What are mycoplasmas: The relationship of tempo and mode in bacterial evolution

Summary In phenotype the mycoplasmas are very different from ordinary bacteria. However, genotypically (i.e., phylogenetically) they are not. On the basis of ribosomal RNA homologies the mycoplasmas belong with the clostridia, and indeed havespecific clostridial relatives. Mycoplasmas are, however, unlike almost all other bacteria in the evolutionary characteristics of their ribosomal RNAs. These RNAs contain relatively few of the highly conserved oligonucleotide sequences characteristic of normal eubacterial ribosomal RNAs. This is interpreted to be a reflection of an elevated mutation rate in mycoplasma lines of descent. A general consequence of this would be that the variation associated with a mycoplasma population is augmented both in number and kind, which in turn would lead to an unusual evolutionary course, one unique in all respects. Mycoplasmas, then, are actually tachytelic bacteria. The unusual evolutionary characteristics of their ribosomal RNAs are the imprints of their rapid evolution.     

The tempo and mode of barnacle evolution

Previous phylogenetic attempts at resolving barnacle evolutionary relationships are few and have relied on limited taxon sampling. Here we combine DNA sequences from three nuclear genes (18S, 28S and H3) and 44 morphological characters collected from 76 thoracican (ingroup) and 15 rhizocephalan (outgroup) species representing almost all the Thoracica families to assess the tempo and mode of barnacle evolution. Using phylogenetic methods of maximum parsimony, maximum likelihood, and Bayesian inference and 14 fossil calibrations, we found that: (1) Iblomorpha form a monophyletic group; (2) pedunculated barnacles without shell plates (Heteralepadomorpha) are not ancestral, but have evolved, at least twice, from plated forms; (3) the ontogenetic pattern with 5-->6-->8-->12+ plates does not reflect Thoracica shell evolution; (4) the traditional asymmetric barnacles (Verrucidae) and the Balanomorpha are each monophyletic and together they form a monophyletic group; (5) asymmetry and loss of a peduncle have evolved twice in the Thoracica, resulting in neither the Verrucomorpha nor the Sessilia forming monophyletic groups in their present definitions; (6) the Scalpellomorpha are not monophyletic; (7) the Thoracica suborders evolved since the Early Carboniferous (340mya) with the final radiation of the Sessilia in the Upper Jurassic (147mya). These results, therefore, reject many of the underlying hypotheses about character evolution in the Cirripedia Thoracica, stimulate a variety of new thoughts on thoracican radiation, and suggest the need for a major rearrangement in thoracican classification based on estimated phylogenetic relationships.     

The tempo and mode of evolution: body sizes of island mammals

The tempo and mode of body size evolution on islands are believed to be well known. It is thought that body size evolves relatively quickly on islands toward the mammalian modal value, thus generating extreme cases of size evolution and the island rule. Here, we tested both theories in a phylogenetically explicit context, by using two different species-level mammalian phylogenetic hypotheses limited to sister clades dichotomizing into an exclusively insular and an exclusively mainland daughter nodes. Taken as a whole, mammals were found to show a largely punctuational mode of size evolution. We found that, accounting for this, and regardless of the phylogeny used, size evolution on islands is no faster than on the continents. We compared different selection regimes using a set of Ornstein-Uhlenbeck models to examine the effects of insularity of the mode of evolution. The models strongly supported clade-specific selection regimes. Under this regime, however, an evolutionary model allowing insular species to evolve differently from their mainland relatives performs worse than a model that ignores insularity as a factor. Thus, insular taxa do not experience statistically different selection from their mainland relatives.     

Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus

Non-LTR retrotransposons R1 and R2 have persisted in rRNA gene loci (rDNA) since the origin of arthropods despite their continued elimination by the recombinational mechanisms of concerted evolution. This study evaluated the short-term evolutionary dynamics of the rDNA locus by measuring the divergence among replicate Drosophila melanogaster lines after 400 generations. The total number of rDNA units on the X chromosome of each line varied from 140 to 310, while the fraction of units inserted with R1 and R2 retrotransposons ranged from 37 to 65%. This level of variation is comparable to that found in natural population surveys. Variation in locus size and retrotransposon load was correlated with large changes in the number of uninserted and R1-inserted units, yet the numbers of R2-inserted units were relatively unchanged. Intergenic spacer (IGS) region length variants were also used to evaluate changes in the rDNA loci. All IGS length variants present in the lines showed significant increases and decreases of copy number. These studies, combined with previous data following specific R1 and R2 insertions in these lines, help to define the type and distribution, both within the locus and within the individual units, of recombinational events that give rise to the concerted evolution of the rDNA locus.     

The tempo and mode of three-dimensional morphological evolution in male reproductive structures

Various evolutionary forces may shape the evolution of traits that influence the mating decisions of males and females. Phenotypic traits that males and females use to judge the species identify of potential mates should evolve in a punctuated fashion, changing significantly at the time of speciation but changing little between speciation events. In contrast, traits experiencing sexual selection or sexually antagonistic interactions are generally expected to change continuously over time because of the directional selection pressures imposed on one sex by the actions of the other. To test these hypotheses, we used spherical harmonic representations of the shapes of male mating structures in reconstructions of the evolutionary tempo of these structures across the history of the Enallagma damselfly clade. Our analyses show that the evolution of these structures is completely consistent with a punctuated model of evolutionary change and a constant evolutionary rate throughout the clade's history. In addition, no interpopulation variation in shape was detected across the range of one species. These results indicate that male mating structures in this genus are used primarily for identifying the species of potential mates and experience little or no selection from intraspecific sexual selection or sexual antagonism. The implications of these results for speciation are discussed.     

Diversification within glacial refugia: tempo and mode of evolution of the polytypic fish Barbus sclateri

A diversity of evolutionary processes can be responsible for generating and maintaining biodiversity. Molecular markers were used to investigate the influence of Plio-Pleistocene climatic oscillations on the evolutionary history of taxa restricted to the freshwaters of a classical glacial refugium. Population genetic, phylogenetic and phylogeographical methods allowed the inference of temporal dynamics of cladogenesis and processes shaping present-day genetic constitution of Barbus sclateri , a polytypic taxon found in several independent river drainages in southern Iberian Peninsula. Results from different analyses consistently indicate several range expansions, high levels of allopatric fragmentation, and admixture following secondary contacts throughout its evolutionary history. Using a Bayesian demographical coalescent model on mitochondrial DNA sequences calibrated with fossil evidence, all cladogenetic events within B. sclateri are inferred to have occurred during the Pleistocene and were probably driven by environmental factors. Our results suggest that glaciation cycles did not inhibit cladogenesis and probably interacted with regional geomorphology to promote diversification. We conclude that this polytypic taxon is a species complex that recently diversified in allopatry, and that Pleistocene glaciation–deglaciation cycles probably contributed to the generation of biological diversity in a classical glacial refugium with high endemicity.     

Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders

A statistical analysis of complete DNA sequence data of mitochondrial genomes from human, bovine, and mouse (and partial sequence of rat) indicates that the transversion rate is lower in bovine than in human and murids, and that it is probably lower in human than in murids. However, it is unknown whether the transition rate is also lower in bovine. It is shown that the L-strand of human mitochondrial DNA has significantly higher C content and lower T and A contents than those of bovine and murids. This suggests that a directional mutation pressure which tends to change base composition has been operating in the human lineage.     

