Comparative genomics reveals birth and death of fragile regions in mammalian evolution

Comparative genomics reveals birth and death of fragile regions in mammalian evolution: "Background:
An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals raised some doubts about their existence.
Results:
Here we demonstrate that fragile regions are subject to a birth and death process, implying that fragility has a limited evolutionary lifespan.
Conclusions:
This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions as a phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome."

EXPRESSION OF DEFENSE GENES IN DROSOPHILA EVOLVES UNDER A DIFFERENT SELECTIVE REGIME FROM EXPRESSION OF OTHER GENES

EXPRESSION OF DEFENSE GENES IN DROSOPHILA EVOLVES UNDER A DIFFERENT SELECTIVE REGIME FROM EXPRESSION OF OTHER GENES: "

ABSTRACT

Genes involved in host-pathogen interactions are expected to be evolving under complex coevolutionary dynamics, including positive directional and/or frequency dependent selection. Empirical work has largely focused on the evolution of immune genes at the level of the protein sequence. We examine components of genetic variance for transcript abundance of defense genes in D. melanogaster and D. simulans using a diallel and a round robin breeding design, respectively, and infer modes of evolution from patterns of segregating genetic variation. Defense genes in D. melanogaster are overrepresented relative to non-defense genes among genes with evidence of significant additive variance for expression. Directional selection is expected to deplete additive genetic variance, whereas frequency dependent selection is expected to maintain additive variance. However, relaxed selection (reduced or no purifying selection) is an alternative interpretation of significant additive variation. Of the three classes of defense genes, the recognition and effector classes show an excess of genes with significant additive variance; whereas signaling genes, in contrast, are overrepresented for dominance variance. Analysis of protein coding sequences revealed no evidence for an association between additive or dominance variation in expression and directional selection. Both balancing selection driven by host-pathogen coevolution and relaxed selection for expression of uninduced defense genes are viable interpretations of these data.

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THE SPECIES CONCEPT AS AN EMERGENT PROPERTY OF POPULATION BIOLOGY

THE SPECIES CONCEPT AS AN EMERGENT PROPERTY OF POPULATION BIOLOGY: "

ABSTRACT

Resurgent interest in the genetics of population divergence and speciation coincides with recent critical evaluation of species concepts and proposals for species delimitation. An important result of these parallel trends is a slight but important conceptual shift in focus away from species diagnoses based on prior species concepts or definitions, and toward analyses of the processes acting on lineages of metapopulations that eventually lead to differences recognizable as species taxa. An advantage of this approach is that it identifies quantitative metapopulation differences in continuous variables, rather than discrete entities that do or do not conform to a prior species concept, and species taxa are recognized as an emergent property of population-level processes. The tension between species concepts and diagnosis versus emergent recognition of species taxa is at least as old as Darwin, and is unlikely to be resolved soon in favor of either view, because the products of both approaches (discrete utilitarian taxon names for species, process-based understanding of the origins of differentiated metapopulations) continue to have important applications.

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Phenotypic Consequences of Copy Number Variation: Insights from Smith-Magenis and Potocki-Lupski Syndrome Mouse Models

Phenotypic Consequences of Copy Number Variation: Insights from Smith-Magenis and Potocki-Lupski Syndrome Mouse Models: "

The characterization of mice with different number of copies of the same genomic segment shows that structural changes influence the phenotypic outcome independently of gene dosage.

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Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species: "Author Summary

In order for a gene to be active, it must be turned on, or “expressed.” Instructions determining when, where, and how much a gene will be expressed are encoded by DNA sequences known as enhancers. The precise DNA sequence of a particular enhancer changes over evolutionary time, which may or may not change its effects on gene expression. Many genes are controlled by multiple enhancers and prior work has shown that the location of these enhancers within the genome tends to remain stable for long periods of evolutionary time. Here, we examine the enhancers controlling expression of a gene (yellow) involved in generating pigmentation diversity among fruit fly (Drosophila) species. Surprisingly, we find that not only have the sequence and function of individual enhancers changed among Drosophila species, but so has the location of these enhancers within the genome of each species. This finding is important because it demonstrates a type of evolutionary change affecting DNA sequence elements critical for gene expression that is currently under appreciated and should be considered when searching for enhancers in related species.

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CRYPTIC GENETIC VARIATION AND BODY SIZE EVOLUTION IN THREESPINE STICKLEBACK

CRYPTIC GENETIC VARIATION AND BODY SIZE EVOLUTION IN THREESPINE STICKLEBACK: "

ABSTRACT

The role of environment as a selective agent is well-established. Environment might also influence evolution by altering the expression of genetic variation associated with phenotypes under selection. Far less is known about this phenomenon, particularly its contribution to evolution in novel environments. We investigated how environment affected the evolvability of body size in the threespine stickleback (Gasterosteus aculeatus). Gasterosteus aculeatus is well suited to addressing this question due to the rapid evolution of smaller size in the numerous freshwater populations established following the colonization of new freshwater habitats by an oceanic ancestor. The repeated, rapid evolution of size following colonization contrasts with the general observation of low phenotypic variation in oceanic stickleback. We reared an oceanic population of stickleback under high and low salinity conditions, mimicking a key component of the ancestral environment and freshwater colonization respectively. There was low genetic variation for body size under high salinity, but this variance increased significantly when fish were reared under low salinity. We therefore conclude that oceanic populations harbor the standing genetic variation necessary for the evolution of body size, but that this variation only becomes available to selection upon colonization of a new habitat.

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THE EFFECT OF DEVELOPMENTAL TEMPERATURE ON THE GENETIC ARCHITECTURE UNDERLYING SIZE AND THERMAL CLINES IN DROSOPHILA MELANOGASTER AND D. SIMULANS FROM THE EAST COAST OF AUSTRALIA

THE EFFECT OF DEVELOPMENTAL TEMPERATURE ON THE GENETIC ARCHITECTURE UNDERLYING SIZE AND THERMAL CLINES IN DROSOPHILA MELANOGASTER AND D. SIMULANS FROM THE EAST COAST OF AUSTRALIA: "

ABSTRACT

Body size and thermal tolerance clines in Drosophila melanogaster occur along the east coast of Australia. However the extent to which temperature affects the genetic architecture underlying the observed clinal divergence remains unknown. Clinal variation in these traits is associated with cosmopolitan chromosome inversions which cline in D. melanogaster. Whether this association influences the genetic architecture for these traits in D. melanogaster is unclear. D. simulans shows linear clines in body size, but non-linear clines in cold resistance. Clinally varying inversions are absent in D. simulans. Line-cross and clinal analyses were performed between tropical and temperate populations of D. melanogaster and D. simulans from the east coast of Australia to investigate whether clinal patterns and genetic effects contributing to clinal divergence in wing centroid size, thorax length, wing-to-thorax ratio, cold and heat resistance differed under different developmental temperatures (18°, 25° and 29°C). Developmental temperature influenced the genetic architecture in both species. Similarities between D. melanogaster and D. simulans suggest clinally varying inversion polymorphisms have little influence on the genetic architecture underlying clinal divergence in size in D. melanogaster. Differing genetic architectures across different temperatures highlight the need to consider different environments in future evolutionary and molecular studies of phenotypic divergence.

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MidExDB: A database of Drosophila CNS midline cell gene expression

MidExDB: A database of Drosophila CNS midline cell gene expression: "Background:
The Drosophila CNS midline cells are an excellent model system to study neuronal and glial development because of their diversity of cell types and the relative ease in identifying and studying the function of midline-expressed genes. In situ hybridization experiments generated a large dataset of midline gene expression patterns. To help synthesize these data and make them available to the scientific community, we developed a web-accessible database.DescriptionMidExDB (Drosophila CNS Midline Gene Expression Database) is comprised of images and data from our in situ hybridization experiments that examined midline gene expression. Multiple search tools are available to allow each type of data to be viewed and compared. Descriptions of each midline cell type and their development are included as background information.
Conclusion:
MidExDB integrates large-scale gene expression data with the ability to identify individual cell types providing the foundation for detailed genetic, molecular, and biochemical studies of CNS midline cell neuronal and glial development and function. This information has general relevance for the study of nervous system development in other organisms, and also provides insight into transcriptional regulation."

Adaptive Divergence in the Thyroid Hormone Signaling Pathway in the Stickleback Radiation

Adaptive Divergence in the Thyroid Hormone Signaling Pathway in the Stickleback Radiation: "Jun Kitano, Sean C. Lema, J. Adam Luckenbach, Seiichi Mori, Yui Kawagishi, Makoto Kusakabe, Penny Swanson, Catherine L. Peichel. During adaptive radiations, animals colonize diverse environments, which requires adaptation in multiple phenotypic traits [1]. Because hormones mediate the dynamic regulation of suites of phenoty...."

