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ABSTRACT Killer whales (Orcinus orca) have been documented to prey on white sharks (Carcharodon carcharias), in some cases causing localised shark displacement and triggering ecological cascades. Notably, a series of such predation events have been reported from South Africa over the last decade, with killer whales specifically targeting sharks' liver. However, observations of these interactions are rare, and knowledge of their frequency across the world's oceans remains limited. In October 2023, a 4.7 m (total length) white shark carcass washed ashore in southeastern Australia, coinciding with reports from citizen scientists of killer whales hunting a large, unidentified prey item in the area. Visual inspection of the carcass revealed that the liver, digestive, and reproductive organs were missing, and the presence of four distinctive bite wounds, one of which was characteristic of killer whale liver extraction as seen in South Africa. Genomic analyses performed on swabs taken from the bite wounds confirmed the presence of killer whale DNA in the major bite area, while the other bites were embedded with genetic material from the scavenging broadnose sevengill shark (Notorynchus cepedianus). These results provide confirmed evidence of killer whale predation on white sharks in Australia and the likely selective consumption of the liver, suggesting predations of this nature are more globally prevalent than currently assumed.

ABSTRACT Genetic mixing aims to increase the genetic diversity of small or isolated populations, by mitigating genetic drift and inbreeding depression, either by maximally increasing genetic diversity, or minimising the prevalence of recessive, deleterious alleles. However, few studies investigate this beyond a single generation of mixing. Here, we model genetic mixing using captive, low‐diversity recipient population of the threatened Southern brown bandicoot (Isoodon obesulus) over 50 generations and compare wild populations across south‐eastern Australia as candidate source populations. We first assess genetic differentiation between 12 populations, including the first genomic assessment of three mainland Australian and three Tasmanian populations. We assess genetic diversity in the 12 populations using an individualised autosomal heterozygosity pipeline, using these results to identify a candidate recipient population for genetic mixing simulations. We found that populations fell into four major groups of genetic similarity: Adelaide Hills, western Victoria, eastern Victoria, and Tasmania, but populations within these groups were also distinct, and additional substructure was observed in some populations. Our autosomal heterozygosity pipeline indicated significant variability in mean heterozygosity between populations, identifying one extremely genetically degraded population on Inner Sister Island, Tasmania. Genetic mixing simulations of a low heterozygosity captive population in Victoria suggested the greatest increase in heterozygosity would be reached by using highly differentiated populations as mixing sources. However, when removing populations that may represent taxonomically discrete lineages, neither metrics of differentiation nor heterozygosity was strongly correlated with modelled heterozygosity increase, indicating the value of simulation‐based approaches when selecting source populations for population mixing.

Abstract The number of human–shark interactions has increased worldwide during the past decade resulting in injuries and fatalities. In Australia, the white shark (Carcharodon carcharias), tiger shark (Galeocerdo cuvier), and bull shark (Carcharhinus leucas) are responsible for the majority of fatal incidents. On the southeast coast of Australia, monitoring programs currently rely on SMART (Shark‐Management‐Alert‐in‐Real‐Time) drumlines and mesh nets to catch, tag, and monitor shark movement. However, these methods are laborious, costly, and involve the capture of only a fraction of the total shark population. Here, we develop a multiplex environmental DNA assay capable of detecting all three shark species simultaneously from water samples by targeting conserved but specific mitochondrial sequences that are characteristic of each species. The specificity of the assay was validated by testing for cross‐amplification across a range of non‐target but co‐occurring shark species from eastern Australia. We test the sensitivity of the assay on water samples collected from shark capture events and sites where these shark species are known to frequent, and undertake DNA sequencing on positive samples to confirm species haplotype authenticity. Samples collected from one of these sites also demonstrate that eDNA detections are dependent on shark activity in the area. This assay will allow for rapid detection of DNA from each shark species in water samples, providing a cost‐effective alternative for monitoring sharks along the east coast of Australia and potentially elsewhere.

Abstract Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade‐offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short‐ and long‐term strategies are integrated into a decision framework that also considers nongenetic aspects of management.

