Variation in ecology and evolutionary biology: from phenotypes to meta-analyses

Phenotypic variation is the heart of evolutionary biology. Getting to the heart of the matter requires statistical and computational tools. This thesis explores two diverse research streams that have flowed from one versatile tool — the multilevel model (also known as a mixed, or hierarchical, model). First, multilevel models can discern similarities and differences between individuals within the same population. Chapter 2 builds on previous research into individual differences in personality and plasticity, by incorporating individual differences in predictability. Through a conceptual guide and an empirical worked example, I show how measuring the integration of multiple aspects of phenotypic variation can better capture individuality. In Chapter 3, I use zebrafish (Danio rerio) as a study species to measure thermal developmental plasticity, and test a popular idea for the maintenance of integrated personality: pace of life syndrome. My results do not support the concept’s implied predictions, and the accumulation of other studies with weak evidence suggests a once bright flame has dimmed. Next, we turn to the second powerful use of multilevel models: aggregating multiple independent studies in a meta-analysis (a type of quantitative review of the literature) to answer, and generate, research questions. Using this technique, Chapter 4 finds that warm developmental temperatures generally increase phenotypic variance in fishes, but cool temperatures do not have the same effect. However, these patterns are highly variable, and we should not assume that meta-analyses always provide the definitive answer to a research question. To calibrate our confidence in the conclusions of any meta-analysis, we need to know how the review was conducted. In Chapter 5, I systematically assess the quality of reporting of meta-analysis in ecology and evolutionary biology publications, and report results from my survey of community attitudes towards reporting. I find both a need and a willingness to improve reporting quality. Chapter 6 provides a solution, with a checklist and guide to reporting for authors, reviewers, and editors of systematic reviews and meta-analyses. Overall, this thesis shows how multilevel models can be used for the study of phenotypic variation, and advocates for how we can better use these tools in the future

A century of limnological evolution and interactive threats in the Panama Canal: Long-term assessments from a shallow basin

Large tropical river dam projects are expected to accelerate over the forthcoming decades to satisfy growing demand for energy, irrigation and flood control. When tropical rivers are dammed the immediate impacts are relatively well studied, but the long-term (decades-centuries) consequences of impoundment remain poorly known. We combined historical records of water quality, river flow and climate with a multi-proxy (macrofossils, diatoms, biomarkers and trace elements) palaeoecological approach to reconstruct the limnological evolution of a shallow basin in Gatun Lake (Panama Canal, Panama) and assess the effects of multiple linked factors (river damming, forest flooding, deforestation, invasive species, pollution and hydro-climate) on the study area. Results show that a century after dam construction, species invasion, deforestation and salt intrusions have forced a gradual change in the study basin from a swamp-type environment towards a more saline lake-governed system of benthic–littoral production likely associated with the expansion of macrophyte stands. Hydrology still remains the most important long-term (decades) structural factor stimulating salinity intrusions, primary productivity, deposition of minerals, and reduction of water transparency during wet periods. During dry periods, physical-chemical conditions are in turn linked to clear water and aerobic conditions while nutrients shift to available forms for the aquatic biota in the detrital-rich reductive sediments. Our study suggests that to preserve the natural riverine system functioning of this area of the Panama Canal, management activities must address long-term ecosystem structural drivers such as river flow, runoff patterns and physical-chemical conditions

orchaRd 2.0 : an R package for visualising meta-analyses with orchard plots

1. Although meta-analysis has become an essential tool in ecology and evolution, reporting of meta-analytic results can still be much improved. To aid this, we have introduced the orchard plot, which presents not only overall estimates and their confidence intervals, but also shows corresponding heterogeneity (as prediction intervals) and individual effect sizes. 2. Here, we have added significant enhancements by integrating many new functionalities into orchaRd 2.0. This updated version allows the visualisation of heteroscedasticity (different variances across levels of a categorical moderator), marginal estimates (e.g. marginalising out effects other than the one visualised), conditional estimates (i.e. estimates of different groups conditioned upon specific values of a continuous variable) and visualisations of all types of interactions between two categorical/continuous moderators. 3. orchaRd 2.0 has additional functions which calculate key statistics from multilevel meta-analytic models such as $I^{2}$ and $R^{2}$. Importantly, orchaRd 2.0 contributes to better reporting by complying with PRISMA-EcoEvo (preferred reporting items for systematic reviews and meta-analyses in ecology and evolution). Taken together, orchaRd 2.0 can improve the presentation of meta-analytic results and facilitate the exploration of previously neglected patterns. 4. In addition, as a part of a literature survey, we found that graphical packages are rarely cited (~3%). We plea that researchers credit developers and maintainers of graphical packages, for example, by citations in a figure legend, acknowledging the use of relevant packages

