ORCID Profile
0000-0003-3813-682X
Current Organisations
UNSW Sydney
,
Centre for Population Genomics
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Proceedings of the National Academy of Sciences
Date: 27-05-2014
Abstract: Tests of bio ersity theory have been controversial partly because alternative formulations of the same theory seemingly yield different conclusions. This has been a particular challenge for neutral theory, which has dominated tests of bio ersity theory over the last decade. Neutral theory attributes differences in species abundances to chance variation in in iduals’ fates, rather than differences in species traits. By identifying common features of different neutral models, we conduct a uniquely robust test of neutral theory across a global dataset of marine assemblages. Consistently, abundances vary more among species than neutral theory predicts, challenging the hypothesis that community dynamics are approximately neutral, and implicating species differences as a key driver of community structure in nature.
Publisher: Springer Science and Business Media LLC
Date: 15-02-2023
DOI: 10.1038/S41467-023-36606-W
Abstract: Following the diagnosis of a paediatric disorder caused by an apparently de novo mutation, a recurrence risk of 1–2% is frequently quoted due to the possibility of parental germline mosaicism but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing in idualized recurrence risk. By combining locus-specific sequencing of multiple tissues to detect occult mosaicism with long-read sequencing to determine the parent-of-origin of the mutation, we show that we can stratify the majority of couples into one of seven discrete categories associated with substantially different risks to future offspring. Among 58 families with a single affected offspring (representing 59 de novo mutations in 49 genes), the recurrence risk for 35 (59%) was decreased below 0.1%, but increased owing to parental mixed mosaicism for 5 (9%)—that could be quantified in semen for paternal cases (recurrence risks of 5.6–12.1%). Implementation of this strategy offers the prospect of driving a major transformation in the practice of genetic counselling.
Publisher: University of Chicago Press
Date: 09-2010
DOI: 10.1086/655219
Abstract: Positive density dependence (i.e., the Allee effect AE) often has important implications for the dynamics and conservation of populations. Here, we show that density-dependent sex ratio adjustment in response to sexual selection may be a common AE mechanism. Specifically, using an analytical model we show that an AE is expected whenever one sex is more fecund than the other and sex ratio bias toward the less fecund sex increases with density. We illustrate the robustness of this pattern, using Monte Carlo simulations, against a range of body size-fecundity relationships and sex-allocation strategies. Finally, we test the model using the sex-changing polygynous reef fish Parapercis cylindrica positive density dependence in the strength of sexual selection for male size is evidenced as the causal mechanism driving local sex ratio adjustment, hence the AE. Model application may extend to invertebrates, reptiles, birds, and mammals, in addition to over 70 reef fishes. We suggest that protected areas may often outperform harvest quotas as a conservation tool since the latter promotes population fragmentation, reduced polygyny, a balancing of the sex ratio, and hence up to a 50% decline in per capita fecundity, while the former maximizes polygyny and source-sink potential.
Publisher: Wiley
Date: 13-06-2020
DOI: 10.1111/DDI.13073
Publisher: Wiley
Date: 04-2012
DOI: 10.1890/11-1753.1
Abstract: Bio ersity may provide insurance against ecosystem collapse by stabilizing assemblages that perform particular ecological functions (the “portfolio effect”). However, the extent to which this occurs in nature and the importance of different mechanisms that generate portfolio effects remain controversial. On coral reefs, herbivory helps maintain coral dominated states, so volatility in levels of herbivory has important implications for reef ecosystems. Here, we used an extensive time series of abundances on 35 reefs of the Great Barrier Reef of Australia to quantify the strength of the portfolio effect for herbivorous fishes. Then, we disentangled the contributions of two mechanisms that underlie it (compensatory interactions and differential responses to environmental fluctuations [“response ersity”]) by fitting a community‐dynamic model that explicitly includes terms for both mechanisms. We found that portfolio effects operate strongly in herbivorous fishes, as shown by nearly independent fluctuations in abundances over time. Moreover, we found strong evidence for high response ersity, with nearly independent responses to environmental fluctuations. In contrast, we found little evidence that the portfolio effect in this system was enhanced by compensatory ecological interactions. Our results show that portfolio effects are driven principally by response ersity for herbivorous fishes on coral reefs. We conclude that portfolio effects can be very strong in nature and that, for coral reefs in particular, response ersity may help maintain herbivory above the threshold levels that trigger regime shifts.
