Interplays of a waterborne disease model linking within- and between- host dynamics with waning vaccine-induced immunity

In this paper, we propose a multi-scale waterborne disease model and are concerned with a heterogenous process of waning vaccine-induced immunity. A completely nested rule has been adopted to link the within- and between-host systems. We prove the existence, positivity and asymptotical smoothness of the between-host system. We derive the basic reproduction numbers associated with the two-scale system in explicit forms, which completely determine the behavior of each system. Uncertainty analysis reveals the trade-offs of the kinetics of the within-host system and the transmission of the between-host system. Numerical simulations suggest that the vaccine waning process plays a significant role in the estimation of the prevalence at population level. Furthermore, the environmental heterogeneity complicates the transmission patterns at the population level.

Subtle East–West Phylogeographic Break of Asteropyrum (Ranunculaceae) in Subtropical China and Adjacent Areas

East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, we estimated the divergence time of Asteropyrum populations through coalescent-based approaches based on DNA sequences of ten nuclear loci and evaluated the contribution of environmental heterogeneity to population differentiation. The results showed that there were two chloroplast clades and nuclear groups within Asteropyrum, displaying a subtle pattern of east–west differentiation. The divergence time of the two nuclear groups was dated to ~1.2 Ma, which is associated with climate changes during the Mid-Pleistocene transition. A genetic admixture event between the two genetic groups happened at ~0.46 Ma, resulting in several admixed populations. Isolation by environmental distance (IBE) explained the majority (46.32%) of population differentiation, but that isolation by geographic distance (IBD) only contributed 4.66%. The results of this study suggest that climate changes during the Pleistocene may be a major cause for the east–west phylogeographic break in subtropical China. However, the complex terrain and high environmental heterogeneity in the west of subtropical China (and adjacent regions such as the Hengduan Mountains and the Himalayan Moutains) caused by strong geological uplift may have profoundly shaped the population structure of plant species in subtropical China.

Synchrony and idiosyncrasy in the gut microbiome of wild primates

Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in diets, environments, and medications, but it could also emerge from fundamental ecological forces that shape primate microbiota more generally. Here we leverage extensive gut microbiome time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, we find strong evidence for idiosyncrasy. Over time, samples from the same baboon were much more similar than samples from different baboons, and host-specific factors collectively explained 30% of the deviance in microbiome dynamics, compared to just 3% for factors shared across hosts. Hence, individualization may be common to mammalian gut microbiota, and designing universal microbiome interventions may face challenges beyond heterogeneity in human lifestyles.

Comparison of Ostracoda (Crustacea) species composition between lakes and streams at high elevations in Turkey

Ostracods are one of the most suitable organisms because of their ecological and morphological preferences for habitat types to study the diversity between streams and lakes. Here, 24 streams and 16 lakes were sampled in 2019 to evaluate the species compositions between streams and lakes. Environmental heterogeneity in the sense of the physico-chemical variables was found among the habitats. 24 of the 29 species with 923 individuals were found in the lakes when 13 species with 898 individuals were found in the streams. Eight species were common in both habitat types. Species contributing about 70.81% to the significant differences in the species composition between the habitats showed cosmopolitan characteristics. Species variation among the replicates of lakes were higher than streams. Results indicated that the species composition was probably associated to dissolved oxygen in lakes, while electrical conductivity in streams. Relationship amid elevational range and ostracod species richness was negative in lakes when there was no clear relationship in the streams. Overall, results suggested that determination of influential regional factors in different aquatic bodies can provide important contributions to the estimation of which habitat types can be chosen by species, and the using of species as bioindicators.

A Quantitative Assessment of Ra'ui (a Traditional Approach to Marine Protected Areas) on the Fishes and Invertebrates of Rarotonga, Cook Islands

