Environmental energy and evolutionary rates in flowering plants

The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.     

Interactions between evolutionary processes at high mutation rates

Evolution at high mutation rates is minimally affected by six processes: mutation-selection balance, error catastrophes, Muller's Ratchet, robustness and compensatory evolution, and clonal interference. Including all of these processes in a tractable, analytical model is difficult, but they can be captured in simulations that utilize realistic genotype-phenotype-fitness maps, as done here by modeling RNA folding. Subjecting finite, asexual populations to a range of mutation rates revealed simple criteria that predict when particular evolutionary processes are important. Populations were initiated with a genotype encoding the most fit phenotype. When purifying selection was strong relative to mutation, the initial genotype was replaced by one more mutationally robust, and the maximally fit phenotype was maintained in a mutation-selection balance where the deleterious mutation rate determined mean fitness. With weaker purifying selection, the most fit genotypes were lost. Although loss of the best genotype was ongoing and might have led to a progressive fitness decline, continual compensatory evolution led to an approximate fitness equilibration. Per total genomic mutation rate, mean fitness was similar for strong and weak purifying selection. These results represent a first step at separating interactions between evolutionary processes at high mutation rate, but additional theory is needed to interpret some outcomes.     

Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern affecting shell albedo in the majority of populations within its native range in Europe. We tested for evolutionary changes in shell albedo that might have been driven by the warming of the climate in Europe over the last half century by compiling an historical dataset for 6,515 native populations of C. nemoralis and comparing this with new data on nearly 3,000 populations. The new data were sampled mainly in 2009 through the Evolution MegaLab, a citizen science project that engaged thousands of volunteers in 15 countries throughout Europe in the biggest such exercise ever undertaken. A known geographic cline in the frequency of the colour phenotype with the highest albedo (yellow) was shown to have persisted and a difference in colour frequency between woodland and more open habitats was confirmed, but there was no general increase in the frequency of yellow shells. This may have been because snails adapted to a warming climate through behavioural thermoregulation. By contrast, we detected an unexpected decrease in the frequency of Unbanded shells and an increase in the Mid-banded morph. Neither of these evolutionary changes appears to be a direct response to climate change, indicating that the influence of other selective agents, possibly related to changing predation pressure and habitat change with effects on micro-climate.     

Small variance in growth rates in annual plants has large effects on genetic drift

? Premise of the Study: Effective population size (N(e)) is a critical index of the evolutionary capacity of populations. Low N(e) indicates that standing genetic diversity is susceptible to loss via stochastic processes (and inbreeding) and is, therefore, unavailable for natural selection to act upon. Reported N(e) in plant populations is often quite low. What biological and ecological factors might produce such low N(e) ? Methods: We conducted a simulation model to test the effect of randomly assigned and autocorrelated growth rates of annual plants on plant-size distributions at the end of the growing season. Because plant size is directly correlated with reproductive output in annual plants, variation in plant size reflects variation in reproduction, and thus our modeled size distributions can be used to estimate N(e). ? Key Results: Randomly assigned growth rates had a negligble effect on N(e)/N. Autocorrelated growth rates decreased N(e)/N as the length of the growing season increased. This was the case even when the variance in growth rates was as low as 0.1% of the mean. ? Conclusions: While intrinsic plant biology can affect the degree of growth autocorrelation, ecological factors such as competition, herbivory, and abiotic stress can increase or decrease levels of growth autocorrelation. Ecological factors that increase growth autocorrelation can have significant effects on genetic drift within populations.     

Heavy metal tolerance in plants: A model evolutionary system

Evolved tolerance to toxic concentrations of heavy metals in plants inhabiting spoil heaps of mines is a well known phenomenon that has been the subject of much research in the last two decades. These plants are useful models for studying processes involved in the early stages of the speciation of edaphic endemics. Recent work has revealed the importance of several phenomena in the differentiation of tolerant populations, including natural selection, founder effects and ‘hitch-hiking’, and has demonstrated the early evolution of morphological differentiation and reproductive isolating mechanisms. Further studies of the biochemistry and molecular biology of heavy metal tolerance will help to show why some plant groups, such as Agrostis, are far more prone to evolve tolerance than others.     

Reconstruction of historical pollination rates reveals linked declines of pollinators and plants

Widespread reports of low pollination rates suggest a recent anthropogenic decline in pollination that could threaten natural and agricultural ecosystems. Nevertheless, unequivocal evidence for a decline in pollination over time has remained elusive because it was not possible to determine historical pollination rates. Here we demonstrate a widely applicable method for reconstructing historical pollination rates, thus allowing comparison with contemporary rates from the same sites. We focused on the relationship between the oil‐collecting bee Rediviva peringueyi (Melittidae) and the guild of oil‐secreting orchid species (Coryciinae) that depends on it for pollination. The guild is distributed across the highly transformed and fragmented lowlands of the Cape Region of South Africa. We show that rehydrated herbarium specimens of Pterygodium catholicum, the most abundant member of the guild, contain a record of past pollinator activity in the form of pollinarium removal rates. Analysis of a pollination time series showed a recent decline in pollination on Signal Hill, a small urban conservation area. The same herbaria contain historical species occurrence data. We analyzed this data and found that there has been a contemporaneous shift in orchid guild composition in urban areas due to the local extirpation of the non‐clonal species, consistent with their greater dependence on seeds and pollination for population persistence.     

