When did theropods become feathered?--evidence for pre-Archaeopteryx feathery appendages

Filamentous impressions associated with locomotive theropod tracks in the Lower Jurassic Turners Falls Formation of western Massachusetts, U.S.A. represent the oldest evidence of feathered dinosaurs. Feather impressions are preserved with sitting traces which bear integumentary structures along the outlines of the pre-pubic and ischiadic impressions. Extant palaeognathous down feathers provide a valuable comparative model for these filamentous integumental structures and for similar structures described in Chinese theropods from younger deposits. The described morphologies are congruent with Stage II of Prum ('99) and support that plumulaceous morphologies evolved before the origin of the rhachis and the planar vane. Appearance of feathery appendages in theropods may be linked to evolution of higher metabolic rates, improved locomotory abilities, and/or distinct behavior(s) and visual communication. Development of feathery integument might have also played a crucial role in the competitiveness and successful radiation of maniraptoriform theropods and their actively flying descendants in the Jurassic.     

When and where was the most recent common ancestor?

 The structured coalescent is investigated for single-locus, digenic samples in the diffusion limit of the unidimensional stepping-stone model for homogeneous, isotropic migration and random genetic drift. Let T denote the scaled time to the most recent common ancestor (MRCA) of the two genes, and let Z designate the scaled deviation of the position of the MRCA from the average position of the two genes. The joint probability density of T and Z is evaluated explicitly. Both the marginal and conditional distributions of T have infinite expectation, as does the marginal distribution of Z. Conditioned on T = τ, the distribution of Z is Gaussian with mean zero and variance 2τ. The main results are extended to anisotropic migration. The results establish the existence of and define in the diffusion limit a retrospective stochastic process for digenic samples in one spatial dimension. Received: 1 May 2001 / Revised version: 2 September 2001 / Published online: 8 February 2002     

When did the house mouse colonize Europe?

This paper is a reply to a recent proposal by Sage and co-workers giving an early date for the colonization of Europe by the house mouse, based on mitochondria! DNA nucleotide divergence estimates. The large discrepancy in time between the date given by these authors and our own is discussed in the light of available palaeontological and genetic data. This leads us to reject the hypothesis supported by Sage and co-workers, and suggest a much more recent date of colonization.     

When did plants become important to leaf‐nosed bats? Diversification of feeding habits in the family Phyllostomidae

A great proportion of bats of the New World family Phyllostomidae feed on fruit, nectar and pollen, and many of them present adaptations to feed also on insects and small vertebrates. So far, attempts to examine the diversification of feeding specialization in this group, and particularly the evolution of nectarivory and frugivory, have provided contradictory results. Here we propose a molecular phylogenetic hypothesis for phyllostomids. On the basis of a matrix of feeding habits that takes into account geographical and seasonal variation, we tested different hypotheses of the evolution of feeding specializations in the group. We find strong support for the evolutionary model of a direct dietary diversification from insectivory. The estimates of divergence times of phyllostomid bats and the reconstruction of ancestral states with a Bayesian approach support the parallel evolution of frugivory in five lineages and of nectarivory in three lineages during the Miocene. On the basis of these findings, and recent dietary studies, we propose that during the evolution of phyllostomids switches to new feeding mechanisms to access to abundant and/or underexploited resources provided selective advantages that favoured the appearance of ecological innovations independently in different lineages of the family. We did not find evidences to support or reject the hypothesis that the insectivorous most recent common ancestor of all phyllostomids was also phytophagous.     

The Nabidae (Insecta,Hemiptera, Heteroptera) of?Argentina

In Argentina, five genera and 14 species are recorded in the subfamilies Prostemmatinae and Nabinae: Hoplistoscelis sordidus Reuter, Lasiomerus constrictus Champion, Metatropiphorus alvarengai Reuter, Nabis argentinus Meyer-Dür, Nabis (Tropiconabis) capsiformis Germar, Nabis faminei Stål, Nabis paranensis Harris, Nabis punctipennis Blanchard, Nabis roripes Stål, Nabis setricus Harris, Nabis tandilensis Berg, Pagasa (Pagasa) costalis Reuter, Pagasa (Lampropagasa) fuscipennis Reuter and Pagasa (Pagasa) signatipennis Reuter.     

When did the human population size start increasing?

