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Investigators in the cognitive neurosciences have turned to Big Data to address persistent replication and reliability issues by increasing sample sizes, statistical power, and representativeness of data. While there is tremendous potential to advance science through open data sharing, these efforts unveil a host of new questions about how to integrate data arising from distinct sources and instruments. We focus on the most frequently assessed area of cognition - memory testing - and demonstrate a process for reliable data harmonization across three common measures. We aggregated raw data from 53 studies from around the world which measured at least one of three distinct verbal learning tasks, totaling N = 10,505 healthy and brain-injured individuals. A mega analysis was conducted using empirical bayes harmonization to isolate and remove site effects, followed by linear models which adjusted for common covariates. After corrections, a continuous item response theory (IRT) model estimated each individual subject’s latent verbal learning ability while accounting for item difficulties. Harmonization significantly reduced inter-site variance by 37% while preserving covariate effects. The effects of age, sex, and education on scores were found to be highly consistent across memory tests. IRT methods for equating scores across AVLTs agreed with held-out data of dually-administered tests, and these tools are made available for free online. This work demonstrates that large-scale data sharing and harmonization initiatives can offer opportunities to address reproducibility and integration challenges across the behavioral sciences.
For the Western Plains of New South Wales, 213 plant communities are classified and described and their protected area and threat status assessed. The communities are listed on the NSW Vegetation Classification and Assessment database (NSWVCA). The full description of the communities is placed on an accompanying CD together with a read-only version of the NSWVCA database.
The NSW Western Plains is 45.5 million hectares in size and covers 57% of NSW. The vegetation descriptions are based on over 250 published and unpublished vegetation surveys and maps produced over the last 50 years (listed in a bibliography), rapid field checks and the expert knowledge on the vegetation. The 213 communities occur over eight Australian bioregions and eight NSW Catchment Management Authority areas. As of December 2005, 3.7% of the Western Plains was protected in 83 protected areas comprising 62 public conservation reserves and 21 secure property agreements. Only one of the eight bioregions has greater than 10% of its area represented in protected areas. 31 or 15% of the communities are not recorded from protected areas. 136 or 64% have less than 5% of their pre-European extent in protected areas. Only 52 or 24% of the communities have greater than 10% of their original extent protected, thus meeting international guidelines for representation in protected areas. 71 or 33% of the plant communities are threatened, that is, judged as being ‘critically endangered’, ‘endangered’ or ‘vulnerable’.
While 80 communities are recorded as being of ‘least concern’ most of these are degraded by lack of regeneration of key species due to grazing pressure and loss of top soil and some may be reassessed as being threatened in the future. Threatening processes include vegetation clearing on higher nutrient soils in wetter regions, altered hydrological regimes due to draw-off of water from river systems and aquifers, high continuous grazing pressure by domestic stock, feral goats and rabbits, and in some places native herbivores — preventing regeneration of key plant species, exotic weed invasion along rivers and in fragmented vegetation, increased salinity, and over the long term, climate change.
To address these threats, more public reserves and secure property agreements are required, vegetation clearing should cease, re-vegetation is required to increase habitat corridors and improve the condition of native vegetation, environmental flows to regulated river systems are required to protect inland wetlands, over-grazing by domestic stock should be avoided and goat and rabbit numbers should be controlled and reduced. Conservation action should concentrate on protecting plant communities that are threatened or are poorly represented in protected areas.
A vegetation classification titled, NSW Vegetation Classification and Assessment (NSWVCA), is described. It aims to classify the native vegetation of New South Wales, Australia covering 80 million hectares distributed across 18 Australian bioregions. It is estimated that between 800 and 1200 plant communities will be described. The best available data is used to establish the classification including vegetation map descriptions, floristic groups derived from plot data and expert advice. Extensive field checking assists with the classification and status assessments. Plant communities are listed under five hierarchical levels and are recorded on a database containing 90 fields supported by 45 tables and 64 forms. 39 database reports list plant communities for several types of planning regions and under State and national broad vegetation classifications. Database fields include plant community scientific name, common name, three layers of characteristic species, an ‘Authority’ field that cites references supporting the definition of a community, substrate, soils, landform, distribution by various regions including bioregions and Catchment Management Authority areas, descriptions and lists of threatening processes and aspects of condition. Estimates of pre-European extent, current extent and areas in public reserves and secure property agreements are recorded and qualified with accuracy levels. One of five threat categories: ‘critically endangered’, ‘endangered’, ‘vulnerable’, ‘near threatened’ or ‘least concern’ is assigned to each plant community based on the application of six criteria including: the proportion of remaining extent compared to an estimated pre-European extent, loss of key species and plant community integrity.
