ORCID Profile
0000-0002-3279-7005
Current Organisation
UNSW Sydney
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Invasive Species Ecology | Genetics | Population, Ecological and Evolutionary Genetics | Biological Adaptation | Epigenetics (incl. Genome Methylation and Epigenomics) | Evolutionary Impacts of Climate Change | Animal Behaviour | Host-Parasite Interactions | Ecology | Evolutionary Biology | Behavioural Ecology
Control of Pests, Diseases and Exotic Species at Regional or Larger Scales | Expanding Knowledge in the Biological Sciences | Forest and Woodlands Flora, Fauna and Biodiversity | Ecosystem Adaptation to Climate Change | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Publisher: Springer Science and Business Media LLC
Date: 17-10-2017
DOI: 10.1038/S41598-017-13476-Z
Abstract: Genetic ersity at community, population and in idual levels is thought to influence the spread of infectious disease. At the in idual level, inbreeding and heterozygosity are associated with increased risk of infection and disease severity. Host genotype rarity may also reduce infection risk if pathogens are co-adapted to common or local hosts, but to date, no studies have investigated the relative importance of genotype rarity and heterozygosity for infection in a wild, sexually reproducing vertebrate. With beak and feather disease virus (BFDV) infection in a wild parrot ( Platycercus elegans ), we show that both heterozygosity and genotype rarity of in idual hosts predicted infection, but in contrasting ways. Heterozygosity was negatively associated with probability of infection, but not with infection load. In contrast, increased host genotype rarity was associated with lower viral load in infected in iduals, but did not predict infection probability. These effects were largely consistent across subspecies, but were not evident at the population level. Subspecies and age were also strongly associated with infection. Our study provides novel insights into infection dynamics by quantifying rarity and ersity simultaneously. We elucidate roles that host genetic ersity can play in infection dynamics, with implications for understanding population ergence, intraspecific ersity and conservation.
Publisher: Springer Science and Business Media LLC
Date: 07-2022
DOI: 10.1007/S00265-022-03194-6
Abstract: In general, males mate with multiple females to increase in idual reproductive success. Whether or not, and under what circumstances, females benefit from multiple mating has been less clear. Our review of 154 studies covering 184 populations of hibians and reptiles showed that polyandry was widespread and variable among and within taxonomic groups. We investigated whether hibian and reptile females had greater reproductive output as the number of sires for offspring increased. Meta-analysis revealed significant heterogeneity in the dataset of all taxa. Expected heterozygosity was a significant moderator (covariate) of positive relationships between female reproductive output and the number of sires, but a sensitivity test showed the result was tenuous. Significant heterogeneity remained despite controlling for expected heterozygosity and other variables but was resolved for most taxonomic groups with subgroup meta-analyses. Subgroup meta-analyses showed that only female salamanders (Caudata) had significantly greater reproductive output with an increased number of sires. For many species of Caudata, males cannot coerce females into accepting spermatophores. We therefore suggest that if females control the number of matings, they can use polyandry to increase their fitness. Caudata offers ideal models with which to test this hypothesis and to explore factors enabling and maintaining the evolution of female choice. Outstanding problems may be addressed by expanding taxonomic coverage and data collection and improving data reporting. Many factors and combinations of factors drive polyandry. Whether or not females benefit from mating with more than one male remains equivocal. Focusing on hibians and reptiles, our analyses demonstrate that female salamanders produced more offspring when mated with multiple males, whereas this was not the case for reptiles. Unlike many other species in our dataset, the polyandrous female salamanders fully control sperm intake and have chosen to mate multiple times. We further highlight problems and key directions for future research in the field.
Publisher: Cold Spring Harbor Laboratory
Date: 11-07-2021
DOI: 10.1101/2021.07.10.451923
Abstract: Factors such as host age, sex, diet, health status and genotype constitute the environmental envelope shaping microbial communities in the host’s gut. It has also been proposed that gut microbiota may be influenced by host epigenetics. Although the relationship between the host’s genotype/epigenotype and its associated microbiota has been the focus of a number of recent studies, the relative importance of these interactions and their biological relevance are still poorly understood. We used methylation-sensitive genotyping by sequencing to genotype and epigenotype invasive cane toads ( Rhinella marina ) from the species’ Australian range-core (three sites) and the invasion-front (three sites), and 16S rRNA gene sequencing to characterize their gut bacterial communities. We tested the effect of host genotype and epigenotype (i.e., methylome) on gut bacterial communities. Our results indicate that the genotypes, epigenotypes and gut communities of the range-core and invasion-front are significantly different from one another. We found a positive association between host pairwise genetic and epigenetic distances. More importantly, a positive relationship was found between the host’s epigenetic and gut bacterial pairwise distances. Interestingly, this association was stronger in in iduals with low genetic differentiation. Our findings suggest that in range-expanding populations, where in iduals are often genetically similar, the interaction between gut bacterial communities and host methylome may provide a mechanism through which invaders increase the plasticity of their response to novel environments, potentially increasing their invasion success.
