflects more enery and transmits less than the open water, therefore there is less fluctuation in temperature in the water 10 cm and more below the floating plant surface. This results in a diurnal thermal stratification. At the surface of the open water changes in temperature tended to be smaller and slower, related to the air temperature; and, with wind disturbance, the water profile maintained relatively homogeneous temperatures.     

Geographical patterns and determinants of species richness in Mexico across selected families of vascular plants: implications for conservation

Mexico is considered a megadiverse country containing more than 10% of the world's biodiversity. The distribution of this species richness and endemism is different among the different Mexican states. We examined the species richness patterns of 13 families of vascular plants (including ferns, gymnosperms and angiosperms) in Mexico using political divisions (states) as units of analysis. We analysed the species richness values (absolute richness, endemic richness and restrictive richness) of these plant families using stepwise multiple regression analysis, assessing their relationship with a set of 10 environmental variables (expressed as heterogeneity coefficients). A combined cluster analysis with multidimensional scaling analysis (MDS) and an analysis of similarities were also undertaken to define the spatial–geographical patterns. Additionally, we proposed a methodological strategy to determine which states of Mexico have priorities for conservation. Our results suggested that the three species richness values used were significantly predicted by environmental factors, especially by climatic heterogeneity. Notwithstanding that a linear pattern was recognized, the Mexican states were gathered in four groups, which were confirmed by the MDS and the cluster analysis: (1) the Yucatan Peninsula, (2) arid Mexico, (3) the Mexican Transition Zone and (4) the megadiverse states. We proposed that 12 Mexican states include all the environmental conditions and are candidates for developing conservation programmes: (1) Quintana Roo, Tabasco and Yucatán, (2) Baja California, Chihuahua and Sinaloa, (3) Guerrero, Jalisco and Nuevo León and (4) Chiapas, Oaxaca and Veracruz.     

Environmental control for the large-scale production of plants through in vitro techniques

Leafy or chlorophyllous explants of a number of plant species currently micropropagated have been found to have high photosynthetic ability. Their growth and development have been promoted on sugar-free medium rather than on sugar-containing medium, provided that the environmental factors, such as CO₂ concentration, light intensity and relative humidity, are controlled for promoting photosynthesis and transpiration of explants/shoots/plantlets in vitro. Thus, environmental control is essential for promoting photosynthetic growth and development of in vitro plantlets. Several types of sugar-free (photoautotrophic) culture systems for large-scale micropropagation of plants have been developed. Advantages of sugar-free over conventional (heterotrophic or photomixotrophic) micropropagation systems are as follows: growth and development of plantlets in vitro are faster and more uniform, plantlets in vitro have less physiological and morphological disorders, biological contamination in vitro is less, plantlets have a higher percentage of survival during acclimatization ex vitro, and larger culture vessels could be used because of less biological contamination. Hence, production costs could be reduced and plant quality could be improved significantly with photoautotrophic micropropagation. Methods for the measurement and control of in vitro environments and the beneficial effects of environmental control on photosynthetic growth, development, and morphogenesis in large-scale production of micropropagated plantlets are presented. This revised version was published online in June 2006 with corrections to the Cover Date.