In recent years, three major innovations have occurred in ecology. (1) The emergence of new statistical methods for analysing community data; (2) the rapid detection of species and whole communities from environmental DNA (eDNA) and bulk-sample DNA; and (3) the wide availability of remotely sensed environmental covariates. The efficiency gains are such that hundreds or even thousands of species can now be detected and, to an extent, quantified in hundreds or even thousands of samples. Collectively, these three innovations have the potential to relieve the problems of data limitation and analysis that environmental management has been struggling with, opening the way to near-real-time tracking of state and change in biodiversity and its functions and services over whole landscapes. The aim of our project is to develop an integrated statistical framework for DNA-based surveys of biodiversity. The framework will allow the estimation of community compositions and the identification of the landscape characteristics that drive them. We will develop a Bayesian hierarchical model accounting for the probabilistic nature of DNA-based data due to observation error and taxonomic uncertainty and for model uncertainty due to the unknown strength and direction of landscape effects on the system. We will build sophisticated and efficient algorithms within a Bayesian framework for identifying the important landscape covariates that predict community structure and provide guidelines on optimal allocation of resources in DNA-based surveys for achieving the required power to infer species distributions and to link them to landscape covariates. The huge potential contribution of DNA-based data to landscape decision-making is demonstrated by how Natural England, Local Planning Authorities, and the NatureSpace Partnership use eDNA to create a biodiversity-offset market ('District Licensing') for the protected Great Crested Newt (GCN). Water samples from 500 ponds across the South Midlands (spanning ~3320 sq km) were tested for GCN and used to create a distribution map, which was then zoned into four 'impact risk' levels. Builders pay a known, sliding-scale fee, and a portion of the fee is used to build and manage new habitat. District Licensing is only feasible with eDNA's greater efficiency. GCN District Licensing expands to at least 16 LPAs in 2020, aiming to go nationwide, which would make it the largest biodiversity-focused, land-use decision scheme in the UK, if not the world. The natural-and highly desirable-extension to the GCN scheme would be to map 'all biodiversity' and to make land-use decisions (e.g. impact risk maps, offset markets, habitat creation) on this broader basis. In fact, samples originally collected for GCN can be repurposed for this larger goal by using 'metabarcoding,' meaning that the eDNA is PCR-amplified for a larger range of taxa. Given the District-Licensing expansion plans, pond eDNA metabarcoding alone could provide an efficient way to map biodiversity across much of the UK. This is far from the only such programme. Ecologists in industry and academia around the world are plunging ahead with large-scale DNA-sampling campaigns, and there is, as yet, no comprehensive set of statistical methods for modelling the individual steps of the new observation processes, quantifying the resulting uncertainty, and assessing how it affects decision-making at the landscape level. Our proposed modelling framework will provide such tools by explicitly capturing measurement bias within biodiversity models as a set of observation processes, and not merely as error. Improving sampling designs and workflows as a result of our proposed models will profoundly increase the efficiency and credibility of inference and therefore reduce the risk of biodiversity loss during the political process of allocating land to different uses.

Conservation monitoring schemes are constrained by time and cost and as such study design needs to be optimised to make the most of these available resources. Removal studies are conducted to protect target species from sites planned for development and the aim of such sampling is to capture and remove the entire population. Typically the studies are designed in an ad-hoc way with some repeated surveys on a single day, and some with simply daily visits. Sampling of sites is often avoided when weather conditions are considered not favourable. Removed species are trans-located to other habitats considered suitable for the specific species. However, measures to determine whether such translocations, and related re-introduction programmes have been successful are currently lacking. Developing robust approaches for both removal and re-introduction programmes will allow resources to be allocated optimally to ensure monitoring can be carried out for a sufficient period of time, to minimise the risk to the species under study. This project will develop new statistical approaches to make the most of the information available from removal and re-introduction data. The types of data which can be collected on animal populations are wide-ranging - for example, simple population counts, presence/absence data, presence only data, batch-marked data, and capture-recapture data. The difficulty and survey intensity required to collect these data will also depend on the associated skill set of data collector as well as the resources available to the team or individual responsible for designing the scheme. As well as proposing optimal study design for removal count data, the project will also address how to optimise study design if multiple types of data are collected simultaneously on a population. Further, we will explore how populations could be monitored with multiple types of data collection to better determine how successfully the population has established itself following some form of intervention (such as trans-location of individuals or re-introducing a previously locally extinct species back into an area). When fitting models to data it is possible to consider different structures to the model, for example to account for time-variation within detectability of the species, and therefore a model selection procedure needs to be implemented to select the structure of the model that best represents the observed data. Current approaches require an understanding of the statistical procedures implemented within this model selection step, however the methodological developments proposed within this project are aimed at a user-base who may have no such knowledge. Therefore within the project we will investigate the development of an automated procedure which will both select a best model(s) out of the models considered for the data set and will also assess how well the model(s) fits the observed data. A best candidate model may in fact fit the observed data very poorly and therefore this check of model fit is crucial if the results of the model will be used to make management decisions as otherwise erroneous conclusions could be drawn. Software with a graphical-user-interface will be developed to make the statistical developments accessible to those with no programming experience. The software will be web-based which will overcome operating system compatibility issues and user-manuals and tutorials will be produced to help end-users to make the most of the software's capabilities.

Conservation monitoring schemes are constrained by time and cost and as such study design needs to be optimised to make the most of these available resources. Removal studies are conducted to protect target species from sites planned for development and the aim of such sampling is to capture and remove the entire population. Typically the studies are designed in an ad-hoc way with some repeated surveys on a single day, and some with simply daily visits. Sampling of sites is often avoided when weather conditions are considered not favourable. Removed species are trans-located to other habitats considered suitable for the specific species. However, measures to determine whether such translocations, and related re-introduction programmes have been successful are currently lacking. Developing robust approaches for both removal and re-introduction programmes will allow resources to be allocated optimally to ensure monitoring can be carried out for a sufficient period of time, to minimise the risk to the species under study. This project will develop new statistical approaches to make the most of the information available from removal and re-introduction data. The types of data which can be collected on animal populations are wide-ranging - for example, simple population counts, presence/absence data, presence only data, batch-marked data, and capture-recapture data. The difficulty and survey intensity required to collect these data will also depend on the associated skill set of data collector as well as the resources available to the team or individual responsible for designing the scheme. As well as proposing optimal study design for removal count data, the project will also address how to optimise study design if multiple types of data are collected simultaneously on a population. Further, we will explore how populations could be monitored with multiple types of data collection to better determine how successfully the population has established itself following some form of intervention (such as trans-location of individuals or re-introducing a previously locally extinct species back into an area). When fitting models to data it is possible to consider different structures to the model, for example to account for time-variation within detectability of the species, and therefore a model selection procedure needs to be implemented to select the structure of the model that best represents the observed data. Current approaches require an understanding of the statistical procedures implemented within this model selection step, however the methodological developments proposed within this project are aimed at a user-base who may have no such knowledge. Therefore within the project we will investigate the development of an automated procedure which will both select a best model(s) out of the models considered for the data set and will also assess how well the model(s) fits the observed data. A best candidate model may in fact fit the observed data very poorly and therefore this check of model fit is crucial if the results of the model will be used to make management decisions as otherwise erroneous conclusions could be drawn. Software with a graphical-user-interface will be developed to make the statistical developments accessible to those with no programming experience. The software will be web-based which will overcome operating system compatibility issues and user-manuals and tutorials will be produced to help end-users to make the most of the software's capabilities.