Publisher: Springer Science and Business Media LLC
Date: 06-06-2009
Publisher: Public Library of Science (PLoS)
Date: 24-07-2017
Publisher: American Society for Microbiology
Date: 17-12-2020
DOI: 10.1128/AEM.02002-20
Abstract: Identifying selection from SNP data obtained from whole-genome sequencing studies is challenging. Some current measures used to identify and quantify selection acting on genomes rely on fixed differences thus, these are inappropriate for SNP data where variants are not fixed. With the increase in whole-genome sequencing studies, it is important to consider SNP data in the context of evolutionary processes. How SNPs are counted and analyzed can help in understanding mutation accumulation and trajectories of strains. We developed a tool for identifying possible evidence of selection and for comparative analysis with other SNP data. We propose a model that provides a rule-of-thumb guideline and two new visualization techniques that can be used to interpret and compare SNP data. We quantify the expected proportion of nonsynonymous SNPs in coding regions under neutrality and demonstrate its use in identifying evidence of positive and negative selection from simulations and empirical data.
Publisher: Wiley
Date: 24-10-2012
DOI: 10.1111/ELE.12019
Publisher: Oxford University Press (OUP)
Date: 03-2012
DOI: 10.1093/JPE/RTR043
Publisher: Cold Spring Harbor Laboratory
Date: 24-02-2019
DOI: 10.1101/559666
Abstract: Terrestrial Antarctica, a predominantly microbial realm, encompasses some of the most unique environments on Earth where resident soil microbiota play key roles in the sustainability and evolution of the ecosystem. Yet the fundamental ecological processes that govern the assemblage of these natural communities remain unclear. Here, we combined multivariate analyses, co-occurrence networks and fitted species abundance distributions of licon sequencing data to disentangle community assemblage patterns of polar soil microbiomes across two ice-free deserts (Windmill Islands and Vestfold Hills) situated along the coastline of eastern Antarctica. Our findings report that communities were predominantly structured by non-neutral processes, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. In contrast, both eukaryotic and archaeal communities exhibited multimodal distributions, indicating the potential emergence of neutrality. Between the three microbial domains, polar soil bacterial communities consistently demonstrated the greatest taxonomic ersity, estimated richness, network connectivity and linear response to contemporary environmental soil parameters. We propose that reduced niche overlap promotes greater phylogenetic ersity enabling more bacterial species to co-exist and essentially thrive under adversity. However, irrespective of overall relative abundance, consistent and robust associations between co-existing community members from all three domains of life highlights the key roles that erse taxa play in ecosystem dynamics. In the face of a warming Antarctica, contemporary dynamics between polar soil microbial communities will inevitably change due to the climate-induced expansion of new ice-free areas. Increasing concern about disturbance and rapid bio ersity loss has intensified the need to better understand microbial community structure and function in high-latitude soils. We have taken an integrated approach to elucidate domain-level assemblage patterns across east Antarctic soil microbiomes. These assemblage patterns will be available to feed into policy management and conservation planning frameworks to potentially mitigate future bio ersity loss.
Publisher: Springer Science and Business Media LLC
Date: 04-2020
DOI: 10.1186/S12866-020-01762-2
Abstract: The human gut microbiome plays a critical role in the carcinogenesis of colorectal cancer (CRC). However, a comprehensive analysis of the interaction between the host and microbiome is still lacking. We found correlations between the change in abundance of microbial taxa, butyrate-related colonic metabolites, and methylation-associated host gene expression in colonic tumour mucosa tissues compared with the adjacent normal mucosa tissues. The increase of genus Fusobacterium abundance was correlated with a decrease in the level of 4-hydroxybutyric acid (4-HB) and expression of immune-related peptidase inhibitor 16 ( PI16 ), Fc Receptor Like A ( FCRLA ) and Lymphocyte Specific Protein 1 ( LSP1 ). The decrease in the abundance of another potentially 4-HB-associated genus, Prevotella 2, was also found to be correlated with the down-regulated expression of metallothionein 1 M ( MT1M ). Additionally, the increase of glutamic acid-related family Halomonadaceae was correlated with the decreased expression of reelin ( RELN ). The decreased abundance of genus Paeniclostridium and genus Enterococcus were correlated with increased lactic acid level, and were also linked to the expression change of Phospholipase C Beta 1 ( PLCB1 ) and Immunoglobulin Superfamily Member 9 ( IGSF9 ) respectively. Interestingly, 4-HB, glutamic acid and lactic acid are all butyrate precursors, which may modify gene expression by epigenetic regulation such as DNA methylation. Our study identified associations between previously reported CRC-related microbial taxa, butyrate-related metabolites and DNA methylation-associated gene expression in tumour and normal colonic mucosa tissues from CRC patients, which uncovered a possible mechanism of the role of microbiome in the carcinogenesis of CRC. In addition, these findings offer insight into potential new biomarkers, therapeutic and/or prevention strategies for CRC.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 17-06-2022
Abstract: The world’s coral reefs are experiencing increasing volatility in coral cover, largely because of anthropogenic environmental change, highlighting the need to understand how such volatility will influence the structure and dynamics of reef assemblages. These changes may influence not only richness or evenness but also the temporal stability of species’ relative abundances (temporal beta- ersity). Here, we analyzed reef fish assemblage time series from the Great Barrier Reef to show that, overall, 75% of the variance in abundance among species was attributable to persistent differences in species’ long-term mean abundances. However, the relative importance of stochastic fluctuations in abundance was higher on reefs that experienced greater volatility in coral cover, whereas it did not vary with drivers of alpha- ersity. These findings imply that increased coral cover volatility decreases temporal stability in relative abundances of fishes, a transformation that is not detectable from static measures of bio ersity.
