Patterns of gene conversion in duplicated yeast histones suggest strong selection on a coadapted macromolecular complex

We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies

Ocean Futures Under Ocean Acidification, Marine Protection, and Changing Fishing Pressures Explored Using a Worldwide Suite of Ecosystem Models

Ecosystem-based management (EBM) of the ocean considers all impacts on and uses of marine and coastal systems. In recent years, there has been a heightened interest in EBM tools that allow testing of alternative management options and help identify tradeoffs among human uses. End-to-end ecosystem modeling frameworks that consider a wide range of management options are a means to provide integrated solutions to the complex ocean management problems encountered in EBM. Here, we leverage the global advances in ecosystem modeling to explore common opportunities and challenges for ecosystem-based management, including changes in ocean acidification, spatial management, and fishing pressure across eight Atlantis (atlantis.cmar.csiro.au) end-to-end ecosystem models. These models represent marine ecosystems from the tropics to the arctic, varying in size, ecology, and management regimes, using a three-dimensional, spatially-explicit structure parametrized for each system. Results suggest stronger impacts from ocean acidification and marine protected areas than from altering fishing pressure, both in terms of guild-level (i.e., aggregations of similar species or groups) biomass and in terms of indicators of ecological and fishery structure. Effects of ocean acidification were typically negative (reducing biomass), while marine protected areas led to both “winners” and “losers” at the level of particular species (or functional groups). Changing fishing pressure (doubling or halving) had smaller effects on the species guilds or ecosystem indicators than either ocean acidification or marine protected areas. Compensatory effects within guilds led to weaker average effects at the guild level than the species or group level. The impacts and tradeoffs implied by these future scenarios are highly relevant as ocean governance shifts focus from single-sector objectives (e.g., sustainable levels of individual fished stocks) to taking into account competing industrial sectors\u27 objectives (e.g., simultaneous spatial management of energy, shipping, and fishing) while at the same time grappling with compounded impacts of global climate change (e.g., ocean acidification and warming)

Economic and Ecosystem Effects of Fishing on the Northeast US Shelf

Modeling tools that can demonstrate possible consequences of strategies designed to operationalize ecosystem-based fisheries management (EBFM) should be able to address tradeoffs over a wide suite of considerations representing the scope of marine management objectives. Coupled ecological-economic modeling, where models for ecological and economic subsystems are linked through their inputs and outputs, allows for quantification of such tradeoffs. Here, we link the harvest output from fishery management scenarios implemented in an end-to-end ecosystem model (Atlantis) to an input–output regional economic model for the Northeast United States to calculate changes in socio-economic indicators, including the consequences of management action for regional sales, wages, and employment. We implement three simple scenarios (maintain, decrease, or increase current fishing effort), and compare model-projected values for systematic and sector-specific indicators. Systematic indicators revealed different ecological and economic outcomes, with large ecological responses and clear tradeoffs among the catch and biomass of species groups. Economic indicators for the region responded similarly to fishery yield; however, changes in total sales did not match those in landed catch. Under increased fishing effort, a lower proportional increase in sales relative to total landed catch arose due to increased yield from lower value species groups. Average fisheries income changed little among scenarios, but was highest when effort was maintained at current levels, likely a reflection of fleet and catch stability. Our results serve to demonstrate that consequences of management may be felt disproportionately among species through the region and across different fisheries sectors. With our coupled modeling approach of passing Atlantis ecosystem model outputs to an input–output economic model, we were able to assess effects of fisheries management across a broader suite of indicators that have relevance for policymakers across multiple objectives

High collocation of sand lance and protected top predators: implications for conservation and management

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Silva, T. L., Wiley, D. N., Thompson, M. A., Hong, P., Kaufman, L., Suca, J. A., Llopiz, J. K., Baumann, H., & Fay, G. High collocation of sand lance and protected top predators: implications for conservation and management. Conservation Science and Practice, (2021): 3:e274, doi: 10.1111/csp2.274.Spatial relationships between predators and prey provide critical information for understanding and predicting climate‐induced shifts in ecosystem dynamics and mitigating human impacts. We used Stellwagen Bank National Marine Sanctuary as a case study to investigate spatial overlap among sand lance (Ammodytes dubius), a key forage fish species, and two protected predators: humpback whales (Megaptera novaeangliae) and great shearwaters (Ardenna gravis). We conducted 6 years (2013–2018) of standardized surveys and quantified spatial overlap using the global index of collocation. Results showed strong, consistent collocation among species across seasons and years, suggesting that humpback whales and great shearwater distributions are tightly linked to sand lance. We propose that identifying sand lance habitats may indicate areas where humpbacks and shearwaters aggregate and are particularly vulnerable to human activities. Understanding how sand lance influence predator distributions can inform species protection and sanctuary management under present and future scenarios.This work was supported by the Bureau of Ocean Energy Management [IA agreement M17PG0019], NOAA Stellwagen Bank National Marine Sanctuary, U.S. Geological Survey, the Volgenau Foundation, and the Mudge Foundation