Energy and the tempo of evolution in amphibians

Aim The evolutionary speed hypothesis (ESH) attempts to explain global patterns of species richness on the basis that rates of molecular evolution and speciation in warmer climates have led to a greater accumulation of taxa at lower latitudes. A substantial alternative hypothesis to the ESH is the tropical conservatism hypothesis (TCH). However, recent tests of the TCH, using amphibians as the model taxon, have relied on the assumption that rates of molecular evolution are stable across latitudes and elevations. Here, we test for the first time for systematic variation in rates of molecular evolution across latitude and elevation among amphibians. Location The dataset is geographically diverse with samples from all continents except Antarctica and also from many of the earth's major tropical–warm temperate archipelagos. Methods We tested for substitution rate heterogeneity across climatically varying habitats with the mitochondrial RNA genes 12S and 16S. Thus, we report here on our findings for amphibians – a taxon whose phylogenetic and trophic contexts are remote from those previously tested – using genes that have also not been examined before. The study utilized paired contrasts of sister species (188 species across 18 families, including both caudates and anurans) that are spatially separated in either latitudinal or elevational dimensions. Results We found substantially faster substitution rates for species living in warmer habitats (P= 0.001–0.002) at both lower latitudes (P < 0.02) and lower elevations (P < 0.01). Main conclusions The consistency of these results with the previous studies that used quite different organisms – and in this instance also using different genes – suggests that this is a ubiquitous pattern in nature consistent with the predictions of the ESH. Recent tests of the TCH that, in estimating diversification rates, have relied on the assumption that DNA evolution occurs at a constant rate across latitudes and elevations, require reconsideration in light of the findings presented here. Our results indicate that greater caution is required when estimating dates of divergence using DNA sequence data.     

Macroevolutionary thermodynamics: Temperature and the tempo of evolution in the tropics

An influential hypothesis proposes that the tempo of evolution is faster in the tropics. Emerging evidence, including a study in this issue of PLOS Biology, challenges this view, raising new questions about the causes of Earth’s iconic latitudinal diversity gradient (LDG).