<p>Ra'ui (traditional marine managed areas) in Rarotonga, Cook Islands, are a form of marine protected area re-implemented in the late 1990s when communities became concerned about declining fish and invertebrate stocks in the lagoon. In this thesis I quantified the effects of Ra'ui on fish and invertebrates. First, for a single focal species of abundant reef fish (Ctenochaetus striatus), I developed a novel framework to incorporate environmental heterogeneity into a Control-Impact assessment of Ra'ui effectiveness using an index of habitat selectivity (Manly's alpha) to 'adjust' the density of a reef fish by 'preferred' substrates. My results empirically demonstrated that substrate heterogeneity impinged upon the interpretation of MPA effects. This suggests that habitat heterogeneity should be quantitatively incorporated into analyses of MPA effects to provide a more robust and defensible set of inferences. The novel framework was then used to assess the effects of Ra'ui on densities of other common reef fish and invertebrates, as well as fish functional groups. Averaged across all Ra'ui, a higher percentage of the invertebrate species (20%) had greater abundances inside Ra'ui relative to corresponding Control sites than fish species (15%). This may suggest spatial management is more effective for sessile organisms such as the invertebrates in this study. Even when environmental heterogeneity was 'controlled' in my analyses, responses to Ra'ui were variable between species and sites, illustrating that factors other than environmental heterogeneity may be driving varying patterns of species abundances. However, for the broad-scale functional groups, there were indications of inverse relationships between predator and prey functional groups at 3 of the Ra'ui. I applied meta-analytical techniques to my data to assess whether there was an island-wide effect of Ra'ui on the densities of fish and invertebrate species, and functional groups. There was no evidence in the metaanalyses for an island-wide Ra'ui effect for any species or functional groups. However, analysis of covariance suggested there was an island-wide Ra'ui effect for a number of fish and invertebrate species. The body size of fish and invertebrates is another metric of MPA effectiveness that is expected to increase with protection. However, in determining an island-wide effect of Ra'ui on size, only two fish species, Mulloidichthys flavolineatus and Stegastes nigricans, had greater mean size in Ra'ui relative to Control sites, and Siganus argenteus was the only reef fish to exhibit greater maximum size in the Ra'ui. Two of the lagoon invertebrates (Echinometra mathaei and Tripneustes gratilla) and three of the reefcrest invertebrates (Echinothrix diadema, Echinometra oblonga, and Trochus niloticus) exhibited an island-wide positive response to Ra'ui for mean size. At individual Ra'ui sites, a number of invertebrates had greater mean and maximum size. Further, at individual sites, M. flavolineatus had greater mean size across the most Ra'ui (4 sites), again indicating that the site fidelity of a species may influence its response to protection. Ontogenetic shifts in habitat use are known to occur in fish and invertebrates. For five fish species, juveniles used habitat differently to adults of the same species. Further, of the five species, only densities of both juvenile and adult Acanthurus triostegus exhibited a positive relationship with the proportion of their preferred habitat (juveniles: r2 = 0.44, p = 0.011; adults: r2 = 0.46, p = 0.009). Densities of adult Ctenochaetus striatus also increased linearly with the proportion of preferred substrate cover (r2 = 0.43, p = 0.035). These results suggest that habitat within an MPA may be limiting for different benthic stages of an organism's ontogeny. Some knowledge of the characteristics that underpin MPA effectiveness can aid in their design. Using commonly occurring fish and invertebrate species, I explored the effectiveness of individual Ra'ui using three separate metrics of effectiveness (the proportion of fish and invertebrates exhibiting 1) greater densities, 2) greater mean size, and 3) greater maximum size in Ra'ui relative to Control sites. Ra'ui area and total fish density in each Ra'ui were characteristics that best described the effectiveness of Ra'ui in enhancing mean fish and invertebrate size. The level of compliance with Ra'ui may also have some impact on Ra'ui effectiveness. This study highlights the importance of incorporating environmental heterogeneity into assessments of MPA effects. Further, temporary prohibitions such as Ra'ui may be more effective for some species if certain conditions are met e.g., compliance is good, and the species Ra'ui are protecting / enhancing have high site-fidelity and high growth rates. These findings provide important information for fisheries and conservation managers (e.g., traditional leaders, governmental agencies, non-governmental agencies, communities) that will aid in better design of monitoring programmes and facilitate improved MPA design, not only in the Pacific region, but worldwide.</p>

A Quantitative Assessment of Ra'ui (a Traditional Approach to Marine Protected Areas) on the Fishes and Invertebrates of Rarotonga, Cook Islands