Abstract Invasive predators are responsible for declines in many animal species across the globe. To redress these declines, conservationists have undertaken substantial work to remove invasive predators or mitigate their effects. Yet, the challenges associated with removal of invasive predators mean that most successful conservation programs have been restricted to small islands, enclosures (“safe havens”), or refuge habitats where threatened species can persist. While these approaches have been, and will continue to be, crucial for the survival of many species, in some contexts they may eventually lock in a baseline where native species vulnerable to invasive predators are accepted as permanently absent from the wild (shifting baseline syndrome). We propose an explicit theme in conservation biology termed “coexistence conservation,” that is distinguished by its pursuit of innovative solutions that drive or enable adaptive evolution of threatened species and invasive predators to occur over the long term. We argue evolution has a large role to play but using it to adapt native species to a new environmental order requires a shift in mindset from small, isolated, and short‐term leaps to deliberate, staged steps within a long‐term strategy. A key principle of coexistence conservation is that predation is treated as the threat, rather than the predator, driving a focus on the outcome rather than the agent. Without a long‐term strategy, we face the permanent loss of many species in the wild. Coexistence conservation is a complementary approach to current practice and will play an important role in shifting our current trajectory from continued and rapid invasive predator‐driven defaunation to a world where invasive predators and native prey can coexist.

Abstract Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments. We use a combination of population genetics and niche suitability models to assess the trajectory of a functionally important, but highly fragmented, plant species from south‐eastern Australia (Banksia marginata, Proteaceae). We demonstrate significant genetic structuring among, and high level of relatedness within, fragmented remnant populations, highlighting imminent risks of inbreeding. Population simulations, controlling for effective population size (Ne), suggest that many remnant populations will suffer rapid declines in genetic diversity due to drift in the absence of intervention. Simulations were used to demonstrate how inbreeding and drift processes might be suppressed by assisted migration and population mixing approaches that enhance the size and connectivity of remnant populations. These analyses were complemented by niche suitability models that predicted substantial reductions of suitable habitat by 2080; ~30% of the current distribution of the species climate niche overlaps with the projected distribution of the species climate niche in the geographic region by the 2080s. Our study highlights the importance of conserving remnant populations and establishing new populations in areas likely to support B. marginata in the future, and adopting seed sourcing strategies that can help populations overcome the risks of inbreeding and maladaptation. We also argue that ecological replacement of B. marginata using climatically suited plant species might be needed in the future to maintain ecosystem processes where B. marginata cannot persist. We recommend the need for progressive revegetation policies and practices to prevent further deterioration of species such as B. marginata and the ecosystems they support.

Abstract Biological invasions are increasing globally in number and extent despite efforts to restrict their spread. Knowledge of incursion pathways is necessary to prevent new invasions and to design effective biosecurity protocols at source and recipient locations. This study uses genome‐wide single nucleotide polymorphisms (SNPs) to determine the origin of 115 incursive Aedes aegypti(yellow fever mosquito) detected at international ports in Australia and New Zealand. We also genotyped mosquitoes at three point mutations in the voltage‐sensitive sodium channel (Vssc) gene: V1016G, F1534C and S989P. These mutations confer knockdown resistance to synthetic pyrethroid insecticides, widely used for controlling invertebrate pests. We first delineated reference populations using Ae. aegypti sampled from 15 locations in Asia, South America, Australia and the Pacific Islands. Incursives were assigned to these populations using discriminant analysis of principal components (DAPC) and an assignment test with a support vector machine predictive model. Bali, Indonesia, was the most common origin of Ae. aegypti detected in Australia, while Ae. aegypti detected in New Zealand originated from Pacific Islands such as Fiji. Most incursives had the same allelic genotype across the three Vsscgene point mutations, which confers strong resistance to synthetic pyrethroids, the only insecticide class used in current, widely implemented aircraft disinsection protocols endorsed by the World Health Organization (WHO). Additionally, all internationally assigned Ae. aegypti had Vssc point mutations linked to pyrethroid resistance that are not found in Australian populations. These findings demonstrate that protocols for preventing introductions of invertebrates must consider insecticide resistance, and highlight the usefulness of genomic data sets for managing global biosecurity objectives.

Genetic rescue can be valuable for the conservation of small populations threatened by low genetic diversity, but it carries the perceived risk of outbreeding depression. Here, Weeks et al. report increased hybrid fitness in a rescued population of the mountain pygmy possum, which likely contributed to population growth following genetic rescue.

Abstract Heterozygosity is a metric of genetic variability frequently used to inform the management of threatened taxa. Estimating observed and expected heterozygosities from genome‐wide sequence data has become increasingly common, and these estimates are often derived directly from genotypes at single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of ‘downstream’ analysis with these markers may depend heavily on ‘upstream’ filtering decisions. Here we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of observed and expected heterozygosity using two reduced‐representation sequencing datasets, one from the mosquito Aedes aegypti (ddRADseq) and the other from a threatened grasshopper, Keyacris scurra (DArTseq). We show that estimates based on polymorphic markers only (i.e. SNP heterozygosity) are always biased by global sample size (N), with smaller N producing larger estimates. By contrast, results are unbiased by sample size when calculations consider monomorphic as well as polymorphic sequence information (i.e. genome‐wide or autosomal heterozygosity). SNP heterozygosity is also biased when differentiated populations are analysed together while autosomal heterozygosity remains unbiased. We also show that when nucleotide sites with missing genotypes are included, observed and expected heterozygosity estimates diverge in proportion to the amount of missing data permitted at each site. We make three recommendations for estimating genome‐wide heterozygosity: (a) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (b) sites with any missing data should be omitted and (c) populations should be analysed in independent runs. This should facilitate comparisons within and across studies and between observed and expected measures of heterozygosity.

