Monsoonal wet season influences the migration tendency of a catadromous fish (barramundi Lates calcarifer)

Many animals exhibit partial migration, which occurs when populations contain coexisting contingents of migratory and resident individuals. This individual-level variation in migration behaviour may drive differences in growth, age at maturity and survival. Therefore, partial migration is widely considered to play a key role in shaping population demography. Otolith chemistry and microstructural analysis were used to identify the environmental- and individual-specific factors that influence migratory behaviour in the facultatively catadromous barramundi (Lates calcarifer) at two distinct life history stages: firstly, as juveniles migrating upstream into fresh water; and secondly, as adults or sub-adults returning to the estuarine/marine spawning habitat. Monsoonal climate played an important role in determining the migration propensity of juveniles: individuals born in the driest year examined (weak monsoon) were more than twice as likely to undergo migration to freshwater than those born in the wettest (strong monsoon) year. In contrast, the ontogenetic timing of return migrations to the estuary by adults and sub-adults was highly variable and not strongly associated with the environmental parameters examined. We propose that scarce resources within saline natal habitats during lower rainfall years may provide an ecological incentive for juveniles to migrate upstream, whereas more abundant resources in higher rainfall years may promote resident life histories within estuaries. We conclude that inter-annual climatic variation, here evidenced by monsoonal strength, likely plays an important role in driving the persistence of diversified life histories within wild barramundi populations.

Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia

Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.

The rise of animal biotelemetry and genetics research data integration

The advancement and availability of innovative animal biotelemetry and genomic technologies are improving our understanding of how the movements of individuals influence gene flow within and between populations and ultimately drive evolutionary and ecological processes. There is a growing body of work that is integrating what were once disparate fields of biology, and here, we reviewed the published literature up until January 2023 (139 papers) to better understand the drivers of this research and how it is improving our knowledge of animal biology. The review showed that the predominant drivers for this research were as follows: (1) understanding how individual-based movements affect animal populations, (2) analyzing the relationship between genetic relatedness and social structuring, and (3) studying how the landscape affects the flow of genes, and how this is impacted by environmental change. However, there was a divergence between taxa as to the most prevalent research aim and the methodologies applied. We also found that after 2010 there was an increase in studies that integrated the two data types using innovative statistical techniques instead of analyzing the data independently using traditional statistics from the respective fields. This new approach greatly improved our understanding of the link between the individual, the population, and the environment and is being used to better conserve and manage species. We discuss the challenges and limitations, as well as the potential for growth and diversification of this research approach. The paper provides a guide for researchers who wish to consider applying these disparate disciplines and advance the field.

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

Sex and male breeding state predict intraspecific trait variation in mouth-brooding fishes

Sex-specific reproductive roles contribute to sexual dimorphic morphological trait variations. In uniparental mouth-brooding fishes, the mouth performs a reproductive function in addition to its key roles in feeding and respiration, resulting in the potential for sex-specific functional performance trade-offs. Trait differences related to parental care may occur when the individual matures or be restricted to periods when the parent is mouth-brooding. This study explored sexual dimorphism and morphological trait adaptations related to feeding, breeding, respiration and locomotion performance in two paternal mouth-brooding freshwater fishes (Glossamia aprion and Neoarius graeffei). Eight morphological traits were evaluated for sexual dimorphism (non-brooder males vs. females) and male breeding state differences (brooders vs. non-brooders). Male breeding state was a significant predictor of trait variation in both species. Brooders differed in buccal volume and in several feeding and locomotory traits compared to non-brooder males. Non-brooder males had bigger buccal volumes and relative eye diameters (G. aprion) and larger relative gape sizes (N. graeffei) compared to females, a potential response to both mouth-brooding and feeding requirements. Although there were clear trait differences between brooder and non-brooder males, further research is required to confirm whether individuals return to their former morphology once mouth-brooding has ceased or if trait differences are maintained post-brooding. This study highlights the importance of considering the potential impacts of intraspecific trait variation on the performance of critical life functions, such as feeding, respiration and locomotion across the life history.