<p>Ra'ui (traditional marine managed areas) in Rarotonga, Cook Islands, are a form of marine protected area re-implemented in the late 1990s when communities became concerned about declining fish and invertebrate stocks in the lagoon. In this thesis I quantified the effects of Ra'ui on fish and invertebrates. First, for a single focal species of abundant reef fish (Ctenochaetus striatus), I developed a novel framework to incorporate environmental heterogeneity into a Control-Impact assessment of Ra'ui effectiveness using an index of habitat selectivity (Manly's alpha) to 'adjust' the density of a reef fish by 'preferred' substrates. My results empirically demonstrated that substrate heterogeneity impinged upon the interpretation of MPA effects. This suggests that habitat heterogeneity should be quantitatively incorporated into analyses of MPA effects to provide a more robust and defensible set of inferences. The novel framework was then used to assess the effects of Ra'ui on densities of other common reef fish and invertebrates, as well as fish functional groups. Averaged across all Ra'ui, a higher percentage of the invertebrate species (20%) had greater abundances inside Ra'ui relative to corresponding Control sites than fish species (15%). This may suggest spatial management is more effective for sessile organisms such as the invertebrates in this study. Even when environmental heterogeneity was 'controlled' in my analyses, responses to Ra'ui were variable between species and sites, illustrating that factors other than environmental heterogeneity may be driving varying patterns of species abundances. However, for the broad-scale functional groups, there were indications of inverse relationships between predator and prey functional groups at 3 of the Ra'ui. I applied meta-analytical techniques to my data to assess whether there was an island-wide effect of Ra'ui on the densities of fish and invertebrate species, and functional groups. There was no evidence in the metaanalyses for an island-wide Ra'ui effect for any species or functional groups. However, analysis of covariance suggested there was an island-wide Ra'ui effect for a number of fish and invertebrate species. The body size of fish and invertebrates is another metric of MPA effectiveness that is expected to increase with protection. However, in determining an island-wide effect of Ra'ui on size, only two fish species, Mulloidichthys flavolineatus and Stegastes nigricans, had greater mean size in Ra'ui relative to Control sites, and Siganus argenteus was the only reef fish to exhibit greater maximum size in the Ra'ui. Two of the lagoon invertebrates (Echinometra mathaei and Tripneustes gratilla) and three of the reefcrest invertebrates (Echinothrix diadema, Echinometra oblonga, and Trochus niloticus) exhibited an island-wide positive response to Ra'ui for mean size. At individual Ra'ui sites, a number of invertebrates had greater mean and maximum size. Further, at individual sites, M. flavolineatus had greater mean size across the most Ra'ui (4 sites), again indicating that the site fidelity of a species may influence its response to protection. Ontogenetic shifts in habitat use are known to occur in fish and invertebrates. For five fish species, juveniles used habitat differently to adults of the same species. Further, of the five species, only densities of both juvenile and adult Acanthurus triostegus exhibited a positive relationship with the proportion of their preferred habitat (juveniles: r2 = 0.44, p = 0.011; adults: r2 = 0.46, p = 0.009). Densities of adult Ctenochaetus striatus also increased linearly with the proportion of preferred substrate cover (r2 = 0.43, p = 0.035). These results suggest that habitat within an MPA may be limiting for different benthic stages of an organism's ontogeny. Some knowledge of the characteristics that underpin MPA effectiveness can aid in their design. Using commonly occurring fish and invertebrate species, I explored the effectiveness of individual Ra'ui using three separate metrics of effectiveness (the proportion of fish and invertebrates exhibiting 1) greater densities, 2) greater mean size, and 3) greater maximum size in Ra'ui relative to Control sites. Ra'ui area and total fish density in each Ra'ui were characteristics that best described the effectiveness of Ra'ui in enhancing mean fish and invertebrate size. The level of compliance with Ra'ui may also have some impact on Ra'ui effectiveness. This study highlights the importance of incorporating environmental heterogeneity into assessments of MPA effects. Further, temporary prohibitions such as Ra'ui may be more effective for some species if certain conditions are met e.g., compliance is good, and the species Ra'ui are protecting / enhancing have high site-fidelity and high growth rates. These findings provide important information for fisheries and conservation managers (e.g., traditional leaders, governmental agencies, non-governmental agencies, communities) that will aid in better design of monitoring programmes and facilitate improved MPA design, not only in the Pacific region, but worldwide.</p>