Price of anarchy on heterogeneous traffic-flow networks

The efficiency of routing traffic through a network, comprising nodes connected by links whose cost of traversal is either fixed or varies in proportion to volume of usage, can be measured by the `price of anarchy'. This is the ratio of the cost incurred by agents who act to minimise their individual expenditure to the optimal cost borne by the entire system. As the total traffic load and the network variability - parameterised by the proportion of variable-cost links in the network - changes, the behaviours that the system presents can be understood with the introduction of a network of simpler structure. This is constructed from classes of non-overlapping paths connecting source to destination nodes that are characterised by the number of variable-cost edges they contain. It is shown that localised peaks in the price of anarchy occur at critical traffic volumes at which it becomes beneficial to exploit ostensibly more expensive paths as the network becomes more congested. Simulation results verifying these findings are presented for the variation of the price of anarchy with the network's size, aspect-ratio, variability and traffic load

Mercury Pollution History in Tropical and Subtropical American Lakes: Multiple Impacts and the Possible Relationship with Climate Change

Sediment cores obtained from 11 tropical and subtropical American lakes revealed that local human activities significantly increased mercury (Hg) inputs and pollution levels. Remote lakes also have been contaminated by anthropogenic Hg through atmospheric depositions. Long-term sediment-core profiles revealed an approximately 3-fold increase in Hg fluxes to sediments from c. 1850 to 2000. Generalized additive models indicate that c. 3-fold increases in Hg fluxes also occurred since 2000 in the remote sites, while Hg emissions from anthropogenic sources have remained relatively stable. The tropical and subtropical Americas are vulnerable to extreme weather events. Air temperatures in this region have shown a marked increase since the 1990s, and extreme weather events arising from climate change have increased. When comparing Hg fluxes to recent (1950-2016) climatic changes, results show marked increases in Hg fluxes to sediments during dry periods. The Standardized Precipitation-Evapotranspiration Index (SPEI) time series indicate a tendency toward more extreme drier conditions across the study region since the mid-1990s, suggesting that instabilities in catchment surfaces caused by climate change are responsible for the elevated Hg flux rates. Drier conditions since c. 2000 appear to be promoting Hg fluxes from catchments to lakes, a process that will likely be exacerbated under future climate-change scenarios

A randomised controlled trial of a relationship-focussed mobile phone application for improving adolescents' mental health

Background: This study evaluated the acceptability and effectiveness of a relationship-focussed mobile phone application (WeClick) for improving depressive symptoms and other mental health outcomes in adolescents. Methods: A randomised controlled trial involving 193 youth (M age: 14.82, SD: 0.94, 86.5% female) from Australia was conducted. Youth were recruited via the Internet and randomly allocated to the intervention or a 4-week wait list control condition, stratified for age and gender. The primary outcome was change in depressive symptom scores measured using the Patient Health Questionnaire for Adolescents (PHQ-A) at baseline, 4-week post-test and 12-week follow-up. Secondary outcomes included anxiety, psychological distress, wellbeing, help-seeking intentions for mental health, social self-efficacy and social support. Participants in the intervention condition received access to the intervention for four weeks. Thematic analysis was utilised to identify and examine acceptability. Results: The change in PHQ-A scores from baseline to 4-week post-test did not differ significantly (d = 0.26, p = .138) between the intervention (Mchange = 2.9, SD = 5.3) and wait list control conditions (Mchange = 1.7, SD = 4.3). However, significant between-group improvements were observed in wellbeing (d = 0.37, p = .023), help-seeking intentions (d = 0.36, p = .016) and professional help-seeking intentions for mental health problems (d = 0.36, p = .008). Increases in help-seeking intentions were sustained at follow-up in the intervention condition. No differential effects were found for generalised anxiety, separation anxiety, social self-efficacy or for any social support outcomes. Over 90% of participants indicated the app was enjoyable, interesting and easy to use. The app provided ‘advice and direction’ (n = 42; 46.15%), an ‘opportunity for self-reflection’ (n = 33; 36.3%) and ‘normalised experiences’ (n = 21; 23.1%). Conclusions: The WeClick app was found to be effective for improving wellbeing and help-seeking intentions for mental health in adolescents. A larger, adequately powered trial is now required to establish differential effects on depressive symptoms. This trial was registered with the Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12618001982202. Keywords: Adolescence; depression; mental health; e-health; relationships.P.J.B. is supported by NHMRC Fellowship 1158707. A.L.C. is supported by NHMRC Fellowship 1122544. A.W-S. is supported by a NSW Health Early Career Fellowship. H.C. is supported by NHMRC Fellowship 1155614

