Expected survival and state of all known species: Data packages for the Biodiversity Indicator Program, first assessment

Brief description

This data collection contains the tabular data, R scripts and methods used to generate three indicators specific to vascular plants for the NSW Biodiversity Indicator Program's first assessment (prior to the date of commencement of the Biodiversity Conservation Act 2016): 1.2a expected survival of all known species; 2.1a within-species genetic diversity (for all known species); 2.1b extant area occupied (for all known species). These indicators use representative species sets (provided in a related data collection). The habitat condition indicators (related data collections) are used to infer reduction in geographic range size. These indicators are an application of the ‘expected diversity’ framework. Reduction in the geographic range size of a species due to habitat loss, alteration and fragmentation is well known to decrease within-species genetic diversity and increase extinction risk. Therefore, current range size and proportion of range lost from habitat loss, alteration and fragmentation were estimated for vascular plant species known to occur naturally in New South Wales. The area of effective habitat (i.e. high quality habitat able to support biodiversity) remaining for each species was estimated from two alternative habitat condition indicators (Love et al. 2020): ecological condition of terrestrial habitat and ecological carrying capacity of terrestrial habitat. Because most species in New South Wales have not been formally assessed for possible threatened status (i.e. at heightened risk of extinction), a provisional risk assessment using a limited set of criteria was completed for all NSW vascular plant species for which adequate data were available from the Atlas of Living Australia. For consistency with IUCN recommended Red List methods, the expected survival of all known species uses area of occupancy within 2km grids to classify all species into four categories: lowest risk, lower risk, higher risk and highest risk. Each category was assigned a probability of survival, allowing the proportion of NSW vascular plant species expected to survive in 100 years to be estimated. Extrapolating trends in the rate of biodiversity loss requires that the list of species used in analyses are representative of the overall biodiversity of New South Wales. A subset of NSW vascular plant species that uniformly represent the full variety of natural habitats for vascular plants in New South Wales (called the representative species set) was selected to represent all vascular plant species, including those yet to be discovered. Ecological environments defined by a generalised dissimilarity model of vascular plants were used as a surrogate for the variety of natural habitats. Based on the proportion of remaining effective habitat in each species’ original range, within-species genetic diversity is also estimated. A range of values is given because each species will respond to loss of range size differently, depending on factors like dispersal ability and degree of adaptation to local environmental conditions, and these differences are not precisely known. The data and scripts provided in the data collection will allow the pre-commencement analyses of these indicators to be re-run. The method as applied in the scripts is designed to allow future iterations of the indicators to be run using updated input data. Guidelines on how to re-run the analyses using the scripts and adapt the data package for future iterations of the indicators is provided in the implementation report (Nipperess DA, Faith DP, Williams KJ, King D, Manion G, Ware C, Schmidt R, Love J, Drielsma M, Allen S & Gallagher R 2020. Expected survival and state of all known species, first assessment. Department of Planning, Industry and Environment NSW, Sydney, Australia.). The relevant guidelines extracted from that report are provided with this data package.\nLineage: This Indicator uses a representative sample of vascular plant species (data and method of derivation described in a separate data collection - see ‘related links’ Representative species sets for vascular plants generated for the Biodiversity Indicator Program, first assessment: expected survival and state of all known species - supplementary data package) to derive three indicators: 1.2a expected survival; 2.1a within-species genetic diversity; 2.1b extant area occupied. Expected survival estimates extinction risk of all biodiversity (both known and undiscovered species) beyond those formally assessed by the NSW Scientific Threatened Species Committee. Species from a biological (i.e. taxonomic) group, in this case vascular plants, are sampled to uniformly represent the full range of natural habitats for that group. The representative species are provisionally assigned to risk of extinction categories based on the estimated proportion of their original habitat that remains intact. This is a limited, provisional assessment of risk using commonly available species occupancy data. The method uses species occurrence observations since 1950 in 2km map grids (each being 4km2) and area of occupancy (AOO) thresholds specified by the two criteria to discriminate four risk of extinction categories. Each species is further assessed for a reduction in AOO determined from the ecological condition indicator as a measure of habitat condition and, for comparison, the ecological carrying capacity measure. The reduction in AOO in four classes (<30%, 30-50%, 50-80% and > 80%), and the AOO thresholds (also using ecological condition) provide the dimensions of the risk categorisation. Each category is given a probability of survival which is applied to all representative species in that category. The Indicator is calculated by summing the probabilities of survival for the representative species across all categories and is expressed as a proportion of the total number of species representing the biological group. This serves as an indicator for all known species within the biological group expected to survive in 100 years and, by logic, extends to undiscovered species in that group. Change in the value of the Indicator reflects a change in survival probability due to a change in habitat condition. If sufficient habitat is lost or degraded for a particular species, its extinction risk category will also change. The AOO data are used to estimate the proportion of within-species genetic diversity that still exists and extant area occupied, after considering loss of suitable habitats. Genetic diversity is inferred from species diversity using geographic range and occupancy. A power curve relates the intact fraction of a species’ AOO to the respective fraction of genetic diversity remaining. Two forms of the curve are used: one that simulates spatially high genetic diversity due to high rates of population divergence and the other low. The two curves equate to an upper and lower estimate of fractional within-species genetic diversity. The Indicator is calculated by separately summing the upper and lower fractions of genetic diversity remaining for all species representing the biological group. This serves as an indicator of within-species genetic diversity for all known species within the biological group and, by logic, extends to undiscovered species in that group. It is also used to show the variation in genetic diversity loss across the categories of species survival for indicator 1.2a. The extant area occupied by all known species is the average fraction of original habitat occupied by the representative species. It is also used to show variation in reductions in AOOs across the categories of species survival for indicator 1.2a. Change in the value of the Indicators reflects a change in habitat condition. Details are given in the explanatory notes attached with this package.