Fish lost at sea: the effect of soak time on pelagic longline catches

Our analyses of observer records reveal that abundance estimates are strongly influenced by the timing of longline operations in relation to dawn and dusk and soak time— the amount of time that baited hooks are available in the water. Catch data will underestimate the total mortality of several species because hooked animals are “lost at sea.” They fall off, are removed, or escape from the hook before the longline is retrieved. For example, longline segments with soak times of 20 hours were retrieved with fewer skipjack tuna and seabirds than segments with soak times of 5 hours. The mortality of some seabird species is up to 45% higher than previously estimated. The effects of soak time and timing vary considerably between species. Soak time and exposure to dusk periods have strong positive effects on the catch rates of many species. In particular, the catch rates of most shark and billfish species increase with soak time. At the end of longline retrieval, for example, expected catch rates for broadbill swordfish are four times those at the beginning of retrieval. Survival of the animal while it is hooked on the longline appears to be an important factor determining whether it is eventually brought on board the vessel. Catch rates of species that survive being hooked (e.g. blue shark) increase with soak time. In contrast, skipjack tuna and seabirds are usually dead at the time of retrieval. Their catch rates decline with time, perhaps because scavengers can easily remove hooked animals that are dead. The results of our study have important implications for fishery management and assessments that rely on longline catch data. A reduction in soak time since longlining commenced in the 1950s has introduced a systematic bias in estimates of mortality levels and abundance. The abundance of species like seabirds has been over-estimated in recent years. Simple modifications to procedures for data collection, such as recording the number of hooks retrieved without baits, would greatly improve mortality estimates

The road to oblivion – quantifying pathways in the decline of large old trees

Large old hollow-bearing trees have a wide range of key ecological roles in forest and other ecosystems globally. Patterns and rates of mortality and decay of these trees had profound effects on the size and composition of their populations. Using an 18-year empirical study of large old trees in the Mountain Ash (Eucalyptus regnans) forests of the Central Highlands of Victoria, we sought to determine if there are particular patterns of decline that are shared by a proportion of the trees in a tree population. We also sought to identify drivers of decline of these trees by quantifying relationships between the condition state of trees (viz: tree form) and a range of covariates. We found that time, stand age and fire can individually and in combination, strongly affect the decay (and eventual collapse) of large old trees. In particular, we found compelling evidence that patterns of tree decline were markedly different in old growth forest (stands dating from ~ 1850) relative to three other younger age classes examined. Trees in older forest decayed less rapidly than trees of equivalent tree form in younger forest. Old growth stands also were characterized by trees in an overall much lower (more intact) form category than the other age classes of forest. A key pattern in our study was the rapid deterioration of large old trees in the youngest aged stands (viz: those regenerating after fires in 1939 and following disturbance between 1960 and 1990). In these forests, a very high proportion of large old trees were either in the most advanced state of tree decay (form 8) or had collapsed (form 9). This is a major concern given that 98.8% of the Mountain Ash forest ecosystem supports forest belonging to these (or even younger) age cohorts. Our investigation highlights the need for forest management to: (1) increase levels of protection for all existing large old hollow-bearing trees, (2) expand the protection of existing regrowth forest so there is the potential to significantly expand the currently very limited areas of remaining old growth forest.The work reported in this paper was funded by the Australian Research Council, The Australian Government (National Environmental Science Program Threatened Species Recovery Hub), and the Government of Victoria

Temporal trends in mammal responses to fire reveals the complex effects of fire regime attributes

