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This paper considers vibronic population inversion in the presence of molecular rotation. The objective is to invert the population of a vibronic level with populated rotational levels to a specific vibrational level in the excited electronic state regardless of the detailed population distribution in the final rotational levels. The control of the multilevel population inversion is achieved by design of a pump pulse through optimal control theory. The total energy fluence and the pulse peak intensity are imposed as physical constraints in the design cost functional. A model diatomic molecule is used as an example to investigate molecular rotational effects on the vibronic population inversion and the control properties at different target times. The numerical results indicate that the shape-optimized pulses can achieve nearly complete population inversion and largely overcome the difficulty that a rectangular pulse faces due to energy mismatches and multiple dipole transition moments. [ABSTRACT FROM AUTHOR]

The molecular population structure of eight benthic Foraminifera with the same or similar morphotypes in shallow waters of West Antarctica and southern Patagonia was analyzed based on the SSU rDNA. The data suggest recent gene flow across the Drake Passage for the foraminiferal species Pullenia subcarinata as well as for a molecular operational taxonomic unit (MOTU) of Micrometula but not for the remaining majority of taxa/MOTUs. The molecular population structures of different taxa shown by haplotype networks is highly variable, indicating different dispersal histories. Antarctic species/MOTUs show star-like topologies reflecting post-glacial demographic and/or spatial expansion from limited refugia on the Antarctic continental shelf. Some Patagonian species/MOTUs show reticulate topologies suggesting more steady and prolonged evolution, while others show star-like topologies that could reflect impact of South American glaciations. The time-calibrated Bayesian phylogenetic reconstruction suggests that the isolation between Antarctic and Patagonian species/MOTUs post-dates the Eocene/Oligocene boundary. Large differences in divergence times between the examined Foraminifera support the hypothesis that separation of ecosystems on the opposite sides of the Drake Passage was a gradual process that started >30 Ma. It seems that the shallow-water monothalamids were the first to be impacted. Among the calcareous forms, the majority of the divergence ages were at 15 Ma or younger, suggesting that the mid-Miocene was the most important period concerning the separation between Antarctic and Patagonian shallow-water benthic biota. [ABSTRACT FROM AUTHOR]

The question of how new species evolve has been examined at every level, from macroevolutionary patterns of diversification to molecular population genetic analyses of specific genomic regions between species pairs. Drosophila has been at the center of many of these research efforts. Though our understanding of the speciation process has grown considerably over the past few decades, very few genes have been identified that contribute to barriers to reproduction. The development of advanced molecular genetic and genomic methods provides promising avenues for the rapid discovery of more genes that contribute to speciation, particularly those involving prezygotic isolation. The continued expansion of tools and resources, especially for species other than Drosophila melanogaster, will be most effective when coupled with comparative approaches that reveal the genetic basis of reproductive isolation across a range of divergence times. Future research programs in Drosophila have high potential to answer long-standing questions in speciation. These include identifying the selective forces that contribute to divergence between populations and the genetic basis of traits that cause reproductive isolation. The latter can be expanded upon to understand how the genetic basis of reproductive isolation changes over time and whether certain pathways and genes are more commonly involved. [ABSTRACT FROM AUTHOR]

The Sympetrum vulgatum (Linnaeus, 1758) complex is composed of the subspecies S. vulgatum vulgatum, S. vulgatum decoloratum (Selys, 1884) and S. vulgatum ibericum Ocharan, 1985 in the West Palaearctic. These taxa have parapatric distributions and noticeable morphological differences in colour and body size, and their taxonomic status is debated. Here we revise the systematics of this group using molecular taxonomy, including molecular analyses of mitochondrial (cytochrome c oxidase subunit I, COI) and nuclear (internal transcribed spacer, ITS1) DNA taking into account known morphological differences. Each subspecies has a unique and differentiated COI haplotype, although divergences among them are low (0.4% maximum uncorrected p-distance). The subspecies are not differentiated by the nuclear marker ITS1. The genetic results for these taxa contrast with the deep divergence of the sister species S. striolatum (Charpentier, 1840). Given current evidence, we propose to maintain the subspecifi c status of the S. vulgatum complex and hypothesize their biogeographical history. It is likely that the three subspecies became isolated during one of the latest glacial periods, each in a different refugium: S. vulgatum ibericum possibly occupied the Iberian Peninsula, S. vulgatum vulgatum the Balkan Peninsula or territories further east and S. vulgatum decoloratum Anatolia. [ABSTRACT FROM AUTHOR]

Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt ( Pleurodeles waltl ), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot. [ABSTRACT FROM AUTHOR]

Populus euphratica Oliv. is a poplar species that is distributed mainly in deserts, making it an interesting model in which to investigate molecular mechanisms underlying different stress responses. Here, we used molecular population genetic methods to detect potential selection in candidate genes belonging to the P. euphratica glutathione (GSH) peroxidase ( Gpx) family, which are associated with an enzymatic mechanism that combats oxidative damage caused by reactive oxygen species (ROS) in plant cells; earlier studies have shown that Gpx proteins play important roles in coping with increased ROS levels during biotic and abiotic stresses in plants. We analyzed the nucleotide diversity and divergence patterns of five loci encoding Gpx genes, and 16 reference loci used as controls, in order to detect departures from the neutral expectation. Gpx1 has an excess of mid-frequency alleles; high intraspecific nucleotide diversity, distributed in the upper tail of the simulated neutral model; and extensive LD, showing strong evidence of balancing selection/local adaptation. The Gpx3.2 gene exhibits very low nucleotide diversity and divergence, suggesting that it has evolved under strong purifying selection. We failed to detect any evidence for natural selection at the other loci ( Gpx2, Gpx4, and Gpx5) compared with the reference loci. The results show that nucleotide diversity and/or divergence differ greatly between members of the Gpx gene family, resulting from differential selective pressure acting on genes, and that adaptive evolution influenced the distribution of P. euphratica in desert regions. [ABSTRACT FROM AUTHOR]

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. [ABSTRACT FROM AUTHOR]

Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced-representation sequencing, candidate-gene approaches, linearity of allele-environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies. [ABSTRACT FROM AUTHOR]

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought. [ABSTRACT FROM AUTHOR]

