Biology subjects

Harvey, E.

Publications and source records attributed to Harvey, E..

29 records · Page 2Linked to original sources

bioRxiv2020

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus - each of which have a diverse host range. Members of the genus Hepacivirus are associated with a diverse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the diversity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae, comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co-divergence over evolutionary time-scales.

microbiology↗

bioRxiv2020

Patch size distribution and network connectivity affect species invasion dynamics in dendritic networks

Biological invasions are globally affecting ecosystems, causing local species loss and altering ecosystem functioning. Understanding the success and unfolding of such biological invasions is thus of high priority. Both local properties and the spatial network structure have been shown to be determinants of invasion success, and the identification of spatial invasion hubs directly promoting invasion dynamics is gaining attention. Spatial dynamics, however, could also indirectly alter invasion success by shaping local community structure: in many ecosystems, such as riverine networks, regional properties such as patch size distribution are known drivers of local community structures, which themselves may affect the establishment success of invading species. Using microcosm experiments in dendritic networks, we disentangled how patch size distribution and dispersal along specific network topologies shaped local communities, and, subsequently, affected the establishment success of invading species. We find that inherent patch size distributions shaped composition and diversity of local communities, and, subsequently, modulated invasion success. Specifically, the relationship between local diversity and invasion success changed across an increasing patch size gradient from a negative to a positive correlation, while overall increasing patch size reduced invasion success. Connectivity did not have a direct effect on invasion success but indirectly affected invasions by shaping diversity patterns in the whole network. Our results emphasize the relevance of indirect, landscape-level effects on species invasions, which need to be considered in the management of spatial habitat networks.

ecology↗

bioRxiv2019

Sustained virome diversity in Antarctic penguins and their ticks: geographical connectedness and no evidence for low pathogen pressure

Despite its isolation and extreme climate, Antarctica is home to diverse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. However, there is a limited understanding of virome diversity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To test the idea that penguins have limited microbial diversity we determined the viromes of three species of penguins and their ticks sampled on the Antarctic peninsula. Using total RNA-Sequencing we identified 107 viral species, comprising likely penguin associated viruses (n = 13), penguin diet and microbiome associated viruses (n = 82) and tick viruses (n = 8), two of which may have the potential to infect penguins. Notably, the level of virome diversity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data therefore reject the theory that penguins are subject to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs.

microbiology↗

bioRxiv2019

Metaecosystem dynamics drive community composition in experimental multi-layered spatial networks

Cross-ecosystem subsidies are studied with a focus on resource exchange at local ecosystem boundaries. This perspective ignores regional dynamics that can emerge via constraints imposed by the landscape, potentially leading to spatially-dependent effects of subsidies and spatial feedbacks. Using miniaturized landscape analogues of river dendritic and terrestrial lattice spatial networks, we manipulated and studied resource exchange between the two whole networks. We found that community composition in dendritic networks depended on the resource pulse from the lattice network, with the strength of this effect declining in larger downstream patches. In turn, this spatially-dependent effect imposed constraints on the lattice network with populations in that network reaching higher densities when connected to more central patches in the dendritic network. Consequently, localized cross-ecosystem fluxes, and their respective effects on recipient ecosystems, must be studied in a perspective taking into account the explicit spatial configuration of the landscape.\n\nStatement of authorshipEH, IG, EAF and FA designed the research; EH conducted the lab experiment with support from IG, EAF and FA, processed the experimental data with methodological developments from IG, and carried out the analysis of experimental data; all authors participated in results interpretation; EH wrote the first draft of the manuscript; All authors significantly contributed to further manuscript revisions.

ecology↗

bioRxiv2019

Assessing different components of biodiversity across a river network using eDNA

O_LIAssessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long-standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA-based assessments to previously used approaches. C_LIO_LIWe sampled may-, stone-, and caddisfly genera with contemporary eDNA and kicknet methods at 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our survey data with historical records of total diversity at the catchment level. C_LIO_LIAt the catchment scale, eDNA and kicknet detected similar proportions of the overall and cumulative historically documented species richness (gamma diversity), namely 42% and 46%, respectively. We further found a good overlap (62%) between the two contemporary methods at the regional scale. C_LIO_LIAt the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet. Richness of eDNA was positively related with discharge, a descriptor of network position, while kicknet was not. C_LIO_LIBeta diversity between sites was similar for the two contemporary methods. Contrary to our expectation, however, beta diversity was driven by species replacement and not by nestedness. C_LIO_LIAlthough optimization of eDNA approaches is still needed, our results indicate that this novel technique can capture extensive aspects of gamma diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments, requiring less time and becoming more cost-efficient than classical approaches. Overall, the richness estimated with the two contemporary methods is similar at both local and regional scale but community composition is differently assessed with the two methods at individual sites and becomes more similar with higher discharge. C_LI