We analyze the frequency spectra of all available human nuclear sequence data sets by using a model of constant population size followed by exponential growth. Parameters of growth (more extreme than or) comparable to what has been suggested from mtDNA data can be rejected for 6 out of the 10 largest data sets. When the data are separated into African and non-African samples, a constant size no-growth model can be rejected for 4 out of 8 non-African samples. Long-term growth (i.e., starting 50-100 kya) can be rejected for 2 out of 8 African samples and 5 out of 8 non-African ones. Under more complex demographic models, including a bottleneck or population subdivision, more of the data are compatible with long-term growth. One problem with the data used here is that a subset of loci may reflect the action of natural selection as well as of demography. It remains possible that the correct demographic model is one of constant population size followed by long-term growth but that at several loci the demographic signature has been obscured by balancing or diversifying selection. However, it is not clear that the data at these loci are consistent with a simple model of balancing selection; more complicated selective alternatives cannot be tested unless they are made explicit. An alternative explanation is that population size growth is more recent (e.g., upper Paleolithic) and that some of the loci have experienced recent directional selection. Given the available data, the latter hypothesis seems more likely.     

Is an archaeon the ancestor of eukaryotes?

The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.     

Are semi-aquatic bugs (Heteroptera: Nepomorpha) indicators of hydrological stability of permanent ponds?

The composition of semi-aquatic bug communities from eight permanent ponds from southern Transylvania was investigated between 2001 and 2004. Three of the ponds were sampled repeatedly throughout the active period of the year, while the other five were sampled only once. Microvelia reticulata (Burmeister, 1835) and Gerris argentatus Schummel, 1832 were the dominant species from the thoroughly investigated habitats. Statistical analysis proved that each of the sampled species has specific habitat preferences in relation to the modifications of the hydrological regime of the ponds (reflected by the modifications of open water areas, station sizes, and percentages of vegetation coverage). The results, obtained from the three habitats investigated throughout the active period, were confirmed by the samples taken from the other five habitats opening the discussion about the use of semi-aquatic bug communities as bioindicators of the hydrological regime for permanent ponds.     

When did oxygenic photosynthesis evolve?

The atmosphere has apparently been oxygenated since the 'Great Oxidation Event' ca 2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in ca 2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as ca 2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at ca 3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U-Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.     

How did Death become a Saint in Mexico?

Over the last decade, the cult of La Santa Muerte (St Death) has attracted a remarkable number of followers in Mexico and the USA. Whereas the social context of her devotees, who tend to live on the fringes of society, has attracted ample attention from scholars and journalists, one of the principal puzzles is still how a skeleton image of death has come to be seen as a saint by large numbers of Catholics. How is it possible for this figure to embrace such antagonistic qualities as death and sainthood in a Christian context? In this semiotic-material exploration of the image's genealogy, I suggest that La Santa Muerte should be seen as a coalescing of two radically distinct images of death: the popular-secular Catrina and the occult-biblical Santísima Muerte. The St Death venerated today encompasses the ambiguities of the two and creates an exceptionally vibrant and popular Catholic image.     

Does the 'Ring of Life' ring true?

In a recent stimulating paper, Rivera and Lake applied a new phylogenetic method to study the evolution of genomes, which challenges the classical representation of the Tree of Life. Acknowledging the evolutionary importance of lateral gene transfer, they used the conditioned genome approach to reconstruct the Tree of Life, and in the end proposed a Ring of Life. They explained that the Ring of Life structure is a result of a single fusion event between two prokaryotic genomes at the base of the eukaryotic tree, probably between the ancestors of a photosynthetic bacterium and an archaeon. Because this constitutes an important conclusion with regards to the evolutionary process and origin of the eukaryotic cell, their work deserves further attention before these conclusions can be accepted. Here we question the reconstruction and the meaning of the Ring of Life. In addition to general problems associated with gene-content-based phylogenetic analyses, we discuss some implicit premises and potential weaknesses of the conditioned genome method and conclude that, although Rivera and Lake's conclusions might be right, they have not been established by their current approach.     

How much does the amphioxus genome represent the ancestor of chordates?

One of the main motivations to study amphioxus is its potential for understanding the last common ancestor of chordates, which notably gave rise to the vertebrates. An important feature in this respect is the slow evolutionary rate that seems to have characterized the cephalochordate lineage, making amphioxus an interesting proxy for the chordate ancestor, as well as a key lineage to include in comparative studies. Whereas slow evolution was first noticed at the phenotypic level, it has also been described at the genomic level. Here, we examine whether the amphioxus genome is indeed a good proxy for the genome of the chordate ancestor, with a focus on protein-coding genes. We investigate genome features, such as synteny, gene duplication and gene loss, and contrast the amphioxus genome with those of other deuterostomes that are used in comparative studies, such as Ciona, Oikopleura and urchin.     