A survival analysis of the gulf stream warm core rings

Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 125(10),(2020): e2020JC016507, https://doi.org/10.1029/2020JC016507.Survival of Gulf Stream (GS) warm core rings (WCRs) was investigated using a census consisting of a total of 961 rings formed during the period 1980–2017. Kaplan‐Meier survival probability and Cox hazard proportional models were used for the analysis. The survival analysis was performed for rings formed in four 5° zones between 75° W and 55° W. The radius, latitude, and distance from the shelf‐break of a WCR at formation all had a significant effect on the survival of WCRs. A pattern of higher survival was observed in WCRs formed in Zone 2 (70°–65° W) or Zone 3 (65°–60° W) and then demised in Zone 1 (75°–70° W). Survival probability of the WCRs increased to more than 70% for those formed within a latitude band from 39.5° to 41.5° N. Survival probability is reduced when the WCRs are formed near the New England Seamounts.We are grateful for financial supports from NOAA (NA11NOS0120038), NSF (OCE‐1851242), SMAST, and UMass Dartmouth. G. G. was supported by NSF under grant OCE‐1851261.2021-04-1

The contribution of geogenic particulate matter to lung disease in indigenous children

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. Indigenous children have much higher rates of ear and lung disease than non-Indigenous children, which may be related to exposure to high levels of geogenic (earth-derived) particulate matter (PM). The aim of this study was to assess the relationship between dust levels and health in Indigenous children in Western Australia (W.A.). Data were from a population-based sample of 1077 Indigenous children living in 66 remote communities of W.A. (>2,000,000 km2), with information on health outcomes derived from carer reports and hospitalisation records. Associations between dust levels and health outcomes were assessed by multivariate logistic regression in a multi-level framework. We assessed the effect of exposure to community sampled PM on epithelial cell (NuLi-1) responses to non-typeable Haemophilus influenzae (NTHi) in vitro. High dust levels were associated with increased odds of hospitalisation for upper (OR 1.77 95% CI [1.02–3.06]) and lower (OR 1.99 95% CI [1.08–3.68]) respiratory tract infections and ear disease (OR 3.06 95% CI [1.20–7.80]). Exposure to PM enhanced NTHi adhesion and invasion of epithelial cells and impaired IL-8 production. Exposure to geogenic PM may be contributing to the poor respiratory health of disadvantaged communities in arid environments where geogenic PM levels are high

Human vaccination against RH5 induces neutralizing antimalarial antibodies that inhibit RH5 invasion complex interactions.

The development of a highly effective vaccine remains a key strategic goal to aid the control and eventual eradication of Plasmodium falciparum malaria. In recent years, the reticulocyte-binding protein homolog 5 (RH5) has emerged as the most promising blood-stage P. falciparum candidate antigen to date, capable of conferring protection against stringent challenge in Aotus monkeys. We report on the first clinical trial to our knowledge to assess the RH5 antigen - a dose-escalation phase Ia study in 24 healthy, malaria-naive adult volunteers. We utilized established viral vectors, the replication-deficient chimpanzee adenovirus serotype 63 (ChAd63), and the attenuated orthopoxvirus modified vaccinia virus Ankara (MVA), encoding RH5 from the 3D7 clone of P. falciparum. Vaccines were administered i.m. in a heterologous prime-boost regimen using an 8-week interval and were well tolerated. Vaccine-induced anti-RH5 serum antibodies exhibited cross-strain functional growth inhibition activity (GIA) in vitro, targeted linear and conformational epitopes within RH5, and inhibited key interactions within the RH5 invasion complex. This is the first time to our knowledge that substantial RH5-specific responses have been induced by immunization in humans, with levels greatly exceeding the serum antibody responses observed in African adults following years of natural malaria exposure. These data support the progression of RH5-based vaccines to human efficacy testing

Measuring the Evolutionary Rewiring of Biological Networks

We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or “rewire”, at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of “commonplace” networks such as family trees, co-authorships and linux-kernel function dependencies

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

As organisms adaptively evolve to a new environment, selection results in the improvement of certain traits, bringing about an increase in fitness. Trade-offs may result from this process if function in other traits is reduced in alternative environments either by the adaptive mutations themselves or by the accumulation of neutral mutations elsewhere in the genome. Though the cost of adaptation has long been a fundamental premise in evolutionary biology, the existence of and molecular basis for trade-offs in alternative environments are not well-established. Here, we show that yeast evolved under aerobic glucose limitation show surprisingly few trade-offs when cultured in other carbon-limited environments, under either aerobic or anaerobic conditions. However, while adaptive clones consistently outperform their common ancestor under carbon limiting conditions, in some cases they perform less well than their ancestor in aerobic, carbon-rich environments, indicating that trade-offs can appear when resources are non-limiting. To more deeply understand how adaptation to one condition affects performance in others, we determined steady-state transcript abundance of adaptive clones grown under diverse conditions and performed whole-genome sequencing to identify mutations that distinguish them from one another and from their common ancestor. We identified mutations in genes involved in glucose sensing, signaling, and transport, which, when considered in the context of the expression data, help explain their adaptation to carbon poor environments. However, different sets of mutations in each independently evolved clone indicate that multiple mutational paths lead to the adaptive phenotype. We conclude that yeasts that evolve high fitness under one resource-limiting condition also become more fit under other resource-limiting conditions, but may pay a fitness cost when those same resources are abundant