Mitochondrial phylogeny within the Yellow Chat (Epthianura crocea) does not support subspecific designation of endangered Alligator Rivers population

The delineation of subspecies is important in the evaluation and protection of biodiversity. Subspecies delineation is hampered by inconsistently applied criteria and a lack of agreement and shifting standards on how a subspecies should be defined. The Australian endemic Yellow Chat (Epthianura crocea) is split into three subspecies (E. c. crocea, E. c. tunneyi, and E. c. macgregori) based on minor plumage differences and geographical isolation. Both E. c. tunneyi (Endangered) and E. c. macgregori (Critically Endangered) are recognized under Australian legislation as threatened and are the subject of significant conservation effort. We used mitochondrial DNA to evaluate the phylogeny of the Yellow Chat and determine how much genetic variation is present in each of the three subspecies. We found no significant difference in the cytochrome b sequences (833 base pairs) of E. c. crocea and E. c. tunneyi, but approximately 0.70% or 5.83 bp difference between E. c macgregori and both E. c. crocea and E. c. tunneyi. This analysis supports the delineation of E. c. macgregori as a valid subspecies but does not support separation of E. c. crocea from E. c. tunneyi. We also found very low levels of genetic variation within the Yellow Chat, suggesting it may be vulnerable to environmental change. Our results cast doubt upon the geographic isolation of E. c. crocea from E. c. tunneyi, but more advanced genetic sequencing and a robust comparison of plumage are needed to fully resolve taxonomy.

Diverse parentage relationships in paternal mouthbrooding fishes

While mouthbrooding is not an uncommon parental care strategy in fishes, paternal mouthbrooding only occurs in eight fish families and is little studied. The high cost of paternal mouthbrooding to the male implies a low risk of investment in another male's offspring but genetic parentage patterns are poorly known for paternal mouthbrooders. Here, we used single-nucleotide polymorphism genetic data to investigate parentage relationships of broods of two mouthbrooders of northern Australian rivers, mouth almighty Glossamia aprion and blue catfish Neoarius graeffei. For N. graeffei, we found that the parentage pattern was largely monogamous with the brooder male as the sire. For G. aprion, the parentage pattern was more heterogeneous including observations of monogamous broods with the brooder male as the sire (73%), polygyny (13%), cuckoldry (6%) and a brood genetically unrelated to the brooder male (6%). Findings demonstrate the potential for complex interrelationships of male care, paternity confidence and mating behaviour in mouthbrooding fishes.

Disturbance alters the forest soil microbiome

Billions of microorganisms perform critical below-ground functions in all terrestrial ecosystems. While largely invisible to the naked eye, they support all higher lifeforms, form symbiotic relationships with ~90% of terrestrial plant species, stabilize soils, and facilitate biogeochemical cycles. Global increases in the frequency of disturbances are driving major changes in the structure and function of forests. However, despite their functional significance, the disturbance responses of forest microbial communities are poorly understood. Here, we explore the influence of disturbance on the soil microbiome (archaea, fungi and bacteria) of some of the world's tallest and most carbon-dense forests, the Mountain Ash forests of south-eastern Australia. From 80 sites, we identified 23,277 and 19,056 microbial operational taxonomic units from the 0-10 cm and 20-30 cm depths of soil respectively. From this extensive data set, we found the diversity and composition of these often cryptic communities has been altered by human and natural disturbance events. For instance, the diversity of ectomycorrhizal fungi declined with clearcut logging, the diversity of archaea declined with salvage logging, and bacterial diversity and overall microbial diversity declined with the number of fires. Moreover, we identified key associations between edaphic (soil properties), environmental (slope, elevation) and spatial variables and the composition of all microbial communities. Specifically, we found that soil pH, manganese, magnesium, phosphorus, iron and nitrate were associated with the composition of all microbial communities. In a period of widespread degradation of global forest ecosystems, our findings provide an important and timely insight into the disturbance responses of soil microbial communities, which may influence key ecological functions.

