Australian Museum

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Proponents of optimal foraging theory attempt to predict the behavior of animals while they are foraging; this theory is based on a number of assump­ tions ( 133 , 155 , 2 10, 23 1 ) . First, an individual's contribution to the next generation (i.e. its fitness) depends on its behavior while foraging. This contribution may be measured genetically or culturally as the proportion of an individual's genes or ideas, respectively, in the next generation. In the former case, the theory is simply an extension of Darwin's theory of evolution. Second, it is assumed that there should be a heritable component of foraging behavior, i.e. an animal that forages in a particular manner should be likely to have offspring that tend to forage in the same manner. This heritable compo­ nent can be either the actual foraging responses made by an animal or the rules by which an animal learns to make such responses. In other words, optimal foraging theory may apply regardless of whether the foraging behavior is learned or innate. Given these first two assumptions, it follows that the proportion of individuals in a population foraging in ways that enhance their fitness will tend to increase over time. Unless countervailed by sufficiently strong group selection (see 287, 242), foraging behavior will therefore evolve, and the average foraging behavior will increasingly come to be characterized by those characteristics that enhance individual fitness. The third assumption is that the relationship between foraging behavior and fitness is known. This relationship is usually referred to as the currency of fitness (23 1 ) . In general, any such currency will include a time scale, although in some cases it may be assumed that fitness is a function of some rate.

A global system of harmonized observations is needed to inform scientists and policy-makers.

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163-185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.

Ecosystem reconfigurations arising from climate-driven changes in species distributions are expected to have profound ecological, social, and economic implications. Here we reveal a rapid climate-driven regime shift of Australian temperate reef communities, which lost their defining kelp forests and became dominated by persistent seaweed turfs. After decades of ocean warming, extreme marine heat waves forced a 100-kilometer range contraction of extensive kelp forests and saw temperate species replaced by seaweeds, invertebrates, corals, and fishes characteristic of subtropical and tropical waters. This community-wide tropicalization fundamentally altered key ecological processes, suppressing the recovery of kelp forests.

Abstract Invertebrate species represent more than 99% of animal diversity; however, they receive much less publicity and attract disproportionately minor research effort relative to vertebrates. Nonmarine mollusks (i.e., terrestrial and freshwater) are one of the most diverse and imperiled groups of animals, although not many people other than a few specialists who study the group seem to be aware of their plight. Nonmarine mollusks include a number of phylogenetically disparate lineages and species-rich assemblages that represent two molluscan classes, Bivalvia (clams and mussels) and Gastropoda (snails, slugs, and limpets). In this article we provide an overview of global nonmarine molluscan biodiversity and conservation status, including several case studies documenting the diversity and global decline of nonmarine mollusks. We conclude with a discussion of the roles that mollusks and malacologists should play in conservation, including research, conservation management strategies, and education and outreach.

Fragmentation of animal and plant populations typically leads to genetic erosion and increased probability of extirpation. Although these effects can usually be reversed by re-establishing gene flow between population fragments, managers sometimes fail to do so due to fears of outbreeding depression (OD). Rapid development of OD is due primarily to adaptive differentiation from selection or fixation of chromosomal variants. Fixed chromosomal variants can be detected empirically. We used an extended form of the breeders' equation to predict the probability of OD due to adaptive differentiation between recently isolated population fragments as a function of intensity of selection, genetic diversity, effective population sizes, and generations of isolation. Empirical data indicated that populations in similar environments had not developed OD even after thousands of generations of isolation. To predict the probability of OD, we developed a decision tree that was based on the four variables from the breeders' equation, taxonomic status, and gene flow within the last 500 years. The predicted probability of OD in crosses between two populations is elevated when the populations have at least one of the following characteristics: are distinct species, have fixed chromosomal differences, exchanged no genes in the last 500 years, or inhabit different environments. Conversely, the predicted probability of OD in crosses between two populations of the same species is low for populations with the same karyotype, isolated for <500 years, and that occupy similar environments. In the former case, we recommend crossing be avoided or tried on a limited, experimental basis. In the latter case, crossing can be carried out with low probability of OD. We used crosses with known results to test the decision tree and found that it correctly identified cases where OD occurred. Current concerns about OD in recently fragmented populations are almost certainly excessive.