Parthenogenetic species are assumed to represent evolutionary dead ends, yet parthenogenesis is common in some groups of invertebrates particularly in those found in relatively constant environments. This suggests that parthenogenetic reproduction might be common in pest invertebrates from uniform agricultural environments. Based on the evaluations of two databases from North America and Italy, we found that parthenogenetic species comprised 45 per cent (North America) or 48 per cent (Italy) of pest species derived from genera where parthenogenesis occurred, compared with an overall incidence of 10 per cent or 16 per cent in these genera. In establishing these patterns, we included only genera containing at least some member species that reproduced by parthenogenesis. The high incidence of parthenogenesis in pest species is spread across different families and several insect orders. Parthenogenetic reproduction may be favoured in agricultural environments when particular clones have a high fitness across multiple generations. Increasing the complexity and variability of agricultural environments represents one way of potentially controlling parthenogenetic pest species. [ABSTRACT FROM AUTHOR]

The Australian grains industry is dealing with a shifting complex of invertebrate pests due to evolving management practices and climate change as indicated by an assessment of pest reports over the last 20–30 years. A comparison of pest outbreak reports from the early 1980s to 2006–07 from south-eastern Australia highlights a decrease in the importance of pea weevils and armyworms, while the lucerne flea, Balaustiummites, blue oat mites and Bryobiamites have increased in prominence. In Western Australia, where detailed outbreak records are available from the mid 1990s, the relative incidence of armyworms, aphids and vegetable weevils has recently decreased, while the incidence of pasture cockchafers, Balaustiummites, blue oat mites, redlegged earth mites, the lucerne flea and snails has increased. These changes are the result of several possible drivers. Patterns of pesticide use, farm management responses and changing cropping patterns are likely to have contributed to these shifts. Drier conditions, exacerbated by climate change, have potentially reduced the build-up of migratory species from inland Australia and increased the adoption rate of minimum and no-tillage systems in order to retain soil moisture. The latter has been accompanied by increased pesticide use, accelerating selection pressures for resistance. Other control options will become available once there is an understanding of interactions between pests and beneficial species within a landscape context and a wider choice of ‘softer' chemicals. Future climate change will directly and indirectly influence pest distributions and outbreaks as well as the potential effectiveness of endemic natural enemies. Genetically modified crops provide new options for control but also present challenges as new pest species are likely to emerge. [ABSTRACT FROM AUTHOR]

Balaustium medicagoense and Bryobia sp. (clover or pasture mite) have recently been identified as potential emerging pests of crops and pastures within southern Australia. Recorded damage by these mites has markedly increased in the past decade. There is limited information on the pesticide tolerance of these mites relative to other earth mite pests. This study examined the response of Ba. medicagoense and Bryobia sp., using the redlegged earth mite [Halotydeus destructor (Tucker)] as a comparison, to several currently registered pesticides against earth mites (omethoate, bifenthrin, chlorpyrifos, methidathion and α-cypermethrin). Ba. medicagoense had a much greater level of tolerance to all pesticides tested than H. destructor. Similarly, Bryobia sp. had a higher level of tolerance to bifenthrin, methidathion and α-cypermethrin than H. destructor. However, in the case of omethoate and chlorpyrifos, the tolerance levels were similar for Bryobia sp. and H. destructor. Ba. medicagoense had a higher level of tolerance than Bryobia sp. to the organophosphates tested (omethoate, chlorpyrifos and methidathion), but there was no difference for bifenthrin. We were unable to compare tolerance levels between Ba. medicagoense and Bryobia sp. to α-cypermethrin because of inconsistencies between replicate tests. These emerging pest mite species, therefore, have a high natural tolerance to currently registered pesticides and may prove difficult to control in the field. These findings suggest that other strategies that are not reliant on chemicals should be considered for the control of Ba. medicagoense and Bryobia sp. [ABSTRACT FROM AUTHOR]