ecology↗

bioRxiv2018

Bioinorganic Angiogenesis

Causing a large diameter blood vessel to sprout branches and a capillary network on demand to create a new angiosome is key to harnessing to potential of regenerative medicine and advancing reconstructive surgery. Currently this can only be achieved by connecting a vein graft to an artery by microsurgery, the arteriovenous loop technique (AVL). The arterial blood pressure in the thin-walled vein is thought to drive remodelling to create branches, however the surgical complexity limits the application of the technique. In this study we demonstrate that unexpectedly, a vessel density of luminal branches in excess of that achieved by the surgical AVL approach can be induced simply by placing a vein in contact with a microporous calcium phosphate. Only osteoinductive biomaterials have been reported previously, this is thought to be the first report of an angio-inductive material. Pilot studies indicated that the material type greatly affected the degree of luminal vascularization. Material contact with the vein is not a requirement for luminal angiogenesis of the vein and together these findings point to a bioinorganic effect, wherein the degradation of the material both releases a stimulatory ionic milieu and creates space for the developing angiosome.

bioengineering↗

bioRxiv2018

Extensive Diversity of RNA Viruses in Australian Ticks

Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi senso lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been the subject of a number of studies using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including those that may have the potential to infect mammalian species. We used a meta-transcriptomics approach to reveal the viral diversity within Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel species of RNA virus belonging to 10 families, as well as one previously described RNA virus. The majority of these viruses clustered phylogenetically with arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian associated Hepacivirus and Pestivirus genera (Flaviviridae). Notably, another bandicoot tick yielded a novel Coltivirus (Reoviridae) - a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l.. in any tick sample, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.\n\nIMPORTANCEEach year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi seno lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses were related to known mammalian viruses, including one that fell within the genus Coltivirus and related to the human pathogen, Colorado tick fever virus.

microbiology↗

bioRxiv2018

Regulation of trophic architecture across spatial scales in a major river network

Moving beyond species count data is an essential step to better understand the effects of environmental perturbations on biodiversity and ecosystem functions, and to eventually better predict the strength and direction of those effects. Here, coupling an integrative path analysis approach with data from an extensive countrywide monitoring program, we tested the main spatial, environmental and anthropogenic drivers of change in stream macroinvertebrate trophic structure along the entire Swiss Rhine river catchment. Trophic structure was largely driven by inherent altitudinal variation influencing and cascading to regional scaled factors such as land use change and position in the riverine network, which, in turn, transformed local habitat structure variables. Those cascading effects across scales propagated through the biotic community, first affecting preys and, in turn, predators. Our results illustrate how seemingly less important factors can act as essential transmission belts, propagating through direct and indirect pathways across scales to generate the specific context in which each trophic group will strive or not, leading to characteristic landscape wide variations in trophic community structure.

ecology↗

bioRxiv2018

Worldwide cross-ecosystem carbon subsidies and their contribution to ecosystem functioning

Ecosystems are widely inter-connected by spatial flows of resources1,2, yet primarily studied in a local context. Meta-ecosystem models suggest that cross-ecosystem subsidies can play an essential role in ecosystem functioning, notably by controlling local availability of resources for biological communities3-6. The general contribution of these resource connections to ecosystem functioning, however, remains unclear in natural systems, due to the heterogeneity and dispersion of data across the ecological literature. Here we provide the first quantitative synthesis on spatial flows of carbon connecting ecosystems worldwide. These cross-ecosystem subsidies range over eight orders of magnitude, between 10-3 and 105 gC m-2 yr-1, and are highly diverse in their provenance. We found that spatial carbon flows and local carbon fluxes are of the same order of magnitudes in freshwater and benthic ecosystems, suggesting an underlying dependency of these systems on resources provided by connected terrestrial and pelagic ecosystems respectively. By contrast, in terrestrial systems, cross-ecosystem subsidies were two to three orders of magnitude lower than local production (grasslands and forests), indicating a weaker quantitative influence on functioning. Those subsidies may still be qualitatively important, however, as some have high nutrient content7,8. We also find important gaps in carbon flow quantification, notably of cross-ecosystem subsidies driven by animal movements, which likely leads to general underestimations of the magnitude and direction of cross-ecosystem linkages9. Overall, we demonstrate strong ecosystem couplings, suggesting that ecosystems can be vulnerable to alterations of these flows and pointing to an urgent need to re-think ecosystem functioning in a spatial perspective.

ecology↗

bioRxiv2017

Population turnover reverses classic island biogeography predictions in river-like landscapes

Statement of authorshipEH, IG, EAF and FA designed the research; IG and EAF designed the model; IG programmed and ran the model, analyzed the simulation data with support from EAF and produced the figures; EH conducted the lab experiment with support from IG, EAF and FA, processed the experimental data with support from IG, and carried out the analysis of experimental data; all authors participated in results interpretation; EH wrote the first draft of the manuscript; All authors significantly contributed to further manuscript revisions. EH and IG contributed equally to this work.

ecology↗

bioRxiv2016

Upstream trophic structure modulates downstream community dynamics via resource subsidies.

In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities dynamics can be indirectly coupled by reciprocal among-ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.

ecology↗