Biologists have long puzzled over the spectacular diversity of animals and plants from Earth’s tropical regions. It is true that some tropical environments are not especially rich in species, and some groups of organisms show contrarian patterns with diversity peaks that occur far outside of the warm, humid tropics. Nonetheless, the big picture is clear: A vastly disproportionate fraction of Earth’s terrestrial biodiversity is concentrated in tropical rainforests, and warm water reef environments similarly account for a large fraction of marine diversity. The extremes of tropical diversity transcend the ability of most humans to process it: Some Amazonian rainforests, for example, contain more species of trees in just a few hectares than are found in the entirety of Europe or North America [1]. In general, the most diverse tropical rainforests support order-of-magnitude increases in species richness relative to otherwise comparable temperate zone communities across a wide range of organisms. Despite decades of study, however, the causes of this latitudinal diversity gradient (LDG) remain elusive.One of the most prominent hypotheses for the LDG is, loosely speaking, the idea that biological processes speed up in the tropics, potentially due to the kinetic effects of temperature on the rates of organismal processes. It seems obvious that the pulse of life should be faster under a torrid tropical sun, and—to naturalists who’ve spent time in lowland rainforests in particular—such a view accords well with perceptions of the humid tropics as a raging, steamy mess of species interactions that collectively generate the tangled web that is tropical diversity. It is generally accepted that temperature can affect metabolic rate and many other biological processes, including those involving ecological interactions between species (e.g., competition, predation, and herbivory). The specific mechanisms connecting thermal energy to biodiversity remain unclear. For example, they might involve the influence of temperature on rates of molecular evolution, which might then influence rates of speciation [2]. Or, species in warmer environments might live closer to their optimal body temperatures, thus enabling them to allocate more resources to performance-associated functions and leading to a systematic upgrading in the intensity of antagonistic or coevolutionary interactions between species [3]. Regardless of the specific mechanism, the general idea is captured by Brown [4], who notes that “‘Diversity begets diversity’ in the tropics, because ‘the Red Queen runs faster when she is hot.’”Writing in PLOS Biology, Drury and colleagues [5] demonstrate that a central prediction of these “faster tropics” hypotheses fails to hold up. They predicted that, if certain types of ecological interactions between species are stronger in the tropics, then we should see a signal of those interactions in long-term patterns of trait evolution. In particular, the increased pressure to respond to species interactions in the tropics should result in faster overall rates of morphological evolution for tropical species. To test this hypothesis, the authors studied the rate of morphological evolution in birds, analyzing a large dataset on bill shape and body proportions from other recent studies [6] with a battery of sophisticated statistical models. These models allowed the rate of morphological change to differ systematically with latitude. Intriguingly, the models that best fit the data in some cases were those that allowed for strong interactions between species in driving patterns of divergence among closely related species that occupied that same biogeographic region (e.g., the neotropics). Thus, there is a partial signal of species interactions on the morphologies of species we see living together today, including those from both tropical and temperate regions. As suggested by the authors, these patterns might reflect a form of ecological character displacement, whereby morphologically similar species evolve differences that minimize their ecological overlap. But, surprisingly, the intensity of these effects shows no consistent relationship with latitude. The take-home message is that—at least for birds and the traits considered—species are not evolving more rapidly in the tropics.Drury and colleagues note that their results contradict recent articles that have documented differences in phenotypic evolutionary rates across latitude, although the studies referenced generally looked at different types of traits (e.g., birdsong). They suggest several potential reasons for the discrepancies between their results and those prior studies. But, critically, these earlier studies generally did not report faster evolution in the tropics, but faster evolution in the temperate zone. Hence, the results of Drury and colleagues and the earlier studies all converge to a similar and more general finding, which is that the warm tropics really aren’t so hot for macroevolution, at least as far as phenotypic evolutionary rates are concerned. By rejecting the simple explanations (faster evolution), new questions emerge about how and why tropical bird communities show such dramatic phenotypic and ecological diversity.Morphological evolution is not the only process that fails to show the expected pattern of “heating up” in the tropics. A number of recent studies have found that rates of species formation are either unrelated to latitude or slower in the tropics [7–9]. These results argue strongly against temperature kinetic models of biodiversity, whereby faster speciation emerges from the effects of warmer temperatures in the tropics on mutation and metabolic rates [10]. Many of the same causal pathways that predict increased rates of speciation as a function of temperature would also apply to rates of morphological evolution: Increased mutation rates in the tropics, for example, should accelerate the tempo of phenotypic evolution due to increased mutational variance in traits. But, regardless of whether we consider phenotypic evolution (as in Drury and colleagues) or lineage diversification, there is simply no evidence for faster evolutionary rates in the tropics.The results from Drury and colleagues [5] and other studies do not reject all possible causal pathways by which temperature or species interactions might facilitate high tropical diversity. Many phylogeny-based studies of species diversification and phenotypic evolution frame their interpretations through the lens of interspecific competition, ecological opportunity, and character displacement. Yet, numerous other types of interactions are relevant to global biodiversity patterns, and some of these interactions have scarcely been explored from a macroevolutionary perspective. Many such interactions have the potential to influence species richness and ecological diversity, perhaps through mechanisms that involve an indirect effect of temperature on equilibrium diversity levels. With more data on how host–pathogen, predator–prey, and other biotic interactions vary latitudinally, perhaps we will emerge with a greater understanding of the diverse mechanisms that contribute to the spectacular enrichment of tropical diversity.     

The shape and tempo of language evolution

There are approximately 7000 languages spoken in the world today. This diversity reflects the legacy of thousands of years of cultural evolution. How far back we can trace this history depends largely on the rate at which the different components of language evolve. Rates of lexical evolution are widely thought to impose an upper limit of 6000–10 000 years on reliably identifying language relationships. In contrast, it has been argued that certain structural elements of language are much more stable. Just as biologists use highly conserved genes to uncover the deepest branches in the tree of life, highly stable linguistic features hold the promise of identifying deep relationships between the world''s languages. Here, we present the first global network of languages based on this typological information. We evaluate the relative evolutionary rates of both typological and lexical features in the Austronesian and Indo-European language families. The first indications are that typological features evolve at similar rates to basic vocabulary but their evolution is substantially less tree-like. Our results suggest that, while rates of vocabulary change are correlated between the two language families, the rates of evolution of typological features and structural subtypes show no consistent relationship across families.     

Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest

This paper reviews how and when African rainforest diversity arose, presenting evidence from both plant and animal studies. Preliminary investigations show that these African forests are an assemblage of species of varying age. Phylogenetic evidence, from both African rainforest angiosperms and vertebrates, suggest a Tertiary origin for the major lineages in some of these groups. In groups where savannah species are well represented and rainforest species are a minority, the latter appear to be relics of a Mid-Tertiary rainforest. By contrast, species that are primarily adapted to rainforest have arisen in the past 10 Myr with the main morphological innovations dating from the Late Miocene, and Quaternary speciation dominating in large, morphologically homogeneous groups. The small number of species-level phylogenies for African rainforest plants hinders a more incisive and detailed study into the historical assembly of these continental forests.     

Latitude,elevation and the tempo of molecular evolution in mammals

Faster rates of microevolution have been recorded for plants and marine foraminifera occupying warmer low latitude environments relative to those occurring at higher latitudes. By contrast, because this rate heterogeneity has been attributed to a relationship between thermal habit and mutagenesis via a body temperature linkage, it has been assumed that microevolution in mammals should not also vary systematically with environmental temperature. However, this assumption has not previously been empirically examined. In this study, we tested for a thermally mediated influence on the tempo of microevolution among mammals using a comprehensive global dataset that included 260 mammal species, from 10 orders and 29 families. In contrast to theoretical predictions, we found that substitution rates in the cytochrome b gene have been substantially faster for species living in warmer latitudes and elevations relative to sister species living in cooler habitats. These results could not be attributed to factors otherwise thought to influence rates of microevolution, such as body mass differentials or genetic drift. Instead, the results indicate that the tempo of microevolution among mammals is either responding directly to the thermal environment or indirectly via an ecological mechanism such as the ‘Red Queen’ effect.     

The tempo of genetic evolution in birds: body mass and climate effects

Aim Negative relationships between body mass and substitution rates have previously been reported. However, most of these studies have involved contrasted taxa that, due to their highly divergent phylogenetic histories, also differ in many additional characteristics other than mass. In particular, there has been little examination of the potentially confounding effects of climate or population size. Here we test for differences in rates of microevolution among bird species that, although differing in mass, are nonetheless very closely related phylogenetic pairs. We additionally tested for latitudinal/elevational and population size effects across these contrasts. Location Global. Methods The tempo of microevolution within the cytochrome b gene of mitochondrial DNA was compared between closely related bird species that differed in body mass, using 130 phylogenetically independent species pairs. In order to minimize climate effects, pairs not having overlapping latitudinal ranges were discarded. In addition, a subset of pairs was identified and analysed that involved comparisons between species that have different latitudinal or elevational midpoints. Results Species with smaller mass had substitution rates marginally faster than those with larger mass (small : large median ratio = 1.05). However, this result was only statistically significant when data were pruned to eliminate comparisons in which population or range size also varied substantially between contrasted species. Latitude and elevation had a much stronger association with substitution rates than body mass within the subset of pairs (n = 30) that also differed in their spatial distributions: lower elevation or latitude species had substantially more substitutions than those at higher latitudes or elevations (low : high ratio = 1.35). Furthermore, when the dataset was pruned of pairs in which body mass was confounded by latitude or elevation, the body mass effect was eliminated. Main conclusions Body mass is known to correlate with latitude, so that the latitudinal/elevational association with microevolution we found might either be additive to, or causal of, the body mass effect. These results are consistent with the evolutionary speed hypothesis, which suggests that latitudinal diversity gradients derive from variation in the rate of microevolution. Our findings also serve to raise concerns about biogeographical studies that use genetic distances between taxa to estimate time since divergence.     

