An examination of forest cover change at Angkor, Cambodia, using satellite imagery, interviews and interpretation of historical events

In the three decades since the mid-1970s through to the early 2000s forest cover at the Angkor World Heritage Site, Cambodia has not progressed linearly but in response to different historical events. This research uses multiple methods in comparing satellite image classification with key informant interviews and other forms of data at the landscape scale and at case studies to provide an historical perspective on forest cover change. The earliest date corresponds to the beginning of the civil war in Cambodia through to a time when a number of events had contributed to significant change in forest pattern and extent at Angkor. The change observed is a result of regulatory controls on land use, ongoing subsistence resource use activities and other events and processes, and more broadly reflects a country in transition and a history of conflict relating to resource governance. The research demonstrates that multiple methods combining medium resolution satellite imagery with interview data and processes detectable at specific time periods can be used to understand patterns of forest change and establish links to processes on the ground

Combining remote sensing change detection and qualitative data to examine landscape change in the context of world heritage

Following inscription of Angkor on the World Heritage List in 1992, restrictions on forest use have been imposed on the local communities residing within the Angkor area. The result has been reduced access to forest resources by local villagers living within the WHS management zones, and with it reduced vegetation cover. Boundaries associated with World Heritage inscription, as defined by administrative lines, are often ambiguous where local boundary demarcation has evolved over time. This ambiguity has contributed to differing levels of constraints on access to resources being placed on communities. This research examines vegetation response to changing use levels enforced through forest management policy across the broader Angkor area. Mixed methods (Jiang, 2003; Creswell and Plano-Clark, 2007) are used to examine the influence of World Heritage zoning on subsistence use of forest resources, and to evaluate different approaches for quantifying and monitoring vegetation change. The effectiveness of site management, in the context of World Heritage obligations, for achieving conservation and development objectives is explored, with an emphasis on combining quantitative remote sensing and qualitative methods. Spatio-temporal patterns of vegetation change and forest resource constraints imposed on villagers are compared at locations both within and outside the WHS management zones. Multiple study sites were established in the north-east of the Angkor plain and the higher slopes and plateau of Phnom Kulen National Park. Research methods included semi-structured interviews with local villagers and key informants (including senior representatives of the Authority for the Protection and Management of Angkor and the Region of Siem Reap (APSARA)), field-based vegetation surveys, and analysis of management policies and historical vegetation and relevant management reports. Field-based studies engaged representatives from local communities in semi-structured interviews across 17 villages to understand how restrictions on forest access at the local level have influenced vegetation change. Vegetation change analysis using field-based vegetation surveys and classified high resolution multi-spectral satellite imagery, as well as informal interviews at spatial locations in close correspondence with areas identified from the remote sensing change V detection, further augmented this process by relating levels of subsistence use to different patterns of vegetation change that have occurred at both the local and landscape scale. Bi-temporal Multivariate Alteration Detection (MAD; Canty, 2007; Canty and Nielsen, 2008) was used to identify landscape change as it does not require the identification of discrete unvegetated areas of sufficient size required to use as calibration targets for image normalisation. MAD outputs show different aspects of change in land cover such as vegetation changing to soil or to rice paddy, vegetation growth, vegetation removal or change in vegetation type between the two dates. The Normalised Difference Vegetation Index (NDVI; Rouse et al., 1973) was used to generate vegetation change maps and quantify change at case studies. The issues surrounding management of the Angkor WHS, including access and availability of forest resources for local residents, are evident in the spatio-temporal correspondence between signature patterns observed in remotely sensed imagery and events as described in field interviews. Several findings emerged from this research. Firstly, interpretation of remote sensing change analysis and data collected during community-based interviews suggests that controls imposed by management is targeted at locals yet unregulated activity by outsiders and those able to circumvent the existing zoning regulations, appears to have created significant change. Secondly, while villagers located within the WHS core management Zones 1 and 2, the two zones with the strictest controls, appear to share similar constraints on use of forest resources for subsistence purposes, the restrictions associated with the management across these zones differ. This is most evident at villages located in close proximity to each other but within different management zones, supporting the argument that controls associated with each of the management boundaries have little relevance to the activities occurring on-the-ground. Thirdly, to sufficiently understand the change identified from the remote sensing analysis both social and cultural processes must be examined. Lastly, understanding the implications of landscape change, both within and across borders, is important for heritage management, and Geographic Information Systems (GIS) and remote sensing based mixed methods can contribute to quantifying such change. This research acknowledges the need to incorporate the broader cultural landscapes of Angkor into management, and argues that the regulations imposed on local communities by the inscription of the site have had unintended consequences, particularly in those zones of management where regulations have proved difficult to enforce. Additionally, it recognises the VI importance of understanding links between differing constraints on the subsistence use of forest resources imposed by heritage listing, and observed rates of vegetation change. The value of management approaches that extend WHS boundaries is also demonstrated, including the contribution of both remotely sensed based monitoring techniques and community-based interviews in establishing connectivity between these spatio-temporal trends and the processes underlying observed change

