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.     

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.     

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.     

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.     

Conservation and diversification of HAIRY MERISTEM gene family in land plants

The shoot apical meristems (SAMs) of land plants are crucial for plant growth and organ formation. In several angiosperms, the HAIRY MERISTEM (HAM) genes function as key regulators that control meristem development and stem cell homeostasis. To date, the origin and evolutionary history of the HAM family in land plants remains unclear. Potentially shared and divergent functions of HAM family members from angiosperms and non-angiosperms are also not known. In constructing a comprehensive phylogeny of the HAM family, we show that HAM proteins are widely present in land plants and that HAM proteins originated prior to the divergence of bryophytes. The HAM family was duplicated in a common ancestor of angiosperms, leading to two distinct groups: type I and type II. Type-II HAM members are widely present in angiosperms, whereas type-I HAM members were independently lost in different orders of monocots. Furthermore, HAM members from angiosperms and non-angiosperms (including bryophytes, lycophytes, ferns and gymnosperms) are able to replace the role of the type-II HAM genes in Arabidopsis, maintaining established SAMs and promoting the initiation of new stem cell niches. Our results uncover the conserved functions of HAM family members and reveal the conserved regulatory mechanisms underlying HAM expression patterning in meristems, providing insight into the evolution of key stem cell regulators in land plants.     

The effect of host plants on genotype variability in fitness and honeydew composition of Aphis fabae

Aphid species can be polyphagous, feeding on multiple host plants across genera. As host plant species can have large variation in their phloem composition, this can affect aphid fitness and honeydew composition. Previous research showed significant intraspecific genotype variation in the composition of the honeydew carbohydrates of the black bean aphid Aphis fabae, with the ant attractant trisaccharide melezitose showing especially large variation across different genotypes. In this study, we test if variation in melezitose and carbohydrate composition of aphid honeydew could be linked to the adaptation of specific aphid genotypes to particular host plants. To this end, 4 high and 5 low melezitose secreting genotypes of the black bean aphid Aphis fabae were reared on 4 common host plants: broad bean, goosefoot, beet, and poppy. The carbohydrate composition, and in particular melezitose secretion, showed important aphid genotype and host plant interactions, with some genotypes being high melezitose secreting on 1 host plant but not on another. However, the interaction effects were not paralleled in the fitness measurements, even though there were significant differences in the average fitness across the different host plants. On the whole, this study demonstrates that aphid honeydew composition is influenced by complex herbivore–plant interactions. We discuss the relevance of these findings in the context of ant–aphid mutualisms and adaptive specialization in aphids.     

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。     

Threats of land use to the global diversity of vascular plants

Aim

Land use is a main driver of biodiversity loss worldwide. However, quantifying its effects on global plant diversity remains a challenge due to the limited availability of data on the distributions of vascular plant species and their responses to land use. Here, we estimated the global extinction threat of land use to vascular plant species based on a novel integration of an ecoregion-level species-area model and the relative endemism richness of the ecoregions.

Location

Global.

Methods

First, we assessed ecoregion-level extinction threats using a countryside species–area relationship model based on responses of local plant richness to land use types and intensities and a high-resolution global land use map. Next, we estimated global species extinction threat by multiplying the relative endemism richness of each ecoregion with the ecoregion-level extinction threats.

Results

Our results indicate that 11% of vascular plant species are threatened with global extinction. We found the largest extinction threats in the Neotropic and Palearctic realms, mainly due to cropland of minimal and high intensity, respectively.

Main Conclusions

Our novel integration of the countryside species–area relationship and the relative endemism richness allows for the identification of hotspots of global extinction threat, as well as the contribution of specific land use types and intensities to this threat. Our findings inform where the development of measures to protect or restore plant diversity globally are most needed.     

The effect of geological biases on our perception of early land plant radiation

The Silurian–Devonian plant radiation was a critical development in the evolution of early terrestrial ecosystems. Characterizing the diversity dynamics of this radiation has been a focus of numerous studies. However, little is known about the impact of geological bias on our perception of this biodiversification. Here, we use a new, comprehensive compilation of plant occurrences from North America, together with a Macrostrat lithological dataset, to elucidate the relationships between the palaeobotanical and geological records of early land plants. Results show that observed raw diversity patterns at both species and genus rank are significantly correlated with fluctuations of sedimentary rock volume, especially of non-marine fossiliferous deposits. The lack of terrestrial sedimentary deposits before the Emsian (Early Devonian) makes it difficult to obtain an accurate depiction of the pre-Emsian plant diversification in North America. However, complementary analyses reveal that sampling-standardized diversity patterns partially correct the raw trajectories, especially at the genus-level if enough preserved non-marine sediments are available for sampling. Our findings highlight that geological incompleteness remains a fundamental bias for describing early plant diversification. This indicates that, even when sampling is extensive, observed diversity patterns potentially reflect the heterogeneity of the rock record, which blurs our understanding of the early history of land vegetation.     

轮藻和陆地植物系统发育及其进化

Charophytic algae and land plants together make up a monophyletic group, streptophytes, which represents one of the main lineages of multicellular eukaryotes and has contributed greatly to the change of the environment on earth in the Phanerozoic Eon. Significant progress has been made to understand phylogenetic relationships among members of this group by phylogenetic studies of morphological and molecular data over the last twenty-five years. Mesostigma viride is now regarded as among the earliest diverging unicellular organisms in streptophytes. Characeae are the sister group to land plants. Liverworts represent the first diverging lineage of land plants. Hornworts and lycophytes are extant representatives of bryophytes and vascular plants, respectively, when early land plants changed from gametophyte to sporophyte as the dominant generation in the life cycle. Equisetum, Psilotaceae, and ferns constitute the monophyletic group of monilophytes, which are sister to seed plants. Gnetales are related to conifers, not to angiosperms as previously thought. Amborella, Nymphaeales, Hydatellaceae, Illiciales, Trimeniaceae, and Austrobaileya represent the earliest diverging lineages of extant angiosperms. These phylogenetic results, together with recent progress on elucidating genetic and developmental aspects of the plant life cycle, multicellularity, and gravitropism, will facilitate evolutionary developmental studies of these key traits, which will help us to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.     

The role of land plants,phosphorus weathering and fire in the rise and regulation of atmospheric oxygen

The evolution of vascular plants and their spread across the land surface, beginning ～420 Ma, progressively increased the rate of weathering of phosphorus from rocks. This phosphorus supply promoted terrestrial and marine productivity and the burial of organic carbon, which has been the major source of O₂ over geological timescales. Hence, it is predicted that the rise of plants led to an increase in the O₂ content of the atmosphere from ～12 vol %, 570–400 Ma to its present level of ～21 vol % by ～340 Ma. Previous modelling studies suggest that O₂ then rose to ～35 vol % ～300 Ma. Such high concentrations are difficult to reconcile with the known persistence of forests, because rising O₂ increases the frequency and intensity of vegetation fires, tending to decrease biomass and cause ecological shifts toward faster regenerating ecosystems. Rising O₂ also directly inhibits C3 photosynthetic carbon assimilation and increases the production of toxic reactive oxygen species in cells. These effects suppress plant‐induced phosphorus weathering and hence organic carbon burial, providing a sensitive negative feedback on O₂. A revised model predicts that this mechanism could have regulated atmospheric O₂ within the range 15–25 vol % for the last 350 million years.     

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.