The evolution of plant life span: facts and hypotheses

There are two different views on the evolution of life forms in Cormophyta: from woody plants to herbaceous ones or in opposite direction - from herbs to trees. In accordance with these views it is supposed that life span in plants changed in the course of evolution from many years (perennials) to few years (annuals, biennials), or went in reverse - from few years to many years. The author discusses the problems of senescence and longevity in Cormophyta in the context of various hypotheses of ageing (programmed death theory, mutation accumulation, antagonistic pleiotropy, disposable soma, genes of ageing, genes of longevity). Special attention is given to bio-morphological aspects of longevity and cases of non-ageing plants ("negative senescence", "potential immortality"). It is proposed to distinguish seven models of simple ontogenesis in Cormophyta that can exemplify the diversity of mechanisms of ageing and longevity. The evolution of life span in plants is considered as an indirect result of natural selection of other characteristics of organisms or as a consequence of fixation of modifications (episelectional evolution). It seems that short life span could emerge several times during evolution of one group of plants, thus favoring its adaptive radiation.     

The Rooting of the Universal Tree of Life Is Not Reliable

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.     

The attempt on the life of the Tree of Life: science,philosophy and politics

Lateral gene transfer (LGT), the exchange of genetic information between (primarily prokaryotic) lineages, not only makes construction of a universal Tree of Life (TOL) difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. We could encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit.     

Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life

The origin and diversification of RNA secondary structure were traced using cladistic methods. Structural components were coded as polarized and ordered multi-state characters, following a model of character state transformation outlined by considerations in statistical mechanics. Several classes of functional RNA were analyzed, including ribosomal RNA (rRNA). Considerable phylogenetic signal was present in their secondary structure. The intrinsically rooted phylogenies reconstructed from evolved RNA structure depicted those derived from nucleic acid sequence at all taxonomical levels, and grouped organisms in concordance with traditional classification, especially in the archaeal and eukaryal domains. Natural selection appears therefore to operate early in the information flow that originates in sequence and ends in an adapted phenotype. When examining the hierarchical classification of the living world, phylogenetic analysis of secondary structure of the small and large rRNA subunits reconstructed a universal tree of life that branched in three monophyletic groups corresponding to Eucarya, Archaea, and Bacteria, and was rooted in the eukaryotic branch. Ribosomal characters involved in the translational cycle could be easily traced and showed that transfer RNA (tRNA) binding domains in the large rRNA subunit evolved concurrently with the rest of the rRNA molecule. Results suggest it is equally parsimonious to consider that ancestral unicellular eukaryotes or prokaryotes gave rise to all extant life forms and provide a rare insight into the early evolution of nucleic acid and protein biosynthesis. Received: 13 September 2000 / Accepted: 27 August 2001     

Cladogenesis, coalescence and the evolution of the three domains of life

In this article, we explore the large-scale structure of the tree of life by using a simple model with a constant number of species and rates of speciation that equal the rates of extinction. In addition, we discuss the consequences of horizontal gene transfer for the concept of a most recent common ancestor of all living organisms (cenancestor). A simple null hypothesis based on coalescence theory explains some features of the observed topologies of the tree of life. Simulations of genes and organismal lineages suggest that there was no single common ancestor that contained all the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history that traces back to an individual molecular cenancestor. However, these molecular ancestors were likely to be present in different organisms and at different times.     

The fundamental units,processes and patterns of evolution,and the Tree of Life conundrum

Background

The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject.

Concept

Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts.1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs), that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes) and preferential replication along with the rest of the recipient genome.2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language). Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome.3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or FOL). Search for trends and patterns in the FOL is a productive direction of study that leads to the delineation of ensembles of FUEs that evolve coherently for a certain time span owing to a shared history of vertical inheritance or horizontal gene transfer; these ensembles are commonly known as genomes, taxa, or clades, depending on the level of analysis. A small set of genes (the universal genetic core of life) might show a (mostly) coherent evolutionary trend that transcends the entire history of cellular life forms. However, it might not be useful to denote this trend "the tree of life", or organismal, or species tree because neither organisms nor species are fundamental units of life.

Conclusion

A logical analysis of the units and processes of biological evolution suggests that the natural fundamental unit of evolution is a FUE, that is, a genetic element with an independent evolutionary history. Evolution of a FUE on the macro scale is naturally represented by a tree. Only the full compendium of trees for individual FUEs (the FOL) is an adequate depiction of the evolution of life. Coherent evolution of FUEs over extended evolutionary intervals is a crucial aspect of the history of life but a "species" or "organismal" tree is not a fundamental concept.