Translocations are being increasingly proposed as a way of conserving biodiversity, particularly in the management of threatened and keystone species, with the aims of maintaining biodiversity and ecosystem function under the combined pressures of habitat fragmentation and climate change. Evolutionary genetic considerations should be an important part of translocation strategies, but there is often confusion about concepts and goals. Here, we provide a classification of translocations based on specific genetic goals for both threatened species and ecological restoration, separating targets based on 'genetic rescue' of current population fitness from those focused on maintaining adaptive potential. We then provide a framework for assessing the genetic benefits and risks associated with translocations and provide guidelines for managers focused on conserving biodiversity and evolutionary processes. Case studies are developed to illustrate the framework.

Many species have fragmented distribution with small isolated populations suffering inbreeding depression and/or reduced ability to evolve. Without gene flow from another population within the species (genetic rescue), these populations are likely to be extirpated. However, there have been only ~ 20 published cases of such outcrossing for conservation purposes, probably a very low proportion of populations that would potentially benefit. As one impediment to genetic rescues is the lack of an overview of the magnitude and consistency of genetic rescue effects in wild species, I carried out a meta-analysis. Outcrossing of inbred populations resulted in beneficial effects in 92.9% of 156 cases screened as having a low risk of outbreeding depression. The median increase in composite fitness (combined fecundity and survival) following outcrossing was 148% in stressful environments and 45% in benign ones. Fitness benefits also increased significantly with maternal ΔF (reduction in inbreeding coefficient due to gene flow) and for naturally outbreeding versus inbreeding species. However, benefits did not differ significantly among invertebrates, vertebrates and plants. Evolutionary potential for fitness characters in inbred populations also benefited from gene flow. There are no scientific impediments to the widespread use of outcrossing to genetically rescue inbred populations of naturally outbreeding species, provided potential crosses have a low risk of outbreeding depression. I provide revised guidelines for the management of genetic rescue attempts.

To meet collective obligations towards biodiversity conservation and monitoring, it is essential that the world's governments and non-governmental organisations as well as the research community tap all possible sources of data and information, including new, fast-growing sources such as citizen science (CS), in which volunteers participate in some or all aspects of environmental assessments. Through compilation of a database on CS and community-based monitoring (CBM, a subset of CS) programs, we assess where contributions from CS and CBM are significant and where opportunities for growth exist. We use the Essential Biodiversity Variable framework to describe the range of biodiversity data needed to track progress towards global biodiversity targets, and we assess strengths and gaps in geographical and taxonomic coverage. Our results show that existing CS and CBM data particularly provide large-scale data on species distribution and population abundance, species traits such as phenology, and ecosystem function variables such as primary and secondary productivity. Only birds, Lepidoptera and plants are monitored at scale. Most CS schemes are found in Europe, North America, South Africa, India, and Australia. We then explore what can be learned from successful CS/CBM programs that would facilitate the scaling up of current efforts, how existing strengths in data coverage can be better exploited, and the strategies that could maximise the synergies between CS/CBM and other approaches for monitoring biodiversity, in particular from remote sensing. More and better targeted funding will be needed, if CS/CBM programs are to contribute further to international biodiversity monitoring.

Abstract Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action 1,2 . Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment 3,4 . Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

As wild environments are often inhospitable, many species have to be captive-bred to save them from extinction. In captivity, species adapt genetically to the captive environment and these genetic adaptations are overwhelmingly deleterious when populations are returned to wild environments. I review empirical evidence on (i) the genetic basis of adaptive changes in captivity, (ii) factors affecting the extent of genetic adaptation to captivity, and (iii) means for minimizing its deleterious impacts. Genetic adaptation to captivity is primarily due to rare alleles that in the wild were deleterious and partially recessive. The extent of adaptation to captivity depends upon selection intensity, genetic diversity, effective population size and number of generation in captivity, as predicted by quantitative genetic theory. Minimizing generations in captivity provides a highly effective means for minimizing genetic adaptation to captivity, but is not a practical option for most animal species. Population fragmentation and crossing replicate captive populations provide practical means for minimizing the deleterious effects of genetic adaptation to captivity upon populations reintroduced into the wild. Surprisingly, equalization of family sizes reduces the rate of genetic adaptation, but not the deleterious impacts upon reintroduced populations. Genetic adaptation to captivity is expected to have major effects on reintroduction success for species that have spent many generations in captivity. This issue deserves a much higher priority than it is currently receiving.