Publisher: Wiley
Date: 03-2018
DOI: 10.1002/ECS2.2125
Publisher: Wiley
Date: 14-05-2015
DOI: 10.1111/MEC.13201
Abstract: Polymorphic species have been the focus of important work in evolutionary biology. It has been suggested that colour polymorphic species have specific evolutionary and population dynamics that enable them to persist through environmental changes better than less variable species. We suggest that recent empirical and theoretical work indicates that polymorphic species may be more vulnerable to extinction than previously thought. This vulnerability arises because these species often have a number of correlated sexual, behavioural, life history and ecological traits, which can have a simple genetic underpinning. When exacerbated by environmental change, these alternate strategies can lead to conflict between morphs at the genomic and population levels, which can directly or indirectly affect population and evolutionary dynamics. In this perspective, we identify a number of ways in which the nature of the correlated traits, their underpinning genetic architecture, and the inevitable interactions between colour morphs can result in a reduction in population fitness. The principles illustrated here apply to all kinds of discrete polymorphism (e.g. behavioural syndromes), but we focus primarily on colour polymorphism because they are well studied. We urge further empirical investigation of the genetic architecture and interactions in polymorphic species to elucidate the impact on population fitness.
Publisher: Cold Spring Harbor Laboratory
Date: 04-07-2022
DOI: 10.1101/2022.07.04.498653
Abstract: Adaptive ergence is a fundamental process that shapes genetic ersity within and across species. Structural variants (SVs) are large-scale genetic differences (insertion, deletions, and rearrangements) within a species or population. SVs can cause important functional differences in the in idual’s phenotype. Characterising SVs across invasive species will help fill knowledge gaps regarding how patterns of genetic ersity and genetic architecture shape rapid adaptation in response to new selection regimes. In this project we seek to understand patterns in genetic ersity within the globally invasive European starling, Sturnus vulgaris . We use whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings to examine patterns in genome-wide SNPs and SVs between populations and within Australia. The findings of our research demonstrate that even within recently erged lineages or populations, there may be high amounts of structural variation. Further, patterns of genetic ersity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of ersity along the length of the organism’s chromosomes (owing to enrichment of SVs in sub telomeric repeat regions), or interpopulation ersity 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 ersity within populations is complex and supports the need for further investigation of SVs across a range of taxa to better understand correlations between oft well studied SNP ersity and that of SVs.
Publisher: Wiley
Date: 04-08-2022
DOI: 10.1111/MEC.16633
Abstract: Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short‐term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well‐studied cane toad, Rhinella marina , to examine the effect of short‐term captivity on brain gene expression levels, and determine whether effects of captivity differ between long‐colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild‐caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild‐caught toads from the same population, with an over‐representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long‐colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short‐term captivity can induce large and population‐specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild‐caught organisms from different populations that have been held in captivity.
Publisher: Cold Spring Harbor Laboratory
Date: 23-08-2023
DOI: 10.1101/2023.08.22.554353
Abstract: In an era of global climate change and massive environmental disturbance, bio ersity conservation is receiving increased attention. Conservation efforts are being greatly aided by genetic tools and approaches, which seek to understand patterns of genetic ersity and how they impact species health and ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions around adaptive potential, with a particular focus on how changes in genetic ersity and effective population size interact with the novel selection regime of the invaded range to drive rapid evolution. The common myna ( Acridotheres tristis ) is a globally invasive passerine, which has undergone multiple concurrent and sequential bottlenecks across its globally invasive range, and yet has established itself across a erse array of ecological conditions. It is therefore an excellent model species for research both into the persistence of low- ersity populations and the mechanics of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna, assembled using a backbone of Oxford Nanopore Technologies long reads, alongside an RNA-seq based transcriptome and genome annotation. To provide genomic context for future studies, we describe the genomic landscape of this species, including genome wide allelic ersity, methylation, repeats, and recombination rate, as well as an examination of gene family expansions and contractions. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, but also reveal artefactual impacts of genetic bottlenecks on demographic analysis.