The doubly uniparental inheritance system allows for the use of two independent mitochondrial genomes for population history investigations. Under this system, two lineages of mitochondrial DNA (mtDNA) exist and males are typically heteroplasmic, having the additional, usually divergent, mitochondrial genome inherited from their male parent. This additional mtDNA typically evolves faster, potentially allowing for insight into more recent events in population history. Few studies did explore this possibility in marine mussels Mytilus showing its usefulness. Recent observations of the Mytilus trossulus mussels who have retained their native mtDNA in European waters posed the question of their origin. Are they part of a population present, but previously undetected, or is this a potentially human mediated, ongoing spread of an invasive species? To tackle this question, we amplified with species-specific primers and sequenced an approximately 1,200-bp-long fragment spanning COIII and ND2 genes from both mitochondrial genomes of mussels sampled at five locations worldwide, covering the whole M. trossulus range. The overall pattern of polymorphisms is compatible with the entirely postglacial history of the whole species, indicating a very deep bottleneck at last glacial maximum, with possible retention of the whole species in a single refugium, and the effective population size of no more than a few thousands. Both analyses of molecular variance and isolation with migration (IM) models point at the West Atlantic as the source of the European M. trossulus mussels, at least the ones who retained their native mtDNA. The hypothesis that this is an ongoing, human-mediated process was considered. To this end, comparison with the well-known case: the introduction of congeneric mussel, Mytilus galloprovincialis, from Mediterranean Sea to Asia was used. This introduction occurred within the last 100 years. The results inferred by the IM model suggest that the timing and structure of transatlantic migration of M. trossulus differs significantly from the M. galloprovincialis case: it is more than 1,000 years old and involves a much larger fraction of the ancestral population. Therefore, most likely, this invasion is not a human-mediated process. [ABSTRACT FROM AUTHOR]

In the marine realm, it is important to understand the connectivity and population dynamics of commercially exploited species; this information promotes sustainable fishing practices. The large slipper lobster, Scyllarides latus (Latreille, 1803), is a commercially valuable crustacean that has been over-exploited in many areas throughout its distribution range in the northeastern (hereafter NE) Atlantic and the Mediterranean. Here, we report the first molecular population genetic study of 5. latus based on 9 nuclear microsatellite loci. A total of 128 specimens of S. latus were collected in the Western Mediterranean (2 locations) and four regions (13 locations) in the NE Atlantic, including Southern Portugal and the Macaronesian archipelagos of Azores, Canary Islands and Cape Verde. Maximum number of alleles per locus ranged from 4 to 14, and observed heterozygosity per locus ranged from 0.143 to 0.795 (0.539 ± 0.087, mean ± SE). Pairwise region estimates of FST, RST and Dest were very low (<0.040) and not significant in all comparisons. Bayesian clustering analysis also suggested homogeneity in 5. latus across all regions. The Almeria-Oran front, an important biogeographic boundary between the Atlantic and Mediterranean basins, was not found to have a significant impact on the genetic structuring of S. latus. Overall, all of our analyses of genetic differentiation and migration suggested panmixia in S. latus across its distributional range. Such pattern is likely to result from its high fecundity and long-lived pelagic larva, which can promote high levels of connectivity between geographically distant populations. Future conservation strategies should manage all S. latus populations jointly (one stock). [ABSTRACT FROM AUTHOR]

Background: Cytochrome P450 3A5 (CYP3A5) is an enzyme involved in the metabolism of many therapeutic drugs. CYP3A5 expression levels vary between individuals and populations, and this contributes to adverse clinical outcomes. Variable expression is largely attributed to four alleles, CYP3A5"1 (expresser allele); CYP3A5"3 (rs776746), CYP3A5"6 (rs10264272) and CYP3A5"7 (rs41303343) (low/non-expresser alleles). Little is known about CYP3A5 variability in Africa, a region with considerable genetic diversity. Here we used a multi-disciplinary approach to characterize CYP3A5 variation in geographically and ethnically diverse populations from in and around Africa, and infer the evolutionary processes that have shaped patterns of diversity in this gene. We genotyped 2538 individuals from 36 diverse populations in and around Africa for common low/non-expresser CYP3A5 alleles, and re-sequenced the CYP3A5 gene in five Ethiopian ethnic groups. We estimated the ages of low/non-expresser CYP3A5 alleles using a linked microsatellite and assuming a step-wise mutation model of evolution. Finally, we examined a hypothesis that CYP3A5 is important in salt retention adaptation by performing correlations with ecological data relating to aridity for the present day, 10,000 and 50,000 years ago. Results: We estimate that ∼43% of individuals within our African dataset express CYP3A5, which is lower than previous independent estimates for the region. We found significant intra-African variability in CYP3A5 expression phenotypes. Within Africa the highest frequencies of high-activity alleles were observed in equatorial and Niger-Congo speaking populations. Ethiopian allele frequencies were intermediate between those of other sub-Saharan African and non-African groups. Re-sequencing of CYP3A5 identified few additional variants likely to affect CYP3A5 expression. We estimate the ages of CYP3A5"3 as ∼76,400 years and CYP3A5"6 as ∼218,400 years. Finally we report that global CYP3A5 expression levels correlated significantly with aridity measures for 10,000 [Spearmann's Rho= -0.465, p=0.004] and 50,000 years ago [Spearmann's Rho= -0.379, p=0.02]. Conclusions: Significant intra-African diversity at the CYP3A5 gene is likely to contribute to multiple pharmacogenetic profiles across the continent. Significant correlations between CYP3A5 expression phenotypes and aridity data are consistent with a hypothesis that the enzyme is important in salt-retention adaptation. [ABSTRACT FROM AUTHOR]

Abstract: We examine the possibilities of various coupling mechanisms among a group of identical stochastic oscillators via Chemical Langevin formalism where each oscillator is modeled by stochastic model of testosterone (T) releasing pathway. Our results show that the rate of synchrony among the coupled oscillators depends on various parameters namely fluctuating factor, coupling constants ϵ, and interestingly on system size. The results show that synchronization is achieved much faster in classical deterministic system rather than stochastic system. Then we do large scale simulation of such coupled pathways using stochastic simulation algorithm and the detection of synchrony is measured by various order parameters such as synchronization manifolds, phase plots etc and found that the proper synchrony of the oscillators is maintained in different coupling mechanisms and support our theoretical claims. We also found that the coupling constant follows power law behavior with the systems size (V) by ϵ ∼ AV −γ , where γ =1 and A is a constant. We also examine the phase transition like behavior in all coupling mechanisms that we have considered for simulation. The behavior of the system is also investigated at thermodynamic limit; where V→∞, molecular population, N→∞ but , to see the role of noise in information processing and found the destructive role in the rate of synchronization. [Copyright &y& Elsevier]