Reviewers

This articles was reviewed by Valerian Dolja, W. Ford Doolittle, Nicholas Galtier, and William Martin

     

Contrasting the ancestry patterns of three distinct population groups from the northernmost region of South America

Colombia, located in the north of the South American subcontinent is a country of great interest for population genetic studies given its high ethnic and cultural diversity represented by the admixed population, 102 indigenous peoples and African descent populations. In this study, an analysis of the genetic structure and ancestry was performed based on 46 ancestry informative INDEL markers (AIM-INDELs) and considering the genealogical and demographic variables of 451 unrelated individuals belonging to nine Native American, two African American, and four multiple ancestry populations. Measures of genetic diversity, ancestry components, and genetic substructure were analyzed to build a population model typical of the northernmost part of the South American continent. The model suggests three types of populations: Native American, African American, and multiple ancestry. The results support hypotheses posed by other authors about issues like the peopling of South America and the existence of two types of Native American ancestry. This last finding could be crucial for future research on the peopling of Colombia and South America in that a single origin of all indigenous communities should not be assumed. It then would be necessary to consider other events that could explain their genetic variability and complexity throughout the continent.     

Evolution without speciation but with selection: LUCA, the Last Universal Common Ancestor in Gilbert's RNA world

This is not an attempt to analyze the Last Universal Common Ancestor (LUCA) to understand the origin of living systems. We do not know what came before Gilberts' RNA world. Our analysis starts with the RNA world and with genes (biological replicators alla Dawkings) made up of RNA proteins with enzymatic catalytic functions within units that are not yet modern cells. We offer a scenario where cellular entities are very simple and without individuality; they are only simple primary units of selection (the first level of selection) in which replicators compete in the most Darwinian manner, totally deprived of cooperation and interactions among genes. The information processing system of this RNA world is inaccurate and inefficient when compared to that found in organisms that came later. Among the "genes" and the entities that harbor them, high mutation rate was the most prevalent source of variability and the only inheritance was through lateral gene transfer of mobile elements. There were no chromosomes or any other genomic organization. As millions of years accumulated, complex and organized biological structures and processes evolved thanks to the variability mustered up mostly by lateral gene transfers and mutations. With micro- and mini-satellites, lateral gene transfers became indispensable devices of selection to mold variability. Competition and Darwinian selection gave way to a new transition in evolution, one I consider ineluctable, in which cooperation among interactive genes prevailed for the sake of higher fitness. Compartmentalization constituted a major transition in evolution that spurted new types of genome organization. Minichromosomes is one of these; cellular membranes and cytoplasmic structures completed the picture of the primitive cell. However, the much talked about phylogenetic tree does not exit in that ancient LUCA. The tree has no organism at its base; only clusters of genes evoke a fragile beginning for the increasingly complex cell types that were to emerge later.     

Superfamilies SDR and MDR: From early ancestry to present forms. Emergence of three lines, a Zn-metalloenzyme, and distinct variabilities

Two large gene and protein superfamilies, SDR and MDR (short- and medium-chain dehydrogenases/reductases), were originally defined from analysis of alcohol and polyol dehydrogenases. The superfamilies contain minimally 82 and 25 genes, respectively, in humans, minimally 324 and 86 enzyme families when known lines in other organisms are also included, and over 47,000 and 15,000 variants in existing sequence data bank entries. SDR enzymes have one-domain subunits without metal and MDR two-domain subunits without or with zinc, and these three lines appear to have emerged in that order from the universal cellular ancestor. This is compatible with their molecular architectures, present multiplicity, and overall distribution in the kingdoms of life, with SDR also of viral occurrence. An MDR-zinc, when present, is often, but not always, catalytic. It appears also to have a structural role in inter-domain interactions, coenzyme binding and substrate pocket formation, as supported by domain variability ratios and ligand positions. Differences among structural and catalytic zinc ions may be relative and involve several states. Combined, the comparisons trace evolutionary properties of huge superfamilies, with partially redundant enzymes in cellular redox functions.     

The evolution of demographic tactics in lizards: a test of some hypotheses concerning life history evolution