Publisher: Elsevier BV
Date: 12-2017
Publisher: The Royal Society
Date: 11-07-2012
Abstract: Kin selection theory has been the central model for understanding the evolution of cooperative breeding, where non-breeders help bear the cost of rearing young. Recently, the dominance of this idea has been questioned particularly in obligate cooperative breeders where breeding without help is uncommon and seldom successful. In such systems, the direct benefits gained through augmenting current group size have been hypothesized to provide a tractable alternative (or addition) to kin selection. However, clear empirical tests of the opposing predictions are lacking. Here, we provide convincing evidence to suggest that kin selection and not group augmentation accounts for decisions of whether, where and how often to help in an obligate cooperative breeder, the chestnut-crowned babbler ( Pomatostomus ruficeps ). We found no evidence that group members base helping decisions on the size of breeding units available in their social group, despite both correlational and experimental data showing substantial variation in the degree to which helpers affect productivity in units of different size. By contrast, 98 per cent of group members with kin present helped, 100 per cent directed their care towards the most related brood in the social group, and those rearing half/full-sibs helped approximately three times harder than those rearing less/non-related broods. We conclude that kin selection plays a central role in the maintenance of cooperative breeding in this species, despite the apparent importance of living in large groups.
Publisher: Wiley
Date: 06-02-2022
DOI: 10.1111/MEC.16353
Abstract: 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 ergent evolutionary change between contemporary native and invasive range s les and their common ancestral population. To do this, we use reduced‐representation sequencing of native s les collected recently in northwestern Europe and invasive s les from Australia, together with museum specimens s led 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 ergent 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 s les. Our results demonstrate the value of including historical s les in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Publisher: Wiley
Date: 19-02-2020
Abstract: Noninvasive s ling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive s ling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal s ling methods in adult hibians. In this study, we compare microbiomes from two noninvasive s le types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal s ling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher ersity. Our results indicate that cloacal swabs were more similar to large intestine s les than were faecal s les, and small intestine s les were significantly different from both nonlethal s le types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal s ling of hibian gut microbiota.
Publisher: Oxford University Press (OUP)
Date: 2011
Publisher: Wiley
Date: 18-07-2011
DOI: 10.1111/J.1558-5646.2011.01391.X
Abstract: Despite decades of research, whether vertebrates can and do adaptively adjust the sex ratio of their offspring is still highly debated. However, this may have resulted from the failure of empirical tests to identify large and predictable fitness returns to females from strategic adjustment. Here, we test the effect of diet quality and maternal condition on facultative sex ratio adjustment in the color polymorphic Gouldian finch (Erythrura gouldiae), a species that exhibits extreme maternal allocation in response to severe and predictable (genetically-determined) fitness costs. On high-quality diets, females produced a relatively equal sex ratio, but over-produced sons in poor dietary conditions. Despite the lack of sexual size dimorphism, nutritionally stressed foster sons were healthier, grew faster, and were more likely to survive than daughters. Although these findings are in line with predictions from sex allocation theory, the extent of adjustment is considerably lower than previously reported for this species. Females therefore have strong facultative control over sex allocation, but the extent of adjustment is likely determined by the relative magnitude of fitness gains and the ability to reliably predict sex-specific benefits from environmental (vs. genetic) variables. These findings may help explain the often inconsistent, weak, or inconclusive empirical evidence for adaptive sex ratio adjustment in vertebrates.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 20-08-2010
Abstract: Extra-pair copulations benefit males by increasing their potential number of offspring. However, whether they have adaptive significance for females has long been debated. Pryke et al. (p. 964 ), provided female finches four different scenarios to test when extra-pair copulations occurred and measured the paternity of the resulting offspring. By varying the potential fathers from a supposedly adaptive, compatible male through a neutral context, to a supposedly maladaptive scenario, females biased paternity to the extra-pair male when his contribution was adaptive and away from the extra-pair male when his contribution was maladaptive. Thus, despite bias in copulation frequency in favor of the social pair, cryptic female choice may show a fertilization bias toward compatible genes.
Publisher: PeerJ
Date: 06-10-2017
DOI: 10.7717/PEERJ.3856
Abstract: The cane toad ( Rhinella marina ) has undergone rapid evolution during its invasion of tropical Australia. Toads from invasion front populations (in Western Australia) have been reported to exhibit a stronger baseline phagocytic immune response than do conspecifics from range core populations (in Queensland). To explore this difference, we injected wild-caught toads from both areas with the experimental antigen lipopolysaccharide (LPS, to mimic bacterial infection) and measured whole-blood phagocytosis. Because the hypothalamic-pituitary-adrenal axis is stimulated by infection (and may influence immune responses), we measured glucocorticoid response through urinary corticosterone levels. Relative to injection of a control (phosphate-buffered saline), LPS injection increased both phagocytosis and the proportion of neutrophils in the blood. However, responses were similar in toads from both populations. This null result may reflect the ubiquity of bacterial risks across the toad’s invaded range utilization of this immune pathway may not have altered during the process of invasion. LPS injection also induced a reduction in urinary corticosterone levels, perhaps as a result of chronic stress.