Publisher: Elsevier BV
Date: 11-2020
Publisher: Springer Science and Business Media LLC
Date: 16-03-2020
DOI: 10.1186/S40168-020-00809-W
Abstract: Resident soil microbiota play key roles in sustaining the core ecosystem processes of terrestrial Antarctica, often involving unique taxa with novel functional traits. However, the full scope of bio ersity and the niche-neutral processes underlying these communities remain unclear. In this study, we combine multivariate analyses, co-occurrence networks and fitted species abundance distributions on an extensive set of bacterial, micro-eukaryote and archaeal licon sequencing data to unravel soil microbiome patterns of nine sites across two east Antarctic regions, the Vestfold Hills and Windmill Islands. To our knowledge, this is the first microbial bio ersity report on the hyperarid Vestfold Hills soil environment. Our findings reveal distinct regional differences in phylogenetic composition, abundance and richness amongst microbial taxa. Actinobacteria dominated soils in both regions, yet Bacteroidetes were more abundant in the Vestfold Hills compared to the Windmill Islands, which contained a high abundance of novel phyla. However, intra-region comparisons demonstrate greater homogeneity of soil microbial communities and measured environmental parameters between sites at the Vestfold Hills. Community richness is largely driven by a variable suite of parameters but robust associations between co-existing members highlight potential interactions and sharing of niche space by erse taxa from all three microbial domains of life examined. Overall, non-neutral processes appear to structure the polar soil microbiomes studied here, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. Eukaryotic and archaeal communities reveal weaker niche-driven signatures accompanied by multimodality, suggesting the emergence of neutrality. We provide new information on assemblage patterns, environmental drivers and non-random occurrences for Antarctic soil microbiomes, particularly the Vestfold Hills, where basic ersity, ecology and life history strategies of resident microbiota are largely unknown. Greater understanding of these basic ecological concepts is a pivotal step towards effective conservation management.
Publisher: Wiley
Date: 19-11-2019
DOI: 10.1002/ECY.2893
Abstract: The extent to which populations in nature are regulated by density-dependent processes is unresolved. While experiments increasingly find evidence of strong density dependence, unmanipulated population time series yield much more ambiguous evidence of regulation, especially when accounting for effects of observation error. Here, we reexamine the evidence for density dependence in time series of population sizes in nature, by conducting an aggregate analysis of the populations in the Global Population Dynamics Database (GPDD). First, following the conventional approach, we fit a density-dependent and a density-independent variant of the Gompertz state-space model to each time series. Then, we conduct an aggregate analysis of the entire database by considering two random-effects density-dependent models that leverage information across data sets. When in idual time series are tested independently, we find very little evidence for density dependence. However, in the aggregate, we find very strong evidence for density dependence, even though, paradoxically, estimated strengths of density dependence for in idual time series tend to be weaker than when each in idual time series is analyzed independently. Furthermore, a hierarchical model that accounts for taxonomic variation in the strength of density dependence reveals that density dependence is consistently stronger in insects and fish than in birds and mammals. Our findings resolve apparent inconsistencies between observational and experimental studies of density dependence by revealing that the observational record does indeed contain strong support for the hypothesis that density dependence is widespread in nature.
Publisher: Elsevier BV
Date: 2007
No related grants have been discovered for Loïc Thibaut.