Morphological (including ultrastructural) and developmental characters utilized in recent literature are critically reviewed as the basis to reassess the phylogenetic relationships of gastropods. The purpose of this paper is to provide a framework of characters for future studies and a testable phylogenetic hypothesis. This is one of the first attempts to use such characters to assess the relationships of all major clades using parsimony methods. The analysis uses 117 characters and includes 40 taxa, predominantly 'prosobranchs'. Five outgroup taxa are included, representing four conchiferan groups and Poly-placophora. Of the 117 characters reviewed and included in the analyses, nine are shell characters (four of these are shell structure), two opercular, two muscular, four ctenidial, 12 renopericardial and 24 reproductive (including 17 based on sperm and spermatogenesis), 27 of the digestive system, 32 of the nervous system and sense organs; the remainder are developmental (3) and of the foot and hypobranchial gland. In the initial analysis the data set included a mixture of binary and multistate characters with all characters unordered. These data were also analysed after scaling so that each character had equal weight. A third data set was constructed in which all characters were coded as binary characters. These analyses resulted in some implausible character transformations, mainly-involving the regaining of lost pallial structures. Additional analyses were run on all three sets of data after removing five characters showing the most unlikely transformations. These analyses resulted in generally similar topologies. The robustness of the clades was tested using clade decay. The adaptive radiation of gastropods and their life history traits are briefly described and discussed and the terminology for simultaneous hermaphroditism refined. A scenario for the evolution of torsion equated with the fossil record is proposed and the effects of torsion and coiling on gastropods are discussed along with asymmetry imposed by limpet-shaped body forms. It is suggested that the first gastropods were ultradextral. The idea that heterochrony has played a major part in gastropod evolution is developed and discussed, particularly the paedomorphic stamp imposed on the apogastropods. The veliger larvae of caenogastropods and heterobranchs are contrasted and found to differ in many respects. The evolution of planktotrophy within gastropods is discussed. Recent phylogenetic hypotheses for gastropods based on molecular data are generally in broad agreement with the present results. On the basis of our analyses we discuss the major monophyletic groups within gastropods. Gastropods appear to be a monophyletic clade, and divide into two primary groups, the Eogastropoda (incorporating the patellogastropods and their (probably sinistrally coiled) ancestors and the Orthogastropoda - the remainder of the gastropods. Orthogastropoda comprises several well defined clades. The vetigastropod clade encompasses most of the groups previously included in the paraphyletic Archaeogastropoda (fissurellids, trochoideans, scissurelloideans, halioroideans pleurotomarioideans) as well as lepeto-driloidean and lepetelloidean limpets and seguenzids. The location of the hot vent taxa Peltospiridae and Neomphalidae varies with each analysis, probably because there is a lack of ultrastructural data for these taxa and parallelism in many characters. They either form a paraphyletic or monophyletic group at or near the base of the vetigastropods or a clade with the neritopsines and cocculinoideans. The neritopsines (Neritoidea etc.) consistently form a clade with the cocculinoidean limpets, but their position on the tree also differs depending on the data set used and (in the case of the scaled data) whether or not the full suite of characters is used. They are either the sister to the rest of the orthogastropods or to the apogastropods. Caenogastropods [Mesogastropoda (+ architaenioglossan groups) + Neogastropoda] are consistently monophyletic as are the heterobranchs ('Heterostropha'+ Opisthobranchia + Pulmo-nata). The caenogastropods and heterobranchs also form a clade in all the analyses and the name Apogastropoda is redefined to encompass this group. New taxa are proposed, Sorbeoconcha for the caenogastropods exclusive of the architaenioglossan taxa, and Hypsogastropoda for the 'higher caenogastropods' – the Sorbeoconcha exclusive of the Cerithioidea and Campaniloidea.