Publisher: Elsevier BV
Date: 08-2013
Publisher: Wiley
Date: 10-11-2017
DOI: 10.1111/JEB.12997
Abstract: In socially monogamous species, in iduals can use extra-pair paternity and offspring sex allocation as adaptive strategies to ameliorate costs of genetic incompatibility with their partner. Previous studies on domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic incompatibility between head colour morphs, the effects of which are more severe in female offspring. Domesticated females use differential sex allocation, and extra-pair paternity with males of compatible head colour, to reduce fitness costs associated with incompatibility in mixed-morph pairings. However, laboratory studies are an oversimplification of the complex ecological factors experienced in the wild and may only reflect the biology of a domesticated species. This study aimed to examine the patterns of parentage and sex ratio bias with respect to colour pairing combinations in a wild population of the Gouldian finch. We utilized a novel PCR assay that allowed us to genotype the morph of offspring before the morph phenotype develops and to explore bias in morph paternity and selection at the nest. Contrary to previous findings in the laboratory, we found no effect of pairing combinations on patterns of extra-pair paternity, offspring sex ratio or selection on morphs in nestlings. In the wild, the effect of morph incompatibility is likely much smaller, or absent, than was observed in the domesticated birds. Furthermore, the previously studied domesticated population is genetically differentiated from the wild population, consistent with the effects of domestication. It is possible that the domestication process fostered the emergence (or enhancement) of incompatibility between colour morphs previously demonstrated in the laboratory.
Publisher: Cold Spring Harbor Laboratory
Date: 28-09-2021
DOI: 10.1101/2021.09.27.462079
Abstract: Understanding the mechanisms underlying rapid adaptation of invasive species in novel environments is key to improving our ability to manage these species. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk-taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads ( Rhinella marina ) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads’ dispersal ability. Common-garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. However, genetic ersity is greatly reduced across the invasive range due to a strong founder effect, and the genetic basis underlying dispersal-related behavioural changes remains unknown. Here we used RNA-seq to compare the brain transcriptomes of toads from the Hawai’ian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, cane toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between range-core and range-front populations. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.
Publisher: Wiley
Date: 23-01-2014
DOI: 10.1111/JEB.12313
Publisher: Springer Science and Business Media LLC
Date: 07-09-2016
Publisher: PeerJ
Date: 05-01-2016
DOI: 10.7717/PEERJ.1550
Abstract: Although the majority of passerine birds are socially monogamous, true genetic monogamy is rare, with extra-pair paternity (EPP) occurring in almost 90% of surveyed socially monogamous species. We present the first molecular data on the genetic breeding system of the long-tailed finch, Poephila acuticauda , a grass finch endemic to the tropical northern savannah of Australia. Although the species forms socially monogamous pair bonds during the breeding season, we found that extra-pair males sired 12.8% of 391 offspring, in 25.7% of 101 broods. Our findings provide only the second estimate of extra-pair paternity in the estrildid finch family.
Publisher: Springer Science and Business Media LLC
Date: 14-06-2015
Publisher: Springer Science and Business Media LLC
Date: 05-02-2018
Publisher: Wiley
Date: 21-04-2011
Publisher: CSIRO Publishing
Date: 10-07-2023
DOI: 10.1071/WR22128
Publisher: Wiley
Date: 28-01-2022
DOI: 10.1111/MEC.16347
Abstract: Understanding the mechanisms allowing invasive species to adapt to novel environments is a challenge in invasion biology. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk‐taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads ( Rhinella marina ) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads’ dispersal ability. Common‐garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. At the molecular level, it is currently unknown whether these changes in dispersal‐related behaviour are underlain by small or large differences in gene expression, nor is known the biological function of genes showing differential expression. Here, we used RNA‐seq to gain a better understanding of the molecular mechanisms underlying dispersal‐related behavioural changes. We compared the brain transcriptomes of toads from the Hawai'ian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between populations located at each end of the invasive range. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.
Publisher: CSIRO Publishing
Date: 06-07-2023
DOI: 10.1071/WR22129
Publisher: Elsevier BV
Date: 04-2019
Publisher: Cold Spring Harbor Laboratory
Date: 17-09-2023
Publisher: CSIRO Publishing
Date: 20-07-2023
DOI: 10.1071/WR22120
Publisher: Springer Science and Business Media LLC
Date: 30-11-2018
Publisher: The Royal Society
Date: 08-2012
Abstract: Theory predicts that mothers should adjust offspring sex ratios when the expected fitness gains or rearing costs differ between sons and daughters. Recent empirical work has linked biased offspring sex ratios to environmental quality via changes in relative maternal condition. It is unclear, however, whether females can manipulate offspring sex ratios in response to environmental quality alone (i.e. independent of maternal condition). We used a balanced within-female experimental design (i.e. females bred on both low- and high-quality diets) to show that female parrot finches ( Erythrura trichroa ) manipulate primary offspring sex ratios to the quality of the rearing environment, and not to their own body condition and health. In idual females produced an unbiased sex ratio on high-quality diets, but over-produced sons in poor dietary conditions, even though they maintained similar condition between diet treatments. Despite the lack of sexual size dimorphism, such sex ratio adjustment is in line with predictions from sex allocation theory because nutritionally stressed foster sons were healthier, grew faster and were more likely to survive than daughters. These findings suggest that mothers may adaptively adjust offspring sex ratios to optimally match their offspring to the expected quality of the rearing environment.
