Molecular dating, evolutionary rates, and the age of the grasses.

Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a data set of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae ∼51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups.

Constraints on Miocene oceanography and climate in the Western and Central Paratethys: O-, Sr-, and Nd-isotope compositions of marine fish and mammal remains

The Paratethys evolved as a marginal sea during the Alpine-Himalayan orogeny in the Oligo-Miocene. Sediments from the northern Alpine Molasse Basin, the Vienna, and the Pannonian Basins located in the western and central part of the Paratethys thus provide unique information on regional changes in climate and oceanography during a period of active Alpine uplift Oxygen isotope compositions of well-preserved phosphatic fossils recovered from the sediments support deposition under sub-tropical to warm-temperate climate with water temperatures of 14 to 28 degrees C for the Miocene. delta(18)O values of fossil shark teeth are similar to those reported for other Miocene marine sections and, using the best available estimates of their biostratigraphic age, show a variation until the end of the Badenian similar to that reported for composite global record. The (87)Sr/(86)Sr isotope ratios of the fossils follow the global Miocene seawater trend, albeit with a much larger scatter. The deviations of (87)Sr/(86)Sr in the samples from the well-constrained seawater curve are interpreted as due to local input of terrestrially-derived Sr. Contribution of local sources is also reflected in the epsilon(Nd) values, consistent with input from ancient crystalline rocks (e.g., Bohemian Massif and/or Mesozoic sediments with epsilon(Nd) < -9. On the other hand, there is evidence for input from areas with Neogene volcanism as suggested by samples with elevated epsilon(Nd) values >-7. Excluding samples showing local influence on the water column, an average epsilon(Nd) value of -7.9 +/- 0.5 may be inferred for the Miocene Paratethys. This value is indistinguishable from the epsilon(Nd) value of the contemporaneous Indian Ocean, supporting a dominant role of this ocean in the Western and Central Paratethys. (C) 2008 Elsevier B.V. All rights reserved.

Evolutionary footprint of coevolving positions in genes.

MOTIVATION: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson-Crick constraint, are usually considered a priori in current measures of coevolution. RESULTS: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of 'independent' evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution.

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA.

We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.

Comment on 'The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway'

Letter to the Editor on Wang M, Wang Q, Wang Z, Zhang X, Pan Y. The molecular evolutionary patterns of the insulin/FOXO signaling pathway

Tectonomagmatic evolution of Western Amazonia: Geochemical characterization and zircon U-Pb geochronologic constraints from the Peruvian Eastern Cordilleran granitoids

The results of a coupled, in situ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) U-Pb study on zircon and geochemical characterization of the Eastern Cordilleran intrusives of Peru reveal 1.15 Ga of intermittent magmatism along central Western Amazonia, the Earth's oldest active open continental margin. The eastern Peruvian batholiths are volumetrically dominated by plutonism related to the assembly and breakup of Pangea during the Paleozoic-Mesozoic transition. A Carboniferous-Permian (340-285 Ma) continental arc is identified along the regional orogenic strike from the Ecuadorian border (6 degrees S) to the inferred inboard extension of the Arequipa-Antofalla terrane in southern Peru (14 degrees S). Widespread crustal extension and thinning, which affected western Gondwana throughout the Permian and Triassic resulted in the intrusion of the late- to post-tectonic La Merced-San Ramon-type anatectites dated between 275 and 220 Ma, while the emplacement of the southern Cordillera de Carabaya peraluminous granitoids in the Late Triassic to Early Jurassic (220-190 Ma) represents, temporally and regionally, a separate tectonomagmatic event likely related to resuturing of the Arequipa-Antofalla block. Volcano-plutonic complexes and stocks associated with the onset of the present Andean cycle define a compositionally bimodal alkaline suite and cluster between 180 and 170 Ma. A volumetrically minor intrusive pulse of Oligocene age (ca. 30 Ma) is detected near the southwestern Cordilleran border with the Altiplano. Both post-Gondwanide (30-170 Ma), and Precambrian plutonism (691-1123 Ma) are restricted to isolated occurrences spatially comprising less than 15% of the Eastern Cordillera intrusives. Only one remnant of a Late Ordovician intrusive belt is recognized in the Cuzco batholith (446.5 +/- 9.7 Ma) indicating that the Famatinian arc system previously identified in Peru along the north-central Eastern Cordillera and the coastal Arequipa-Antofalla terrane also existed inboard of this parautochthonous crustal fragment. Hitherto unknown occurrences of late Mesoproterozoic and middle Neoproterozoic granitoids from the south-central cordilleran segment define magmatic events at 691 +/- 13 Ma, 751 +/- 8 Ma, 985 +/- 14 Ma, and 1071-1123 +/- 23 Ma that are broadly coeval with the Braziliano and Grenville-Sunsas orogenies, respectively. Our data suggest the existence of a continuous orogenic belt in excess of 3500 km along Western Amazonia during the formation of Rodinia, its ``early'' fragmentation prior to 690 Ma, and support a model of reaccretion of the Paracas-Arequipa-Antofalla terrane to western Gondwana in the Early Ordovician with subsequent detachment of the Paracas segment in form of the Mexican Oaxaquia microcontinent in Middle Ordovician. A tectonomagmatic model involving slab detachment, followed by underplating of cratonic margin by asthenospheric mantle is proposed for the genesis of the volumetrically dominant Late Paleozoic to early Mesozoic Peruvian Cordilleran batholiths.

