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bioRxiv2019

Viruses of the eukaryotic plankton are predicted to increase carbon export efficiency in the global sunlit ocean

The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earths carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral "shunt" and "shuttle"). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

ecology↗

bioRxiv2019

How range residency and long-range perception change encounter rates

Encounter rates link movement strategies to intra- and inter-specific interactions, and therefore translate individual movement behavior into higher-level ecological processes. Indeed, a large body of interacting population theory rests on the law of mass action, which can be derived from assumptions of Brownian motion in an enclosed container with exclusively local perception. These assumptions imply completely uniform space use, individual home ranges equivalent to the population range, and encounter dependent on movement paths actually crossing. Mounting empirical evidence, however, suggests that animals use space non-uniformly, occupy home ranges substantially smaller than the population range, and are often capable of nonlocal perception. Here, we explore how these empirically supported behaviors change pairwise encounter rates. Specifically, we derive novel analytical expressions for encounter rates under Ornstein-Uhlenbeck motion, which features non-uniform space use and allows individual home ranges to differ from the population range. We compare OU-based encounter predictions to those of Reflected Brownian Motion, from which the law of mass action can be derived. For both models, we further explore how the interplay between the scale of perception and home range size affects encounter rates. We find that neglecting realistic movement and perceptual behaviors can systematically bias encounter rate predictions.

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bioRxiv2019

Seagrass mediates microalgal community structure at a distance

Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for thirteen major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least fifteen meters outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming Harmful Algal Blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.

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bioRxiv2019

Habitat affinity and density-dependent movement as indicators of fish habitat restoration efficacy

Conceptual and methodological tools from behavioral ecology can inform studies of habitat quality and their potential for evaluating habitat restoration in conservation efforts is explored here. Such approaches provide mechanistic detail in understanding the relationship between organisms and their habitats and are thus more informative than correlations between density and habitat characteristics. Several Pacific salmon species have been the target of habitat restoration efforts for the past 2-3 decades, but most post-restoration effectiveness studies have been limited to correlative data described above. In mark-recapture assays from four different study years, the affinity of sub-yearling Chinook salmon (Oncorhynchus tschawytscha) and steelhead (O. mykiss) for stream pools restored with or created by engineered log structures was greater than that for pools without restoration, though with high interannual variability. From corresponding distribution and density data, it was clear that habitat affinity data are not always concordant with single observations of density. The same was true of the correlation between either affinity or density and physical characteristics of pools, although depth and current velocity had some explanatory power for both responses in Chinook. Movement into pools by Chinook during the assays indicated that restored pools can support more immigrants at a given density than can unrestored pools; however no such pattern emerged for steelhead. Variation among individuals in body condition has implications for population-wide fitness, and such low variation was correlated with stronger affinity for pools in Chinook regardless of restoration status. This suggests that pools may mediate habitat-related trade-offs and that restoring them might have a positive effect on fitness. Thus affinity, immigration, and condition data give much-needed mechanistic indication of habitat selection for restored habitat via an apparent capacity increase and those potential fitness benefits. This is stronger support for restoration effectiveness than density differences alone because density data 1) may simply indicate redistribution of fish from poor to good habitats and 2) are not adequate to show correlations between restoration and positive change in traits correlated with fitness.

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bioRxiv2019

Arbovirus Vectors of Epidemiological Concern in the Americas: A Scoping Review of Entomological Studies on Zika, Dengue and Chikungunya Virus Vectors