Publisher: Oxford University Press (OUP)
Date: 27-11-2017
Publisher: Wiley
Date: 14-05-2016
DOI: 10.1111/MEC.13632
Abstract: Polymorphism describes two or more distinct, genetically determined, phenotypes that co-occur in the same population, where the rarest morph is maintained at a frequency above the mutation rate (Ford 1945 Huxley 1955). In a recent opinion piece, we explored a new idea regarding the role of genetic architectures and morph interactions in colour polymorphisms and how this can negatively affect population performance (Bolton et al. 2015). In this issue of Molecular Ecology, Forsman (2016) thoroughly discusses the current evidence for polymorphisms enhancing population performance and critiques the validity of the definitions of polymorphism we use in our original paper. We respond by clarifying that the negative consequences of polymorphisms that we discussed are likely to be most pertinent in species that have a particular set of characteristics, such as strong sexual or social interactions between morphs and discrete genetic architectures. Although it was not our intention to redefine polymorphism, we do believe that there should be further discussion about refining or characterizing balanced polymorphisms with respect to the degree of morph sympatry, discreteness of traits and their underlying genetic architecture, and the types of selection that drive and maintain the variation. The latter describes whether polymorphism is primarily maintained by external factors such as predation pressure or internal factors such as interactions with members of the same species. The contribution of Forsman (2016) is useful to this discussion, and we hope that our exchange of opinions will inspire new empirical and theoretical ideas on the origin and maintenance of colour polymorphisms.
Publisher: Public Library of Science (PLoS)
Date: 09-12-2016
Publisher: The Royal Society
Date: 19-04-2021
Abstract: In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here, we use an iconic invader, the cane toad ( Rhinella marina ), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e. the costs of producing the inducible defence) were minimized in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within the sodium channel epithelial 1 subunit gamma gene ( SCNN1G ) in alarm cue exposed in iduals and their offspring. This gene is a key to the regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early life experiences of tadpoles induce intergenerational effects through epigenetic mechanisms, which enhance larval fitness. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’
Publisher: The Royal Society
Date: 03-2022
Abstract: Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. We used a co-introduced, invasive host–parasite system (the lungworm Rhabdias pseudosphaerocephala and cane toads Rhinella marina ), where rapid adaptation and dispersal have led to population differences in infection resistance. We quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which juvenile hosts became infected following standardized exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the host's body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) were higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge juvenile toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host–parasite arms race, changing outcomes appear to be driven by shifts in host immunocompetence.
Publisher: Wiley
Date: 16-10-2013
DOI: 10.1002/ECE3.824
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.BEPROC.2014.08.020
Abstract: The existence of animal personality is well-established across a wide range of species, with the majority of evidence for this being obtained from in iduals held in captivity. However, there has been little work assessing the influence of commonly-measured personality traits on fitness, which is pertinent when the genetic basis of personality is considered. We measured whether the reproductive behaviour and success of zebra finches in a captive mixed-sex aviary environment was influenced by an aspect of their personality, their exploratory behaviour in a single-sex social aviary. We found that more exploratory males made a greater number of breeding attempts and raised more nestlings than less exploratory males. These results were not confounded by extra-pair paternity, which was not related to personality, or by the in iduals that did not initiate any reproductive attempts at all. Our work provides evidence that attributes of personality may influence the degree to which in iduals cope with, and thrive in a captive environment and this should be accounted for in both experimental design and the interpretation of results. Furthermore, this suggests that there may be selection on these traits as part of the domestication process.
Publisher: Cold Spring Harbor Laboratory
Date: 22-06-2023
DOI: 10.1101/2023.06.19.545515
Abstract: Parasites may suppress the immune function of an infected host using microRNAs (miRNAs) to prevent protein production. Nonetheless, little is known about the ersity of miRNAs and their mode(s) of action. In this study, we investigated the effects of infection by a parasitic lungworm ( Rhabdias pseudosphaerocephala ) on miRNA and mRNA expression of its host, the invasive cane toad ( Rhinella marina ). We compared miRNA and mRNA expression in naïve toads that had never been infected by lungworms to toads that were infected with lungworms for the first time in their lives, and to toads that were infected the second time in their lives (i.e., had two consecutive infections). In total, we identified 434 known miRNAs and 106 potential novel miRNAs. Compared to uninfected toads, infected animals upregulated five (single-infection treatment) or four (multiple-infection treatment) miRNAs. Seven of these differentially expressed miRNAs were associated with gene pathways related to the immune response, potentially reflecting immunosuppression of cane toads by their parasites. Infected hosts did not respond with substantial mRNA transcription, with only one differentially expressed gene between control and single-infection hosts. Our study suggests that miRNA-mediated interactions may play a role in mediating the interaction between the parasite and its host. Our findings clarify the role of miRNAs in host-parasite interactions, in a system in which an ongoing range expansion by the host has generated substantial ergence in host-parasite interactions.