The NSWVCA will progress over four geographical sections of NSW commencing with the mainly arid and semi-arid Western Plains (this volume), progressing eastwards to the Western Slopes, the Tablelands and finally the biologically complex Coast and Escarpment. The NSWVCA will assist with: selecting new protected areas, guiding incentive payments and land use decisions in the NSW property vegetation planning process, site assessment in environmental impact assessments, assisting with nominations and definitions of threatened ecological communities in State and Federal laws, prioritizing CMA and other regional targets for the protection and restoration of vegetation and assisting in public education about native vegetation.
A CD accompanying the paper contains a read-only version of the database and outputs of Part 1 of the NSWVCA project – the vegetation of the NSW Western Plains.
Foreword
(2006)
This issue of Cunninghamia contains the first two papers of a project involving the classification and assessment of the native vegetation of New South Wales, Australia (NSWVCA). Besides developing a comprehensive typology of the vegetation, the project aims to assess the protected area and threat status of the State’s vegetation. It collates information on vegetation composition, geographic distribution of plant communities, physiographic features, threats, aspects of condition, planning and management and representation in protected areas into a single database system. A photographic library is also being collated for use with the database and use in publications and education programs.
Wollemia nobilis Jones et al. (Wollemi Pine) is restricted to four sites growing in warm temperate rainforest typical of the canyons in the Blue Mountains and Wollemi National Parks. 88 vascular plant species were recorded from four sites. The tree canopy at all sites is dominated by Wollemia nobilis, Ceratopetalum apetalum, Doryphora sassafras and Acmena smithii. A large number of fern and vine species dominate the forest floor. Site 1 contains more species than the other sites, possibly due to its diversity of topographic features. Similarity analysis indicates that sites 2 and 3 are the most similar and sites 1 and 4 are least similar in floristic composition. 54% of plant species were recorded at one site only. Ceratopetalum apetalum, Blechnum cartilagineum and Wollemia nobilis were found to contribute most to the similarity between sites.
This fourth paper in the NSW Vegetation Classification and Assessment series covers the Brigalow Belt South-/1(BBS) and Nandewar (NAN) Bioregions and the western half of the New England Bioregion (NET), an area of 9.3 million hectares being 11.6% of NSW. It completes the NSWVCA coverage for the Border Rivers-Gwydir and Namoi CMA areas and records plant communities in the Central West and Hunter–Central Rivers CMA areas. In total, 585 plant communities are now classified in the NSWVCA covering 11.5 of the 18 Bioregions in NSW (78% of the State). Of these 226 communities are in the NSW Western Plains and 416 are in the NSW Western Slopes. 315 plant communities are classified in the BBS, NAN and west-NET Bioregions including 267 new descriptions since Version 2 was published in 2008. Descriptions of the 315 communities are provided in a 919 page report on the DVD accompanying this paper along with updated reports on other inland NSW bioregions and nine Catchment Management Authority areas fully or partly classified in the NSWVCA to date. A read-only version of Version 3 of the NSWVCA database is on the DVD for use on personal computers. A feature of the BBS and NAN Bioregions is the array of ironbark and bloodwood Eucalyptusdominated shrubby woodlands on sandstone and acid volcanic substrates extending from Dubbo to Queensland. This includes iconic natural areas such as Warrumbungle and Mount Kaputar National Parks and the 500,000 ha Pilliga Scrub forests. Large expanses of basalt-derived soils support grassy box woodland and native grasslands including those on the Liverpool Plains; near Moree; and around Inverell, most of which are cleared and threatened. Wetlands occur on sodic soils near Yetman and in large clay gilgais in the Pilliga region. Sedgelands are rare but occupy impeded creeks. Aeolian lunettes occur at Narran Lake and near Gilgandra. Areas of deep sand contain Allocasuarina, eucalypt mallee and Melaleuca uncinata heath. Tall grassy or ferny open forests occur on mountain ranges above 1000m elevation in the New England Bioregion and on the Liverpool Range while grassy box woodlands occupy lower elevations with lower rainfall and higher temperatures. The vegetation classification and assessment is based on over 100 published and unpublished vegetation surveys and map unit descriptions, expert advice, extra plot sampling and data analysis and over 25 000 km of road traverse with field checking at 805 sites. Key sources of data included floristic analyses produced in western regional forest assessments in the BBS and NAN Bioregions, floristic analyses in over 60 surveys of conservation reserves and analysis of plot data in the western NET Bioregion and covering parts of the Namoi and Border Rivers- Gwydir CMA areas. Approximately 60% of the woody native vegetation in the study area has been cleared resulting in large areas of “derived” native grasslands. As of June 2010, 7% of the area was in 136 protected areas and 127 of the 315 plant communities were assessed to be adequately protected in reserves. Using the NSWVCA database threat criteria, 15 plant communities were assessed as being Critically Endangered, 59 Endangered, 60 Vulnerable, 99 Near Threatened and 82 Least Concern. 61 of these communities are assessed as part of NSW or Commonwealth-listed Threatened Ecological Communities. Current threats include expanding dryland and irrigated cropping on alluvial plains, floodplains and gently undulating topography at lower elevations; over-grazing of steep hills; altered water tables and flooding regimes; localized mining; and the spread of exotic species, notably Coolatai Grass (Hyparrhenia hirta).