An evolutionary approach reveals a high protein-coding capacity of the human genome

We developed a new evolutionary method for identifying exons from genomic sequences and found 19000 potential coding exons that are absent from all existing annotations of the human genome. Of these, 13700 satisfied very stringent criteria and can with confidence be considered as novel exons. Evidently, a large number of new human genes can be identified using evolutionary approaches.     

Cloning of the human activin receptor cDNA reveals high evolutionary conservation.

The entire coding region of the human activin receptor was obtained from a human testis cDNA library. Analysis of the 1539 nucleotide (513 amino acid) sequence of the receptor reveals that there are only 83 nucleotide differences compared to the coding sequence of the mouse activin receptor. Similar to its ligands, the amino acid sequence of the activin receptor is highly conserved with only two conservative amino acid differences (Lys-39 and Val-92 in human versus Arg-39 and Ile-92 in the mouse). This high degree of conservation of the activin receptor illustrates a strong evolutionary selection and confirms that activin and its receptor play an important role in development.     

A population dynamics model for annual plants subject to inbreeding depression

Summary We present a population dynamics model for annual plants subject to density dependent competition and a decline in mean individual fitness with inbreeding. An analysis of this model provides three distinct sets of parameter values that define the relative influence of inbreeding depression and density on population growth. First, a population with a relatively high finite rate of increase and a relatively small environmental carrying capacity can persist in spite of low levels of inbreeding depression. These types of population may occur during a bottleneck event that is caused by pure predation (or collecting) pressure rather than loss of habitat. Second, there can exist a minimum viable population size when the finite rate of increase is relatively low and the population is also affected by density: the growth or decline of the population will depend on the initial population size. Third, when the population is small enough to be simultaneously effected by density and by inbreeding depression, there can be no viable population.     

Genome-wide evolutionary response to a heat wave in Drosophila

Extreme climatic events can substantially affect organismal performance and Darwinian fitness. In April 2011, a strong heat wave struck extensive geographical areas of the world, including Western Europe. At that time, we happened to resume and extend a long-term time series of seasonal genetic data in the widespread fly Drosophila subobscura, which provided a unique opportunity to quantify the intensity of the genetic perturbation caused by the heat wave. We show that the spring 2011 genetic constitution of the populations transiently shifted to summer-like frequencies, and that the magnitude of the genetic anomaly quantitatively matched the temperature anomaly. The results provide compelling evidence that direct effects of rising temperature are driving adaptive evolutionary shifts, and also suggest a strong genetic resilience in this species.     

Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species

Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co‐occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next‐generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein‐encoding genes, with the Complex IV genes (coxI‐III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.     

Photosynthetic characterization of flavodoxin-expressing tobacco plants reveals a high light acclimation-like phenotype

Flavodoxins are electron carrier flavoproteins present in bacteria and photosynthetic microorganisms which duplicate the functional properties of iron-sulphur containing ferredoxins and replace them under adverse environmental situations that lead to ferredoxin decline. When expressed in plant chloroplasts, flavodoxin complemented ferredoxin deficiency and improved tolerance to multiple sources of biotic, abiotic and xenobiotic stress. Analysis of flavodoxin-expressing plants grown under normal conditions, in which the two carriers are present, revealed phenotypic effects unrelated to ferredoxin replacement. Flavodoxin thus provided a tool to alter the chloroplast redox poise in a customized way and to investigate its consequences on plant physiology and development. We describe herein the effects exerted by the flavoprotein on the function of the photosynthetic machinery. Pigment analysis revealed significant increases in chlorophyll a, carotenoids and chlorophyll a/b ratio in flavodoxin-expressing tobacco lines. Results suggest smaller antenna size in these plants, supported by lower relative contents of light-harvesting complex proteins. Chlorophyll a fluorescence and P700 spectroscopy measurements indicated that transgenic plants displayed higher quantum yields for both photosystems, a more oxidized plastoquinone pool under steady-state conditions and faster plastoquinone dark oxidation after a pulse of saturating light. Many of these effects resemble the phenotypes exhibited by leaves adapted to high irradiation, a most common environmental hardship faced by plants growing in the field. The results suggest that flavodoxin-expressing plants would be better prepared to cope with this adverse situation, and concur with earlier observations reporting that hundreds of stress-responsive genes were induced in the absence of stress in these lines.     

DNA evolutionary rates in nine-primaried passerine birds

Differences in single-copy nuclear-DNA sequences among 13 species of passerine birds were measured using DNA-DNA hybridization. A matrix of pairwise dissimilarity values (delta mode distances) was constructed from analysis of fitted thermal dissociation curves. A least-squares method of phylogenetic estimation was used to construct two topologies from the distance matrix, one constraining branch lengths of sister taxa to be equal and the other permitting such lengths to vary. These topologies were identical in the pattern of branching of taxa, and the difference in their sums of squares was not statistically significant, suggesting that rates of DNA evolution in sister groups of nine- primaried oscines are equal. A nonparametric test for nonrandom variation in distances of sister groups to outgroup taxa revealed no statistically significant deviation from random variation that would be expected as a result of measurement error. However, the level of measurement error was such that rates of DNA evolution in sister taxa could vary by as much as 10% without being detected with the statistical methods used here.