We analyze, with an augmented data base, patterns of covariation of the three primary demographic parameters (age at maturity, fecundity, adult survival, all measured in the same unit of time) in lizards. This also constitutes a first attempt to use all three of these parameters for this group of species. We attempt to place these analyses in the framework of recent theories on life history evolution (Ferrière and Clobert, 1992; Charnov, 1993). Life history data were collected from the literature and from our original work, and a composite phylogeny was assembled, based on a variety of published sources. Using a phylogenetically based statistical method (independent contrasts), the allometric (log-log) relationship of fecundity (and of clutch size) in relation to snout-vent length was found to differ significantly between the two major clades of extant lizards, Iguania (43 species in our data set) and Scleroglossa (47 species). We therefore emphasize analyses done separately for the two clades. Without removing correlations with body size, the relationships between fecundity and survival, and between fecundity and age at maturity, were also found to differ between clades, which differs from Charnov's (1993) predictions. When correlations with body size were removed statistically, however, the two clades did not differ significantly in these relationships. In a principal components analysis (PCA) of the three demographic variables plus snout-vent length, the first axis explained the majority (53–57%) of variation in both clades, while the second axis explained 27–31% of the variation and loaded mainly on fecundity. In a PCA of size-adjusted demographic variables residuals (from log-log regressions on snout-vent length), the first axis explained 66–68% of the variation and was clearly interpretable as the classical “slow-fast” continuum, which has been described in birds and mammals. The PCA of residuals did not provide clear evidence of additional significant patterns of covariation. However, the rate of evolution of mortality (size-corrected), but not of fecundity or age at maturity, differed significantly between clades. Furthermore, fecundity and age at maturity, both corrected for variation in adult mortality (in addition to body size), were still significantly related, indicating the existence of other patterns of variation in these life history traits. In other words, the ratios between age at maturity and adult mortality, or between fecundity and adult mortality, were not found to be invariant, because the variation not accounted for by these ratios was significantly associated with variation in another variable. This result contradicts the prediction of Charnov (1993), and suggests the existence of other directions of evolution in these life history traits.     

Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution

HLA class I molecules can be classified into supertypes associated with overlapping peptide-binding motifs and repertoires. Herein, overlaps in peptide-binding and T-cell recognition repertoires were demonstrated between mouse and human molecules. Since rodent and primate lineages separated before the current allelic variation of mouse and human class I molecules, these data demonstrate that supertypic specificities originated by convergent evolution. Phylogenetic and structural analyses demonstrated that convergent evolution also occurs amongst primates and within the human species, resulting from the selection of different pocket structures having similar specificity or independent repeated selection of the same pocket structure.     

Testing adaptive hypotheses on the evolution of larval life history in acorn and stalked barnacles

Despite strong selective pressure to optimize larval life history in marine environments, there is a wide diversity with regard to developmental mode, size, and time larvae spend in the plankton. In the present study, we assessed if adaptive hypotheses explain the distribution of the larval life history of thoracican barnacles within a strict phylogenetic framework. We collected environmental and larval trait data for 170 species from the literature, and utilized a complete thoracican synthesis tree to account for phylogenetic nonindependence. In accordance with Thorson's rule, the fraction of species with planktonic‐feeding larvae declined with water depth and increased with water temperature, while the fraction of brooding species exhibited the reverse pattern. Species with planktonic‐nonfeeding larvae were overall rare, following no apparent trend. In agreement with the “size advantage” hypothesis proposed by Strathmann in 1977, egg and larval size were closely correlated. Settlement‐competent cypris larvae were larger in cold water, indicative of advantages for large juveniles when growth is slowed. Planktonic larval duration, on the other hand, was uncorrelated to environmental variables. We conclude that different selective pressures appear to shape the evolution of larval life history in barnacles.     

Space, time, form: viewing the Tree of Life

There are numerous ways to display a phylogenetic tree, which is reflected in the diversity of software tools available to phylogenetists. Displaying very large trees continues to be a challenge, made ever harder as increasing computing power enables researchers to construct ever-larger trees. At the same time, computing technology is enabling novel visualisations, ranging from geophylogenies embedded on digital globes to touch-screen interfaces that enable greater interaction with evolutionary trees. In this review, I survey recent developments in phylogenetic visualisation, highlighting successful (and less successful) approaches and sketching some future directions.     

Analysis of molecular differentiation in a hybrid zone between chromosomally distinct races of the common shrew Sorex araneus (Insectivora: Soricidae) suggests their common ancestry

During postglacial colonization, populations that diverged in different refugia produced a patchwork of genomes, often delimited with sharp hybrid zones. The outcome of hybridization following the secondary contact of two genetically distinct populations is hard to predict. In this context, the present study investigated the genetic structure of the hybrid zone between the Drnholec and Białowieża chromosome races of the common shrew ( Sorex araneus ) in Poland using biparentally inherited (seven autosomal microsatellites) and uniparentally inherited (Y-linked microsatellite and mtDNA) molecular markers. On the basis of diagnostic chromosomes, the Drnholec and Białowieża races were classified to different karyotypic groups, which were believed to have independent glacial histories. It was found that genetic differentiation between the Drnholec and Białowieża races was weak and nonsignificant with respect to all molecular markers. However, these results are in contrast with the chromosomal structure of this hybrid zone. The very sharp frequency clines of the diagnostic chromosomes strongly suggest that gene flow between the Drnholec and Białowieża races was reduced. Nonsignificant correlations between genetic differentiation and both the presence of an environmental barrier and geographical distance reveal that only differences in karyotypes might be a reason for limited gene exchange between the races. It is assumed that a lack of molecular differences between the Drnholec and Białowieża races results from a shared ancestral variation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 79–90.     