The molecular population structure of 20 populations of the subalpine plant Gentiana pannonica was studied by use of amplified fragment length polymorphism (AFLP) and sequencing of non-coding regions of plastid DNA. Of the populations sampled, 18 were native (11 were from the Eastern Alps, which is the distribution centre of the species, and seven were from the Bohemian Forest, which is on the margin of the distribution range), and two were from the Giant Mts and of unclear status. No plastid DNA polymorphisms were found within the entire 6,185 bp investigated. The AFLP data revealed grouping of populations at the regional level. However, differentiation at the regional level (10.3 %) and at the interpopulation level (14.2 %) was low. Even though current populations are isolated and contain small numbers of individuals, the within-population variation (75.511 %) was high. Genetic variation was higher for alpine populations than for Bohemian Forest populations, probably because of fundamental differences in historical changes in population size between these regions. Within-population variation was intermediate for populations in the Giant Mts. The results indicate the possibility of a large distribution of species in the unglaciated areas of Central Europe, irrespective of altitude, during the late Pleistocene and early Holocene. Our results do not confirm that G. pannonica was introduced in the Giant Mts, and native status in the Giant Mts is possible. [ABSTRACT FROM AUTHOR]

The activity of the full-length hammerhead ribozyme requires a tertiary interaction between its distal loops leading to the closure of the molecule and its stabilization in the active conformation. In this study, the conformational changes accompanying the cis-cleavage reaction of Chrysanthemum chlorotic mottle viroid hammerhead ribozyme were investigated by high-pressure experiments on the complete cleavage reaction. Two activation volumes (Δ V≠) were measured, pointing to the presence of two different populations of molecules corresponding to fast-cleaving and slow-cleaving ribozymes in the reaction mixture. The fast population, with a small Δ V≠ of 2.6 mL·mol−1, most likely represents molecules in the near-active conformation, whereas the slow population, with a larger Δ V≠ of 11.6 mL·mol−1, represents molecules that need a larger conformational change to induce activity. In addition, pH-dependence experiments suggest that the group whose deprotonation is required for activity intervenes in the formation of the transition state or in the chemistry of the reaction, but not in the conformational change that precedes it. [ABSTRACT FROM AUTHOR]

Forests and woodlands are under continuing pressure from urban and agricultural development. Tree-dependent mammals that rarely venture to the ground are likely to be highly sensitive to forest fragmentation. The Australian squirrel glider (Petaurus norfolcensis) provides an excellent case study to examine genetic (functional) connectivity among populations. It has an extensive range that occurs in a wide band along the east coast. However, its forest and woodland habitat has become greatly reduced in area and is severely fragmented within the southern inland part of the species' range, where it is recognised as threatened. Within central and northern coastal regions, habitat is much more intact and we thus hypothesise that genetic connectivity will be greater in this region than in the south. To test this we employed microsatellite analysis in a molecular population biology approach. Most sampling locations in the highly modified south showed signatures of genetic isolation. In contrast, a high level of genetic connectivity was inferred among most sampled populations in the more intact habitat of the coastal region, with samples collected 1400 km apart having similar genetic cluster membership. Nonetheless, some coastal populations associated with urbanisation and agriculture are genetically isolated, suggesting the historic pattern observed in the south is emerging on the coast. Our study demonstrates that massive landscape changes following European settlement have had substantial impacts on levels of connectivity among squirrel glider populations, as predicted on the basis of the species' ecology. This suggests that landscape planning and management in the south should be focused on restoring habitat connectivity where feasible, while along the coast, existing habitat connectivity must be maintained and recent losses restored. Molecular population biology approaches provide a ready means for identifying fragmentation effects on a species at multiple scales. Such studies are required to examine the generality of our findings for other tree-dependent species. [ABSTRACT FROM AUTHOR]

Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, Populus tremula, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene PPO1 has a 600 bp region with a highly elevated KA/KS ratio and reduced synonymous diversity. PPO1 also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that PPO1 has been subjected to recurrent selective sweeps. The gene PPO2 shows a marked excess of high frequency, derived variants and shows many of the same trends as PPO1 does, even though the pattern is less pronounced, suggesting that PPO2 might have been the target of a recent selective sweep. Our results supports data from both Populus and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution. [ABSTRACT FROM AUTHOR]

Chromosomal inversion polymorphism play a major role in the evolutionary dynamics of populations and species because of their effects on the patterns of genetic variability in the genomic regions within inversions. Though there is compelling evidence for the adaptive character of chromosomal polymorphisms, the mechanisms responsible for their maintenance in natural populations is not fully understood. For this type of analysis, Drosophila subobscura is a good model species as it has a rich and extensively studied chromosomal inversion polymorphism system. Here, we examine the patterns of DNA variation in two natural populations segregating for chromosomal arrangements that differentially affect the surveyed genomic region; in particular, we analyse both nucleotide substitutions and insertion/deletion variations in the genomic region encompassing the odorant-binding protein genes Obp83a and Obp83b (Obp83 region). We show that the two main gene arrangements are genetically differentiated, but are consistent with a monophyletic origin of inversions. Nevertheless, these arrangements interchange some genetic information, likely by gene conversion. We also find that the frequency spectrum-based tests indicate that the pattern of nucleotide variation is not at equilibrium; this feature probably reflects the rapid increase in the frequency of the new gene arrangement promoted by positive selection (that is an adaptive change). Furthermore, a comparative analysis of polymorphism and divergence patterns reveals a relaxation of the functional constraints at the Obp83b gene, which might be associated with particular ecological or demographic features of the Canary island endemic species D. guanche [ABSTRACT FROM AUTHOR]

The article discusses a study which analyzed discrepancies among results of commonly used methods for Anopheles gambiae M and S molecular form identification. The genotyping of more than 400 Anopheles gambiae specimens from nine African countries, and the sequencing of the IGS-amplicon of 115 of them, found discrepancies among results obtained by the different approaches due to different kinds of biases.