BackgroundThree arthorpod-borne viruses (arboviruses) causing human disease have been the focus of a large number of studies in the Americas since 2013 due to their global spread and epidemiological impacts: Zika, dengue, and chikungunya viruses. A large proportion of infections by these viruses are asymptomatic. However, all three viruses are associated with moderate to severe health consequences in a small proportion of cases. Two mosquito species, Aedes aegypti and Aedes albopictus, are among the worlds most prominent arboviral vectors, and are known primary vectors for all three viruses in the Americas.\n\nObjectivesThis review summarizes the state of the entomological literature surrounding the biology and ecology of vectors of Zika, dengue and chikungunya viruses and factors affecting virus transmission. The rationale of the review was to elucidate consensus and discord between studies, and guide future research based on identified knowledge gaps.\n\nResultsA total of 196 studies were included in the scoping review after initial screening and subsequent exclusion of out-of-scope studies, secondary data publications, duplicate records, and studies unavailable in English language.\n\nKey findingsTemperature and humidity have the strongest impact on mosquito distribution and dynamics, development of immatures and arborviral infection rates. Low socioeconomic status and related factors, including poor infrastructure, inconsistent access to water, and high household resident density, have been consistently associated with arbovirus vector occurrence. Effects of interspecific competition on arboviral vector species is currently poorly understood. Vector competence for Zika virus is well established for Ae. aegypti and Ae. albopictus. Information on Zika virus vector transmission dynamics is sparse in contrast to the wealth of research available for dengue and chikungunya viruses.\n\nConclusionsBased on the internationally recognized urgency of Zika virus infection as a public health concern, further research on arbovirus vectors and transmission dynamics is of pressing need.

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bioRxiv2019

Hydrothermal activity and water mass composition shape microbial eukaryote diversity and biogeography in the Okinawa Trough

Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but factors shaping protist diversity, such as dispersal barriers and environmental selection, remain difficult to parse. Deep-sea water masses, which form geographic barriers, and hydrothermal vents, which represent isolated productivity hotspots, are ideal opportunities for studying the effects of dispersal barriers and environmental selection on protist communities. The Okinawa Trough, a deep, back-arc spreading basin, contains distinct water masses in the bottom waters of northern and southern regions and at least twenty-five active hydrothermal vents. In this study, we used metabarcoding to characterize protist communities from fourteen stations spanning the length of the Okinawa Trough, including three hydrothermal vent sites. Significant differences in community structure reflecting regional oceanography and water mass composition were present, indicating the importance of geographic factors in shaping protist communities. Protist communities in bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.

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bioRxiv2019

PyLandStats: An open-source Pythonic library to compute landscape metrics

Quantifying the spatial pattern of landscapes has become a common task of many studies in landscape ecology. Most of the existing software to compute landscape metrics is not well suited to be used in interactive environments such as Jupyter notebooks nor to be included as part of automated computational workflows. This article presents PyLandStats, an open-source Python library to compute landscape metrics within the scientific Python stack. The PyLandStats package provides a set of methods to undertake recurrent approaches to quantify landscape patterns, such as the analysis of the spatiotemporal patterns of land use/land cover change or gradient analysis. The implementation is based on the prevailing Python libraries for geospatial data analysis in a way that they can be forthwith integrated into complex computational workflows. Notably, the provided methods offer a large variety of options so that users can employ PyLandStats in the way that best supports their needs. The source code is publicly available, and is organized in a modular object-oriented structure that enhances its maintainability and extensibility.

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bioRxiv2019

New residential perennial floras reflect distinctive decisions of residential developers and new homeowners

Urban patterns reflect the people who build and manage urban space. However, most field research on residential vegetation focuses on household or neighborhood preferences, norms, or socioeconomic drivers of observed patterns and plant traits. Very few urban ecology researchers have studied residential real estate developers, who configure the space and establish the initial plant communities. How do the landscaping decisions of developers and homeowners shape residential perennial floras? To answer this question, I collected a stratified random sample of perennials at 60 newly built and sold homes in the Seattle, WA area. Through field sampling, conversations with new homeowners, and archival research, I assigned each individual perennial to one of three origins: remnant, planted by developers, or planted by homeowners. After describing landscaping decisions using plant traits (as presented in gardening literature), I evaluated whether planting decisions of developers and homeowners were heterogeneous and whether urban form or economic drivers influenced planted species richness. I also tested whether homeowner yard and plant buying preferences could be linked to planted richness. Given that developers and homeowners have different incentives, I hypothesized that they would choose different types of perennials and that urban metrics related to area and economics would increase species richness. I also predicted that homeowner preferences would be linked to species richness patterns. Developers planted most of the trees, shrubs, and graminoids. Homeowners planted fewer woody and more herbaceous perennial species. Parcel planting area, wealth related metrics, and parcel density increased species richness for some perennials. However, homeowner preferences were stronger predictors of their planting behavior than urban metrics. Because assembly of residential perennial flora communities is heterogeneous, future investigations in other urban ecosystems should incorporate preferences of developers and homeowners, site-specific constraints, and broader scale influences. More work is needed to understand developer incentives and preferences.