Managing multifunctional landscapes: local insights from a Pacific Island Country context

Across Pacific Island Countries, projects and policies are incorporating objectives related to managing landscape multifunctionality to sustain flows of multiple, valued ecosystem services. Strategies to manage natural resources are often not effective, or do not have intended outcomes, if they do not account for local contexts and the varied needs and constraints of stakeholders who rely upon natural resources for their livelihoods. Through fieldwork in Ba, Fiji, local insights were generated concerning the institutional, geographic, and socio-economic factors which determine and challenge i) different stakeholders’ ability to access landscape resources, and ii) stakeholders’ capacities to benefit from ecosystem services. The following insights were generated from this research which are important for guiding management of landscape multifunctionality. In Ba, hierarchical governance systems present barriers to effective management of landscape multifunctionality, and projects or policies with aims to manage landscapes should establish context appropriate multi-scale governance. Such governance systems should facilitate communication and interaction between different stakeholders, build upon community knowledge, and support communities as key actors in landscape management. Consideration of the spatial footprint of landscape resources, stakeholders’ different physical and financial capacities, and the institutional structures that mediate access to resources should be central to landscape management and planning. Various climatic stressors affect flows of ecosystem services from the Ba landscape and people’s capacity to access landscape resources; therefore, it is important that management of landscapes also builds resilience to climate stressor

Further evidence of Chelonid herpesvirus 5 (ChHV5) latency : High levels of ChHV5 DNA detected in clinically healthy marine turtles

The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCRbased studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals' clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP

Ancient Plant Genomics in Archaeology, Herbaria, and the Environment : Annual Review of Plant Biology

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research

Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community

Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant

An open - source mobile geospatial platform for promoting climate - smart livelihood - landscape systems in Fiji and Tonga

Communities in Fiji and Tonga rely on landscape services to support a variety of livelihoods. These communities are increasingly vulnerable to climate (e.g. increasing cyclone occurrence and intensity) and environmental (e.g. mining and deforestation) stressors. Within these landscape systems, accurate and timely monitoring of human-climate-environment interactions is important to inform landscape management, land use policies, and climate-smart sustainable development. Data collection and monitoring approaches exist to capture landscape-livelihood information such as surveys, participatory GIS (PGIS), and remote sensing. However, these monitoring approaches are challenged by data collection and management burdens, timely integration of databases and data streams, aligning system requirements with local needs, and socio-technical issues associated with low-resource development contexts. Such monitoring approaches only provide static representation of livelihood-landscape interactions failing to capture the dynamic nature of vulnerabilities, and benefit only a small user base. We present a prototype of a mobile, open-source geospatial tool being collaboratively developed with the Ministries of Agriculture in Fiji and Tonga and local stakeholders, to address the above shortcomings of PGIS and other environmental monitoring and data sharing approaches. The tool is being developed using open-source mobile GIS technologies following a formal ICT for Development (ICT4D) framework. We discuss the results for each component of the ICT4D framework which involves multiple landscape stakeholders across the two Small Island Developing States. Based on the ICT4D user requirements analysis, we produced a prototype open-source mobile geospatial data collection, analysis and sharing tool. New dynamic spatial data layers related to landscape use and climate were specifically developed for use in the tool. We present the functionality of the tool alongside the results of field-testing with stakeholders in Fiji and Tonga

New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases &gt;20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained &lt;3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size &lt; 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method. </jats:p

Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information. (Résumé d'auteur