The still poorly explored world of microbial functioning is about to be uncovered by a combined application of old and new technologies. Bacteria, especially, are still in the dark with respect to their phylogenetic affiliations as well as their metabolic capabilities and functions. However, with the advent of sophisticated flow cytometric and cell sorting technologies in microbiological labs, there is now the possibility to gain this knowledge at the single-cell level without cumbersome cultivation approaches. Cytometry also facilitates the understanding of physiological diversity in seemingly likewise acting populations. Both individuality and diversity lead to the complex and concerted actions of microbial consortia. This review provides an overview of the state of the art in the field. It deals with the handling of microorganisms from the very beginning (i.e. sampling, and detachment and fixation procedures) and goes on to discuss the pitfalls and problems in analysing cells without any further treatment. If information cannot be gained by specific staining procedures, phylogenetic technologies, transcriptomic and proteomic approaches may be options for achieving advanced insights. All in all, flow cytometry will be a mediator technology to gain a deeper insight into the heterogeneity of populations and the functioning of microbial communities. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models. [ABSTRACT FROM AUTHOR]

Gene flow from diploid to polyploid species could have significant effects on the morphology and ecology of polyploids. The potential of such introgression for bringing about evolutionary change within polyploids has long been recognized, although there are few examples of the process in the wild. Here, we focus on introgression between the diploid species, Senecio squalidus, and the tetraploid, S. vulgaris, which resulted in the origin of a variant form of S. vulgaris that produces radiate rather than nonradiate flower heads. The radiate variant of S. vulgaris is more attractive to pollinators and has a higher outcrossing rate. We review recent work that has isolated and characterized two regulatory genes, RAY1 and RAY2, that control presence of ray florets in radiate flower heads, and which have been introgressed into S. vulgaris from S. squalidus in the recent past. We identify a copy of RAY2 in S. vulgaris ( RAY2b) homeologous to the copy ( RAY2a) previously isolated, thus providing further evidence that S. vulgaris is allotetraploid. We also show that the RAY2a-R allele, which is fixed in radiate S. vulgaris, occurs at intermediate frequency in S. squalidus. Thus, based on this result, it is not possible to distinguish whether radiate S. vulgaris originated once or multiple times following hybridization between nonradiate S. vulgaris and S. squalidus. [ABSTRACT FROM AUTHOR]

New genomic resources and genetic tools of the past few years have advanced the nematode genus Caenorhabditis as a model for comparative biology. However, understanding of natural genetic variation at molecular and phenotypic levels remains rudimentary for most species in this genus, and for C. briggsae in particular. Here we characterize phenotypic variation in C. briggsae’s sensitivity to the potentially important and variable environmental toxin, ethanol, for globally diverse strains. We also quantify nucleotide variation in a new sample of 32 strains from four continents, including small islands, and for the closest-known relative of this species ( C. sp. 9). We demonstrate that C. briggsae exhibits little heritable variation for the effects of ethanol on the norm of reaction for survival and reproduction. Moreover, C. briggsae does not differ significantly from C. elegans in our assays of its response to this substance that both species likely encounter regularly in habitats of rotting fruit and vegetation. However, we uncover drastically more molecular genetic variation than was known previously for this species, despite most strains, including all island strains, conforming to the broad biogeographic patterns described previously. Using patterns of sequence divergence between populations and between species, we estimate that the self-fertilizing mode of reproduction by hermaphrodites in C. briggsae likely evolved sometime between 0.9 and 10 million generations ago. These insights into C. briggsae’s natural history and natural genetic variation greatly expand the potential of this organism as an emerging model for studies in molecular and quantitative genetics, the evolution of development, and ecological genetics. [ABSTRACT FROM AUTHOR]

The coalescent with recombination is a very useful tool in molecular population genetics. Under this framework, genealogies often represent the evolution of the substitution unit, and because of this, the few coalescent algorithms implemented for the simulation of coding sequences force recombination to occur only between codons. However, it is clear that recombination is expected to occur most often within codons. Here we have developed an algorithm that can evolve coding sequences under an ancestral recombination graph that represents the genealogies at each nucleotide site, thereby allowing for intracodon recombination. The algorithm is a modification of Hudson's coalescent in which, in addition to keeping track of events occurring in the ancestral material that reaches the sample, we need to keep track of events occurring in ancestral material that does not reach the sample but that is produced by intracodon recombination. We are able to show that at typical substitution rates the number of nonsynonymous changes induced by intracodon recombination is small and that intracodon recombination does not generally result in inflated estimates of the overall nonsynonymous/synonymous substitution ratio (ω). On the other hand, recombination can bias the estimation of ω at particular codons, resulting in apparent rate variation among sites and in the spurious identification of positively selected sites. Importantly, in this case, allowing for variable synonymous rates across sites greatly reduces the falsepositive rate and recovers statistical power. Finally, coalescent simulations with intracodon recombination could be used to better represent the evolution of nuclear coding genes or fast-evolving pathogens such as HIV-1. We have implemented this algorithm in a computer program called NetRecodon, freely available at http://darwin.uvigo.es. [ABSTRACT FROM AUTHOR]

Pentatricopeptide Repeat (PPR) proteins comprise a family of nuclear-encoded transcriptional regulators of cytoplasmic genes. They have shown dramatic expansion in copy number in plants and although the functional importance of many remains unclear, a subset has been repeatedly implicated as nuclear restorers for cytoplasmic male sterility. Here we investigate the molecular population genetics and molecular evolution of seven single-copy PPR genes in the outcrossing model plant Arabidopsis lyrata. In comparison with neutral reference loci, we find on average elevated levels of polymorphism and an excess of high frequency variants at these PPR genes, suggesting that natural selection is maintaining polymorphism at some of these loci. This elevation in diversity persists when we control for divergence and generally decreases in the flanking regions, suggesting that these genes are themselves the targets of selection. Some of the PPR genes also demonstrate elevated population differentiation, consistent with spatially varying selection. In contrast, no comparable patterns are observed at these loci in A. thaliana, providing no evidence for the action of balancing selection in this selfing species. Taken together, these results suggest that a subset of PPR genes may be subject to balancing selection associated with ongoing cytonuclear coevolution in the outcrossing A. lyrata, possibly mediated either by intergenomic conflict or compensatory evolution. [ABSTRACT FROM AUTHOR]