Stable isotope (C, O, S) systematics of the mercury mineralization at Idrija, Slovenia: constraints on fluid source and alteration processes

The world-class Idrija mercury deposit (western Slovenia) is hosted by highly deformed Permocarboniferous to Middle Triassic sedimentary rocks within a complex tectonic structure at the transition between the External Dinarides and the Southern Alps. Concordant and discordant mineralization formed concomitant with Middle Triassic bimodal volcanism in an aborted rift. A multiple isotopic (C, O, S) investigation of host rocks and ore minerals was performed to put constraints on the source and composition of the fluid, and the hydrothermal alteration. The distributions of the delta(13)C and delta(18)O values of host and gangue carbonates are indicative of a fracture-controlled hydrothermal system, with locally high fluid-rock ratios. Quantitative modeling of the delta(13)C and delta(18)O covariation for host carbonates during temperature dependent fluid-rock interaction, and concomitant precipitation of void-filling dolomites points to a slightly acidic hydrothermal fluid (delta(13)Capproximate to-4parts per thousand and delta(18)Oapproximate to+10parts per thousand), which most likely evolved during isotopic exchange with carbonates under low fluid/rock ratios. The delta(34)S values of hydrothermal and sedimentary sulfur minerals were used to re-evaluate the previously proposed magmatic and evaporitic sulfur sources for the mineralization, and to assess the importance of other possible sulfur sources such as the contemporaneous seawater sulfate, sedimentary pyrite, and organic sulfur compounds. The delta(34)S values of the sulfides show a large variation at deposit down to hand-specimen scale. They range for cinnabar and pyrite from -19.1 to +22.8parts per thousand, and from -22.4 to +59.6parts per thousand, respectively, suggesting mixing of sulfur from different sources. The peak of delta(34)S values of cinnabar and pyrite close to 0parts per thousand is compatible with ore sulfur derived dominantly from a magmatic fluid and/or from hydrothermal leaching of basement rocks. The similar stratigraphic trends of the delta(34)S values of both cinnabar and pyrite suggest a minor contribution of sedimentary sulfur (pyrite and organic sulfur) to the ore formation. Some of the positive delta(34)S values are probably derived from thermochemical reduction of evaporitic and contemporaneous seawater sulfates.

Developmental constraints on vertebrate genome evolution.

Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates: zebrafish, using a microarray experiment spanning 14 stages of development, and mouse, using EST counts for 26 stages of development. We show that, in both species, genes expressed early in development (1) have a more dramatic effect of knock-out or mutation and (2) are more likely to revert to single copy after whole genome duplication, relative to genes expressed late. This supports high constraints on early stages of vertebrate development, making them less open to innovations (gene gain or gene loss). Results are robust to different sources of data -- gene expression from microarrays, ESTs, or in situ hybridizations; and mutants from directed KO, transgenic insertions, point mutations, or morpholinos. We determine the pattern of these constraints, which differs from the model used to describe vertebrate morphological conservation ("hourglass" model). While morphological constraints reach a maximum at mid-development (the "phylotypic" stage), genomic constraints appear to decrease in a monotonous manner over developmental time.

Prepupal Building Behavior in Drosophila melanogaster and Its Evolution under Resource and Time Constraints.

Structures built by animals are a widespread and ecologically important 'extended phenotype'. While its taxonomic diversity has been well described, factors affecting short-term evolution of building behavior within a species have received little experimental attention. Here we describe how, given the opportunity, wandering Drosophila melanogaster larvae often build long tunnels in agar substrates and embed their pupae within them. These embedded larvae are characterized by a longer egg-to-pupariation developmental time than larvae that pupate on the surface. Assuming that such building behaviors are likely to be energetically costly and/or time consuming, we hypothesized that they should evolve to be less pronounced under resource or time limitation. In accord with this prediction, larvae from populations evolved for 160 generations under a regime that combines larval malnutrition with limited developmental time dug shorter tunnels than larvae from control unselected populations. However, the proportion of larvae that embedded before pupation did not differ between the malnutrition-adapted and control populations, suggesting that tunnel length and likelihood of embedding before pupation are controlled by different genetic loci. The behaviors exhibited by wandering larvae of Drosophila melanogaster prior to pupation offer a model system to study evolution of animal building behaviors because the tunneling and embedding phenotypes are simple, facultative and highly variable.

Avian Evolutionary Genomics: Studies of Ficedula Flycatchers

In this thesis, different genetic tools are used to investigate both natural variation and speciation in the Ficedula flycatcher system: pied (Ficedula hypoleuca) and collared (F. albicollis) flycatchers. The molecular evolution of a gene involved in postnatal body growth, GH, has shown high degree of conservation at the mature protein between birds and mammals, whereas the variation observed in its signal peptide seems to be adaptive in pied flycatcher (I & II). Speciation is the process by which reproductive barriers to gene flow evolve between populations, and understanding the mechanisms involved in pre- and post-zygotic isolation have been investigated in Ficedula flycatchers. The Z chromosome have been suggested to be the hotspot for genes involved in speciation, thus sequencing of 13 Z-linked coding genes from the two species in allopatry and sympatry have been conducted (III). Surprisingly, the majority of Z-linked genes seemed to be highly conserved, suggesting instead a potential involvement of regulatory regions. Previous studies have shown that genes involved in hybrid fitness, female preferences and male plumage colouration are sex-linked. Hence, three pigmentation genes have been investigated: MC1R, AGRP, and TYRP1. Of these three genes, TYRP1 was identified as a strong candidate to be associated with black-brown plumage variation in sympatric populations, and hence is a strong candidate for a gene contributing to pre-zygotic isolation (IV). In sympatric areas, where pied and collared flycatchers have overlapping breeding areas, hybridization sometimes occurs leading to the production of unfit hybrids. By using a proteomic approach a novel expression pattern in hybrids was revealed compared to the parental species (V) and differentially expressed proteins subsequently identified by sequence similarity (VI). In conclusion, the Z chromosome appears to play an important role in flycatcher speciation, but probably not at the coding level. In addition the novel expression patterns might give new insights into the maladaptive hybrids.

Positive time-frequency distributions based on joint marginal constraints

This correspondence studies the formulation of members ofthe Cohen-Posch class of positive time-frequency energy distributions.Minimization of cross-entropy measures with respect to different priorsand the case of no prior or maximum entropy were considered. It isconcluded that, in general, the information provided by the classicalmarginal constraints is very limited, and thus, the final distributionheavily depends on the prior distribution. To overcome this limitation,joint time and frequency marginals are derived based on a "directioninvariance" criterion on the time-frequency plane that are directly relatedto the fractional Fourier transform.

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.