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bioRxiv2019

On Some Problems of Estimating Fundamental Niche from Physiological Data

Hutchinson proposed the idea of the fundamental niche, determined by physiological properties of a species, more than 50 years ago. The idea remains both central to ecological thinking and largely unexplored experimentally. In this note, we describe some problems of using physiological experiments databases to estimate fundamental niches, show some solutions, and the apply our solution to testing the prediction that fundamental niches contain realized niches, for some species of marine fishes and terrestrial beetles. Our results were concordant with Hutchinsons predictions.

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bioRxiv2019

Identifying the fitness consequences of sex in complex natural environments

In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. Here we use a large-scale transplant experiment of a North American wildflower to show that sex is associated with reduced lifetime fitness, despite lower herbivory. We separate the effects of sex from hybridity, finding that over-winter survival is elevated in asexuals regardless of hybridity, but herbivores target hybrid asexuals. Survival is lowest in homozygous sexual lineages, implicating inbreeding depression as a cost of sex. Our results show that the consequences of sex are shaped by complex natural environments, correlated traits, and the identity of mates, rather than sex itself.

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bioRxiv2019

Microbial degradation of plastic in aqueous solutions demonstrated by CO2 evolution and quantification.

The environmental accumulation of plastics worldwide is a consequence of the durability of the material. Alternative polymers, marketed as biodegradable, present a potential solution to mitigate their ecological damage. However, understanding of biodegradability has been hindered by a lack of reproducible testing methods. Here, we present a new approach to assess biodegradability by monitoring bacterial respiration, in an aqueous media supplemented with a polymer as a single carbon source. Rhodococcus rhodochrous and Alcanivorax borkumensis are good model organisms for soil and marine systems respectively, allowing simulations of plastic biodegradation in these key environments. We demonstrate that polymer molecular weight reduction is the critical factor in the biodegradability of low-density polyethylene. Additionally, we tested a wide variety of plastics, including environmentally weathered and laboratory aged samples, using the same method allowing direct comparisons of the relative biodegradability of various polymers.

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bioRxiv2019

Disease as an evolutionary weapon

Disease and predation are both highly important in ecology, and pathogens with multiple host species have turned out to be common. Nonetheless, the interplay between multi-host epidemics and predation has received relatively little attention. Here, we analyse a model of a predator-prey system with disease in both prey and predator populations and determine reasonable parameter values using allometric mass scaling relations. Our analysis focuses on the possibility of extinction events rather than the linear stability of the model equations. We find that if the predator is a specialist, epidemics frequently drive the predator species to extinction. If the predator has an additional, immune prey species, predators will usually survive. Coexistence of predator and disease is impossible in the single-prey model. We conclude that for the prey species, carrying a pathogen can be an effective weapon against predators, and that being a generalist is a major advantage for a predator.

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bioRxiv2019

Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus

Changing ocean conditions driven by anthropogenic activity may have a negative impact on fisheries by increasing stress and disease with the mucosal microbiome as a potentially important intermediate role. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, GI, and pyloric caeca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning one year from the Scripps Institution of Oceanography Pier, making this the largest and longest wild marine fish microbiome survey. Mucosal sites had unique communities significantly different from the surrounding sea water and sediment communities with over 10 times more diversity than sea water alone. Although, external surfaces such as skin and gill were more similar to sea water, digesta was similar to sediment. Both alpha and beta diversity of the skin and gill was explained by environmental and biological factors, especially sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by migrations of chub mackerel sub-populations by nanopore sequencing a 14 769 bp region of the 16 568 bp mitochondria. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year, but highest in the skin, GI, and digesta between June and September. Our study evaluates the extent which the environment and host biology drives mucosal microbial ecology, establishing a baseline for long term monitoring surveys for linking environment stressors to mucosal health of wild marine fish.