Publisher: American Society for Microbiology
Date: 09-2018
DOI: 10.1128/JVI.00768-18
Abstract: Cane toads are poisonous hibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study s les cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.
Publisher: Cold Spring Harbor Laboratory
Date: 19-10-2021
DOI: 10.1101/2021.10.19.464902
Abstract: Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. Using a co-introduced, invasive host-parasite system (the lungworm Rhabdias pseudosphaerocephala and the cane toad Rhinella marina), we quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which hosts became infected following standardised exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the host’s body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) was higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host-parasite arms-race, changing outcomes appear to be driven by shifts in host immunocompetence.
Publisher: Elsevier BV
Date: 07-2014
Publisher: PeerJ
Date: 29-03-2018
DOI: 10.7717/PEERJ.4573
Abstract: 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 in iduals 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 in idual 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.
Publisher: Cold Spring Harbor Laboratory
Date: 23-08-2021
DOI: 10.1101/2021.08.22.457241
Abstract: 1. During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation 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 ergent evolutionary change between contemporary native and invasive range s les and their common ancestral population. To do this, we use reduced-representation sequencing of native s les collected recently in north-western Europe and invasive s les from Australia, together with museum specimens s led in the UK during the mid-19 th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants (e.g. TCDD) and food carbohydrate content. We also identified ergent 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 s les. Our results demonstrate the value of including historical s les in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Publisher: Wiley
Date: 15-02-2012
Publisher: Public Library of Science (PLoS)
Date: 11-06-2015
Publisher: Wiley
Date: 03-05-2011
DOI: 10.1111/J.1558-5646.2011.01314.X
Abstract: Because selection is often sex-dependent, alleles can have positive effects on fitness in one sex and negative effects in the other, resulting in intralocus sexual conflict. Evolutionary theory predicts that intralocus sexual conflict can drive the evolution of sex limitation, sex-linkage, and sex chromosome differentiation. However, evidence that sex-dependent selection results in sex-linkage is limited. Here, we formally partition the contribution of Y-linked and non-Y-linked quantitative genetic variation in coloration, tail, and body size of male guppies (Poecilia reticulata)-traits previously implicated as sexually antagonistic. We show that these traits are strongly genetically correlated, both on and off the Y chromosome, but that these correlations differ in sign and magnitude between both parts of the genome. As predicted, variation in attractiveness was found to be associated with the Y-linked, rather than with the non-Y-linked component of genetic variation in male ornamentation. These findings show how the evolution of Y-linkage may be able to resolve sexual conflict. More generally, they provide unique insight into how sex-specific selection has the potential to differentially shape the genetic architecture of fitness traits across different parts of the genome.
Publisher: Wiley
Date: 20-04-2015
DOI: 10.1111/MEC.13184
Abstract: The process of biological invasion exposes a species to novel pressures, in terms of both the environments it encounters and the evolutionary consequences of range expansion. Several invaders have been shown to exhibit rapid evolutionary changes in response to those pressures, thus providing robust opportunities to clarify the processes at work during rapid phenotypic transitions. The accelerating pace of invasion of cane toads (Rhinella marina) in tropical Australia during its 80-year history has been well characterized at the phenotypic level, including common-garden experiments that demonstrate heritability of several dispersal-relevant traits. In iduals from the invasion front (and their progeny) show distinctive changes in morphology, physiology and behaviour that, in combination, result in far more rapid dispersal than is true of conspecifics from long-colonized areas. The extensive body of work on cane toad ecology enables us to place into context studies of the genetic basis of these traits. Our analyses of differential gene expression from toads from both ends of this invasion-history transect reveal substantial upregulation of many genes, notably those involved in metabolism and cellular repair. Clearly, then, the dramatically rapid phenotypic evolution of cane toads in Australia has been accompanied by substantial shifts in gene expression, suggesting that this system is well suited to investigating the genetic underpinnings of invasiveness.
Publisher: Wiley
Date: 18-07-2022
Abstract: 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.