Development and preliminary validation of the 'Caring for Country' questionnaire: measurement of an Indigenous Australian health determinant

<p>Abstract</p> <p>Background</p> <p>'Caring for Country' is defined as Indigenous participation in interrelated activities with the objective of promoting ecological and human health. Ecological services on Indigenous-owned lands are belatedly attracting some institutional investment. However, the health outcomes associated with Indigenous participation in 'caring for country' activities have never been investigated. The aims of this study were to pilot and validate a questionnaire measuring caring for country as an Indigenous health determinant and to relate it to an external reference, obesity.</p> <p>Methods</p> <p>Purposively sampled participants were 301 Indigenous adults aged 15 to 54 years, recruited during a cross-sectional program of preventive health checks in a remote Australian community. Questionnaire validation was undertaken with psychometric tests of internal consistency, reliability, exploratory factor analysis and confirmatory one-factor congeneric modelling. Accurate item weightings were derived from the model and used to create a single weighted composite score for caring for country. Multiple linear regression modelling was used to test associations between the caring for country score and body mass index adjusting for socio-demographic factors and health behaviours.</p> <p>Results</p> <p>The questionnaire demonstrated adequate internal consistency, test-retest validity and proxy-respondent validity. Exploratory factor analysis of the 'caring for country' items produced a single factor solution that was confirmed via one-factor congeneric modelling. A significant and substantial association between greater participation in caring for country activities and lower body mass index was demonstrated. Adjusting for socio-demographic factors and health behaviours, an inter-quartile range rise in caring for country scores was associated with 6.1 Kg and 5.3 Kg less body weight for non-pregnant women and men respectively.</p> <p>Conclusion</p> <p>This study indicates preliminary support for the validity of the caring for country concept and a questionnaire designed to measure it. This study also highlights the importance of investigating Indigenous-asserted health promotion activities. Further studies in similar populations are merited to test the generalisability of this questionnaire and to explore associations with other important Indigenous health outcomes.</p

Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations

The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations

First Measurement of the Hubble Constant from a Dark Standard Siren using the Dark Energy Survey Galaxies and the LIGO/Virgo Binary-Black-hole Merger GW170814

We present a multi-messenger measurement of the Hubble constant H 0 using the binary–black-hole merger GW170814 as a standard siren, combined with a photometric redshift catalog from the Dark Energy Survey (DES). The luminosity distance is obtained from the gravitational wave signal detected by the Laser Interferometer Gravitational-Wave Observatory (LIGO)/Virgo Collaboration (LVC) on 2017 August 14, and the redshift information is provided by the DES Year 3 data. Black hole mergers such as GW170814 are expected to lack bright electromagnetic emission to uniquely identify their host galaxies and build an object-by-object Hubble diagram. However, they are suitable for a statistical measurement, provided that a galaxy catalog of adequate depth and redshift completion is available. Here we present the first Hubble parameter measurement using a black hole merger. Our analysis results in ${H}_{0}={75}_{-32}^{+40}\,\mathrm{km}\,{{\rm{s}}}^{-1}\,{\mathrm{Mpc}}^{-1}$, which is consistent with both SN Ia and cosmic microwave background measurements of the Hubble constant. The quoted 68% credible region comprises 60% of the uniform prior range [20, 140] km s−1 Mpc−1, and it depends on the assumed prior range. If we take a broader prior of [10, 220] km s−1 Mpc−1, we find {H}_{0 {78}_{-24}^{+96}\,\mathrm{km}\,{{\rm{s}}}^{-1}\,{\mathrm{Mpc}}^{-1} (57% of the prior range). Although a weak constraint on the Hubble constant from a single event is expected using the dark siren method, a multifold increase in the LVC event rate is anticipated in the coming years and combinations of many sirens will lead to improved constraints on H 0