Population genomics and conservation management of a declining tropical rodent

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (F_ST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.

Direct and indirect disturbance impacts in forests

Human and natural disturbances are key drivers of change in forest ecosystems. Yet, the direct and indirect mechanisms which underpin these changes remain poorly understood at the ecosystem level. Here, using structural equation modelling across a 150+ year chronosequence, we disentangle the direct and indirect effects of major disturbances in a temperate forest ecosystem. We show that wildfires, logging and post-fire (salvage) logging can affect plant and microbial communities and abiotic soil properties both directly and indirectly through plant-soil-microbial interactions. We quantified 68 direct and indirect disturbance effects across these components, with the majority resulting in ecosystem-wide adverse effects. Indirect disturbance effects accounted for 43% of total disturbance effects, with some amplifying or partially mitigating direct disturbance effects. Overall, human disturbances were associated with more negative effects than natural disturbances. Our analyses provide novel insights into the multifaceted dynamics of forest disturbances and the mechanisms which underpin their relative impacts.

Scale-dependent signatures of local adaptation in a foundation tree species

Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.

Adapting reintroduction tactics in successive trials increases the likelihood of establishment for an endangered carnivore in a fenced sanctuary

Threatened species recovery programs are increasingly turning to reintroductions to reverse biodiversity loss. Here we present a real-world example where tactics (techniques which influence post-release performance and persistence) and an adaptive management framework (which incorporates feedback between monitoring and future actions) improved reintroduction success. Across three successive trials we investigated the influence of tactics on the effective survival and post-release dispersal of endangered eastern quolls (Dasyurus viverrinus) reintroduced into Mulligans Flat Woodland Sanctuary, Australian Capital Territory. Founders were monitored for 42 days post-release, and probability of survival and post-release dispersal were tested against trial, origin, sex, den sharing and presence of pouch young. We adopted an adaptive management framework, using monitoring to facilitate rapid learning and to implement interventions that improved reintroduction success. Founders released in the first trial were less likely to survive (28.6%, n = 14) than those founders released the second (76.9%, n = 13) and third trials (87.5%, n = 8). We adapted several tactics in the second and third trials, including the selection of female-only founders to avoid elevated male mortality, and post-mating releases to reduce stress. Founders that moved dens between consecutive nights were less likely to survive, suggesting that minimising post-release dispersal can increase the probability of survival. The probability of moving dens was lower in the second and third trials, for females, and when den sharing with another founder. This study demonstrates that, through iterative trials of tactics involving monitoring and learning, adaptive management can be used to significantly improve the success of reintroduction programs.

Pervasive admixture between eucalypt species has consequences for conservation and assisted migration

Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south-eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.

Relationship between effective and demographic population size in continuously distributed populations

Genetic monitoring of wild populations can offer insights into demographic and genetic information simultaneously. However, widespread application of genetic monitoring is hindered by large uncertainty in the estimation and interpretation of target metrics such as contemporary effective population size, Ne . We used four long-term genetic and demographic studies (≥9 years) to evaluate the temporal stability of the relationship between Ne and demographic population size (Nc ). These case studies focused on mammals that are continuously distributed, yet dispersal-limited within the spatial scale of the study. We estimated local, contemporary Ne with single-sample methods (LDNE, Heterozygosity Excess, and Molecular Ancestry) and demographic abundance with either mark-recapture estimates or catch-per-unit effort indices. Estimates of Ne varied widely within each case study suggesting interpretation of estimates is challenging. We found inconsistent correlations and trends both among estimates of Ne and between Ne and Nc suggesting the value of Ne as an indicator of Nc is limited in some cases. In the two case studies with consistent trends between Ne and Nc , FIS was more stable over time and lower, suggesting FIS may be a good indicator that the population was sampled at a spatial scale at which genetic structure is not biasing estimates of Ne . These results suggest that more empirical work on the estimation of Ne in continuous populations is needed to understand the appropriate context to use LDNe as a useful metric in a monitoring programme to detect temporal trends in either Ne or Nc .