This third paper in the NSW Vegetation Classification and Assessment series covers the NSW South-western Slopes Bioregion of 8.192 million hectares being 10% of NSW. A total of 135 plant communities, comprising 97 new communities and 38 previously described communities, are classified. Their protected area and threat status is assessed. A full description of the 135 plant communities is provided in a 400 page report, generated from the NSWVCA database, on the CD accompanying this paper. Eucalyptus-dominated grassy or shrubby woodlands and open forests are the main types of vegetation in the bioregion. The CD also contains a read-only version of Version 2 of the NSWVCA database that includes updated information on the plant communities previously published in Version 1 of the NSWVCA covering the NSW Western Plains. Six new communities are added to the Western Plains. The vegetation classification and assessment is based on published and unpublished vegetation surveys and map unit descriptions that are listed in the NSWVCA Bibliography on the CD, expert advice and extensive field checking. Over 80% of the native vegetation in the NSW South-western Slopes Bioregion has been cleared making it the most cleared and fragmented of the 18 IBRA Bioregions in NSW. Exotic plant species dominate the ground cover outside conservation reserves, state forests, roadsides and travelling stock reserves. As of September 2008 about 1.9% of the Bioregion was in 105 protected areas and 28 of the 135 plant communities were assessed to be adequately protected in reserves. Using NSWVCA Threat Criteria, 18 plant communities were assessed as being Critically Endangered, 33 Endangered, 29 Vulnerable, 25 Near Threatened and 30 Least Concern. Current threats include over-grazing, especially during drought, exotic species dominance of the ground cover, impacts of fragmentation on species persistence and genetic diversity and impacts of lower rainfall due to climate change. To address these threats, linking and enlarging vegetation remnants through revegetation (including regenerating native ground cover) is required. Some progress is being made through re-vegetation schemes driven by the NSW 2003 Natural Resource reforms, however, more incentive funding for landholders would accelerate the re-vegetation program.
Aerial photo interpretation of high resolution airborne imagery (ADS40) was used in a three-dimensional (3-D) digital Geographic Information System (GIS) environment to map native plant communities defined in the NSW Vegetation Classification and Assessment (NSW VCA) in central-southern New South Wales. NSW VCA plant community types form part of the NSW BioMetric vegetation type dataset underpinning NSW natural resource management (NRM) planning frameworks. This region was previously devoid of detailed vegetation mapping. In addition to developing a novel method for mapping plant communities, the use of ADS40 imagery allowed for capture of multiple attributes in each map polygon including attributes pertaining to dominant species and vegetation condition. Such data informs multi-attribute models used in conservation planning, providing utility beyond that of a singular plant community map.
A total of 546,150 hectares of native vegetation in 100 native plant communities was mapped across the study area (Coolamon, Cootamundra, Junee, Lockhart, Narrandera, Tarcutta, Urana, Wagga Wagga and Yanco 1:100,000 mapsheets and Ariah Park, Wallaroobie Range and Yoogali 1:50,000 mapsheets). Exotic pine plantations and native species plantings were also mapped. Remnants of greater than one hectare were captured through on-screen GIS digitising at scales of approximately 1:4,000. The plant community type mapping was independently assessed using random blind validation points as having a user accuracy of 87%. This level of accuracy demonstrates the applicability of the methodology for mapping open forests, woodlands and open woodlands of south-eastern Australia and probably other vegetation elsewhere. Such accurate mapping provides end users with confidence when using vegetation maps in environmental assessment and land use planning.