479 research outputs found
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The roles of provenance and phylogeny in recruitment, community assembly, and species coexistence in invaded California grasslands
Biological invasions pose one of the greatest threats to global biodiversity, but many naturalized invaders coexist with the native community. Community ecology theory provides a framework for understanding the mechanisms by which invaders might coexist with native species or exclude them from the community, thus informing management practices to maximize their effectiveness at conserving native biodiversity. Differences in functional or phylogenetic similarity of invaders to native residents can affect invasion success and the probability they will coexist with natives. For example, functionally dissimilar species may not compete strongly and distantly related species may share fewer natural enemies. Furthermore, environmental heterogeneity can promote species coexistence by providing the opportunity for a greater number of coexistence mechanisms to operate, thereby mitigating the potential for species invasions to lead to native extinction.
My thesis examines how provenance (i.e., native origin) and phylogenetic relatedness of plant species affect community dynamics and species interactions in the invaded California grasslands. To do this I have assembled two unique community data sets, one spanning 48 years across a 1000-ha site and one spanning 7 years along a 500-km latitudinal transect. I show that native and exotic species abundance and diversity is highly variable in both time and space, but these provenance group responses are rarely negatively correlated (Chapter 2). Thus, exotic species do not generally appear to exclude natives from communities. Long-term abundance patterns further suggest that the system remains in a state of transience, and populations of several native species are declining at local scales (Chapter 3). Recruitment limitation due to the build-up of plant litter associated with exotic grasses may be generally responsible for these declines, but habitat suitability, land-use history, and community composition also affect native recruitment. Across the grasslands, disturbance and resource supply can interact to affect both species and phylogenetic diversity (Chapter 4). Disturbance in particular can increase diversity, likely by increasing opportunities for colonization by removing plant litter that previously limited recruitment. Both phylogeny and provenance can also affect biotic interactions, such as with communities of soil organisms (Chapter 5). Thus, I have shown that spatio-temporal heterogeneity, alterations to the biotic environment mediated by exotic invasion, and phylogenetic relationships among species are all important considerations when evaluating impacts of invasion and designing management strategies to conserve native biodiversity, especially in light of anthropogenic influence on disturbance regimes and resource supply
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Seed and establishment limitation contribute to long-term native forb declines in California grasslands
The effects of exotic species invasions on biodiversity vary with spatial scale, and documentation of local-scale changes in biodiversity following invasion is generally lacking. Coupling long-term observations of local community dynamics with experiments to determine the role played by exotic species in recruitment limitation of native species would inform both our understanding of exotic impacts on natives at local scales and regional-scale management efforts to promote native persistence. We used field experimentation to quantify propagule and establishment limitation in a suite of native annual forbs in a California reserve, and compared these findings to species abundance trends within the same sites over the past 48 years. Observations at 11 paired sites (inside and outside the reserve) indicated that exotic annual plants have continued to increase in abundance over the past 48 years. This trend suggests the system has not reached equilibrium >250 years after exotic species began to spread, and 70 years after livestock grazing ceased within the reserve. Long-term monitoring observations also indicated that six native annual forb species went extinct from more local populations than were colonized. To determine the potential role of exotic species in these native plant declines, we added seed of these species into plots adjacent to monitoring sites where plant litter and live grass competition were removed. Experimental results suggest both propagule and establishment limitation have contributed to local declines observed for these native forbs. Recruitment was highest at sites that had current or historical occurrences of the seeded species, and in plots where litter was removed. Grazing history (i.e., location within or outside the reserve) interacted with exotic competition removal, such that removal of live grass competition increased recruitment in more recently grazed sites. Abundance of forbs was positively related to recruitment, while abundance of exotic forbs was negatively related. Thus, exotic competition is likely only one factor contributing to local declines of native species in invaded ecosystems, with a combination of propagule limitation, site quality, and land use history also playing important and interactive roles in native plant recruitment.This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://www.esa.org/.Keywords: Recruitment limitation, Community assembly, Livestock grazing, USA grasslands, Exotic species, California, Competition, Invasion, Propagule limitationKeywords: Recruitment limitation, Community assembly, Livestock grazing, USA grasslands, Exotic species, California, Competition, Invasion, Propagule limitatio