When do objects become landmarks? A VR study of the effect of task relevance on spatial memory

We investigated how objects come to serve as landmarks in spatial memory, and more specifically how they form part of an allocentric cognitive map. Participants performing a virtual driving task incidentally learned the layout of a virtual town and locations of objects in that town. They were subsequently tested on their spatial and recognition memory for the objects. To assess whether the objects were encoded allocentrically we examined pointing consistency across tested viewpoints. In three experiments, we found that spatial memory for objects at navigationally relevant locations was more consistent across tested viewpoints, particularly when participants had more limited experience of the environment. When participants' attention was focused on the appearance of objects, the navigational relevance effect was eliminated, whereas when their attention was focused on objects' locations, this effect was enhanced, supporting the hypothesis that when objects are processed in the service of navigation, rather than merely being viewed as objects, they engage qualitatively distinct attentional systems and are incorporated into an allocentric spatial representation. The results are consistent with evidence from the neuroimaging literature that when objects are relevant to navigation, they not only engage the ventral "object processing stream", but also the dorsal stream and medial temporal lobe memory system classically associated with allocentric spatial memory.     

How did Saccharomyces evolve to become a good brewer?

Brewing and wine production are among the oldest technologies and their products are almost indispensable in our lives. The central biological agents of beer and wine fermentation are yeasts belonging to the genus Saccharomyces, which can accumulate ethanol. Recent advances in comparative genomics and bioinformatics have made it possible to elucidate when and why yeasts produce ethanol in high concentrations, and how this remarkable trait originated and developed during their evolutionary history. Two research groups have shed light on the origin of the genes encoding alcohol dehydrogenase and the process of ethanol accumulation in Saccharomyces cerevisiae.     

When does Intraspecific C-value Variation become Taxonomically Significant?

AIMS: To examine what possible role intraspecific DNA C-value variation may play in plant taxonomy. SCOPE: Although many of the original examples of intraspecific C-value variation have been shown to be the result of experimental variation, new examples using the appropriate standards and controls continue to be published. The evidence that intraspecific C-value variation alters phenotypes can be equivocal, and detailed studies are needed to clarify any possible relationship. However, populations within species have been shown to have varying DNA amounts that can be correlated with eco-geographic variables, suggesting that the variation is adaptive and that these may be examples of incipient speciation. CONCLUSIONS: Where intraspecific C-value variation appears most significant for taxonomy is as an indicator of taxonomic heterogeneity, pointing to the need for a re-evaluation of the delimitation of the species in question. There is also the need to test whether intraspecific C-value variants produce fertile F(1) hybrids or not, as this would be a good indication of whether they belong in the same biological species.     

Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera,?Pentatomidae)

The sequences of 18S and 28S rDNAs have been used as molecular markers to resolve phylogenetic relationships of Heteroptera for two decades. The complete sequences of 18S rDNAs have been used in many studies, while in most studies only partial sequences of 28S rDNAs have been used due to technical difficulties of amplifying the complete lengths. In this study, we amplified the complete 18S and 28S rDNA sequences of Eurydema maracandica Oshanin, 1871, and reconstructed the secondary structure models of the corresponding rRNAs. In addition, and more importantly, all of the length variable regions of 18S rRNA were compared among 37 families of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was compared among 51 families based on 84 sequences. It was found that 8 length variable regions could potentially serve as molecular synapomorphies for some monophyletic groups. Therefore discoveries of more molecular synapomorphies for specific clades can be anticipated from amplification of complete 18S and 28S rDNAs of more representatives of Heteroptera.     

How old is the most recent ancestor of two copies of an allele?

An important clue to the evolutionary history of an allele is the structure of the neighboring region of the genome, which we term the genomic background of the allele. Consider two copies of the allele. How similar we expect their genomic background to be is strongly influenced by the age of their most recent common ancestor (MRCA). We apply diffusion theory, first used by Motoo Kimura as a tool for predicting the changes in allele frequencies over time and developed by him in many articles in this journal, to prove a variety of new results on the age of the MRCA under the simplest demographic assumptions. In particular, we show that the expected age of the MRCA of two copies of an allele with population frequency f is just 2Nf generations, where N is the effective population size. Our results are a first step in running exact coalescent simulations, where we also simulate the history of the population frequency of an allele.     

Parallels between the proximal–distal development of vertebrate and arthropod appendages: homology without an ancestor?

Evolutionary studies suggest that the limbs of vertebrates and the appendages of arthropods do not share a common origin. However, recent genetic studies show new similarities in their developmental programmes. These similarities might be caused by the independent recruitment of homologous genes for similar functions or by the conservation of an ancestral proximal-distal development programme. This basic programme might have arisen in an ancestral outgrowth and been independently co-opted in vertebrate and arthropod appendages. It has subsequently diverged in both phyla to fine-pattern the limb and to control phylum-specific cellular events. We suggest that although vertebrate limbs and arthropod appendages are not strictly homologous structures they retain remnants of a common ancestral developmental programme.