The Last Universal Common Ancestor (LUCA) and the Ancestors of Archaea and Bacteria were Progenotes

The tRNA split genes of Nanoarchaeum equitans and the Met-tRNA^fMet → fMet-tRNA^fMet pathway, identifiable as ancestral traits, and the late appearance of DNA are used to understand the evolutionary stage at which the progenote → genote transition took place. The arguments are such as to impose that not only was the last universal common ancestor (LUCA) a progenote, but the ancestors of Archaea and Bacteria were too. Therefore, the progenote → genote transition took place in a very advanced stage of the evolution of the tree of life, and only when the ancestors of Archaea and Bacteria were already defined. These conclusions are in disagreement with commonly held beliefs.     

What life cycle graphs can tell about the evolution of life histories

We analyze long-term evolutionary dynamics in a large class of life history models. The model family is characterized by discrete-time population dynamics and a finite number of individual states such that the life cycle can be described in terms of a population projection matrix. We allow an arbitrary number of demographic parameters to be subject to density-dependent population regulation and two or more demographic parameters to be subject to evolutionary change. Our aim is to identify structural features of life cycles and modes of population regulation that correspond to specific evolutionary dynamics. Our derivations are based on a fitness proxy that is an algebraically simple function of loops within the life cycle. This allows us to phrase the results in terms of properties of such loops which are readily interpreted biologically. The following results could be obtained. First, we give sufficient conditions for the existence of optimisation principles in models with an arbitrary number of evolving traits. These models are then classified with respect to their appropriate optimisation principle. Second, under the assumption of just two evolving traits we identify structural features of the life cycle that determine whether equilibria of the monomorphic adaptive dynamics (evolutionarily singular points) correspond to fitness minima or maxima. Third, for one class of frequency-dependent models, where optimisation is not possible, we present sufficient conditions that allow classifying singular points in terms of the curvature of the trade-off curve. Throughout the article we illustrate the utility of our framework with a variety of examples.     

Phylogeny of the Ascaridoidea (Nematoda: Ascaridida) based on three genes and morphology: hypotheses of structural and sequence evolution

Ascaridoid nematodes parasitize the gastrointestinal tract of vertebrate definitive hosts and are represented by more than 50 described genera. We used 582 nucleotides (83% of the coding sequence) of the mitochondrial gene cytochrome oxidase subunit 2, in combination with published small- and large-subunit nuclear rDNA sequences (2,557 characters) and morphological data (20 characters), to produce a phylogenetic hypothesis for representatives of this superfamily. This combined evidence phylogeny strongly supported clades that, with 1 exception, were consistent with Fagerholm's 1991 classification. Parsimony mapping of character states on the combined evidence tree was used to develop hypotheses for the evolution of morphological, life history, and amino acid characters. This analysis of character evolution revealed that certain key features that have been used by previous workers for developing taxonomic and evolutionary hypotheses represent plesiomorphic states. Cytochrome oxidase subunit 2 nucleotides show a strong compositional bias to A+T and a substitution bias to thymine. These biases are most apparent at third positions of codons and 4-fold degenerate sites, which is consistent with the nonrandom substitution pattern of A+T pressure. Despite nucleotide bias, cytochrome oxidase amino acid sequences show conservation and retention of critical functional residues, as inferred from comparisons to other organisms.     

Tree invasions: a comparative test of the dominant hypotheses and functional traits

Trees act as ecosystem engineers and invasions by exotic tree species profoundly impact recipient communities. Recently, research on invasive trees has dramatically increased, enabling the assessment of general trends in tree invasion. Analysing 90 studies dealing with 45 invasive tree species, we conducted a quantitative review and a meta-analysis to estimate the relevance of eight leading hypotheses for explaining tree invasions. We also tested whether species functional traits (growth rate, density/cover, germination, biomass and survival) equally promote tree invasiveness. Overall, our results suggest that several hypotheses, linked to invasibility or invasiveness, are pertinent to explain tree invasions. Furthermore, more than one hypothesis has been supported for a given species, which indicates that multiple factors lead to the success of invasive tree species. In addition, growth rate appears to be the most efficient predictor of invasiveness for invasive trees and could thus be used as a means to identify potential alien tree invasions. We conclude that further investigations are needed to test the consistency of some hypotheses across a broader pool of invasive tree species, whilst experimental studies with the same tree species across a larger range of sites would help to reveal the full suite of factors that affect tree invasions.     

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

Background

Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record.

Scope and Conclusions

The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.     

Life, Autonomy and Cognition: An Organizational Approach to the Definition of the Universal Properties of Life

This article addresses the issue of defining the universal properties of living systems through an organizational approach, according to which the distinctive properties of life lie in the functional organization which correlates its physicochemical components in living systems, and not in these components taken separately. Drawing on arguments grounded in this approach, this article identifies autonomy, with a set of related organizational properties, as universal properties of life, and includes cognition within this set.