Giving stakeholders a voice in governance: Biodiversity priorities for New Zealand's agriculture
Mainstreaming biodiversity across government and society is recognised by international policy as critical to achieving positive conservation outcomes. With ‘participatory governance’ increasingly being applied to achieve collective action in conservation, there are growing calls to critically review such processes to capture their complexity and manage for emergent outcomes. This paper critically reviews a case study, aiming to give a broad range of stakeholders a voice in setting biodiversity priorities for New Zealand's agricultural landscape, in relation to four principles for knowledge co-production in sustainability: context-based, pluralistic, goal-orientated and interactive. Aiming to facilitate an inclusive but rapid participation process, while not overburdening those willing to participate, three pathways for engagement were offered. Stakeholder participants were recruited from public, private and civic sectors involved in managing New Zealand's farmland biodiversity. An initial scoping exercise helped elevate biodiversity groups and management actions distinct to New Zealand's social and environmental context. Online surveys then gave stakeholders, from a diverse range of roles and sectors, a nationwide voice to express their own biodiversity interests and needs; these were reviewed by an advisor panel to reach consensus on final priorities that reflected the biodiversity outcomes that matter most to stakeholders involved in managing New Zealand's agricultural landscape and the management practices they considered most relevant to achieving those outcomes. This knowledge co-production process delivered multiple gains that would not have been achieved had a more traditional science-based process been applied, such as wide stakeholder engagement, identification of a tangible starting point, mitigation of bias or conflict risks, enhanced researcher and practitioner capabilities and a shared understanding of the opportunities and challenges for future development. Institutes addressing conservation challenges within local contexts need to: be ‘boundary-spanning’ to manage cross-scale influences and enable desired conservation behaviours; plan explicitly for the substantial effort required to overcome existing power hierarchies and facilitate transparent and structured decision processes that deliver social justice; better capture the relational values of nature to more successfully leverage peoples’ connection to nature in conservation policies and practices; and incorporate wider environmental (e.g. biosecurity), social, economic and political considerations. A free Plain Language Summary can be found within the Supporting Information of this article
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Polyploidy on Islands: Its Emergence and Importance for Diversification.
Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa
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Polyploidy on Islands: Its Emergence and Importance for Diversification.
Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa
Retinal inner nuclear layer volume reflects inflammatory disease activity in multiple sclerosis;a longitudinal OCT study
Background: The association of peripapillary retinal nerve fibre layer (pRNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness with neurodegeneration in multiple sclerosis (MS) is well established. The relationship of the adjoining inner nuclear layer (INL) with inflammatory disease activity is less well understood. Objective: The objective of this paper is to investigate the relationship of INL volume changes with inflammatory disease activity in MS. Methods In this longitudinal, multi-centre study, optical coherence tomography (OCT) and clinical data (disability status, relapses and MS optic neuritis (MSON)) were collected in 785 patients with MS (68.3% female) and 92 healthy controls (63.4% female) from 11 MS centres between 2010 and 2017 and pooled retrospectively. Data on pRNFL, GCIPL and INL were obtained at each centre. Results: There was a significant increase in INL volume in eyes with new MSON during the study (N = 61/1562, beta = 0.01mm(3), p<.001). Clinical relapses (other than MSON) were significantly associated with increased INL volume (beta = 0.005, p =.025). INL volume was independent of disease progression (beta = 0.002mm(3), p =.474). Conclusion: Our data demonstrate that an increase in INL volume is associated with MSON and the occurrence of clinical relapses. Therefore, INL volume changes may be useful as an outcome marker for inflammatory disease activity in MSON and MS treatment trials
Progress in the development of a recombinant vaccine for human hookworm disease: The Human Hookworm Vaccine Initiative