Logging and fire regimes alter plant communities

Disturbances are key drivers of plant community composition, structure, and function. Plant functional traits, including life forms and reproductive strategies are critical to the resilience and resistance of plant communities in the event of disturbance. Climate change and increasing anthropogenic disturbance are altering natural disturbance regimes globally. When these regimes shift beyond the adaptive resilience of plant functional traits, local populations and ecosystem functions can become compromised. We tested the influence of multiple disturbances, of varying intensity and frequency, on the composition and abundance of vascular plant communities and their respective functional traits (life forms and reproductive strategies) in the wet sclerophyll, Mountain Ash Eucalyptus regnans forests of southeastern Australia. Specifically, we quantified the effect of the type and number of disturbances (including fires, clearcut logging, and salvage logging) on plant community composition. We found that clearcut and salvage logging and the number of fires significantly influenced plant community composition and functional traits. Specifically, multiple fires resulted in lower populations of species that depend on on-site seeding for persistence. This includes the common tree species Eucalyptus regnans, Pomaderris aspera, and Acacia dealbata. In contrast, clearcut and salvage logged sites supported abundant on-site seeder species. However, species that depend on resprouting by surviving individuals, such as common and keystone "tree ferns" Dicksonia antarctica and Cyathea australis, declined significantly. Our data have important implications for understanding the relationship between altered disturbance regimes and plant communities and the respective effects on ecosystem function. In a period of rapid global environmental change, with disturbances predicted to increase and intensify, it is critical to address the impact of altered disturbance regimes on biodiversity.

The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure.

Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others

The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.

Non-linear growth in tree ferns, Dicksonia antarctica and Cyathea australis

Tree ferns are an important structural component of forests in many countries. However, because their regeneration is often unrelated to major disturbances, their age is often difficult to determine. In addition, rates of growth may not be uniform, which further complicates attempts to determine their age. In this study, we measured 5 years of growth of Cyathea australis and Dicksonia antarctica after a large wildfire in 2009 in south-eastern Australia. We found growth rates of these two species were unaffected by aspect and elevation but slope had a minor effect with D. antarctica growing 0.3mm faster for each additional degree of slope. Geographic location influenced growth in both species by up to 12 - 14mm/yr. The most consistent factor influencing growth rate, however, was initial height at the time of the 2009 fire; a finding consistent in both species and all geographic locations. For both tree fern species, individuals that were taller at the commencement of the study had greater overall growth for the duration of the study. This effect did not decrease even among the tallest tree ferns in our study (up to 6 metres tall). Overall, Cyathea australis averaged 73 (± 22)mm/year of growth (± 1SD), with the rate increasing 5mm/yr per metre of additional height. Dicksonia antarctica averaged 33 (± 13)mm/year, increasing by 6mm/yr/m. Growth rates dependent on initial height were unexpected and we discuss possible reasons for this finding. Variable growth rates also suggest that common age estimation methods of dividing height by average growth rate are likely to underestimate the age of short tree ferns, while overestimating the age of tall tree ferns, particularly if they have been subject to a fire.

Short- and long-term effects of habitat fragmentation differ but are predicted by response to the matrix

Habitat loss and fragmentation are major threats to biodiversity and ecosystem processes. Our current understanding of the impacts of habitat loss and fragmentation is based largely on studies that focus on either short-term or long-term responses. Short-term responses are often used to predict long-term responses and make management decisions. The lack of studies comparing short- and long-term responses to fragmentation means we do not adequately understand when and how well short-term responses can be extrapolated to predict long-term responses, and when or why they cannot. To address this gap, we used data from one of the world's longest-running fragmentation experiments, The Wog Wog Habitat Fragmentation Experiment. Using data for carabid beetles, we found that responses in the long term (more than 22 yr post-fragmentation ≈22 generations) often contrasted markedly with those in the short term (5 yr post-fragmentation). The total abundance of all carabids, species richness and the occurrence of six species declined in the short term in the fragments but increased over the long term. The occurrence of three species declined initially and continued to decline, whilst another species was positively affected initially but decreased in the long term. Species' responses to the matrix that surrounds the fragments strongly predicted both the direction (increase/decline in occurrence) and magnitude of their responses to fragmentation. Additionally, species' responses to the matrix were somewhat predicted by their preferences for different types of native habitat (open vs. shaded). Our study highlights the degree of the matrix's influence in fragmented landscapes, and how this influence can change over time. We urge caution in using short-term responses to forecast long-term responses in cases where the matrix (1) impacts species' responses to fragmentation (by isolating them, creating new habitat or altering fragment habitat) and (2) is likely to change through time.

A morphological and phylogenetic investigation into divergence among sympatric Australian southern bull kelps (Durvillaea potatorum and D. amatheiae sp. nov.)

Genetic analyses can reveal a wealth of hitherto undiscovered cryptic biodiversity. For co-occurring and morphologically similar species, the combination of molecular, ecological and morphological analyses provides an excellent opportunity for understanding some of the processes that can lead to divergence and speciation. The Australian endemic brown macroalga Durvillaea potatorum (Phaeophyceae) was examined with a combination of genetic and morphological approaches to confirm the presence of two separate species and to infer the processes that led to their divergence. A total of 331 individuals from 11 sites around coastal Tasmania were collected and measured in situ for a range of morphological and ecological characteristics. Tissue samples were also collected for each individual to allow genetic analyses using mitochondrial (COI) and nuclear (28S) markers. Genetic analyses confirmed the presence of two deeply divergent clades. The significant morphological differentiation, despite high levels of intra-lineage variability, further supported their recognition as distinct species. We describe a new species, D. amatheiae sp. nov., which is characterised by a narrower and proportionately shorter stipe, shorter total length, and higher number of stipitate lateral blades and branches than D. potatorum (sensu stricto). The occurrence of both species in sympatry along Tasmania's eastern and western coasts, as well as their contrasting patterns of haplotype diversity, supports a hypothesis of geographical isolation, allopatric speciation and subsequent secondary contact in response to sea level and ocean current change throughout the Pleistocene glaciation cycles. This research contributes to resolving the phylogenetic relationships, taxonomy and evolution of the ecologically keystone kelp genus Durvillaea.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity inN. stellatus Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics.

Do temporal changes in vegetation structure additional to time since fire predict changes in bird occurrence?

Fire is a major ecological process in ecosystems globally. Its impacts on fauna can be both direct (e.g., mortality) and indirect (e.g., altered habitat), resulting in population recovery being driven by several possible mechanisms. Separating direct from indirect impacts of fire on faunal population recovery can be valuable in guiding management of biodiversity in fire-prone environments. However, resolving the influence of direct and indirect processes remains a key challenge because many processes affecting fauna can change concomitantly with time since fire. We explore the mechanisms influencing bird response to fire by posing the question, can temporal changes in vegetation structure predict changes in bird occurrence on sites, and can these be separated from other temporal changes using the surrogate of time since fire? We conducted a 12-yr study of bird and vegetation responses to fire at 124 sites across six vegetation classes in Booderee National Park, Australia. Approximately half of these sites, established in 2002, were burned by a large (>3000 ha) wildfire in 2003. To disentangle collinear effects of temporal changes in vegetation and direct demographic effects on population recovery that are subsumed by time since fire, we incorporated both longitudinal and cross-sectional vegetation effects in addition to time since fire within logistic structural equation models. We identified temporal changes in vegetation structure and richness of plant and bird species that characterized burned and unburned sites in all vegetation classes. For nine bird species, a significant component of the year trend was driven by temporal trends in one of three vegetation variables (number of understory or midstory plant species, or midstory cover). By contrast, we could not separate temporal effects between time since fire and vegetation attributes for bird species richness, reporting rate, and the occurrence of 11 other bird species. Our findings help identify species for which indirect effects of vegetation dominate recovery and thus may benefit from vegetation management where conservation actions are required and, conversely, those species for which direct effects of time since fire drive recovery, where simply leaving a system to recover following the last disturbance will be sufficient.

Disturbance gradient shows logging affects plant functional groups more than fire

Understanding the impacts of natural and human disturbances on forest biota is critical for improving forest management. Many studies have examined the separate impacts on fauna and flora of wildfire, conventional logging, and salvage logging, but empirical comparisons across a broad gradient of simultaneous disturbances are lacking. We quantified species richness and frequency of occurrence of vascular plants, and functional group responses, across a gradient of disturbances that occurred concurrently in 2009 in the mountain ash forests of southeastern Australia. Our study encompassed replicated sites in undisturbed forest (~70 yr post fire), forest burned at low severity, forest burned at high severity, unburned forest that was clearcut logged, and forest burned at high severity that was clearcut salvage logged post-fire. All sites were sampled 2 and 3 yr post fire. Mean species richness decreased across the disturbance gradient from 30.1 species/site on low-severity burned sites and 28.9 species/site on high-severity burned sites, to 25.1 species/site on clearcut sites and 21.7 species/site on salvage logged sites. Low-severity burned sites were significantly more species-rich than clearcut sites and salvage logged sites; high-severity burned sites supported greater species richness than salvage logged sites. Specific traits influenced species' sensitivity to disturbance. Resprouting species dominated undisturbed mountain ash forests, but declined significantly across the gradient. Fern and midstory trees decreased significantly in frequency of occurrence across the gradient. Ferns (excluding bracken) decreased from 34% of plants in undisturbed forest to 3% on salvage logged sites. High-severity burned sites supported a greater frequency of occurrence and species richness of midstory trees compared to clearcut and salvage logged sites. Salvage logging supported fewer midstory trees than any other disturbance category, and were distinctly different from clearcut sites. Plant life form groups, including midstory trees, shrubs, and ferns, were dominated by very few species on logged sites. The differences in biotic response across the gradient of natural and human disturbances have significant management implications, particularly the need to reduce mechanical disturbance overall and to leave specific areas with no mechanical disturbance across the cut area during logging operations, to ensure the persistence of resprouting taxa.

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.

Implications of recurrent disturbance for genetic diversity

Exploring interactions between ecological disturbance, species’ abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well‐understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance‐induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

Identifying the location of fire refuges in wet forest ecosystems

The increasing frequency of large, high-severity fires threatens the survival of old-growth specialist fauna in fire-prone forests. Within topographically diverse montane forests, areas that experience less severe or fewer fires compared with those prevailing in the landscape may present unique resource opportunities enabling old-growth specialist fauna to survive. Statistical landscape models that identify the extent and distribution of potential fire refuges may assist land managers to incorporate these areas into relevant biodiversity conservation strategies. We used a case study in an Australian wet montane forest to establish how predictive fire simulation models can be interpreted as management tools to identify potential fire refuges. We examined the relationship between the probability of fire refuge occurrence as predicted by an existing fire refuge model and fire severity experienced during a large wildfire. We also examined the extent to which local fire severity was influenced by fire severity in the surrounding landscape. We used a combination of statistical approaches, including generalized linear modeling, variogram analysis, and receiver operating characteristics and area under the curve analysis (ROC AUC). We found that the amount of unburned habitat and the factors influencing the retention and location of fire refuges varied with fire conditions. Under extreme fire conditions, the distribution of fire refuges was limited to only extremely sheltered, fire-resistant regions of the landscape. During extreme fire conditions, fire severity patterns were largely determined by stochastic factors that could not be predicted by the model. When fire conditions were moderate, physical landscape properties appeared to mediate fire severity distribution. Our study demonstrates that land managers can employ predictive landscape fire models to identify the broader climatic and spatial domain within which fire refuges are likely to be present. It is essential that within these envelopes, forest is protected from logging, roads, and other developments so that the ecological processes related to the establishment and subsequent use of fire refuges are maintained.

Fine-scale refuges can buffer demographic and genetic processes against short-term climatic variation and disturbance: a 22-year case study of an arboreal marsupial

Ecological disturbance and climate are key drivers of temporal dynamics in the demography and genetic diversity of natural populations. Microscale refuges are known to buffer species' persistence against environmental change, but the effects of such refuges on demographic and genetic patterns in response to short-term environmental variation are poorly understood. We quantified demographic and genetic responses of mountain brushtail possums (Trichosurus cunninghami) to rainfall variability (1992-2013) and to a major wildfire. We hypothesized that there would be underlying differences in demographic and genetic processes between an unburnt mesic refuge and a topographically exposed zone that was burnt in 2009. Fire caused a 2-year decrease in survival in the burnt zone, but the population grew after the fire due to immigration, leading to increased expected heterozygosity. We documented a fire-related behavioural shift, where the rate of movement by individuals in the unburnt refuge to the burnt zone decreased after fire. Irrespective of the fire, there were long-term differences in demographic and genetic parameters between the mesic/unburnt refuge and the nonmesic/burnt zone. Survival was high and unaffected by rainfall in the refuge, but lower and rainfall-dependent in the nonmesic zone. Net movement of individuals was directional, from the mesic refuge to the nonmesic zone, suggesting fine-scale source-sink dynamics. There were higher expected heterozygosity (HE ) and temporal genetic stability in the refuge, but lower HE and marked temporal genetic structure in the exposed habitat, consistent with reduced generational overlap caused by elevated mortality and immigration. Thus, fine-scale refuges can mediate the short-term demographic and genetic effects of climate and ecological disturbance.

Phylogeographic Structure in Penguin Ticks across an Ocean Basin Indicates Allopatric Divergence and Rare Trans-Oceanic Dispersal

The association of ticks (Acarina) and seabirds provides an intriguing system for assessing the influence of long-distance dispersal on the evolution of parasitic species. Recent research has focused on host-parasite evolutionary relationships and dispersal capacity of ticks parasitising flighted seabirds. Evolutionary research on the ticks of non-flighted seabirds is, in contrast, scarce. We conducted the first phylogeographic investigation of a hard tick species (Ixodes eudyptidis) that parasitises the Little Blue Penguin (Eudyptula minor). Using one nuclear (28S) and two mitochondrial (COI and 16S) markers, we assessed genetic diversity among several populations in Australia and a single population on the South Island of New Zealand. Our results reveal two deeply divergent lineages, possibly representing different species: one comprising all New Zealand samples and some from Australia, and the other representing all other samples from Australian sites. No significant population differentiation was observed among any Australian sites from within each major clade, even those separated by hundreds of kilometres of coastline. In contrast, the New Zealand population was significantly different to all samples from Australia. Our phylogenetic results suggest that the New Zealand and Australian populations are effectively isolated from each other; although rare long-distance dispersal events must occur, these are insufficient to maintain trans-Tasman gene flow. Despite the evidence for limited dispersal of penguin ticks between Australia and New Zealand, we found no evidence to suggest that ticks are unable to disperse shorter distances at sea with their hosts, with no pattern of population differentiation found among Australian sites. Our results suggest that terrestrial seabird parasites may be quite capable of short-distance movements, but only sporadic longer-distance (trans-oceanic) dispersal.

The effect of sex-biased dispersal on opposite-sexed spatial genetic structure and inbreeding risk

Natal sex-biased dispersal has long been thought to reduce the risk of inbreeding by spatially separating opposite-sexed kin. Yet, comprehensive and quantitative evaluations of this hypothesis are lacking. In this study, we quantified the effectiveness of sex-biased dispersal as an inbreeding avoidance strategy by combining spatially explicit simulations and empirical data. We quantified the extent of kin clustering by measuring the degree of spatial autocorrelation among opposite-sexed individuals (FM structure). This allowed us to systematically explore how the extent of sex-biased dispersal, generational overlap, and mate searching distance, influenced both kin clustering, and the resulting inbreeding in the absence of complementary inbreeding avoidance strategies. Simulations revealed that when sex-biased dispersal was limited, positive FM genetic structure developed quickly and increased as the mate searching distance decreased or as generational overlap increased. Interestingly, complete long-range sex-biased dispersal did not prevent the development of FM genetic structure when generations overlapped. We found a very strong correlation between FM genetic structure and both FIS under random mating, and pedigree-based measures of inbreeding. Thus, we show that the detection of FM genetic structure can be a strong indicator of inbreeding risk. Empirical data for two species with different life history strategies yielded patterns congruent with our simulations. Our study illustrates a new application of spatial genetic autocorrelation analysis that offers a framework for quantifying the risk of inbreeding that is easily extendable to other species. Furthermore, our findings provide other researchers with a context for interpreting observed patterns of opposite-sexed spatial genetic structure.

The need for a comprehensive reassessment of the Regional Forest Agreements in Australia

Regional Forest Agreements (RFAs) are State–Federal agreements underpinning the management of the majority of Australia’s commercially productive native forests. Introduced between 1997 and 2001, they were designed to deliver certainty to forest industries while, simultaneously, guaranteeing environmental protection, including the conservation of biodiversity. Using examples, we argue that RFAs in some jurisdictions have failed to do either. We strongly recommend a comprehensive reassessment of RFAs. This is needed to: (1) take into account significant new knowledge on forest ecology and management that has been gathered in the past 20 years, including updated prognoses for some critically endangered species; (2) better evaluate the full range of wood and non-wood products and services provided by forests; (3) accommodate new methods of forest inventory and more environmentally sensitive silvicultural systems; and (4) better account for the impacts of natural disturbances, such as fires, on the area available for logging, sustained yield, and forest ecosystem integrity per se. Without a substantial overhaul of the RFAs, there is a significant risk of undervaluing the full range of native forest values, exacerbating species declines, and permanently damaging forest ecosystems.

Geographical variation in body size and sexual size dimorphism in an Australian lizard, Boulenger's Skink (Morethia boulengeri)

Ecogeographical rules help explain spatial and temporal patterns in intraspecific body size. However, many of these rules, when applied to ectothermic organisms such as reptiles, are controversial and require further investigation. To explore factors that influence body size in reptiles, we performed a heuristic study to examine body size variation in an Australian lizard, Boulenger's Skink Morethia boulengeri from agricultural landscapes in southern New South Wales, south-eastern Australia. We collected tissue and morphological data on 337 adult lizards across a broad elevation and climate gradient. We used a model-selection procedure to determine if environmental or ecological variables best explained body size variation. We explored the relationship between morphology and phylogenetic structure before modeling candidate variables from four broad domains: (1) geography (latitude, longitude and elevation), (2) climate (temperature and rainfall), (3) habitat (vegetation type, number of logs and ground cover attributes), and (4) management (land use and grazing history). Broad phylogenetic structure was evident, but on a scale larger than our study area. Lizards were sexually dimorphic, whereby females had longer snout-vent length than males, providing support for the fecundity selection hypothesis. Body size variation in M. boulengeri was correlated with temperature and rainfall, a pattern consistent with larger individuals occupying cooler and more productive parts of the landscape. Climate change forecasts, which predict warmer temperature and increased aridity, may result in reduced lizard biomass and decoupling of trophic interactions with potential implications for community organization and ecosystem function.