Publisher: Cold Spring Harbor Laboratory
Date: 26-10-2023
Publisher: Cold Spring Harbor Laboratory
Date: 17-11-2020
DOI: 10.1101/2020.11.16.385690
Abstract: Gut bacterial communities influence, and are influenced by, the behaviour and ecology of their hosts. Those interactions have been studied primarily in humans and model organisms, but we need field research to understand the relationship between an organism’s gut bacteria and its ecological challenges, such as those imposed by rapid range expansion (as in invasive species) and the presence of host-manipulating parasites. Cane toads ( Rhinella marina ) provide an excellent model system in this respect, because the species’ ongoing colonization of Australia has enforced major changes in phenotypic traits (including behaviour), and lungworm parasites ( Rhabdias pseudosphaerocephala ) modify host gut function in ways that enhance the viability of lungworm larvae. We collected female toads from across the species’ invasive range and studied their morphology, behaviour, parasite infection status and gut bacterial community. Range-core versus range-edge toads differed in morphology, behaviour, gut bacterial composition and predicted gut bacterial function but did not differ in the occurrence of parasite infection nor in the intensity of infection. Toads infected with lungworms differed from uninfected conspecifics in gut bacterial composition and ersity. Our study demonstrates strong associations between gut bacterial community and host ecology and behaviour.
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/WR05106
Abstract: 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 in iduals present, whether populations are expanding or contracting, identifying the origin of invasive in iduals, the number of separate introduction events that have occurred and in which order, and the rate that in iduals 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 ex le 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.
Publisher: Cold Spring Harbor Laboratory
Date: 08-04-2021
DOI: 10.1101/2021.04.07.438753
Abstract: 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 genome ( S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (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. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. 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 counter-intuitive behaviour in traditional BUSCO metrics, and present B uscomp , a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.
Publisher: Oxford University Press (OUP)
Date: 06-01-2016
Abstract: Mitochondria are critical for life, yet their underlying evolutionary biology is poorly understood. In particular, little is known about interaction between two levels of evolution: between in iduals and within in iduals (competition between cells, mitochondria or mitochondrial DNA molecules). Rapid evolution is suspected to occur frequently in mitochondrial DNA, whose maternal inheritance predisposes advantageous mutations to sweep rapidly though populations. Rapid evolution is also predicted in response to changed selection regimes after species invasion or removal of pathogens or competitors. Here, using empirical and simulated data from a model invasive bird species, we provide the first demonstration of rapid selection on the mitochondrial genome within in iduals in the wild. Further, we show differences in mitochondrial DNA copy number associated with competing genetic variants, which may provide a mechanism for selection. We provide evidence for three rarely documented phenomena: selection associated with mitochondrial DNA abundance, selection on the mitochondrial control region, and contemporary selection during invasion.
Publisher: Wiley
Date: 29-09-2021
DOI: 10.1111/MEC.15601
Abstract: 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.
Publisher: Springer Science and Business Media LLC
Date: 31-07-2013
Publisher: Oxford University Press (OUP)
Date: 2015
Publisher: Oxford University Press (OUP)
Date: 06-2015
Publisher: Cold Spring Harbor Laboratory
Date: 03-11-2022
DOI: 10.1101/2022.11.02.514965
Abstract: Transitions from sexual to asexual reproduction have occurred in numerous lineages across the tree of life, but it remains unclear why asexual populations rarely persist. In facultatively parthenogenetic animals, all-female populations can arise when males are absent or become extinct, and such populations can give rise to obligately asexual species. Facultative parthenogens could therefore shed light on the initial stages of transitions to asexuality, and the factors that determine the success or failure of asexual populations. Here, we describe a novel spatial mosaic of mixed-sex and all-female populations of the facultatively parthenogenetic Australian phasmid Megacrania batesii , and use this system to investigate the consequences of reproductive mode variation in the wild. Analysis of single nucleotide polymorphisms (SNPs) indicated multiple, independent transitions between reproductive modes. As expected, all-female populations had drastically reduced heterozygosity and genetic ersity relative to mixed-sex populations. However, we found few consistent differences in fitness-related traits between population types. All-female populations exhibited more frequent and severe (non-functional) wing deformities, but did not show higher rates of appendage loss. All-female populations also harbored more parasites, but only in certain habitats. Reproductive mode explained little variation in female body size, fecundity, or egg hatch-rate. Our results confirm that transitions to parthenogenetic reproduction can lead to dramatic reductions in genetic ersity and heterozygosity. However, our findings also suggest that asexual M. batesii populations consist of high-fitness genotypes that might be able to thrive for many generations, perhaps until they encounter a drastic environmental change to which they are unable to adapt.
Publisher: Springer Science and Business Media LLC
Date: 27-11-2010
Publisher: Wiley
Date: 15-05-2012
DOI: 10.1002/ECE3.259
Publisher: Elsevier BV
Date: 2011
Publisher: Wiley
Date: 06-2015
Publisher: Wiley
Date: 04-2009
Publisher: Cold Spring Harbor Laboratory
Date: 19-05-2021
DOI: 10.1101/2021.05.19.442026
Abstract: A species’ success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings ( Sturnus vulgaris ) established populations in Australia and North America in the 19 th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.
