Biogeographic calibrations for the molecular clock

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.     

The locus of sexual selection: moving sexual selection studies into the post‐genomics era

Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.     

Resolving the value of the dingo in ecological restoration

There is global interest in restoring populations of apex predators, both to conserve them and to harness their ecological services. In Australia, reintroduction of dingoes (Canis dingo) has been proposed to help restore degraded rangelands. This proposal is based on theories and the results of studies suggesting that dingoes can suppress populations of prey (especially medium‐ and large‐sized herbivores) and invasive predators such as red foxes (Vulpes vulpes) and feral cats (Felis catus) that prey on threatened native species. However, the idea of dingo reintroduction has met opposition, especially from scientists who query the dingo's positive effects for some species or in some environments. Here, we ask ‘what is a feasible experimental design for assessing the role of dingoes in ecological restoration?’ We outline and propose a dingo reintroduction experiment—one that draws upon the existing dingo‐proof fence—and identify an area suitable for this (Sturt National Park, western New South Wales). Although challenging, this initiative would test whether dingoes can help restore Australia's rangeland biodiversity, and potentially provide proof‐of‐concept for apex predator reintroductions globally.     

Lethal ovitrap deployment for Aedes aegypti control: potential implications for non‐target organisms

In Australia, dengue control combines source reduction with lethal ovitraps to reduce Aedes aegypti populations during outbreaks. Lethal ovitraps are considered a sustainable and environmentally friendly method of controlling container‐inhabiting mosquitoes, however, to‐date, this claim has not been quantified. This study assesses the potential impact of lethal ovitraps on non‐target organisms when used to control Ae. aegypti in tropical Australia. For retention of specimens, we substituted standard sticky ovitraps for lethal ovitraps. We collected 988 Ae. aegypti and 44,132 non‐target specimens over 13 months from 16 sites. Although Ae. aegypti comprised only 2.2% of the total collection, they were were the eighth most dominant taxa collected, on the 93^rd percentile. Of the non‐target organisms, Collembola were the dominant taxa, 44.2%, with 36.8% and 10.5% Diptera and Hymenoptera, respectively. Of the Dipterans, 61% were family Phoridae. Lethal ovitraps were visited by 90 insect or invertebrate families in total. Ovitraps are attractive to Collembola, Phoridae, Sciaridae, Formicidae, and Culicidae, with minimal attraction by Apidae and other commonly monitored non‐target organisms. For container‐inhabiting mosquitoes, LOs are cost effective operationally, requiring minimal staff resources for placement and retrieval.     

Emerging Object Representations in the Visual System Predict Reaction Times for Categorization

Recognizing an object takes just a fraction of a second, less than the blink of an eye. Applying multivariate pattern analysis, or “brain decoding”, methods to magnetoencephalography (MEG) data has allowed researchers to characterize, in high temporal resolution, the emerging representation of object categories that underlie our capacity for rapid recognition. Shortly after stimulus onset, object exemplars cluster by category in a high-dimensional activation space in the brain. In this emerging activation space, the decodability of exemplar category varies over time, reflecting the brain’s transformation of visual inputs into coherent category representations. How do these emerging representations relate to categorization behavior? Recently it has been proposed that the distance of an exemplar representation from a categorical boundary in an activation space is critical for perceptual decision-making, and that reaction times should therefore correlate with distance from the boundary. The predictions of this distance hypothesis have been born out in human inferior temporal cortex (IT), an area of the brain crucial for the representation of object categories. When viewed in the context of a time varying neural signal, the optimal time to “read out” category information is when category representations in the brain are most decodable. Here, we show that the distance from a decision boundary through activation space, as measured using MEG decoding methods, correlates with reaction times for visual categorization during the period of peak decodability. Our results suggest that the brain begins to read out information about exemplar category at the optimal time for use in choice behaviour, and support the hypothesis that the structure of the representation for objects in the visual system is partially constitutive of the decision process in recognition.     

Mitochondrial damage contributes to Pseudomonas aeruginosa activation of the inflammasome and is downregulated by autophagy

The nucleotide-binding domain, leucine-rich repeat containing family caspase recruitment domain containing 4 (NLRC4) inflammasome can be activated by pathogenic bacteria via products translocated through the microbial type III secretion apparatus (T3SS). Recent work has shown that activation of the NLRP3 inflammasome is downregulated by autophagy, but the influence of autophagy on NLRC4 activation is unclear. We set out to determine how autophagy might influence this process, using the bacterium Pseudomonas aeruginosa, which activates the NLRC4 inflammasome via its T3SS. Infection resulted in T3SS-dependent mitochondrial damage with increased production of reactive oxygen intermediates and release of mitochondrial DNA. Inhibiting mitochondrial reactive oxygen release or degrading intracellular mitochondrial DNA abrogated NLRC4 inflammasome activation. Moreover, macrophages lacking mitochondria failed to activate NLRC4 following infection. Removal of damaged mitochondria by autophagy significantly attenuated NLRC4 inflammasome activation. Mitochondrial DNA bound specifically to NLRC4 immunoprecipitates and transfection of mitochondrial DNA directly activated the NLRC4 inflammasome; oxidation of the DNA enhanced this effect. Manipulation of autophagy altered the degree of inflammasome activation and inflammation in an in vivo model of P. aeruginosa infection. Our results reveal a novel mechanism contributing to NLRC4 activation by P. aeruginosa via mitochondrial damage and release of mitochondrial DNA triggered by the bacterial T3SS that is downregulated by autophagy.     

Molecular Characterization of Notch1 Positive Progenitor Cells in the Developing Retina

The oscillatory expression of Notch signaling in neural progenitors suggests that both repressors and activators of neural fate specification are expressed in the same progenitors. Since Notch1 regulates photoreceptor differentiation and contributes (together with Notch3) to ganglion cell fate specification, we hypothesized that genes encoding photoreceptor and ganglion cell fate activators would be highly expressed in Notch1 receptor-bearing (Notch1⁺) progenitors, directing these cells to differentiate into photoreceptors or into ganglion cells when Notch1 activity is diminished. To identify these genes, we used microarray analysis to study expression profiles of whole retinas and isolated from them Notch1⁺ cells at embryonic day 14 (E14) and postnatal day 0 (P0). To isolate Notch1⁺ cells, we utilized immunomagnetic cell separation. We also used Notch3 knockout (Notch3KO) animals to evaluate the contribution of Notch3 signaling in ganglion cell differentiation. Hierarchical clustering of 6,301 differentially expressed genes showed that Notch1⁺ cells grouped near the same developmental stage retina cluster. At E14, we found higher expression of repressors (Notch1, Hes5) and activators (Dll3, Atoh7, Otx2) of neuronal differentiation in Notch1⁺ cells compared to whole retinal cell populations. At P0, Notch1, Hes5, and Dll1 expression was significantly higher in Notch1⁺ cells than in whole retinas. Otx2 expression was more than thirty times higher than Atoh7 expression in Notch1⁺ cells at P0. We also observed that retinas of wild type animals had only 14% (P < 0.05) more ganglion cells compared to Notch3KO mice. Since this number is relatively small and Notch1 has been shown to contribute to ganglion cell fate specification, we suggested that Notch1 signaling may play a more significant role in RGC development than the Notch3 signaling cascade. Finally, our findings suggest that Notch1⁺ progenitors—since they heavily express both pro-ganglion cell (Atoh7) and pro-photoreceptor cell (Otx2) activators—can differentiate into either ganglion cells or photoreceptors.