Fire is a major ecological process in many ecosystems worldwide. We sought to identify which attributes of fire regimes affect temporal change in the presence and abundance of Australian native mammals. Our detailed study was underpinned by time series data on 11 mammal species at 97 long-term sites in southeastern Australia between 2003 and 2013. We explored how temporal aspects of fire regimes influenced the presence and conditional abundance of species. The key fire regime components examined were: (1) severity of a major fire in 2003, (2) interval between the last major fire (2003) and the fire prior to that, and (3) number of past fires. Our long-term data set enabled quantification of the interactions between survey year and each fire regime variable: an ecological relationship missing from temporally restricted studies. We found no evidence of any appreciable departures from the assumption of independence of the sites. Multiple aspects of fire regimes influenced temporal variation in the presence and abundance of mammals. The best models indicated that six of the 11 species responded to two or more fire regime variables, with two species influenced by all three fire regime attributes. Almost all species responded to time since fire, either as an interaction with survey year or as a main effect. Fire severity or its interaction with survey year was important for most terrestrial rodents. The number of fires at a site was significant for terrestrial rodents and several other species. Our findings contain evidence of the effects on native mammals of heterogeneity in fire regimes. Temporal response patterns of mammal species were influenced by multiple fire regime attributes, often in conjunction with survey year. This underscores the critical importance of long-term studies of biota that are coupled with data sets characterized by carefully documented fire history, severity, and frequency. Long-term studies are essential to predict animal responses to fires and guide management of when and where (prescribed) fire or, conversely, long-unburned vegetation is needed. The complexity of observed responses highlights the need for large reserves in which patterns of heterogeneity in fire regimes can be sustained in space and over time. © 2015 by the Ecological Society of America. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Comparative use of active searches and artificial refuges to detect amphibians in terrestrial environments

Artificial refuges (cover boards) are commonly used to survey and monitor herpetofauna in many parts of the world. Despite the extensive use of artificial refuges in mesic environments, their effectiveness for detecting amphibians in temperate zones has rarely been examined. We compared amphibian detection probabilities between two survey methods; active searches of natural habitat and artificial refuges of three different types (corrugated steel, roofing tiles and timber railway sleepers). Our study area included five bioregions encompassing a 1,180 km latitudinal gradient across a modified, temperate eucalypt woodland vegetation community in south-eastern Australia. We deployed 14,778 artificial refuges in terrestrial environments, within patches of remnant vegetation, and collected presence and abundance data on herpetofauna between 1999 and 2017. We used Bayesian logistic regression to identify the most effective survey method for detecting frog species across all bioregions. We modelled frog detections by fitting survey method, time since refuge deployment, and rainfall prior to each survey. We detected 3970 individuals from 18 frog species. Overall, we found active searches and timber substrates most effective for detecting a broad range of species, although detection rates were driven by the numerically abundant spotted marsh frog Limnodynastes tasmaniensis. Timber refuges were effective for detecting several burrowing species, whereas active searches were effective at detecting habitat generalists. Quadratic effects of rainfall prior to survey as opposed to linear effects of time since artificial refuge placement was important in explaining frog detection rates in some bioregions. Active searches, timber railway sleepers and sheets of corrugated steel provide complimentary survey methods for detecting amphibians, although detection rates are influenced by rainfall patterns. Artificial refuges provide a time-effective and standardised method for studying amphibians in their non-breeding terrestrial environment and should be incorporated into future surveys and biodiversity monitoring programs.The work was funded by the Australian Govern-ment's Caring for Our Country Initiative, the National Environmental Science Program's Threatened Species Recovery Hub and the Australian Research Council, and is supported by the Murray Local Land Services, Riverina Local land Services, Central Tablelands Local land Services, North East Catchment Management Authority, Goulburn Broken Catchment Management Authority, NSW Environment Trust, Ian Potter Foundation and the Vincent Fairfax Family Foundation