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bioRxiv2019

Grazer behavior can regulate large-scale patterns of community states

Ecosystem patterning can arise from environmental heterogeneity, biological feedbacks that produce multiple persistent ecological states, or their interaction. One source of feed-backs is density-dependent changes in behavior that regulates species interactions. By fitting state-space models to large-scale ([~]500km) surveys on temperate rocky reefs, we find that behavioral feedbacks best explain why kelp and urchin barrens form either reef-wide patches or local mosaics. Best-supported models in California include feedbacks where starvation intensifies grazing across entire reefs create reef-scale, alternatively stable kelp- and urchin-dominated states (32% of reefs). Best-fitting models in New Zealand include the feedback of urchins avoiding dense kelp stands that can increase abrasion and predation risk, which drives a transition from shallower urchin-dominated to deeper kelp-dominated zones, with patchiness at 3-8m depths with intermediate wave stress. Connecting locally-studied processes with region-wide data, we highlight how behavior can explain community patterning and why some systems exhibit community-wide alternative stable states.

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bioRxiv2019

Temporal dynamics of nitrogen cycle gene diversity in a hyporheic microbiome

Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness-- defined as the number of unique within-gene phylotypes--across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that (1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and (2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.

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bioRxiv2019

Effects of trap confinement on personality measurements in two terrestrial rodents

In recent years individual differences in the behavior of animals, or personalities, have been shown to influence the response of individuals to changing environments and have important ecological implications. As researchers strive to understand and predict the responses of individuals and populations to anthropogenic changes, personality studies in wild populations will likely continue to increase. Studies of personality in wild populations often require that animals are live-trapped before behavioral observation can occur; however, it is unknown what impact live trapping may have on the behavior of trapped individuals. Specifically, if the duration of trap confinement directly influences behavior, then by obtaining wild animals through live-trapping are we confounding the very measurements we are most interested in? To investigate this question, we performed a study using two small mammal species. We positioned high-definition trail cameras on Longworth small mammal traps in the field to observe capture events and record the time of capture. We then measured personality in captured deer mice (Peromyscus maniculatus) and southern red-backed voles (Myodes gapperi) using three standardized tests. With a repeatability analysis, we confirmed which behaviors could be considered personality traits, and through linear and generalized linear models, we found that the time an animal had spent confined to a trap before testing did not affect the majority of behaviors exhibited. Our results showed two weak behavioral effects of confinement duration on boldness and docility depending on whether an individual had been trapped previously. Our results suggest that personality measurements of wild, trapped small mammals are not determined by trapping procedures, but that researchers should control for whether an animal is naive to trapping during analysis.

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bioRxiv2019

Impact of global warming on insects: are tropical species more vulnerable than temperate species?

The magnitude and ecological impact of climate change varies with latitude. Several recent models have shown that tropical ectotherms face the greatest risk from warming because they currently experience temperatures much closer to their physiological optimum than temperate taxa. Even a small increase in temperature may thus result in steep fitness declines in tropical species but increased fitness in temperate species. This prediction, however, is based on a model that does not account for latitudinal differences in activity periods. Temperate species in particular may often experience considerably higher temperatures than expected during the active season. Here, we integrate data on insect warming tolerance and temperature-dependent development to re-evaluate latitudinal trends in thermal safety margins after accounting for latitudinal trends in insect seasonal activity. Our analyses suggest that temperate and tropical species differ far less in thermal safety margins than commonly assumed, and thus face a similar risk from warming.

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bioRxiv2019

Density-dependent effects of mortality on the optimal body size of a habitat shift: Why smaller is better despite increased mortality risk?

Many animal species across different taxa change their habitat during their development. An ontogenetic habitat shift enables the development of early vulnerable-to-predation stages in a safe nursery habitat with reduced predation mortality, while less vulnerable stages can exploit a more risky, rich feeding habitat. Therefore, the timing of the habitat shift is crucial for individual fitness. We investigate the effect that size-selectivity in mortality in the rich feeding habitat has on the optimal timing of the habitat shift using a population model and the adaptive dynamics approach. We show that the size-selective nature of mortality in this habitat affects density-dependent body growth rate in the nursery habitat and thus the optimal timing of the habitat shift. This is caused by the effect exerted by size-dependent mortality on the size distribution of the population that results in strong competition in the nursery habitat. We furthermore find that, as a consequence of this effect, increased size-selectivity in mortality in the rich feeding habitat causes the optimal body size to shift habitat to decrease. Our results reveal the interdependence between population structure and life history traits, and highlight the need for integrating ecological interactions in the study of the evolution of life histories.

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