Earth mites are a complex of related species introduced into Australia in the early part of last century that cause economic damage to crops, especially canola, and to pastures. A general method of chemical control aimed at interrupting the life cycle at the most effective stage, by spraying in the spring before the mites enter diapause, has recently been adopted for controlling earth mites, particularly the redlegged earth mite Halotydeus destructor (Tucker). Here we use paired-paddock treatments and field enclosures to test the effectiveness of this method on pest populations of H. destructor as well as on other pests over two seasons at multiple pasture sites in Victoria. Halotydeus destructor numbers at the start of the winter growing season were suppressed by up to 85%, but this control level was not sustained. The numbers of H. destructor and other pests were similar to or higher than those in the unsprayed areas by spring. Spring spraying is, therefore, a useful means of suppressing H. destructor in early autumn, but its effects disappear relatively quickly over time in Victoria. This strategy also has little impact on the control of the blue oat mite Penthaleus major (Duges) and other phytophagous invertebrate pests. [ABSTRACT FROM AUTHOR]

Abstract??Drosophila melanogasterinvaded Australia around 100?years ago, most likely through a northern invasion. The wide range of climatic conditions in eastern Australia across whichD. melanogasteris now found provides an opportunity for researchers to identify traits and genes that are associated with climatic adaptation. Allozyme studies indicate clinal patterns for at least four loci including a strong linear cline inAdhand a non-linear cline in ?-Gpdh. Inversion clines were initially established from cytological studies but have now been validated with larger sample sizes using molecular markers for breakpoints. Recent collections indicate that some genetic markers (AdhandIn(3R)Payne) have changed over the last 20?years reflecting continuing evolution. Heritable clines have been established for quantitative traits including wing length/area, thorax length and cold and heat resistance. A cline in egg size independent of body size and a weak cline in competitive ability have also been established. Postulated clinal patterns for resistance to desiccation and starvation have not been supported by extensive sampling. Experiments under laboratory and semi-natural conditions have suggested selective factors generating clinal patterns, particularly for reproductive patterns over winter. Attempts are being made to link clinal variation in traits to specific genes using QTL analysis and the candidate locus approach, and to identify the genetic architecture of trait variation along the cline. This is proving difficult because of inversion polymorphisms that generate disequilibrium among genes. Substantial gaps still remain in linking clines to field selection and understanding the genetic and physiological basis of the adaptive shifts. HoweverD. melanogasterpopulations in eastern Australia remain an excellent resource for understanding past and future evolutionary responses to climate change. [ABSTRACT FROM AUTHOR]

Many intracellular micro-organisms are now known to cause reproductive abnormalities and other phenomena in their hosts. The endosymbiont Wolbachia is the best known of these reproductive manipulators owing to its extremely high incidence among arthropods and the diverse host effects it has been implicated as causing. However, recent evidence suggests that another intracellular bacterium, a Cytophaga-like organism (CLO), may also induce several reproductive effects in its hosts. Here, we present the first survey of arthropod hosts for infection by the CLO. We use a sensitive hemi-nested polymerase chain reaction method to screen 223 species from 20 arthropod orders for infection by the CLO and Wolbachia. The results indicate that, although not as prevalent as Wolbachia, the CLO infects a significant number of arthropod hosts (ca. 7.2%). In addition, double infections of the CLO and Wolbachia were found in individuals of seven arthropod species. Sequencing analysis of the 16S rDNA region of the CLO indicates evidence for horizontal transmission of the CLO strains. We discuss these results with reference to future studies on host effects induced by intracellular micro-organisms. [ABSTRACT FROM AUTHOR]

The endosymbiont Wolbachia has gained widespread notoriety over the past decade because of its high infection frequency among arthropods, and the unique heterogeneity of the host reproductive effects that it has been implicated as causing to enhance its own spread. Recently, another endosymbiotic bacterium from the Cytophaga-Flavobacterium-Bacteroides phylum has been shown to be widespread among arthropods and manipulate its hosts' reproduction to enhance its own spread. We show that infection by this Cytophaga-like organism (CLO) in the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae) is associated with a significant increase in the fecundity of infected females. This adds to the growing list of phenotypes that the CLO can induce in its hosts, which now include feminization, parthenogenesis induction, cytoplasmic incompatibility and fecundity enhancement, rivalling Wolbachia for overall diversity of host reproductive manipulations. [ABSTRACT FROM AUTHOR]