Novel bird responses to successive, large-scale, landscape transformations

Transformation of intact vegetation into new kinds and configurations of human-modified habitats is a well-established driver of biodiversity loss. Following initial conversion, many human-dominated landscapes are then subject to further large-scale changes in land use. The impacts on biodiversity of repeated changes in land use remain poorly known, particularly how changes in the matrix interact with initial patterns of vegetation clearing. We used an 18-yr study of birds in remnant patches of endangered temperate woodland in south-eastern Australia to quantify the spatial and temporal effects of successive land use transformation in the surrounding landscape. We examined bird response to (1) initial patterns of landscape modification (creating semi-cleared grazing land dominated by pastures that surrounded remnant woodland patches), (2) subsequent establishment and maturation of exotic tree plantations on the pastures surrounding woodland patches, and (3) additive and interactive effects of both types of landscape transformation. The majority of the 57 bird species modeled responded to conversion of grazing land to exotic plantations, either independently from initial patterns of landscape transformation (20 species), or interactively (18 species) or additively (15 species) with initial landscape transformation. The occurrence of only one species (the Common Bronzewing) was related to patterns of initial transformation but not subsequent transformation due to plantation establishment. Thus, despite many characteristics of the woodland patches within the plantation remaining largely unaltered throughout our 18-yr investigation, the matrix had a profound effect on the kinds of species inhabiting them, with such impacts often magnified over time as the matrix continued to change. Plantation establishment triggered new regional-level spatial processes with effects on birds detected in woodland patches up to 2 km away from the plantation. Matrix conversion selected for species with different traits (size, diet and movement patterns) compared to the initial transformation, suggesting it is acting as a different filter on the bird community. New kinds of landscape transformation (such as plantation establishment on previously cleared land) can radically affect the species that have persisted for many decades in previously modified landscapes. This highlights the challenges, but also opportunities, for conserving taxa in ever changing human-dominated environments. © 2019 by the Ecological Society of America. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Disentangling the effects of farmland use, habitat edges, and vegetation structure on ground beetle morphological traits

Land-use change due to agriculture has a major influence on arthropod biodiversity, and may influence species differently depending on their traits. It is unclear how species traits vary across different land uses and their edges, with most studies focussing on single habitat types and overlooking edge effects. We examined variation in morphological traits of carabid beetles (Coleoptera:Carabidae) on both sides of edges between woodlands and four adjoining, but contrasting farmland uses in an agricultural landscape. We asked: (1) how do traits differ between woodlands and different adjoining farmland uses (crop, fallow, restoration planting, and woody debris applied over crop), and do effects depend on increasing distances from the farmland–woodland edge? (2) Does vegetation structure explain observed effects of adjoining farmland use and edge effects on these traits? We found that carabid communities varied in body size and shape, including traits associated with diet, robustness, and visual ability. Smaller sized species were associated with woodlands and larger sized species with farmlands. Farmland use further influenced these associations, where woodlands adjoining plantings supported smaller species, while fallows and crops supported larger species. Vegetation structure significantly influenced body size, flying ability, and body shape, and helped explain the effects of farmland use and distance from edges on body size. We highlight the important role of vegetation structure, farmland use, and edge effects in filtering the morphological traits of carabid assemblages across a highly modified agricultural landscape. Our findings suggest that farmland management can influence body size and dispersal-related traits in farmland and adjacent native vegetation. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Visualization of species pairwise associations: A case study of surrogacy in bird assemblages

Quantifying and visualizing species associations are important to many areas of ecology and conservation biology. Species networks are one way to analyze species associations, with a growing number of applications such as food webs, nesting webs, plant-animal mutualisms, and interlinked extinctions. We present a new method for assessing and visualizing patterns of co-occurrence of species. The method depicts interactions and associations in an analogous way with existing network diagrams for studying pollination and trophic interactions, but adds the assessment of sign, strength, and direction of the associations. This provides a distinct advantage over existing methods of quantifying and visualizing co-occurrence. We demonstrate the utility of our new approach by showing differences in associations among woodland bird species found in different habitats and by illustrating the way these can be interpreted in terms of underlying ecological mechanisms. Our new method is computationally feasible for large assemblages and provides readily interpretable effects with standard errors. It has wide applications for quantifying species associations within ecological communities, examining questions about particular species that occur with others, and how their associations can determine the structure and composition of communities