Tempo and mode of morphological evolution are decoupled from latitude in birds

The latitudinal diversity gradient is one of the most striking patterns in nature, yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions—namely, competition—can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.

Analyses of morphological measurements from over 9400 bird species reveal that interactions between species have impacted evolution, but fail to support the longstanding hypothesis that competition is stronger in the tropics.     

Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas

Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in genome sequencing, comparative genome analysis provides a new approach to facilitate our understanding of these bacteria. In this study, our main focus is to investigate the evolution of gene content in phytoplasmas, mycoplasmas, and their common ancestor. By using a phylogenetic framework for comparative analysis of 12 complete genome sequences, we characterized the putative gains and losses of genes in these obligate parasites. Our results demonstrated that the degradation of metabolic capacities in these bacteria has occurred predominantly in the common ancestor of Mollicutes, prior to the evolutionary split of phytoplasmas and mycoplasmas. Furthermore, we identified a list of genes that are acquired by the common ancestor of phytoplasmas and are conserved across all strains with complete genome sequences available. These genes include several putative effectors for the interactions with hosts and may be good candidates for future functional characterization.     

The tempo and modes of evolution of reproductive isolation in fungi

Reproductive isolation is an essential ingredient of speciation, and much has been learned in recent years about the evolution of reproductive isolation and the genetics of reproductive barriers in animals and plants. Fungi have been neglected on these aspects, despite being tractable model eukaryotes. Here, we used a model fitting approach to look at the importance of different barriers to gene flow to explain the decrease of reproductive compatibility with genetic distance in fungi. We found support for the occurrence of reinforcement in the presyngamy compatibility among basidiomycetes. In contrast, no evidence for reinforcement was detected in ascomycetes, concurring with the idea that host/habitat adaptation in this group can pleiotropically cause reproductive isolation. We found no evidence of a snowballing accumulation of postsyngamic reproductive incompatibilities in either ascomycetes or the complex of anther smut fungi. Together with previous studies, our results suggest that ecologically based barriers to gene flow and karyotypic differences may have an important role in hybrid inviability and sterility in fungi. Interestingly, hybrid sterility appeared to evolve faster than hybrid inviability in fungi.     

Specific evolution of F1-like ATPases in mycoplasmas

F(1)F(0) ATPases have been identified in most bacteria, including mycoplasmas which have very small genomes associated with a host-dependent lifestyle. In addition to the typical operon of eight genes encoding genuine F(1)F(0) ATPase (Type 1), we identified related clusters of seven genes in many mycoplasma species. Four of the encoded proteins have predicted structures similar to the α, β, γ and ε subunits of F(1) ATPases and could form an F(1)-like ATPase. The other three proteins display no similarity to any other known proteins. Two of these proteins are probably located in the membrane, as they have three and twelve predicted transmembrane helices. Phylogenomic studies identified two types of F(1)-like ATPase clusters, Type 2 and Type 3, characterized by a rapid evolution of sequences with the conservation of structural features. Clusters encoding Type 2 and Type 3 ATPases were assumed to originate from the Hominis group of mycoplasmas. We suggest that Type 3 ATPase clusters may spread to other phylogenetic groups by horizontal gene transfer between mycoplasmas in the same host, based on phylogeny and genomic context. Functional analyses in the ruminant pathogen Mycoplasma mycoides subsp. mycoides showed that the Type 3 cluster genes were organized into an operon. Proteomic analyses demonstrated that the seven encoded proteins were produced during growth in axenic media. Mutagenesis and complementation studies demonstrated an association of the Type 3 cluster with a major ATPase activity of membrane fractions. Thus, despite their tendency toward genome reduction, mycoplasmas have evolved and exchanged specific F(1)-like ATPases with no known equivalent in other bacteria. We propose a model, in which the F(1)-like structure is associated with a hypothetical X(0) sector located in the membrane of mycoplasma cells.