Organisms that compete for limited resources within a common environment may evolve traits that allow them to exploit distinct ecological niches, thus enabling multiple species to coexist within the same habitat. The process of niche partitioning now has been captured at the molecular level, employing the method of continuous in vitro evolution. Mixed populations of 2 different "species" of RNA enzymes were made to compete for limited amounts of one or more substrates, with utilization of the substrate being necessary for amplification of the RNA. Evolution in the presence of a single substrate led to the extinction of one or the other enzyme. whereas evolution in the presence of 5 alternative substrates led to the accumulation of mutations that allowed each enzyme to exploit a different preferred resource. The evolved enzymes were capable of sustained coevolution within a common environment, exemplifying the emergence of stable ecological niche behavior in a model system. Biochemical characterization of the 2 evolved enzynes revealed marked differences in their kinetic properties and adaptive strategies. One enzyme reacted with its preferred substrate ≈100-fold faster than the other, but the slower-reacting species produced 2- to 3-fold more progeny per reacted parent molecule. The in vitro coevolution of 2 or more species of RNA enzymes will make possible further studies in molecular ecology, including the exploration of more complex behaviors, such as predation or cooperation, under controlled laboratory conditions. [ABSTRACT FROM AUTHOR]

The doubly uniparental system of mitochondrial inheritance (DUI) is best known in marine mussels Mytilus. Under DUI there are two types of mitochondrial DNA (mtDNA). The female type (F) is transmitted to offspring of both genders and the male type (M) exclusively to sons; consequently two distinct mtDNA lineages exist. The M lineage evolves under more relaxed selection than the F lineage resulting in higher polymorphism within the M lineage. Though this polymorphism is expected to make inferences on fine population structure easier using M instead of F data, no comprehensive comparative data exist to support this claim. We sequenced a 1,205 bp fragment of M and F mtDNA comprising parts of the COIII and ND2 genes, and analysed 204 individuals representing three Mytilus species: M. edulis, M. galloprovincialis and M. trossulus from 13 European sampling sites. A clear distinction between Mediterranean and Atlantic populations was found with both M and F data, but much better geographic differentiation was found within the Atlantic using F rather than M data. In particular, Atlantic M. galloprovincialis can be differentiated from Atlantic M. edulis, and further subdivision of Atlantic M. edulis is possible using the F data but not the M data. Multiple tests of selection were carried out to attempt to explain this paradox. We concluded that the overall pattern of polymorphism is consistent with strong purifying selection; not only is this selection relaxed in the M lineage in comparison with the F lineage, but it is also more frequently interrupted by periodic selective sweeps within the M lineage. [ABSTRACT FROM AUTHOR]

Abstract: The evolutionary process as imagined by Darwin 150 years ago is evident not only in nature but also in the manner in which naked nucleic acids and proteins experience the “survival of the fittest” in the test tube during in vitro evolution. This review highlights some of the most apparent evolutionary patterns, such as directional selection, purifying selection, disruptive selection, and iterative evolution (recurrence), and draws parallels between what happens in the wild with whole organisms and what happens in the lab with molecules. Advances in molecular selection techniques, particularly with catalytic RNAs and DNAs, have accelerated in the last 20 years to the point where soon any sort of complex differential hereditary event that one can ascribe to natural populations will be observable in molecular populations, and exploitation of these events can even lead to practical applications in some cases. [Copyright &y& Elsevier]

Lake Tanganyika is not the most species-rich of the Great East African Lakes, but comprises the greatest diversity of cichlid fishes in terms of morphology, ecology, and breeding styles. The lake contains a polyphyletic assemblage of cichlid lineages, which evolved from several ancient species that colonized the emerging lake some 9–12 million years ago. Based on morphological characteristics, the Tanganyikan cichlids have been classified into 12, or, more recently, 16 tribes, which are largely supported by molecular data. The radiations of East African cichlids are believed to be driven by complex interactions between extrinsic factors, such as climatic changes and geological processes, and intrinsic biological characteristics of the involved organisms. Diversification within different lineages occurred simultaneously in response to drastic habitat changes such as the establishment of lacustrine deep-water conditions 5–6 MYA and subsequent major lake-level fluctuations. This seems particularly true for the mouthbrooding lineages whereas the substrate breeders underwent a more gradual process of diversification. This review presents an account of the taxonomy and phylogeny of the Lake Tanganyika cichlid species assemblage, its relationship to the African cichlid fauna, key factors leading to the astonishing diversity and discusses recently proposed alternative age estimates for the Lake Tanganyika cichlid species assemblage. [ABSTRACT FROM AUTHOR]

The population structure of thermo- and mesophilic biogas reactors digesting maize silage as the sole substrate was investigated employing a novel, highly degenerated PCR-primer pair targeting mcrA/mrtA coding for the key enzyme of methanogens. No sequence affiliating with Methanococcales, Methanopyrales, ANME-, rice or fen soil clusters was detected. Direct MeA PCR-cloning results indicated that Methanobacteriales were the most important methanogens in the thermophilic reactors. 57% and 80% of the analysed sequences affiliated with this order, 14% and 20% with Methanosarcinaceae and 0% and 29% with Methanomicrobiales. Methanomicrobiales dominated in the mesophilic reactors at the given conditions, 69% and 84% of the sequences recovered from direct MeA primed cloning affiliated with this order, 31% and 0% with Methanosarcinaceae and 0% and 16% with Methanobacteriales. No sequence affiliating with Methanosaetaceae was found. MeA primed PCR-single-strand conformation polymorphism indicated that population fluctuations occurred. According to sequence analysis of excised bands, Methanosarcinaceae dominated and Methanobacteriales were significantly represented in the thermophilic fermenter. Only 1 Methanosaetaceae sequence was found. Hydrogenotrophs appear to have a much higher and obligate acetoclastic methanogens a much lower importance than previously thought in biogas production from renewable resources. [ABSTRACT FROM AUTHOR]

Aquatic microbial ecology aims at nothing less than explaining the world from “ecological scratch”. It develops theories, concepts and models about the small and invisible living world that is at the bottom of every macroscopic aquatic system. In this paper we propose to look at the development of Aquatic Microbial Ecology as a reiteration of classical eukaryotic limnology and oceanography. This was conceptualized moving historically from the socalled water desertto microcosmto ecosystem. Each of these concepts characterizes a particular historical field of knowledge that embraces also practices and theories about living beings in aquatic environments. Concerning the question of “who is there”, however, Aquatic Microbial Ecology historically developed in reverse order. Repetition, reiteration and replication notwithstanding, Aquatic Microbial Ecology has contributed new ideas, theories and methods to the whole field of ecology as well as to microbiology. The disciplining of Aquatic Microbial Ecology happened in the larger field of plankton biology, and it is still attached to this biological domain, even conceiving of itself very selfconsciously as a discipline of its own. Today, Aquatic Microbial Ecology as a discipline is much broader than plankton ecology ever was, for it includes not only oceans and freshwaters but also benthic, interstitial and groundwater systems. The success of Aquatic Microbial Ecology is expressed by its influence on other fields in ecology. The challenge is to further develop its theoretical and methodological features while at the same time contributing to current pressing problems such as climate change or the management of global water resources.And then it may not be fanciful to suppose that even in the year nineteen hundred and nineteen a great number of minds are still only partially lit up by the cold light of knowledge. It is the most capricious illuminant. They are still apt to ruminate, without an overpowering bias to the truth, whether a kingfishers body shows which way the wind blows; whether an ostrich digests iron; whether owls and ravens herald illfortune; and the spilling of salt bad luck; what the tingling of ears forebodes, and even to toy pleasantly with more curious speculations as to the joints of elephants and the politics of storks, which came within the province of the more fertile and betterinformed brain of the author 1919Virginia Woolf from the essay “Reading”, In:Leonard Woolf ed., 1950: The Captains Death Bed and Other Essays, – London: Hogarth Press, p. 157. © 2008 WILEYVCH Verlag GmbH & Co. KGaA, Weinheim [ABSTRACT FROM AUTHOR]

Abstract: To think ecologically is to think complexly, recognising that reality is rarely singular, and that there is usually more than just one thing going on at the same time. Additionally, the world is lumpy, in that some few aspects of a phenomenon usually matter much more than others, and so the world is not actually infinitely variable. Besides, the physically tangible world that we care most about is usually shaped by apparently intangible sets of processes and functions. What we see is rarely all that we get. Under these conditions, planning becomes the informative telling of context, and the savvy tracing of consequence. I propose an ecosystem approach to planning, and lay out the parameters of the worldview necessary to take such an approach to an integrative regional planning. Nested scale hierarchic ecosystem ecology, or process-function ecology, provides a pragmatically robust frame from within which to come to know what it means to plan ecologically. The key insights from such a view are: (a) that complex systems are best seen to be organised into nested levels, with purposively named systems emergent from subsystems, and interactively giving rise to suprasystems; (b) that descriptions of such systems are inherently purposive and perspectival, and so why we make a description, and where we position ourselves to make that description, will significantly influence what it is we can come to see; and (c) that such systems can only be known meaningfully if they are considered to have multiple process-driven boundaries, and are depicted using multiple functionally relevant spatial and temporal scales. I use cases from the interwoven history of ecological science and social theory, habitat conservation planning, heat island mitigation, urban forestry, and impervious surface management to synthesise a description of what it means, pragmatically, to think and plan in an ecologically integrative way. [Copyright &y& Elsevier]

Abstract  Population dynamics and zonation of the amphipods Bathyporeia pilosa and B. sarsi, co-occurring on some beaches, were studied through monthly sampling of eight cross-shore transects along the Belgian coast (October 2003–October 2004). Their biomass and production were assessed for the first time. Abundance and biomass of B. pilosa were ten times higher along western ultra-dissipative transects than along slightly more reflective, eastern transects. For B. sarsi (less prominent), differences between the two westernmost transects (2–5× higher) and all others were observed, whereas P/B ratio was comparable for all. B. pilosa could reach two times higher abundance and biomass and higher levels of production (max B. sarsi = 7,580 g m−2 y−1; max B. pilosa = 16,040 g m−2 y−1), while the species was nearly absent from the eastern transects. Continuous reproduction and recruitment with three relative peaks of the latter (February, July, October) were observed. Fecundity showed parallel temporal variation for both species, peaking in February and September–October. Interestingly, the July relative “recruitment” peak could not be explained by relative abundance of gravid females or fecundity, but was probably caused by adult mortality. Both species displayed comparable gonad production (B. pilosa: P g  = 0.73 mg/ind year; B. sarsi: P g  = 0.71 mg/ind year), but B. pilosa produced fewer yet larger embryos. Peak abundances were found at 436 ± 25 SD cm (B. pilosa) and 357 ± 40 SD cm (B. sarsi) above MLLWS, corresponding to a 40–62 m cross-shore distance between the peaks of both species. The occupied cross-shore range was larger for B. sarsi than for B. pilosa (35–54 m), for females than for males (15–23 m), and for adults than for juveniles of B. pilosa (5–8 m). Both species displayed many comparable life history features. Differences in abundance and biomass may be related to beach morphodynamics and zonation. [ABSTRACT FROM AUTHOR]

Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion. [Copyright &y& Elsevier]

The article focuses on the effects of climate change on the Arctic marine mammals. Changes in the environment can affect the behavior and fitness of individual organisms and the viability of populations. It notes that genetic analyses can have a detailed understanding on how species use their environment and how past climate-induced environmental change affected them. It states that molecular genetic approaches are being used to determine distribution and migration patterns, dispersal and breeding behavior, population structure and the effects of past, and present climate change in Arctic marine mammals.

Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has become essential in training the modern scientist. The following article offers preparatory and problem-solving questions for engaging students in the understanding of microarray technologies for use in conjunction with other course materials relating to discussions of microarray technology. [ABSTRACT FROM AUTHOR]

The article offers information on the significant simulation approach of environmental heterogeneity for the delay on the resistance development of allele. It notes that the simulation of the herbicide resistance in a weed is showed up using a population genetics model and the alternation of two unrelated herbicides in time and space. Moreover the simulation of environmental heterogeneity level has led by a size variation of herbicide-treated areas. The research suggests to depend on the interaction between the breeding systems and the dominance of the resistance allele in the presence of herbicide, value of fitness cost and the dominance of this fitness cost.

