Sea urchin reproductive performance in a changing ocean: Poor males improve while good males worsen in response to ocean acidification

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: The datasets supporting this article have been uploaded as part of the electronic supplementary material.Ocean acidification (OA) is predicted to be a major driver of ocean biodiversity change. At projected rates of change, sensitive marine taxa may not have time to adapt. Their persistence may depend on pre-existing inter-individual variability. We investigated individual male reproductive performance under present-day and OA conditions using two representative broadcast spawners, the sea urchins Lytechinus pictus and Heliocidaris erythrogramma. Under the non-competitive individual ejaculate scenario, we examined sperm functional parameters (e.g. swimming speed, motility) and their relationship with fertilization success under current and near-future OA conditions. Significant inter-individual differences in almost every parameter measured were identified. Importantly, we observed strong inverse relationships between individual fertilization success rate under current conditions and change in fertilization success under OA. Individuals with a high fertilization success under current conditions had reduced fertilization under OA, while individuals with a low fertilization success under current conditions improved. Change in fertilization success ranged from −67% to +114% across individuals. Our results demonstrate that while average population fertilization rates remain similar under OA and present-day conditions, the contribution by different males to the population significantly shifts, with implications for how selection will operate in a future ocean.European Union Horizon 2020Marie Curie Alumni AssociationCompany of BiologistsNSW Environmental Trus

Enhancing accuracy and precision of transparent synthetic soil modelling

Over recent years non-intrusive modelling techniques have been developed to investigate soil-structure interaction problems of increasingly complex geometry. This paper concerns the development of a small-scale, 1 g, modelling technique using a transparent analogue for soil with particle image velocimetry for internal displacement measurement. Larger model geometry achieved in this research using fine-grained transparent synthetic soils has led to an increased need for rigorous photogrammetric correction techniques. A correction framework, based upon a modified version of the pinhole camera model, is presented that corrects for lens and camera movement induced errors as well as scaling from image space to object space. An additional statistical approach is also developed to enhance the system precision, by minimising the impact of increased non-coplanarity between the photogrammetry control plane and the target plane. The enhanced data correction and statistical precision is demonstrated using a case study examining the failure mechanism around a double helical screw pile installed in transparent synthetic soil representative of a soft clay

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater)

Brown-headed Cowbirds (Molothrus ater) are the most widespread avian brood parasite in North America, laying their eggs in the nests of approximately 250 host species that raise the cowbird nestlings as their own. It is currently unknown how these heterospecific hosts influence the cowbird gut microbiota relative to other factors, such as the local environment and genetics. We test a Nature Hypothesis (positing the importance of cowbird genetics) and a Nurture Hypothesis (where the host parents are most influential to cowbird gut microbiota) using the V6 region of 16S rRNA as a microbial fingerprint of the gut from 32 cowbird samples and 16 potential hosts from nine species. We test additional hypotheses regarding the influence of the local environment and age of the birds.We found no evidence for the Nature Hypothesis and little support for the Nurture Hypothesis. Cowbird gut microbiota did not forma clade, but neither did members of the host species. Rather, the physical location, diet and age of the bird, whether cowbird or host, were the most significant categorical variables. Thus, passerine gut microbiota may be most strongly influenced by environmental factors. To put this variation in a broader context, we compared the bird data to a fecal microbiota dataset of 38 mammal species and 22 insect species. Insects were always the most variable; on some axes, we found more variation within cowbirds than across all mammals. Taken together, passerine gut microbiota may be more variable and environmentally determined than other taxonomic groups examined to date. © 2014 Hird et al

Poor fit to the multispecies coalescent is widely detectable in empirical data

Model checking is a critical part of Bayesian data analysis, yet it remains largely unused in systematic studies. Phylogeny estimation has recently moved into an era of increasingly complex models that simultaneously account for multiple evolutionary processes, the statistical fit of these models to the data has rarely been tested. Here we develop a posterior predictive simulation-based model check for a commonly used multispecies coalescent model, implemented in *BEAST, and apply it to 25 published data sets. We show that poor model fit is detectable in the majority of data sets; that this poor fit can mislead phylogenetic estimation; and that in some cases it stems from processes of inherent interest to systematists. We suggest that as systematists scale up to phylogenomic data sets, which will be subject to a heterogeneous array of evolutionary processes, critically evaluating the fit of models to data is an analytical step that can no longer be ignored. [Gene duplication and extinction; gene tree; hybridization; model fit; multispecies coalescent; next-generation sequencing; posterior predictive simulation; species delimitation; species tree.] © The Author(s) 2013

Many Body Theory of Charge Transfer in Hyperthermal Atomic Scattering

We use the Newns-Anderson Hamiltonian to describe many-body electronic processes that occur when hyperthermal alkali atoms scatter off metallic surfaces. Following Brako and Newns, we expand the electronic many-body wavefunction in the number of particle-hole pairs (we keep terms up to and including a single particle-hole pair). We extend their earlier work by including level crossings, excited neutrals and negative ions. The full set of equations of motion are integrated numerically, without further approximations, to obtain the many-body amplitudes as a function of time. The velocity and work-function dependence of final state quantities such as the distribution of ion charges and excited atomic occupancies are compared with experiment. In particular, experiments that scatter alkali ions off clean Cu(001) surfaces in the energy range 5 to 1600 eV constrain the theory quantitatively. The neutralization probability of Na$^+$ ions shows a minimum at intermediate velocity in agreement with the theory. This behavior contrasts with that of K$^+$, which shows ... (7 figures, not included. Figure requests: [email protected])Comment: 43 pages, plain TeX, BUP-JBM-

Localisation of RNAs into the germ plasm of vitellogenic xenopus oocytes

We have studied the localisation of mRNAs in full-grown Xenopus laevis oocytes by injecting fluorescent RNAs, followed by confocal microscopy of the oocyte cortex. Concentrating on RNA encoding the Xenopus Nanos homologue, nanos1 (formerly Xcat2), we find that it consistently localised into aggregated germ plasm ribonucleoprotein (RNP) particles, independently of cytoskeletal integrity. This implies that a diffusion/entrapment-mediated mechanism is active, as previously reported for previtellogenic oocytes. Sometimes this was accompanied by localisation into scattered particles of the “late”, Vg1/VegT pathway; occasionally only late pathway localisation was seen. The Xpat RNA behaved in an identical fashion and for neither RNA was the localisation changed by any culture conditions tested. The identity of the labelled RNP aggregates as definitive germ plasm was confirmed by their inclusion of abundant mitochondria and co-localisation with the germ plasm protein Hermes. Further, the nanos1/Hermes RNP particles are interspersed with those containing the germ plasm protein Xpat. These aggregates may be followed into the germ plasm of unfertilized eggs, but with a notable reduction in its quantity, both in terms of injected molecules and endogenous structures. Our results conflict with previous reports that there is no RNA localisation in large oocytes, and that during mid-oogenesis even germ plasm RNAs localise exclusively by the late pathway. We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. Our results support the view that mechanistically the two modes of localisation are extremely similar, and that in an injection experiment RNAs might utilise either pathway, the distinction in fates being very subtle and subject to variation. We discuss these results in relation to their biological significance and the results of others