Complex rift geometries resulting from inheritance of pre-existing structures: Insights and regional implications from the Barmer Basin rift

Structural studies of the Barmer Basin in Rajasthan, northwest India, demonstrate the important effect that pre-existing faults can have on the geometries of evolving fault systems at both the outcrop and basin-scale. Outcrop exposures on opposing rift margins reveal two distinct, non-coaxial extensional events. On the eastern rift margin northwest–southeast extension was accommodated on southwest- and west-striking faults that form a complex, zig-zag fault network. On the western rift margin northeast–southwest extension was accommodated on northwest-striking faults that form classical extensional geometries. Combining these outcrop studies with subsurface interpretations demonstrates that northwest–southeast extension preceded northeast–southwest extension. Structures active during the early, previously unrecognised extensional event were variably incorporated into the evolving fault systems during the second. In the study area, an inherited rift-oblique fault transferred extension from the rift margin to a mid-rift fault, rather than linking rift margin fault systems directly. The resultant rift margin accommodation structure has important implications for early sediment routing and depocentre evolution, as well as wider reaching implications for the evolution of the rift basin and West Indian Rift System. The discovery of early rifting in the Barmer Basin supports that extension along the West Indian Rift System was long-lived, multi-event, and likely resulted from far-field plate reorganisations

Complex rift geometries resulting from inheritance of pre-existing structures: Insights and regional implications from the Barmer Basin rift

Structural studies of the Barmer Basin in Rajasthan, northwest India, demonstrate the important effect that pre-existing faults can have on the geometries of evolving fault systems at both the outcrop and basin-scale. Outcrop exposures on opposing rift margins reveal two distinct, non-coaxial extensional events. On the eastern rift margin northwest–southeast extension was accommodated on southwest- and west-striking faults that form a complex, zig-zag fault network. On the western rift margin northeast–southwest extension was accommodated on northwest-striking faults that form classical extensional geometries.Combining these outcrop studies with subsurface interpretations demonstrates that northwest–southeast extension preceded northeast–southwest extension. Structures active during the early, previously unrecognised extensional event were variably incorporated into the evolving fault systems during the second. In the study area, an inherited rift-oblique fault transferred extension from the rift margin to a mid-rift fault, rather than linking rift margin fault systems directly. The resultant rift margin accommodation structure has important implications for early sediment routing and depocentre evolution, as well as wider reaching implications for the evolution of the rift basin and West Indian Rift System. The discovery of early rifting in the Barmer Basin supports that extension along the West Indian Rift System was long-lived, multi-event, and likely resulted from far-field plate reorganisations

Origin of Lower Cretaceous Quartzose Arenites in northern India and the Indus Basins of Pakistan – the result of provenance composition, weathering or diagenesis?

Lower Cretaceous (Aptian-Albian) sandstones of the Ghaggar-Hakra Formation in the Barmer Basin of northwest Rajasthan, India, have a complex depositional history which is confusing given they are quartzose arenites. The heavy mineral grains are very well-rounded and the assemblage is dominated by zircon and rutile grains suggesting that the sediments have been recycled multiple times, whilst the presence of staurolite indicates a metapelite provenance component. Petrographical analysis suggests that extreme diagenesis cannot account for the quartzose arenite composition, despite Early Cretaceous soil formation and at least two periods of subsequent telogenetic modification. An alternative explanation to extreme chemical weathering in the provenance area is that the Ghaggar-Hakra sandstones are multi-cycle sediments derived, at least in part, from the quartzose arenites of the Cambrian Jodhpur Group.This analysis suggest that variations in detrital mineralogy across the Western India Rift System and Indus Basins are the result of transcontinental fluvial transport systems sourcing sediment from specific basement highs (Nagar Parker High, Devikot High, Deodar Ridge and Aravalli Mountain Range) mixed with varying proportions of sediment derived from sandstones of the Jodhpur Group. Consequently, we suggest that Cretaceous fluvial systems were controlled by the local palaeogeographies within the failed rifts of the Barmer and Cambay Basins, and that both basins formed barriers to sediment transport from the Aravalli Mountain Range across the north-west Indian plate and into surrounding basins

Do Individual Females Differ Intrinsically in Their Propensity to Engage in Extra-Pair Copulations?