The nature of evolutionary changes recorded by the fossil record has long been controversial, with particular disagreement concerning the relative frequency of gradual change versus stasis within lineages. Here, I present a large-scale, statistical survey of evolutionary mode in fossil lineages. Over 250 sequences of evolving traits were fit by using maximum likelihood to three evolutionary models: directional change, random walk, and stasis. Evolution in these traits was rarely directional; in only 5% of fossil sequences was directional evolution the most strongly supported of the three modes of change. The remaining 95% of sequences were divided nearly equally between random walks and stasis. Variables related to body size were significantly less likely than shape traits to experience stasis. This finding is in accord with previous suggestions that size may be more evolutionarily labile than shape and is consistent with some but not all of the mechanisms proposed to explain evolutionary stasis. In general, similar evolutionary patterns are observed across other variables, such as dade membership and temporal resolution, but there is some evidence that directional change in planktonic organisms is more frequent than in benthic organisms. The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria and suggests that truly directional evolution is infrequent or, perhaps more importantly, of short enough duration so as to rarely register in paleontological sampling. [ABSTRACT FROM AUTHOR]

The portfolio effect is the increase of the stability of a system to random fluctuations with the increase of the number of random state variables due to spreading the risk among these variables; many examples exist in various areas of science and technology. We report the existence of an opposite effect, the decrease of stability to random fluctuations due to an increase of the number of random state variables. For successive industrial or biochemical processes of independent, random efficiencies, the stability of the total efficiency decreases with the increase of the number of processes. Depending on the variables considered, the same process may display both a portfolio as well as an anti-portfolio behavior. In disordered kinetics, the activation energy of a reaction or transport process is the result of a sum of random components. Although the total activation energy displays a portfolio effect, the rate coefficient displays an anti-portfolio effect. For random- channel kinetics, the stability of the total rate coefficient increases with the average number of reaction pathways, whereas the stability of the survival function has an opposite behavior: it decreases exponentially with the increase of the average number of reaction pathways (anti-portfolio effect). In molecular biology, the total rate of a nucleotide substitution displays a portfolio effect, whereas the probability that no substitutions occur displays an anti-portfolio effect, resulting in faster evolutionary processes due to fluctuations. The anti-portfolio effect emerges for products of random variables or equations involving multiplicative convolution products. [ABSTRACT FROM AUTHOR]

Inbreeding causes reduction of genetic variability that may have severe fitness consequences. In spite of its potentially huge impact on viability and evolutionary processes especially in small populations, quantitative demonstrations of genetic and demographic effects of inbreeding in natural populations are few. Here, we examine the relationship between individual inbreeding coefficients ( F) and individual standardized multilocus heterozygosity ( H) in an insular metapopulation of house sparrows ( Passer domesticus) in northern Norway in order to evaluate whether H is a good predictor for F. We then relate variation in fitness (i.e. the probability of surviving from fledging to recruitment) to F and H, which enables us to examine whether inbreeding depression is associated with a reduction in genetic variability. The average level of inbreeding in the house sparrow metapopulation was high, and there was large inter-individual variation in F. As expected, standardized multilocus heterozygosity decreased with the level of inbreeding. The probability of recruitment was significantly negatively related to F, and, accordingly, increased with H. However, H explained no significant additional variation in recruitment rate than was explained by F. This suggests that H is a good predictor for F in this metapopulation, and that an increase in F is likely to be associated with a general increase in the level of homozygosity on loci across the genome, which has severe fitness consequences. [ABSTRACT FROM AUTHOR]

The presence of two gender-associated mitochondrial genornes iii marine mussels provides a unique opportunity to investigate the dynamics of mtDNA evolution without complications inherent in interspecific comparisons. Here, we assess the relative importance of selection, mutation, and differential constraint in shaping the patterns of polymorphism within and divergence between the male (M) and female (F) mitochondrial genomes of the California sea mussel, Mytilus californianus. Partial sequences were obtained from homologous regions of four genes (nad2, cox1, atp6, and nad5) totaling 2307 bp in length. The M and F mtDNA molecules of M. calfornianus exhibited extensive levels of nucleotide polymorphism and were more highly diverged than observed in other mytilids (overall Tamura-Nei distances >40%). Consistent with previomis studies, the M molecule had significantly higher levels of silent and replacement polymorphism relative to F. Both genomes possessed large numbers of singleton and low-frequency mutations that gave rise to significantly negative Tajima's D values. Mutation-rate scalars estimated for silent and replacement mutations were elevated in the M. genome but were not sufficient to account for its higher level of polymorphism. McDonald-Kreitman tests were highly significant at all loci due to excess numbers of fixed replacement mutations between molecules. Strong purifying selection was evident in both genomes in keeping the majority of replacement mutations at low population frequencies but appeared to be slightly relaxed in M. Our results suggest that a reduction in selective constraintacting on the M genome remains the best explanation for its greater levels of polymorphism and faster rate of evolution. [ABSTRACT FROM AUTHOR]

One of the central goals of evolutionary biology is to understand the genetic basis of adaptive evolution. The availability of nearly complete genome sequences from a variety of organisms has facilitated the collection of data on naturally occurring genetic variation on the scale of hundreds of loci to whole genomes. Such data have changed the focus of molecular population genetics from making inferences about adaptive evolution at single loci to identifying which loci, out of hundreds to thousands, have been recent targets of natural selection. A major challenge in this effort is distinguishing the effects of selection from those of the demographic history of populations. Here we review some current progress and remaining challenges in the field.Heredity (2007) 98, 340–348. doi:10.1038/sj.hdy.6800967; published online 2 May 2007 [ABSTRACT FROM AUTHOR]

Molecular population genetic studies are providing new perspectives on the evolution of genes that confer resistance to pathogens and herbivores. Here, we compare the evolutionary history of different components of the defense response (detection, signaling and response) and of genes with parallel function in plants and Drosophila. A review of the literature indicates that the dominant form of selection acting on defense genes (balancing, positive and purifying) differs among components of defense. Sampling of particular classes of genes and genes from non-model organisms, however, remains limited. Future studies combining molecular evolutionary analyses with ecological genetic and functional analyses should better reveal how natural selection has shaped defense gene evolution. [Copyright &y& Elsevier]

