BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series

Motivation Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables Included The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and Grain Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and Grain The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of Measurement The database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Format csv and. SQL

Qualitative mathematical models to support ecosystem-based management of Australia's Northern Prawn Fishery

A major decline in the catch of the banana prawn [shrimp], Penaeus (Fenneropenaeus) merguiensis, occurred over a six-year period in the Weipa region of the northeastern Gulf of Carpentaria, Australia. Three main hypotheses have been developed to explain this decline: (1) prawn recruitment collapsed due to overfishing; (2) recruitment collapsed due to a change in the prawn's environment; and (3) adult banana prawns were still present, but fishers could no longer effectively find or catch them. Qualitative mathematical models were used to link population biology, environmental factors, and fishery dynamics to evaluate the alternative hypotheses. This modeling approach provides the means to rapidly integrate knowledge across disciplines and consider alternative hypotheses about how the structure and function of an ecosystem affects its dynamics. Alternative models were constructed to address the different hypotheses and also to encompass a diversity of opinion about the underlying dynamics of the system. Key findings from these analyses are that: instability in the system can arise when discarded fishery bycatch supports relatively high predation pressure; system stability can be enhanced by management of fishing effort or stock catchability; catch per unit effort is not necessarily a reliable indicator of stock abundance; a change in early-season rainfall should affect all stages in the banana prawn's life cycle; and a reduced catch in the Weipa region can create and reinforce a shift in fishing effort away from Weipa. Results from the models informed an approach to test the hypotheses (i.e., an experimental fishing program), and promoted understanding of the system among researchers, management agencies, and industry. The analytical tools developed in this work to address stages of a prawn life cycle and fishery dynamics are generally applicable to any exploited natural resource

Seasonal, interannual and spatial variability in the reproductive dynamics of Penaeus merguiensis

Penaeid prawns (shrimp) are short-lived and fecund, with a complicated life cycle that includes offshore spawning followed by a coastal or estuarine postlarval and juvenile phase. Factors affecting survival during the early life-history stages, and during movement between these stages, will affect variability in recruitment to the nursery ground, the offshore subadult and adult population, and, ultimately, catch. The inability to predict recruitment, and ultimately commercial offshore catch, has been complicated by an incomplete understanding of these factors. The reproductive dynamics of Penaeus (Fenneropenaeus) merguiensis were investigated by simultaneous adult and larval sampling on 66 lunar-monthly surveys from March 1986 to March 1992 in Albatross Bay, northeastern Gulf of Carpentaria, Australia. Egg production was seasonal, with the highest production from 6-mo-old newly recruited spawners, and another peak from 12mo-old spawners. Larval abundance (no. m-2) followed the same seasonal pattern as the abundance of eggs. However, interannual variation in egg and larval abundance was large, and there was a weak correlation between monthly egg and larval abundance. Larval abundance appeared to be further influenced by fluctuations in chlorophyll a concentration, a measure of food availability. There was evidence of a match/mismatch relationship between larval abundance and episodic chlorophyll increases. While there was no direct spawner (egg production)-fishery recruit relationship in P. merguiensis over the 6-yr study, there was a strong relationship between total larval abundance in spring and the size of the commercial catch 3 to 6 mo later. Therefore, factors affecting larval survival, including food availability, have significant implications for fishery production.</jats:p

Multispecies fisheries management and conservation: Tactical applications using models of intermediate complexity

Stakeholders increasingly expect ecosystem assessments as part of advice on fisheries management. Quantitative models to support fisheries decision-making may be either strategic ('big picture', direction-setting and contextual) or tactical (focused on management actions on short timescales), with some strategic models informing the development of tactical models. We describe and review 'Models of Intermediate Complexity for Ecosystem assessments' (MICE) that have a tactical focus, including use as ecosystem assessment tools. MICE are context- and question-driven and limit complexity by restricting the focus to those components of the ecosystem needed to address the main effects of the management question under consideration. Stakeholder participation and dialogue is an integral part of this process. MICE estimate parameters through fitting to data, use statistical diagnostic tools to evaluate model performance and account for a broad range of uncertainties. These models therefore address many of the impediments to greater use of ecosystem models in strategic and particularly tactical decision-making for marine resource management and conservation. MICE are capable of producing outputs that could be used for tactical decision-making, but our summary of existing models suggests this has not occurred in any meaningful way to date. We use a model of the pelagic ecosystem in the Coral Sea and a linked catchment and ocean model of the Gulf of Carpentaria, Australia, to illustrate how MICE can be constructed. We summarize the major advantages of the approach, indicate opportunities for the development of further applications and identify the major challenges to broad adoption of the approach