The arbovirus vectors Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are both common throughout the Indo-Pacific region, where 70% of global dengue transmission occurs. For Ae. aegypti all Indo-Pacific populations are invasive, having spread from an initial native range of Africa, while for Ae. albopictus the Indo-Pacific includes invasive populations and those from the native range: putatively, India to Japan to Southeast Asia. This study analyses the population genomics of 480 of these mosquitoes sampled from 27 locations in the Indo-Pacific. We investigated patterns of genome-wide genetic differentiation to compare pathways of invasion and ongoing gene flow in both species, and to compare invasive and native-range populations of Ae. albopictus. We also tested landscape genomic hypotheses that genetic differentiation would increase with geographical distance and be lower between locations with high connectivity to human transportation routes, the primary means of dispersal at these scales. We found that genetic distances were generally higher in Ae. aegypti, with Pacific populations the most highly differentiated. The most differentiated Ae. albopictus populations were in Vanuatu, Indonesia and Sri Lanka, the latter two representing potential native-range populations and potential cryptic subspeciation respectively. Genetic distances in Ae. aegypti increased with geographical distance, while in Ae. albopictus they decreased with higher connectivity to human transportation routes. Contrary to the situation in Ae. aegypti, we found evidence of long-distance Ae. albopictus colonisation events, including colonisation of Mauritius from East Asia and of Fiji from Southeast Asia. These direct genomic comparisons indicate likely differences in dispersal ecology in these species, despite their broadly sympatric distributions and similar use of human transport to disperse. Our findings will assist biosecurity operations to trace the source of invasive material and for biocontrol operations that benefit from matching genetic backgrounds of released and local populations.

The maternally inherited intracellular bacteria Wolbachia can manipulate host reproduction in various ways that foster frequency increases within and among host populations. Manipulations involving cytoplasmic incompatibility (CI), where matings between infected males and uninfected females produce non-viable embryos, are common in arthropods and produce a reproductive advantage for infected females. CI was associated with the spread of Wolbachia variant wRi in Californian populations of Drosophila simulans, which was interpreted as a bistable wave, in which local infection frequencies tend to increase only once the infection becomes sufficiently common to offset imperfect maternal transmission and infection costs. However, maternally inherited Wolbachia are expected to evolve towards mutualism, and they are known to increase host fitness by protecting against infectious microbes or increasing fecundity. We describe the sequential spread over approximately 20 years in natural populations of D. simulans on the east coast of Australia of two Wolbachia variants (wAu and wRi), only one of which causes significant CI, with wRi displacing wAu since 2004. Wolbachia and mtDNA frequency data and analyses suggest that these dynamics, as well as the earlier spread in California, are best understood as Fisherian waves of favourable variants, in which local spread tends to occur from arbitrarily low frequencies. We discuss implications for Wolbachia-host dynamics and coevolution and for applications of Wolbachia to disease control.

The genetic population structure of Aedes (Stegomyia) aegypti (L.), the main vector of dengue virus, is being investigated in areas where a novel dengue suppression program is to be implemented. The aim of the program is to release and establish mosquito populations with impaired virus transmission capabilities. To model effects of the release and devise protocols for its implementation, information about the genetic structure of populations at a range of spatial scales is required.This study investigates a potential release site in the Hua Sam Rong Subdistrict of Plaeng Yao District, Chachoengsao Province, in eastern Thailand which comprises a complex of five villages within a 10 km radius. Aedes aegypti resting indoors was sampled at four different times of year from houses within the five villages. Genetic markers were used to screen the mosquitoes: two Exon Primed Intron Crossing (EPIC) markers and five microsatellite markers. The raw allele size was determined using several statistical software packages to analyze the population structure of the mosquito. Estimates of effective population size for each village were low, but there was no evidence of genetic isolation by geographic distance.The presence of temporary genetic structure is possibly caused by genetic drift due to large contributions of adults from a few breeding containers. This suggests that the introduction of mosquitoes into an area needs to proceed through multiple releases and targeting of sites where mosquitoes are emerging in large numbers.

Wolbachia are maternally inherited bacteria that commonly spread through host populations by causing cytoplasmic incompatibility, often expressed as reduced egg hatch when uninfected females mate with infected males. Infected females are frequently less fecund as a consequence of Wolbachia infection. However, theory predicts that because of maternal transmission, these "parasites" will tend to evolve towards a more mutualistic association with their hosts. Drosophila simulans in California provided the classic case of a Wolbachia infection spreading in nature. Cytoplasmic incompatibility allowed the infection to spread through individual populations within a few years and from southern to northern California (more than 700 km) within a decade, despite reducing the fecundity of infected females by 15%-20% under laboratory conditions. Here we show that the Wolbachia in California D. simulans have changed over the last 20 y so that infected females now exhibit an average 10% fecundity advantage over uninfected females in the laboratory. Our data suggest smaller but qualitatively similar changes in relative fecundity in nature and demonstrate that fecundity-increasing Wolbachia variants are currently polymorphic in natural populations.