Effects of personality on territory defence in communication networks: a playback experiment with radio-tagged great tits

Effects of personality on territory defence in communication networks: a playback experiment with radio-tagged great tits: "

Individuals often differ consistently in behaviour across time and contexts, and such consistent behavioural differences are commonly described as personality. Personality can play a central role in social behaviour both in dyadic interactions and in social networks. We investigated whether explorative behaviour, as proxy of personality of territorial male great tits (Parus major), predicts their own and their neighbours' territorial responses towards simulated intruders. Several weeks prior to playback, subjects were taken from the wild to test their exploratory behaviour in a standard context in the laboratory. Exploratory behaviour provides a proxy of personality along a slow–fast explorer continuum. Upon release, males were radio-tracked and subsequently exposed to interactive playback simulating a more or a less aggressive territorial intruder (by either overlapping or alternating broadcast songs with the subjects' songs). At the same time, we radio-tracked a neighbour of the playback subject. Male vocal responses during playback and spatial movements after playback varied according to male explorative behaviour and playback treatment. Males with lower exploration scores approached the loudspeaker less, and sang more songs, shorter songs and songs with slower element rates than did males with higher exploration scores. Moreover, neighbour responses were related to the explorative behaviour of the subject receiving the playback but not to their own explorative behaviour. Our overall findings reveal for the first time how personality traits affect resource defence within a communication network providing new insights on the cause of variation in resource defence behaviour.

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I just like this one because the title made me laugh...

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers: "

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

Nature Communications 1, 99 (2010). doi:10.1038/ncomms1102

Authors: Justin Crocker, Nathan Potter & Albert Erives

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Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells: "Guillaume J. Filion, Joke G. van Bemmel, Ulrich Braunschweig, Wendy Talhout, Jop Kind, Lucas D. Ward, Wim Brugman, Inês J. de Castro, Ron M. Kerkhoven, Harmen J. Bussemaker, Bas van Steensel. Chromatin is important for the regulation of transcription and other functions, yet the diversity of chromatin composition and the distribution along chromosomes are still poorly characterized. By...."

Insights Into Species Divergence and the Evolution of Hermaphroditism From Fertile Interspecies Hybrids of Caenorhabditis Nematodes [Population and evolutionary genetics]

Insights Into Species Divergence and the Evolution of Hermaphroditism From Fertile Interspecies Hybrids of Caenorhabditis Nematodes [Population and evolutionary genetics]: "

The architecture of both phenotypic variation and reproductive isolation are important problems in evolutionary genetics. The nematode genus Caenorhabditis includes both gonochoristic (male/female) and androdioecious (male/hermaprodite) species. However, the natural genetic variants distinguishing reproductive mode remain unknown, and nothing is known about the genetic basis of postzygotic isolation in the genus. Here we describe the hybrid genetics of the first Caenorhabditis species pair capable of producing fertile hybrid progeny, the gonochoristic Caenorhabditis sp. 9 and the androdioecious C. briggsae. Though many interspecies F₁ arrest during embryogenesis, a viable subset develops into fertile females and sterile males. Reciprocal parental crosses reveal asymmetry in male-specific viability, female fertility, and backcross viability. Selfing and spermatogenesis are extremely rare in XX F₁, and almost all hybrid self-progeny are inviable. Consistent with this, F₁ females do not express male-specific molecular germline markers. We also investigated three approaches to producing hybrid hermaphrodites. A dominant mutagenesis screen for self-fertile F₁ hybrids was unsuccessful. Polyploid F₁ hybrids with increased C. briggsae genomic material did show elevated rates of selfing, but selfed progeny were mostly inviable. Finally, the use of backcrosses to render the hybrid genome partial homozygous for C. briggsae alleles did not increase the incidence of selfing or spermatogenesis relative to the F₁ generation. These hybrid animals were genotyped at 23 loci, and significant segregation distortion (biased against C. briggsae) was detected at 13 loci. This, combined with an absence of productive hybrid selfing, prevents formulation of simple hypotheses about the genetic architecture of hermaphroditism. In the near future, this hybrid system will likely be fruitful for understanding the genetics of reproductive isolation in Caenorhabditis.

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