ABSTRACT The demand for accurate forecasting of the effects of global warming on biodiversity is growing, but current methods for forecasting have limitations. In this article, we compare and discuss the different uses of four forecasting methods: (1) models that consider species individually, (2) niche-theory models that group species by habitat (more specifically, by environmental conditions under which a species can persist or does persist), (3) general circulation models and coupled ocean–atmosphere–biosphere models, and (4) species–area curve models that consider all species or large aggregates of species. After outlining the different uses and limitations of these methods, we make eight primary suggestions for improving forecasts. We find that greater use of the fossil record and of modern genetic studies would improve forecasting methods. We note a Quaternary conundrum: While current empirical and theoretical ecological results suggest that many species could be at risk from global warming, during the recent ice ages surprisingly few species became extinct. The potential resolution of this conundrum gives insights into the requirements for more accurate and reliable forecasting. Our eight suggestions also point to constructive synergies in the solution to the different problems.

▪ Abstract Species extinctions and the deterioration of other biodiversity features worldwide have led to the adoption of systematic conservation planning in many regions of the world. As a consequence, various software tools for conservation planning have been developed over the past twenty years. These tools implement algorithms designed to identify conservation area networks for the representation and persistence of biodiversity features. Budgetary, ethical, and other sociopolitical constraints dictate that the prioritized sites represent biodiversity with minimum impact on human interests. Planning tools are typically also used to satisfy these criteria. This chapter reviews both the concepts and technical choices that underlie the development of these tools. Conservation planning problems can be formulated as optimization problems, and we evaluate the suitability of different algorithms for their solution. Finally, we also review some key issues associated with the use of these tools, such as computational efficiency, the effectiveness of taxa and abiotic parameters at choosing surrogates for biodiversity, the process of setting explicit targets of representation for biodiversity surrogates, and dealing with multiple criteria. The review concludes by identifying areas for future research, including the scheduling of conservation action over extensive time periods and incorporating data about site vulnerability.

Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.

All Australian land mammals, reptiles, and birds weighing more than 100 kilograms, and six of the seven genera with a body mass of 45 to 100 kilograms, perished in the late Quaternary. The timing and causes of these extinctions remain uncertain. We report burial ages for megafauna from 28 sites and infer extinction across the continent around 46,400 years ago (95% confidence interval, 51,200 to 39,800 years ago). Our results rule out extreme aridity at the Last Glacial Maximum as the cause of extinction, but not other climatic impacts; a "blitzkrieg" model of human-induced extinction; or an extended period of anthropogenic ecosystem disruption.

Abstract This article highlights how the loose definition of the term ‘refugia’ has led to discrepancies in methods used to assess the vulnerability of species to the current trend of rising global temperatures. The term ‘refugia’ is commonly used without distinguishing between macrorefugia and microrefugia, ex situ refugia and in situ refugia, glacial and interglacial refugia or refugia based on habitat stability and refugia based on climatic stability. It is not always clear which definition is being used, and this makes it difficult to assess the appropriateness of the methods employed. For example, it is crucial to develop accurate fine‐scale climate grids when identifying microrefugia, but coarse‐scale macroclimate might be adequate for determining macrorefugia. Similarly, identifying in situ refugia might be more appropriate for species with poor dispersal ability but this may overestimate the extinction risk for good dispersers. More care needs to be taken to properly define the context when referring to refugia from climate change so that the validity of methods and the conservation significance of refugia can be assessed.

Abstract The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable consequences for many species. Many small isolated populations are going extinct unnecessarily. In many cases, such populations can be genetically rescued by gene flow into them from another population within the species, but this is very rarely done. This novel and authoritative book addresses the issues involved in genetic management of fragmented animal and plant populations, including inbreeding depression, loss of genetic diversity and elevated extinction risk in small isolated populations, augmentation of gene flow, genetic rescue, causes of outbreeding depression and predicting its occurrence, desirability and implementation of genetic translocations to cope with climate change, and defining and diagnosing species for conservation purposes.

Abstract Thousands of small populations are at increased risk of extinction because genetics and evolutionary biology are not well‐integrated into conservation planning–a major lost opportunity for effective actions. We propose that if the risk of outbreeding depression is low, the default should be to evaluate restoration of gene flow to small inbred populations of diploid outbreeding organisms that were isolated by human activities within the last 500 years, rather than inaction. We outline the elements of a scientific‐based genetic management policy for fragmented populations of plants and animals, and discuss the reasons why the current default policy is, inappropriately, inaction.