A hallmark of positive selection (adaptive evolution) in protein-coding regions is a dN/dS ratio >1, where dN is the number of nonsynonymous substitutions/nonsynonymous sites and dS is the number of synonymous substitutions/synonymous sites. Zonadhesin is a male reproductive protein localized on the sperm head, comprising many domains known to be involved in cell-cell interaction or cell adhesion. Previous studies have shown that VWD domains (homologous to the D domains of the von Willebrand factor) are involved directly in binding to the female zona pellucida (ZP) in a speciesspecific manner. In this study, we sequenced 47 coding exons in 12 primate species and, by using maximum-likelihood methods to determine sites under positive selection, we show that VWD2, membrane/A5 antigen mu receptor, and mucin-like domains in zonadhesin are rapidly evolving and, thus, may be involved in binding to the ZP in a speciesspecific manner in primates. In addition, polymorphism data from 48 human individuals revealed significant polymorphism-to-divergence heterogeneity and a significant departure from equilibrium-neutral expectations in the frequency spectrum, suggesting balancing selection and positive selection occurring in zonadhesin (ZAN) within human populations. Finally, we observe adaptive evolution in haplotypes segregating for a frameshift mutation that was previously thought to indicate that ZAN was a potential pseudogene. [ABSTRACT FROM AUTHOR]

The brittle-star Acrocnida brachiata (Montagu) lives in sandy-bottom habitat of both intertidal and subtidal zones along the coasts of the northwestern Europe. An allozyme frequency-based survey (five enzyme loci) was combined with a mitochondrial (mt) COI haplotype analysis (598-bp sequences) on 17 populations to trace back past colonization pathways from the actual population structure of the species. Both genetic markers display a sharp genetic break between intertidal (clade I) and subtidal populations (clade S). This break corresponds to an allele frequency inversion at three enzyme loci ( Hk, Pgm and Pgi) and a deep divergence of about 20% in mtCOI sequences between most of the intertidal populations and other samples. The geographic distribution of clade I seems to be more restricted than clade S as it is absent from the intertidal of the eastern English Channel and North Sea and may be replaced by clade S in south Brittany. Applying previously published rates of mutation, divergence between the two clades is estimated to pre-date 5 million years ago and may be due to allopatric speciation processes at the Mio–Pliocene transition. The occurrence of putative hybrids in a few localities, however, suggests incomplete cryptic speciation with secondary contact zones. The relative importance of colonization history vs. habitat specialization are discussed in the light of neutral evolution as tested from mtCOI gene sequences. While differential selection seems to have contributed little to the separation of the lineages, it may have played a role in the emergence of adaptive polymorphisms in the hybrid zone. Furthermore, congruent spatial patterns of differentiation were observed in both clades suggesting a recent increase in population size. These findings are in agreement with a recent expansion of the populations during or after the formation of the English Channel, from a southern refuge for the subtidal clade whereas the intertidal clade may have persisted further north. As previously suspected for a species with a very short pelagic larval phase, contemporary gene flow between distant or adjacent populations appears to be extremely reduced or even absent. [ABSTRACT FROM AUTHOR]

Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations. [ABSTRACT FROM AUTHOR]

Small populations at the edge of a species’ distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully ( n = 34) from the next nearest population, off Labrador ( n = 127; microsatellites – FST= 0.0243, P<0.0001; mtDNA –ΦST = 0.0456, P<0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations ( h = 0.51, π = 0.14%), a pattern which may be due to selective sweeps associated with this species’ extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales. [ABSTRACT FROM AUTHOR]

Previous research has shown that members of the unisexual hybrid complex of the genus Ambystoma possess a mitochondrial genome that is unrelated to their nuclear parental species, but the origin of this mitochondrion has remained unclear. We used a 744-bp fragment of the mitochondrial gene cytochrome b within a comparative phylogenetic framework to infer the maternal ancestor of this unisexual lineage. By examining a broader range of species than has previously been compared, we were able to uncover a recent maternal ancestor to this complex. Unexpectedly, Ambystoma barbouri, a species whose nuclear DNA has not been identified in the unisexuals, was found to be the recent maternal ancestor of the individuals examined through the discovery of a shared mtDNA haplotype between the unisexuals and A. barbouri. Based on a combination of sequence data and glacial patterning, we estimate that the unisexual lineage probably originated less than 25 000 years ago. In addition, all unisexuals examined showed extremely similar mtDNA sequences and the resultant phylogeny was consistent with a single origin for this lineage. These results confirm previous suggestions that the unisexual Ambystoma complex was formed from a hybridization event in which the nuclear DNA of the original maternal species was subsequently lost. [ABSTRACT FROM AUTHOR]

Dispersal is a fundamental process influencing evolution, social behaviour, and the long-term persistence of populations. We use both observational and genetic data to investigate dispersal, kin-clustering and intergroup relatedness in the white-breasted thrasher, Ramphocinclus brachyurus, a cooperatively breeding bird that is globally endangered. Mark-resighting data suggested sex-biased dispersal, with females dispersing over greater distances while males remained philopatric. Accordingly, spatial autocorrelation analysis showed highly significant fine-scale genetic structure among males, but not among females. This fine-scale genetic structuring of the male population resulted in very high levels of relatedness between dominant males at neighbouring nests, similar to that seen within cooperative groups in many species where kin selection is cited as a cause of cooperation. By implication, between-group as well as within-group cooperation may be important, potentially creating a feedback loop in which short-distance dispersal by males leads to the formation of male kin clusters that in turn facilitate nepotistic interactions and favour further local recruitment. The strength of spatial autocorrelation, as measured by the autocorrelation coefficient, r, was approximately two to three times greater than that reported in previous studies of animals. Relatively short dispersal distances by both males and females may have a negative impact on the white-breasted thrasher's ability to colonize new areas, and may influence the long-term persistence of isolated populations. This should be taken into account when designating protected areas or selecting sites for habitat restoration. [ABSTRACT FROM AUTHOR]