BACKGROUND: While many studies have investigated the occurrence of extra-pair paternity in wild populations of birds, we still know surprisingly little about whether individual females differ intrinsically in their principal readiness to copulate, and to what extent this readiness is affected by male attractiveness. METHODOLOGY/FINDINGS: To address this question I used captive zebra finches (Taeniopygia guttata) as a model system. I first measured female readiness to copulate when courted by a male for the first time in life. Second, I conducted choice-chamber experiments to assess the mating preferences of individual females prior to pair formation. I then paired females socially with a non-desired mate and once they had formed a stable pair bond, I observed the inclination of these females to engage in extra-pair copulations with various males. Females showing a high readiness to copulate when courted by a male for the first time in life were much more likely to engage in extra-pair copulations later in life than others. Male attractiveness, as measured in choice tests, was a useful predictor of whether females engaged in extra-pair copulations with these males, but, surprisingly, the attractiveness of a female's social partner had no effect on her fidelity. However, it remained unclear what made some males more attractive than others. Contrary to a widespread but rarely tested hypothesis, females did not preferentially copulate with males having a redder beak or singing at a higher rate. Rather it seemed that song rate was a confounding factor in choice-chamber experiments: song attracted the female's attention but did not increase the male's attractiveness as a copulation partner. CONCLUSIONS/SIGNIFICANCE: Intrinsic variation in female readiness to copulate as well as variation in the attractiveness of the extra-pair male but not the social partner decided the outcome of extra-pair encounters

Getting a Head Start: Diet, Sub-Adult Growth, and Associative Learning in a Seed-Eating Passerine

Developmental stress, and individual variation in response to it, can have important fitness consequences. Here we investigated the consequences of variable dietary protein on the duration of growth and associative learning abilities of zebra finches, Taeniopygia guttata, which are obligate graminivores. The high-protein conditions that zebra finches would experience in nature when half-ripe seed is available were mimicked by the use of egg protein to supplement mature seed, which is low in protein content. Growth rates and relative body proportions of males reared either on a low-protein diet (mature seed only) or a high-protein diet (seed plus egg) were determined from body size traits (mass, head width, and tarsus) measured at three developmental stages. Birds reared on the high-protein diet were larger in all size traits at all ages, but growth rates of size traits showed no treatment effects. Relative head size of birds reared on the two diets differed from age day 95 onward, with high-diet birds having larger heads in proportion to both tarsus length and body mass. High-diet birds mastered an associative learning task in fewer bouts than those reared on the low-protein diet. In both diet treatments, amount of sub-adult head growth varied directly, and sub-adult mass change varied inversely, with performance on the learning task. Results indicate that small differences in head growth during the sub-adult period can be associated with substantial differences in adult cognitive performance. Contrary to a previous report, we found no evidence for growth compensation among birds on the low-protein diet. These results have implications for the study of vertebrate cognition, developmental stress, and growth compensation

Exploration Behaviour Is Not Associated with Chick Provisioning in Great Tits

In biparental systems, members of the same pair can vary substantially in the amount of parental care they provide to offspring. The extent of this asymmetry should depend on the relative costs and benefits of care. Individual variation in personality is likely to influence this trade-off, and hence is a promising candidate to explain differences in care. In addition, plasticity in parental care may also be associated with personality differences. Using exploration behaviour (EB) as a measure of personality, we investigated these possibilities using both natural and experimental data from a wild population of great tits (Parus major). Contrary to predictions, we found no association between EB and natural variation in provisioning behaviour. Nor was EB linked to responsiveness to experimentally increased brood demand. These results are initially surprising given substantial data from other studies suggesting personality should influence investment in parental care. However, they are consistent with a recent study showing selection on EB is weak and highly context-specific in the focal population. This emphasises the difficulty faced by personality studies attempting to make predictions based on previous work, given that personalities often vary among populations of the same species

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence–structure–function relationships

Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods