Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions

A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.

Contrasting Patterns of Single Nucleotide Polymorphisms and Structural Variation Across Multiple Invasions

Genetic divergence is the fundamental process that drives evolution and ultimately speciation. Structural variants (SVs) are large-scale genomic differences within a species or population and can cause functionally important phenotypic differences. Characterizing SVs across invasive species will fill knowledge gaps regarding how patterns of genetic diversity and genetic architecture shape rapid adaptation under new selection regimes. Here, we seek to understand patterns in genetic diversity within the globally invasive European starling, Sturnus vulgaris. Using whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings, we examine patterns in genome-wide SNPs and SVs between populations and within Australia. Our findings detail the landscape of standing genetic variation across recently diverged continental populations of this invasive avian. We demonstrate that patterns of genetic diversity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of diversity along the length of the organism's chromosomes (owing to enrichment of SVs in subtelomeric repeat regions), or interpopulation diversity patterns (possibly a result of altered selection regimes or introduction history). Finally, we find that levels of balancing selection within the native range differ across SNP and SV of different classes and outlier classifications. Overall, our results demonstrate that the processes that shape allelic diversity within populations is complex and support the need for further investigation of SVs across a range of taxa to better understand correlations between often well-studied SNP diversity and that of SVs.

Evolutionary genomics: Insights from the invasive European starlings

Two fundamental questions for evolutionary studies are the speed at which evolution occurs, and the way that this evolution may present itself within an organism's genome. Evolutionary studies on invasive populations are poised to tackle some of these pressing questions, including understanding the mechanisms behind rapid adaptation, and how it facilitates population persistence within a novel environment. Investigation of these questions are assisted through recent developments in experimental, sequencing, and analytical protocols; in particular, the growing accessibility of next generation sequencing has enabled a broader range of taxa to be characterised. In this perspective, we discuss recent genetic findings within the invasive European starlings in Australia, and outline some critical next steps within this research system. Further, we use discoveries within this study system to guide discussion of pressing future research directions more generally within the fields of population and evolutionary genetics, including the use of historic specimens, phenotypic data, non-SNP genetic variants (e.g., structural variants), and pan-genomes. In particular, we emphasise the need for exploratory genomics studies across a range of invasive taxa so we can begin understanding broad mechanisms that underpin rapid adaptation in these systems. Understanding how genetic diversity arises and is maintained in a population, and how this contributes to adaptability, requires a deep understanding of how evolution functions at the molecular level, and is of fundamental importance for the future studies and preservation of biodiversity across the globe.

Fragmentation by major dams and implications for the future viability of platypus populations

The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (F_ST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; F_ST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, F_ST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.

Transcript- and annotation-guided genome assembly of the European starling

The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.

Weedy and seedy: the rapid evolution of life-history characteristics in an introduced daisy

Despite the importance of life-history characteristics in determining a species' success, we still lack basic information about some fundamental life-history elements found across the life cycle of introduced plants. Our study assesses rapid evolutionary divergence in life-history characteristics of the beach daisy Arctotheca populifolia by comparing introduced Australian and source South African plants and measuring eight key variables including seed mass, germination, reproductive output and survival. This is the first study that compares the life history of an introduced plant species with its single original source population, providing a precise and powerful method for detecting evolutionary divergence. We found that introduced A. populifolia has evolved a suite of weedy life-history characteristics in less than 90 years: the introduced plants use a live-fast die-young strategy of germination and survival and produce significantly more inflorescences and more seeds that germinate faster. This knowledge adds to the remarkable data that we already have on the rapid evolutionary divergence occurring in the morphology, physiology and defence of this introduced plant and highlights the speed and scope of evolutionary divergence possible in plants. To fully understand and manage the future of our plant species, we must consider their potential for ongoing change in key aspects of life history.

Bray-Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment ( A A), and comparative performance in selection detection

Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray‐Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill “Q‐profile” measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within‐population (alpha) variation, undesirable for a between‐population (beta) measure. The first dependency is derived from similarity to GST and FST. The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data‐filtering or by a modified statistic ^AA or “Adjusted AFD”. The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions—which is shown in this article for ^AA, for equilibrium, and nonequilibrium, for the commonly used data type of single‐nucleotide‐polymorphisms (SNPs) in two locations. Thus, ^AA can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of ^AA and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that ^AA is in one of the best such pairwise criteria. For any application, using ^AA, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.

A stochastic model for estimating sustainable limits to wildlife mortality in a changing world

Human-caused mortality of wildlife is a pervasive threat to biodiversity. Assessing the population-level impact of fisheries bycatch and other human-caused mortality of wildlife has typically relied upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional methods. Building on the widely applied potential biological removal (PBR) equation, we devised a new population modeling approach for estimating sustainable limits to human-caused mortality and applied it in a case study of bottlenose dolphins affected by capture in an Australian demersal otter trawl fishery. Our approach, termed sustainable anthropogenic mortality in stochastic environments (SAMSE), incorporates environmental and demographic stochasticity, including the dependency of offspring on their mothers. The SAMSE limit is the maximum number of individuals that can be removed without causing negative stochastic population growth. We calculated a PBR of 16.2 dolphins per year based on the best abundance estimate available. In contrast, the SAMSE model indicated that only 2.3-8.0 dolphins could be removed annually without causing a population decline in a stochastic environment. These results suggest that reported bycatch rates are unsustainable in the long term, unless reproductive rates are consistently higher than average. The difference between the deterministic PBR calculation and the SAMSE limits showed that deterministic approaches may underestimate the true impact of human-caused mortality of wildlife. This highlights the importance of integrating stochasticity when evaluating the impact of bycatch or other human-caused mortality on wildlife, such as hunting, lethal control measures, and wind turbine collisions. Although population viability analysis (PVA) has been used to evaluate the impact of human-caused mortality, SAMSE represents a novel PVA framework that incorporates stochasticity for estimating acceptable levels of human-caused mortality. It offers a broadly applicable, stochastic addition to the demographic toolbox to evaluate the impact of human-caused mortality on wildlife.

Social integration influences fitness in allied male dolphins

Understanding determinants of differential reproductive success is at the core of evolutionary biology because of its connection to fitness. Early work has linked variation in reproductive success to differences in age,¹ rank,² or size,^3,4 as well as habitat characteristics.⁵ More recently, studies in group-living taxa have revealed that social relationships also have measurable effects on fitness.^6-8 The influence of social bonds on fitness is particularly interesting in males who compete over reproductive opportunities. In Shark Bay, Western Australia, groups of 4-14 unrelated male bottlenose dolphins cooperate in second-order alliances to compete with rival alliances over access to females.^9-12 Nested within second-order alliances, pairs or trios of males, which can vary in composition, form first-order alliances to herd estrus females. Using 30 years of behavioral data, we examined how individual social factors, such as first-order alliance stability, social connectivity, and variation in social bond strength within second-order alliances, affect male fitness. Analyzing the reproductive careers of 85 males belonging to 10 second-order alliances, we found that the number of paternities a male achieved was positively correlated with his cumulative social bond strength but negatively correlated with his variation in bond strength. Thus, well-integrated males with more homogeneous social bonds to second-order allies obtained most paternities. Our findings provide novel insights into the fitness benefits of polyadic cooperation among unrelated males and highlight the adaptive value of social bonds in this context.

Detecting steps in spatial genetic data: Which diversity measures are best?

Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, G_ST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, G_ST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (G_ST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.

Genetics and Plasticity Are Responsible for Ecogeographical Patterns in a Recent Invasion

Patterns of covariation between phenotype and environment are presumed to be reflective of local adaptation, and therefore translate to a meaningful influence on an individual’s overall fitness within that specific environment. However, these environmentally driven patterns may be the result of numerous and interacting processes, such as genetic variation, epigenetic variation, or plastic non-heritable variation. Understanding the relative importance of different environmental variables on underlying genetic patterns and resulting phenotypes is fundamental to understanding adaptation. Invasive systems are excellent models for such investigations, given their propensity for rapid evolution. This study uses reduced representation sequencing data paired with phenotypic data to examine whether important phenotypic traits in invasive starlings (Sturnus vulgaris) within Australia appear to be highly heritable (presumably genetic) or appear to vary with environmental gradients despite underlying genetics (presumably non-heritable plasticity). We also sought to determine which environmental variables, if any, play the strongest role shaping genetic and phenotypic patterns. We determined that environmental variables—particularly elevation—play an important role in shaping allelic trends in Australian starlings and may also reinforce neutral genetic patterns resulting from historic introduction regime. We examined a range of phenotypic traits that appear to be heritable (body mass and spleen mass) or negligibly heritable (e.g. beak surface area and wing length) across the starlings’ Australian range. Using SNP variants associated with each of these phenotypes, we identify key environmental variables that correlate with genetic patterns, specifically that temperature and precipitation putatively play important roles shaping phenotype in this species. Finally, we determine that overall phenotypic variation is correlated with underlying genetic variation, and that these interact positively with the level of vegetation variation within a region, suggesting that ground cover plays an important role in shaping selection and plasticity of phenotypic traits within the starlings of Australia.

Historical museum samples enable the examination of divergent and parallel evolution during invasion

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced‐representation sequencing of native samples collected recently in northwestern Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid‐19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

Cooperative partner choice in multi-level male dolphin alliances

Investigations into cooperative partner choice should consider both potential and realised partners, allowing for the comparison of traits across all those available. Male bottlenose dolphins form persisting multi-level alliances. Second-order alliances of 4–14 males are the core social unit, within which 2–3 males form first-order alliances to sequester females during consortships. We compared social bond strength, relatedness and age similarity of potential and realised partners of individual males in two age periods: (i) adolescence, when second-order alliances are formed from all available associates, and (ii) adulthood, when first-order allies are selected from within second-order alliances. Social bond strength during adolescence predicted second-order alliance membership in adulthood. Moreover, males preferred same-aged or older males as second-order allies. Within second-order alliances, non-mating season social bond strength predicted first-order partner preferences during mating season consortships. Relatedness did not influence partner choice on either alliance level. There is thus a striking resemblance between male dolphins, chimpanzees and humans, where closely bonded non-relatives engage in higher-level, polyadic cooperative acts. To that end, our study extends the scope of taxa in which social bonds rather than kinship explain cooperation, providing the first evidence that such traits might have evolved independently in marine and terrestrial realms.

Signatures of selection in a recent invasion reveal adaptive divergence in a highly vagile invasive species

A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful alien introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris, and seek to understand how these have been influenced by introduction history. We used reduced representation sequencing to determine population structure, and identify Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We found that since their introduction into Australia, starling populations have become genetically differentiated despite the potential for high levels of dispersal, and that starlings have responded to selective pressures imposed by a wide range of environmental conditions across their geographic range. Isolation by distance appears to have played a strong role in determining genetic substructure across the starling's Australian range. Analyses of candidate SNPs that are putatively under selection indicated that aridity, precipitation and temperature may be important factors driving adaptive variation across the starling's invasive range in Australia. However, we also noted that the historic introduction regime may leave footprints on sites flagged as being under adaptive selection, and encourage critical interpretation of selection analyses in non-native populations.

Evolution of defense and herbivory in introduced plants-Testing enemy release using a known source population, herbivore trials, and time since introduction

The enemy release hypothesis is often cited as a potential explanation for the success of introduced plants; yet, empirical evidence for enemy release is mixed. We aimed to quantify changes in herbivory and defense in introduced plants while controlling for three factors that might have confounded past studies: using a wide native range for comparison with the introduced range, measuring defense traits without determining whether they affect herbivore preferences, and not considering the effect of time since introduction. The first hypothesis we tested was that introduced plants will have evolved lower levels of plant defense compared to their source population. We grew South African (source) and Australian (introduced) beach daisies (Arctotheca populifolia) in a common-environment glasshouse experiment and measured seven defense traits. Introduced plants had more ash, alkaloids, and leaf hairs than source plants, but were also less tough, with a lower C:N ratio and less phenolics. Overall, we found no difference in defense between source and introduced plants. To determine whether the feeding habits of herbivores align with changes in defense traits, we conducted preference feeding trials using five different herbivore species. Herbivores showed no overall preference for leaves from either group. The second hypothesis we tested was that herbivory on introduced plant species will increase through time after introduction to a new range. We recorded leaf damage on herbarium specimens of seven species introduced to eastern Australia and three native control species. We found no change in the overall level of herbivory experienced by introduced plants since arriving in Australia.

CONCLUSION

In the field of invasion ecology, we need to rethink the paradigm that species introduced to a new range undergo simple decreases in defenses against herbivores. Instead, plants are likely to employ a range of defense traits that evolve in both coordinated and opposing ways in response to a plethora of different biotic and abiotic selective pressures.

Affiliation history and age similarity predict alliance formation in adult male bottlenose dolphins

Male alliances are an intriguing phenomenon in the context of reproduction since, in most taxa, males compete over an indivisible resource, female fertilization. Adult male bottlenose dolphins (Tursiops aduncus) in Shark Bay, Western Australia, form long-term, multilevel alliances to sequester estrus females. These alliances are therefore critical to male reproductive success. Yet, the long-term processes leading to the formation of such complex social bonds are still poorly understood. To identify the criteria by which male dolphins form social bonds with other males, we adopted a long-term approach by investigating the ontogeny of alliance formation. We followed the individual careers of 59 males for 14 years while they transitioned from adolescence (8-14 years of age) to adulthood (15-21 years old). Analyzing their genetic relationships and social associations in both age groups, we found that the vast majority of social bonds present in adolescence persisted through time. Male associations in early life predict alliance partners as adults. Kinship patterns explained associations during adolescence but not during adulthood. Instead, adult males associated with males of similar age. Our findings suggest that social bonds among peers, rather than kinship, play a central role in the development of adult male polyadic cooperation in dolphins.

Differences in gene regulation in a tephritid model of prezygotic reproductive isolation

The two tephritid fruit fly pests, Bactrocera tryoni and Bactrocera neohumeralis, are unusually well suited to the study of the genetics of reproductive isolating mechanisms. Sequence difference between the species is no greater than between a pair of conspecific Drosophila melanogaster populations. The two species exist in close sympatry, yet do not hybridize in the field, apparently kept separate by a strong premating isolation mechanism involving the time of day at which mating occurs. This spurred us to search for key genes for which time of day expression is regulated differently between the species. Using replicated, quantitative transcriptomes from head tissues of males of the two species, sampled in the day and night, we identified 141 transcripts whose abundance showed a significant interaction between species and time of day, indicating a difference in gene regulation. The brain transcripts showing this interaction were enriched for genes with a neurone function and 90% of these were more abundant at night than day in B. tryoni. Features of the expression patterns suggest that there may be a difference in the regulation of sleep-wake cycles between the species. In particular several genes, which in D. melanogaster are expressed in circadian pacemaker cells, are promising candidates to further explore the genetic differentiation involved in this prezygotic reproductive isolation mechanism.

Rapid evolution of leaf physiology in an introduced beach daisy

Photosynthesis is a key biological process. However, we know little about whether plants change their photosynthetic strategy when introduced to a new range. We located the most likely source population for the South African beach daisy Arctotheca populifolia introduced to Australia in the 1930s, and ran a common-garden experiment measuring 10 physiological and morphological leaf traits associated with photosynthesis. Based on predictions from theory, and higher rainfall in the introduced range, we hypothesized that introduced plants would have a (i) higher photosynthetic rate, (ii) lower water-use efficiency (WUE) and (iii) higher nitrogen-use efficiency. However, we found that introduced A. populifolia had a lower photosynthetic rate, higher WUE and lower nitrogen-use efficiency than did plants from Arniston, South Africa. Subsequent site visits suggested that plants in Arniston may be able to access moisture on a rocky shelf, while introduced plants grow on sandy beaches where water can quickly dissipate. Our unexpected findings highlight that: (1) it is important to compare introduced species to their source population for an accurate assessment of evolutionary change; (2) rainfall is not always a suitable proxy for water availability and (3) introduced species often undergo evolutionary changes, but without detailed ecological information we may not be able to accurately predict the direction of these changes.

The Introduction of Entropy and Information Methods to Ecology by Ramon Margalef

In ecology and evolution, entropic methods are now used widely and increasingly frequently. Their use can be traced back to Ramon Margalef's first attempt 70 years ago to use log-series to quantify ecological diversity, including searching for ecologically meaningful groupings within a large assemblage, which we now call the gamma level. The same year, Shannon and Weaver published a generally accessible form of Shannon's work on information theory, including the measure that we now call Shannon-Wiener entropy. Margalef seized on that measure and soon proposed that ecologists should use the Shannon-Weiner index to evaluate diversity, including assessing local (alpha) diversity and differentiation between localities (beta). He also discussed relating this measure to environmental variables and ecosystem processes such as succession. Over the subsequent decades, he enthusiastically expanded upon his initial suggestions. Finally, 2019 also would have been Margalef's 100th birthday.

Is MHC diversity a better marker for conservation than neutral genetic diversity? A case study of two contrasting dolphin populations

Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia-one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty-three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population-for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human-induced changes to the coastal ecosystem it inhabits.

Rapid reshaping: the evolution of morphological changes in an introduced beach daisy

Thousands of species have been introduced to new ranges worldwide. These introductions provide opportunities for researchers to study evolutionary changes in form and function in response to new environmental conditions. However, almost all previous studies of morphological change in introduced species have compared introduced populations to populations from across the species' native range, so variation within native ranges probably confounds estimates of evolutionary change. In this study, we used microsatellites to locate the source population for the beach daisy Arctotheca populifolia that had been introduced to eastern Australia. We then compared four introduced populations from Australia with their original South African source population in a common-environment experiment. Despite being separated for less than 100 years, source and introduced populations of A. populifolia display substantial heritable morphological differences. Contrary to the evolution of increased competitive ability hypothesis, introduced plants were shorter than source plants, and introduced and source plants did not differ in total biomass. Contrary to predictions based on higher rainfall in the introduced range, introduced plants had smaller, thicker leaves than source plants. Finally, while source plants develop lobed adult leaves, introduced plants retain their spathulate juvenile leaf shape into adulthood. These changes indicate that rapid evolution in introduced species happens, but not always in the direction predicted by theory.

Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers

Empirical genetic datasets used for estimating contemporary dispersal in wild populations and to correctly identify dispersers are rarely tested to determine if they are capable of providing accurate results. Here we test whether a genetic dataset provides sufficient information to accurately identify first-generation dispersers. Using microsatellite data from three wild populations of common starlings (Sturnus vulgaris), we artificially simulated dispersal of a subset of individuals; we term this ‘Simulated Disperser Analysis’. We then ran analyses for diminishing numbers of loci, to assess at which point simulated dispersers could no longer be correctly identified. Not surprisingly, the correct identification of dispersers varied significantly depending on the individual chosen to ‘disperse’, the number of loci used, whether loci had high or low Polymorphic Information Content and the location to which the dispersers were moved. A review of the literature revealed that studies that have implemented first-generation migrant detection to date have used on average 10 microsatellite loci. Our results suggest at least 27 loci are required to accurately identify dispersers in the study system evaluated here. We suggest that future studies use the approach we describe to determine the appropriate number of markers needed to accurately identify dispersers in their study system; the unique nature of natural systems means that the number of markers required for each study system will vary. Future studies can use Simulated Disperser Analysis on pilot data to test marker panels for robustness to contemporary dispersal identification, providing a powerful tool in the efficient and accurate design of studies using genetic data to estimate dispersal.

Information Theory Broadens the Spectrum of Molecular Ecology and Evolution

Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance.

De Novo Assembly of the Liver Transcriptome of the European Starling, Sturnus vulgaris

The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader.

Genes are information, so information theory is coming to the aid of evolutionary biology

Speciation is central to evolutionary biology, and to elucidate it, we need to catch the early genetic changes that set nascent taxa on their path to species status (Via 2009). That challenge is difficult, of course, for two chief reasons: (i) serendipity is required to catch speciation in the act; and (ii) after a short time span with lingering gene flow, differentiation may be low and/or embodied only in rare alleles that are difficult to sample. In this issue of Molecular Ecology Resources, Smouse et al. (2015) have noted that optimal assessment of differentiation within and between nascent species should be robust to these challenges, and they identified a measure based on Shannon's information theory that has many advantages for this and numerous other tasks. The Shannon measure exhibits complete additivity of information at different levels of subdivision. Of all the family of diversity measures ('0' or allele counts, '1' or Shannon, '2' or heterozygosity, F(ST) and related metrics) Shannon's measure comes closest to weighting alleles by their frequencies. For the Shannon measure, rare alleles that represent early signals of nascent speciation are neither down-weighted to the point of irrelevance, as for level 2 measures, nor up-weighted to overpowering importance, as for level 0 measures (Chao et al. 2010, )2015. Shannon measures have a long history in population genetics, dating back to Shannon's PhD thesis in 1940 (Crow 2001), but have received only sporadic attention, until a resurgence of interest in the last ten years, as reviewed briefly by Smouse et al. (2015).

Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis

Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.

The relative importance of reproduction and survival for the conservation of two dolphin populations

It has been proposed that in slow‐growing vertebrate populations survival generally has a greater influence on population growth than reproduction. Despite many studies cautioning against such generalizations for conservation, wildlife management for slow‐growing populations still often focuses on perturbing survival without careful evaluation as to whether those changes are likely or feasible. Here, we evaluate the relative importance of reproduction and survival for the conservation of two bottlenose dolphin (Tursiops cf aduncus) populations: a large, apparently stable population and a smaller one that is forecast to decline. We also assessed the feasibility and effectiveness of wildlife management objectives aimed at boosting either reproduction or survival. Consistent with other analytically based elasticity studies, survival had the greatest effect on population trajectories when altering vital rates by equal proportions. However, the findings of our alternative analytical approaches are in stark contrast to commonly used proportional sensitivity analyses and suggest that reproduction is considerably more important. We show that

in the stable population reproductive output is higher, and adult survival is lower;

the difference in viability between the two populations is due to the difference in reproduction;

reproductive rates are variable, whereas survival rates are relatively constant over time;

perturbations on the basis of observed, temporal variation indicate that population dynamics are much more influenced by reproduction than by adult survival;

for the apparently declining population, raising reproductive rates would be an effective and feasible tool to reverse the forecast population decline; increasing survival would be ineffective.

Our findings highlight the importance of reproduction – even in slow‐growing populations – and the need to assess the effect of natural variation in vital rates on population viability. We echo others in cautioning against generalizations based on life‐history traits and recommend that population modeling for conservation should also take into account the magnitude of vital rate changes that could be attained under alternative management scenarios.

Paternity and male mating strategies of a ground squirrel ( Ictidomys parvidens ) with an extended mating season

Animal mating systems are driven by the temporal and spatial distribution of sexually receptive females. In mammals, ground-dwelling squirrels represent an ideal clade for testing predictions regarding the effects of these parameters on male reproductive strategies. While the majority of ground squirrel species have a short, highly synchronous annual breeding season that occurs immediately after females emerge from hibernation, the Mexican or Rio Grande ground squirrel ( Ictidomys parvidens ) differs markedly in having an extended mating season (2 months) and a long delay between emergence from hibernation and female receptivity (1–2 months). Both traits are expected to favor polygyny by increasing the chances that a male can secure matings with multiple females (e.g., females that come into estrus on different days). To test this prediction, we used microsatellite markers to characterize the mating system of a population of Rio Grande ground squirrels from Carlsbad, New Mexico. Our analyses indicated a high frequency of multiple paternity of litters in this population. Paternity was not related to spatial overlap between known mothers and assigned fathers, suggesting that territory defense is unlikely to be an effective male reproductive strategy in the study population. Dominance interactions among males were frequent, with heavier males typically winning dyadic interactions. Surprisingly, however, males with lower dominance scores appeared to have higher reproductive success, as did males that were active over a greater extent of the study site. Collectively, these results suggest that the mating system of the Rio Grande ground squirrel is best described as scramble competition polygyny, with the primary male reproductive strategy consisting of searching for estrous females. Similar patterns of male–male competition have been reported for a few other ground squirrel species, providing potentially important opportunities for comparative studies of the factors favoring this form of male reproductive strategy.

Extraordinary conservation of entire chromosomes in insects over long evolutionary periods

Comparison of the genomes of different Drosophila species has shown that six different chromosomes, the so-called ''Muller elements," constitute the building blocks for all Drosophila species. Here, we confirm previous results suggesting that this conservation of the Muller elements extends far beyond Drosophila, to at least tephritid fruit flies, thought to have diverged from drosophilids 60-70 mYr ago. Less than 10 percent of genes differ in chromosome location between the two insect groups. Within chromosomes, however, the order is highly scrambled, as expected from the comparison between Drosophila species. The data also support the notion that the sex chromosomes of tephritid flies originated from an ancestor of the dot chromosome 4 of Drosophila. Overall, therefore, no new chromosome has been created for perhaps a billion generations over the two evolutionary lines. This stability at the chromosome level, which appears to extend to all Diptera including mosquitoes, is in stark contrast to other groups such as mammals, birds, fish and plants, in which chromosome numbers and organization vary enormously among species that have diverged over much fewer generations.

Tracking invasion and invasiveness in Queensland fruit flies: From classical genetics to ‘omics’

Three Australian tephritid fruit flies (Bactrocera tryoni - Q-fly, Bactrocera neohumeralis - NEO, and Bactrocera jarvisi - JAR) are promising models for genetic studies of pest status and invasiveness. The long history of ecological and physiological studies of the three species has been augmented by the development of a range of genetic and genomic tools, including the capacity for forced multigeneration crosses between the three species followed by selection experiments, a draft genome for Q-fly, and tissue- and stage-specific transcriptomes. The Q-fly and NEO species pair is of particular interest. The distribution of NEO is contained entirely within the wider distribution of Q-fly and the two species are ecologically extremely similar, with no known differences in pheromones, temperature tolerance, or host-fruit utilisation. However there are three clear differences between them: humeral callus colour, complete pre-mating isolation based on mating time-of-day, and invasiveness. NEO is much less invasive, whereas in historical times Q-fly has invaded southeastern Australia and areas of Western Australia and the Northern Territory. In southeastern fruit-growing regions, microsatellites suggest that some of these outbreaks might derive from genetically differentiated populations overwintering in or near the invaded area. Q-fly and NEO show very limited genome differentiation, so comparative genomic analyses and QTL mapping should be able to identify the regions of the genome controlling mating time and invasiveness, to assess the genetic bases for the invasive strains of Q-fly, and to facilitate a variety of improvements to current sterile insect control strategies for that species.

Is there evidence of selection in the dopamine receptor D4 gene in Australian invasive starling populations?

Although population genetic theory is largely based on the premise that loci under study are selectively neutral, it has been acknowledged that the study of DNA sequence data under the influence of selection can be useful. In some circumstances, these loci show increased population differentiation and gene diversity. Highly polymorphic loci may be especially useful when studying populations having low levels of diversity overall, such as is often the case with threatened or newly established invasive populations. Using common starlings Sturnus vulgaris sampled from invasive Australian populations, we investigated sequence data of the dopamine receptor D4 gene (DRD4), a locus suspected to be under selection for novelty-seeking behaviour in a range of taxa including humans and passerine birds. We hypothesised that such behaviour may be advantageous when species encounter novel environments, such as during invasion. In addition to analyses to detect the presence of selection, we also estimated population differentiation and gene diversity using DRD4 data and compared these estimates to those from microsatellite and mitochondrial DNA sequence data, using the same individuals. We found little evidence for selection on DRD4 in starlings. However, we did find elevated levels of within-population gene diversity when compared to microsatellites and mitochondrial DNA sequence, as well as a greater degree of population differentiation. We suggest that sequence data from putatively nonneutral loci are a useful addition to studies of invasive populations, where low genetic variability is expected.

The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species

Background

The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations.

Results

We produced a draft de novo genome assembly of Australia’s major tephritid pest species, Bactrocera tryoni. The male genome (650 -700 Mbp) includes approximately 150Mb of interspersed repetitive DNA sequences and 60Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions.

Conclusions

This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1153) contains supplementary material, which is available to authorized users.

Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique

Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies.

A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations

Stock enhancement, restocking and sea ranching are being increasingly applied in both fisheries and conservation. The contribution of hatchery stock to fishery harvest and the maintenance of the genetic structure of stocked populations are both important considerations when releasing captive-bred organisms into natural systems. Use of wild-caught broodstock generally overcomes some of the genetic problems associated with domesticated hatchery populations, but there is still a need to ensure that a sufficient proportion of the natural population contribute to production of the stocked cohort to realise the genetic benefits of using wild-caught broodstock. Releases of Penaeus (Melicertus) plebejus are under investigation as a means of increasing prawn production in recruitment-limited areas. We used the highly variable mitochondrial control region (mtCR) to assign post-larvae to maternal lineages in the hatchery and also to investigate the reproductive performance of female broodstock in terms of contribution to the production of the cohorts of post-larvae in the hatchery. Our data showed that mtCR can be a useful tool for tracking lineages and provided genetic evidence that unequal contribution and underproducing females can occur even in wild-caught broodstock. This work therefore highlights the importance of monitoring the genetic composition of pre-release hatchery stocks.

Cultural transmission of tool use combined with habitat specializations leads to fine-scale genetic structure in bottlenose dolphins

Socially learned behaviours leading to genetic population structure have rarely been described outside humans. Here, we provide evidence of fine-scale genetic structure that has probably arisen based on socially transmitted behaviours in bottlenose dolphins (Tursiops sp.) in western Shark Bay, Western Australia. We argue that vertical social transmission in different habitats has led to significant geographical genetic structure of mitochondrial DNA (mtDNA) haplotypes. Dolphins with mtDNA haplotypes E or F are found predominantly in deep (more than 10 m) channel habitat, while dolphins with a third haplotype (H) are found predominantly in shallow habitat (less than 10 m), indicating a strong haplotype-habitat correlation. Some dolphins in the deep habitat engage in a foraging strategy using tools. These 'sponging' dolphins are members of one matriline, carrying haplotype E. This pattern is consistent with what had been demonstrated previously at another research site in Shark Bay, where vertical social transmission of sponging had been shown using multiple lines of evidence. Using an individual-based model, we found support that in western Shark Bay, socially transmitted specializations may have led to the observed genetic structure. The reported genetic structure appears to present an example of cultural hitchhiking of mtDNA haplotypes on socially transmitted foraging strategies, suggesting that, as in humans, genetic structure can be shaped through cultural transmission.

Genetic monitoring reveals significant population structure in eastern quolls: implications for the conservation of a threatened carnivorous marsupial

The eastern quoll (Dasyurus viverrinus), while still relatively abundant in Tasmania, is now threatened by the recently introduced European red fox (Vulpes vulpes). Due to a lack of demographic information on eastern quolls, molecular data become a crucial surrogate to inform the management of the species. The aim of this study was to acquire baseline genetic data for use in current and future conservation strategies. Genetic variation, at seven microsatellite loci, was lower in Tasmanian eastern quolls than in quoll species from the Australian mainland. Within Tasmania, genetic variation was greater in central than peripheral populations, with the lowest levels detected on Bruny Island. Significant genetic population structure, consistent with regional differentiation, appears related to geographic distance among populations. Levels of gene flow appeared moderate, with genetic admixture greatest among central populations. Therefore, eastern quolls from genetically diverse central Tasmanian populations will become an important source for conservation initiatives if widespread declines begin to occur. Ongoing genetic monitoring of existing populations will allow conservation strategies to be adaptive. However, in order for translocations to be successful, managers must not only consider the genetic composition of founding individuals, but also habitat-specific adaptations, disease and threatening processes at translocation sites.

High genetic diversity is not essential for successful introduction

Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.

A novel mammalian social structure in Indo-Pacific bottlenose dolphins (Tursiops sp.): complex male alliances in an open social network

Terrestrial mammals with differentiated social relationships live in 'semi-closed groups' that occasionally accept new members emigrating from other groups. Bottlenose dolphins (Tursiops sp.) in Shark Bay, Western Australia, exhibit a fission-fusion grouping pattern with strongly differentiated relationships, including nested male alliances. Previous studies failed to detect a group membership 'boundary', suggesting that the dolphins live in an open social network. However, two alternative hypotheses have not been excluded. The community defence model posits that the dolphins live in a large semi-closed 'chimpanzee-like' community defended by males and predicts that a dominant alliance(s) will range over the entire community range. The mating season defence model predicts that alliances will defend mating-season territories or sets of females. Here, both models are tested and rejected: no alliances ranged over the entire community range and alliances showed extensive overlap in mating season ranges and consorted females. The Shark Bay dolphins, therefore, present a combination of traits that is unique among mammals: complex male alliances in an open social network. The open social network of dolphins is linked to their relatively low costs of locomotion. This reveals a surprising and previously unrecognized convergence between adaptations reducing travel costs and complex intergroup-alliance relationships in dolphins, elephants and humans.

Corrigendum to: Inbreeding and testicular abnormalities in a bottlenecked population of koalas (Phascolarctos cinereus)

Habitat destruction and fragmentation, interactions with introduced species or the relocation of animals to form new populations for conservation purposes may result in a multiplication of population bottlenecks. Examples are the translocations of koalas to French Island and its derivative Kangaroo Island population, with both populations established as insurance policies against koala extinction. In terms of population size, these conservation programs were success stories. However, the genetic story could be different. We conducted a genetic investigation of French and Kangaroo Island koalas by using 15 microsatellite markers, 11 of which are described here for the first time. The results confirm very low genetic diversity. French Island koalas have 3.8 alleles per locus and Kangaroo Island koalas 2.4. The present study found a 19% incidence of testicular abnormality in Kangaroo Island animals. Internal relatedness, an individual inbreeding coefficient, was not significantly different in koalas with testicular abnormalities from that in other males, suggesting the condition is not related to recent inbreeding. It could instead result from an unfortunate selection of founder individuals carrying alleles for testicular abnormalities, followed by a subsequent increase in these alleles' frequencies through genetic drift and small population-related inefficiency of selection. Given the low diversity and possible high prevalence of deleterious alleles, the genetic viability of the population remains uncertain, despite its exponential growth so far. This stands as a warning to other introductions for conservation reasons.

Nature and nurture: A step towards investigating their interactions in the wild

The debate about the relative importance of nature versus nurture has been around for decades, but despite this, there has been very little evidence about how these might in fact interact to drive evolution in the wild. Recently, the identification of a comparable methodology for analyzing both genetic and social effects of phenotypic variation revealed that fitness variation in a free-living population of dolphin was driven by a strong social and genetic interaction. This study not only provides evidence that nature and nurture do interact to drive phenotypic evolution but also represents a step towards partitioning the effects of genetic, social, environmental factors and their multiway interactions to better understand phenotypic evolution in the wild.

A new level of complexity in the male alliance networks of Indian Ocean bottlenose dolphins (Tursiops sp.)

Male bottlenose dolphins in Shark Bay, Western Australia form two levels of alliances; two to three males cooperate to herd individual females and teams of greater than three males compete with other groups for females. Previous observation suggested two alliance tactics: small four to six member teams of relatives that formed stable pairs or trios and unrelated males in a large 14-member second-order alliance that had labile trio formation. Here, we present evidence for a third level of alliance formation, a continuum of second-order alliance sizes and no relationship between first-order alliance stability and second-order alliance size. These findings challenge the 'two alliance tactics' hypothesis and add to the evidence that Shark Bay male bottlenose dolphins engage in alliance formation that likely places considerable demands on their social cognition.

Inbreeding tolerance and fitness costs in wild bottlenose dolphins

In wild populations, inbreeding tolerance is expected to evolve where the cost of avoidance exceeds that of tolerance. We show that in a wild population of bottlenose dolphins found in East Shark Bay, Western Australia, levels of inbreeding are higher than expected by chance alone, and demonstrate that inbreeding is deleterious to female fitness in two independent ways. We found that inbred females, and females with inbred calves, have reduced fitness (lower calving success). We further show that one of the costs of inbreeding is extended weaning age, and that females' earlier calves are more likely to be inbred. While the exact causes of inbreeding remain obscure, our results indicate that one factor is female age, and thus experience. Any inbreeding avoidance mechanisms such as female evasion of kin, or male dispersal, do not seem to be completely effective in this population, which supports the view that inbreeding avoidance does not always evolve wherever inbreeding incurs a cost.

Inbreeding and testicular abnormalities in a bottlenecked population of koalas (Phascolarctos cinereus)

Habitat destruction and fragmentation, interactions with introduced species or the relocation of animals to form new populations for conservation purposes may result in a multiplication of population bottlenecks. Examples are the translocations of koalas to French Island and its derivative Kangaroo Island population, with both populations established as insurance policies against koala extinction. In terms of population size, these conservation programs were success stories. However, the genetic story could be different. We conducted a genetic investigation of French and Kangaroo Island koalas by using 15 microsatellite markers, 11 of which are described here for the first time. The results confirm very low genetic diversity. French Island koalas have 3.8 alleles per locus and Kangaroo Island koalas 2.4. The present study found a 19% incidence of testicular abnormality in Kangaroo Island animals. Internal relatedness, an individual inbreeding coefficient, was not significantly different in koalas with testicular abnormalities from that in other males, suggesting the condition is not related to recent inbreeding. It could instead result from an unfortunate selection of founder individuals carrying alleles for testicular abnormalities, followed by a subsequent increase in these alleles’ frequencies through genetic drift and small population-related inefficiency of selection. Given the low diversity and possible high prevalence of deleterious alleles, the genetic viability of the population remains uncertain, despite its exponential growth so far. This stands as a warning to other introductions for conservation reasons.

Measurement of biological information with applications from genes to landscapes

Biological diversity is quantified for reasons ranging from primer design, to bioprospecting, and community ecology. As a common index for all levels, we suggest Shannon's (S)H, already used in information theory and biodiversity of ecological communities. Since Lewontin's first use of this index to describe human genetic variation, it has been used for variation of viruses, splice-junctions, and informativeness of pedigrees. However, until now there has been no theory to predict expected values of this index under given genetic and demographic conditions. We present a new null theory for (S)H at the genetic level, and show that this index has advantages including (i) independence of measures at each hierarchical level of organization; (ii) robust estimation of genetic exchange over a wide range of conditions; (iii) ability to incorporate information on population size; and (iv) explicit relationship to standard statistical tests. Utilization of this index in conjunction with other existing indices offers powerful insights into genetic processes. Our genetic theory is also extendible to the ecological community level, and thus can aid the comparison and integration of diversity at the genetic and community levels, including the need for measures of community diversity that incorporate the genetic differentiation between species.

Population genetic tools for pest management: a review

Population genetic tools have the potential to answer key questions in pest management including quantifying the number of genetically distinct populations represented in an invasion, the number of individuals present, whether populations are expanding or contracting, identifying the origin of invasive individuals, the number of separate introduction events that have occurred and in which order, and the rate that individuals are moving between populations. Genetic methods have only recently gained sufficient resolution to address these questions due to advances in laboratory techniques coupled with an increase in computational power. In combination, these methods may lead to a more comprehensive understanding of the dynamics of invasions. The expansion of the European starling (Sturnus vulgaris) into Western Australia is used as an applied example of how genetic methods can be integrated to provide vital information to improve pest-management strategies. Invasion events also may provide a unique opportunity to test some of these methodologies.