The Leadbeater's Possum Review

This document reviews current science on Leadbeater’s Possum and its montane ash forest habitat in the Central Highlands of Victoria. The report comprises seven chapters on key topics related to the conservation and current management of Leadbeater’s Possum and the forest habitats on which the species depends. Chapter 1 gives a brief history of major events that effect Leadbeater’s Possum and its forest habitat in the Central Highlands of Victoria. Chapter 2 explores work on hollow-bearing trees, as they are the most critical habitat element that will dictate the species’ survival. Chapter 3 reviews some of the recent policies for the management of the species, while Chapters 4 and 5 provide a summary of some of the statistics and other information relating to Leadbeater’s Possum and the forests in which it is found. Chapter 6 explores information about and insights into the Mountain Ash ecosystem and why it is currently classified as Critically Endangered under IUCN Red List of Ecosystems criteria. Chapter 7 reviews many relevant government documents. Chapter 8 contains some general conclusions about the management of Leadbeater’s Possum and the forests in which it occurs. Throughout this report, unless otherwise specified, reference to ANU means the ANU scientists who have conducted research in the Victorian Central Highlands ecosystem over the past 34+ years, or the scientific work that they have produced. We examine the threats to Leadbeater’s Possum as well as critically appraise the effectiveness of management actions and protective measures designed to conserve the species. We examine the Critically Endangered listing of both Leadbeater’s Possum and the Mountain Ash ecosystem in which it lives, and why both are in a parlous state. The review looks back over the history of decisions and other factors that have led us to the current situation, and explores possible futures based on decisions currently being made. Our review relies heavily on the substantial scientific literature on Leadbeater’s Possum and Mountain Ash forest. Long term data and scientifically robust research will play an important role in rigorously assessing many current claims about the status of populations of Leadbeater’s Possum and its habitat and providing clarity on information to guide enhanced decision making. The area of remaining 1939 age forest in the Central Highlands is reaching low levels, and important decisions need to be made about how the forests of this age are managed. The next 5-10 years will be critical for how the Central Highlands ash forests and the species that inhabit them persist (or otherwise) over the next century

Spatiotemporal effects of logging and fire on tall, wet temperate eucalypt forest birds

Forests globally are subject to disturbances such as logging and fire that create complex temporal variation in spatial patterns of forest cover and stand age. However, investigations that quantify temporal changes in biodiversity in response to multiple forms of disturbance in space and time are relatively uncommon. Over a 10-yr period, we investigated the response of bird species to spatiotemporal changes in forest cover associated with logging and wildfire in the mountain ash (Eucalyptus regnans) forests of southeastern Australia. Specifically, we examined how bird occurrence changed with shifts in the proportion of area burned or logged in a 4.5 km radius surrounding our 88 long-term field survey sites, each measuring 1 ha in size. Overall species richness was greatest in older forest patches, but declined as the amount of fire around each site increased. At the individual species level, 31 of the 37 bird species we modeled exhibited a negative response to the amount of fire in the surrounding landscape, while one species responded positively to fire. Only nine species exhibited signs of recovery in the 6 yr of surveys following the fire. Five species were more likely to be detected as the proportion of logged forest surrounding a site increased, suggesting a possible "concentration effect" with displaced birds moving into unlogged areas following harvesting of adjacent areas. We also identified relationships between the coefficients of life history attributes and spatiotemporal changes in forest cover and stand age. Large-bodied birds and migratory species were associated with landscapes subject to large amounts of fire in 2009. There were associations between old growth stands and small-bodied bird species and species that were not insectivores. Our study shows that birds in mountain ash forests are strongly associated with old growth stands and exhibit complex, time-dependent, and species-specific responses to landscape disturbance. Despite logging and fire both being high-severity perturbations, no bird species exhibited similar responses to fire and logging in the landscape surrounding our sites. Thus, species responses to one kind of landscape-scale disturbance are not readily predictable based on an understanding of the responses to another kind of (albeit superficially similar) disturbance.Threatened Species Recovery Hub of the National Environmental Science Program, Parks Victoria, and Victorian Government Department of Environment, Land, Water and Plannin