Publisher: Springer Science and Business Media LLC
Date: 06-11-2016
Publisher: Wiley
Date: 15-12-2022
DOI: 10.1111/EVA.13516
Abstract: Knowledge of an animal's chronological age is crucial for understanding and predicting population demographics, survival and reproduction, but accurate age determination for many wild animals remains challenging. Previous methods to estimate age require invasive procedures, such as tooth extraction to analyse growth layers, which are difficult to carry out with large, mobile animals such as cetaceans. However, recent advances in epigenetic methods have opened new avenues for precise age determination. These ‘epigenetic clocks’ present a less invasive alternative and can provide age estimates with unprecedented accuracy. Here, we present a species‐specific epigenetic clock based on skin tissue s les for a population of Indo‐Pacific bottlenose dolphins ( Tursiops aduncus ) in Shark Bay, Western Australia. We measured methylation levels at 37,492 cytosine‐guanine sites (CpG sites) in 165 s les using the mammalian methylation array. Chronological age estimates with an accuracy of ±1 year were available for 68 animals as part of a long‐term behavioral study of this population. Using these s les with known age, we built an elastic net model with Leave‐One‐Out‐Cross‐Validation, which retained 43 CpG sites, providing an r = 0.86 and median absolute age error (MAE) = 2.1 years (5% of maximum age). This model was more accurate for our data than the previously published methylation clock based on skin s les of common bottlenose dolphins ( T. truncatus : r = 0.83, MAE = 2.2) and the multi‐species odontocete methylation clock ( r = 0.68, MAE = 6.8), highlighting that species‐specific clocks can have superior performance over those of multi‐species assemblages. We further developed an epigenetic sex estimator, predicting sex with 100% accuracy. As age and sex are critical parameters for the study of animal populations, this clock and sex estimator will provide a useful tool for extracting life history information from skin s les rather than long‐term observational data for free‐ranging Indo‐Pacific bottlenose dolphins worldwide.
Publisher: Oxford University Press (OUP)
Date: 06-2015
Abstract: 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 ersity. Highly polymorphic loci may be especially useful when studying populations having low levels of ersity overall, such as is often the case with threatened or newly established invasive populations. Using common starlings Sturnus vulgaris s led 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 ersity using DRD4 data and compared these estimates to those from microsatellite and mitochondrial DNA sequence data, using the same in iduals. We found little evidence for selection on DRD4 in starlings. However, we did find elevated levels of within-population gene ersity 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.
Publisher: Informa UK Limited
Date: 30-04-2016
Publisher: Wiley
Date: 27-08-2020
DOI: 10.1002/ECE3.6679
Publisher: Wiley
Date: 28-10-2013
DOI: 10.1002/ECE3.844
Publisher: Cold Spring Harbor Laboratory
Date: 28-02-2023
DOI: 10.1101/2023.02.28.530339
Abstract: Rhabdias pseudosphaerocephala is a well-studied invasive nematode parasite of hibians. However, there are several outstanding questions about R. pseudosphaerocephala that are best answered using genomic data. This species differs phenotypically across its invasive range. These differences are challenging to interpret because this species is part of a complex that is erse and cryptic in its home-range, and we do not know how many species from this complex originally colonised Australia. For this reason, it is unknown whether the phenotypic differences across the introduced range are due to intraspecific differentiation between populations or due to the presence of multiple species. In addition, there is little consensus in the placement of Rhabdiasidae family within the phylum Nematoda, making it difficult to perform comparative analyses with other nematodes. Within this paper, we assemble a reference genome for R. pseudosphaerocephala , the first assembly of any Rhabdiasidae species. We then use resequencing data to address outstanding questions about this species. Specifically, we combine population genetic and phylogenetic analyses to determine that there is likely only a single R. pseudosphaerocephala lineage within Australia, and identify that the invasive range population is closely related to home rage isolates that infect similar host species. We present compelling evidence for a genetic bottleneck following introduction to Australia and genetic differentiation occurring between invasive range populations. We then use genome-scale phylogenomic analysis to place the Rhabdiasidae family in the suborder Rhabditina. Ultimately, this paper brings the study of Rhabdiasidae into the genomic era, and sheds light on its ancient and modern evolutionary history.
Start Date: 2020
End Date: 2024
Funder: Marsden Fund
View Funded ActivityStart Date: 2016
End Date: 12-2021
Amount: $385,700.00
Funder: Australian Research Council
View Funded ActivityStart Date: 04-2015
End Date: 04-2018
Amount: $360,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2019
End Date: 06-2024
Amount: $1,110,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 03-2013
End Date: 02-2017
Amount: $315,000.00
Funder: Australian Research Council
View Funded Activity