Hookworm infection is one of the most important parasitic infections of humans, possibly outranked only by malaria as a cause of misery and suffering. An estimated 1.2 billion people are infected with hookworm in areas of rural poverty in the tropics and subtropics. Epidemiological data collected in China, Southeast Asia, and Brazil indicate that, unlike other soil-transmitted helminth infections, the highest hookworm burdens typically occur in adult populations, including the elderly. Emerging data on the host cellular immune responses of chronically infected populations suggest that hookworms induce a state of host anergy and immune hyporesponsiveness. These features account for the high rates of hookworm reinfection following treatment with anthelminthic drugs and therefore, the failure of anthelminthics to control hookworm. Despite the inability of the human host to develop naturally acquired immune responses to hookworm, there is evidence for the feasibility of developing a vaccine based on the successes of immunizing laboratory animals with either attenuated larval vaccines or antigens extracted from the alimentary canal of adult blood-feeding stages. The major antigens associated with each of these larval and adult hookworm vaccines have been cloned and expressed in prokaryotic and eukaryotic systems. However, only eukaryotic expression systems (e.g., yeast, baculovirus, and insect cells) produce recombinant proteins that immunologically resemble the corresponding native antigens. A challenge for vaccinologists is to formulate selected eukaryotic antigens with appropriate adjuvants in order to elicit high antibody titers. In some cases, antigen-specific IgE responses are required to mediate protection. Another challenge will be to produce anti-hookworm vaccine antigens at high yield low cost suitable for immunizing large impoverished populations living in the developing nations of the tropics
A comparative analysis of virial black hole mass estimates of moderate-luminosity active galactic nuclei using Subaru/FMOS
We present an analysis of broad emission lines observed in moderate-luminosity active galactic nuclei (AGNs), typical of those found in X-ray surveys of deep fields, with the goal of testing the validity of single-epoch virial black hole mass estimates. We have acquired near-infrared spectra of AGNs up to z ~ 1.8 in the COSMOS and Extended Chandra Deep Field-South Survey, with the Fiber Multi-Object Spectrograph mounted on the Subaru telescope. These near-infrared spectra provide a significant detection of the broad Hα line, shown to be a reliable probe of black hole mass at low redshift. Our sample has existing optical spectroscopy that provides a detection of Mg II, typically used for black hole mass estimation at z >~ 1. We carry out a spectral-line fitting procedure using both Hα and Mg II to determine the virial velocity of gas in the broad-line region, the continuum luminosity at 3000 Å, and the total Hα line luminosity. With a sample of 43 AGNs spanning a range of two decades in luminosity, we find a tight correlation between the ultraviolet and emission-line luminosity. There is also a close one-to-one relationship between the full width at half-maximum of Hα and Mg II. Both of these then lead to there being very good agreement between Hα- and Mg II-based masses over a wide range in black hole mass, i.e., M BH ~ 107-9 M ⊙. In general, these results demonstrate that local scaling relations, using Mg II or Hα, are applicable for AGNs at moderate luminosities and up to z ~ 2
A panel of recombinant Leishmania donovani cell surface and secreted proteins identifies LdBPK_323600.1 as a serological marker of symptomatic infection
Visceral leishmaniasis is a deadly infectious disease and is one of the world’s major neglected health problems. Because the symptoms of infection are similar to other endemic diseases, accurate diagnosis is crucial for appropriate treatment. Definitive diagnosis using splenic or bone marrow aspirates is highly invasive, and so, serological assays are preferred, including the direct agglutination test (DAT) or rK39 strip test. These tests, however, are either difficult to perform in the field (DAT) or lack specificity in some endemic regions (rK39), making the development of new tests a research priority. The availability of Leishmania spp. genomes presents an opportunity to identify new diagnostic targets. Here, we use genome data and a mammalian protein expression system to create a panel of 93 proteins consisting of the extracellular ectodomains of the Leishmania donovani cell surface and secreted proteins. We use these panel and sera from murine experimental infection models and natural human and canine infections to identify new candidates for serological diagnosis. We observed a concordance between the most immunoreactive antigens in different host species and transmission settings. The antigen encoded by the LdBPK_323600.1 gene can diagnose Leishmania infections with high sensitivity and specificity in patient cohorts from different endemic regions including Bangladesh and Ethiopia. In longitudinal sampling of treated patients, we observed reductions in immunoreactivity to LdBPK_323600.1 suggesting it could be used to diagnose treatment success. In summary, we have identified new antigens that could contribute to improved serological diagnostic tests to help control the impact of this deadly tropical infectious disease. IMPORTANCE Visceral leishmaniasis is fatal if left untreated with patients often displaying mild and non-specific symptoms during the early stages of infection making accurate diagnosis important. Current methods for diagnosis require highly trained medical staff to perform highly invasive biopsies of the liver or bone marrow which pose risks to the patient. Less invasive molecular tests are available but can suffer from regional variations in their ability to accurately diagnose an infection. To identify new diagnostic markers of visceral leishmaniasis, we produced and tested a panel of 93 proteins identified from the genome of the parasite responsible for this disease. We found that the pattern of host antibody reactivity to these proteins was broadly consistent across naturally acquired infections in both human patients and dogs, as well as experimental rodent infections. We identified a new protein called LdBPK_323600.1 that could accurately diagnose visceral leishmaniasis infections in humans
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