Plastic and Genetic Determination of Population, Community, and Ecosystem Properties in Freshwater Environments

The hierarchy of biological organization, from molecules to ecosystems, describes the relationships among various biological systems. Of particular interest is assessing how the factors that primarily determine the nature of one hierarchical level also have transcendent qualities that affect the ecology and evolution of higher hierarchical levels. The goal of this dissertation was to use a bottom-up approach to examine the transcendent effects of two factors that strongly determine the nature of their associated level of biological organization. The first, phenotypic plasticity, is a primary factor that determines the phenotype of an individual. The second factor, genetic diversity, largely determines the phenotypic distributions associated with populations. Controlled laboratory experiments on taxa from a freshwater tri-trophic food web were employed to examine the transcendent effects of phenotypic plasticity and genetic diversity on the biological hierarchy because relationships between individuals and populations from different trophic levels are well documented for numerous freshwater species. The results show that phenotypic plasticity can induce changes in population means and variances that promote population persistence and evolvability, and that plasticity provides a mechanistic explanation of community stability in response to changing environments. Similarly, genetic diversity may act as a signal that induces phenotypic plasticity in individuals, modulates community richness and ecosystem properties, and suggests a potential mechanism for the changes in biodiversity. Thus, results from this dissertation show that plasticity and genetic variation can shape the attributes of other biological groups higher in the biological hierarchy, and, in some cases, may also provide a mechanistic explanation for variability observed in higher levels of the biological hierarchy. These results highlight the importance of integrating traditionally disparate biological disciplines and may help to unify biology as a field

Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. Conclusions: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory

Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence

BACKGROUND: Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native zooplankton populations to the introduction of non-native salmonids in alpine lakes in the Sierra Nevada of California, USA. We compared morphological and life-history traits in populations of Daphnia with a known history of introduced salmonids and populations that have no history of salmonid introductions. RESULTS: Our results show that Daphnia populations co-existing with fish have undergone rapid adaptive reductions in body size and in the timing of reproduction. Size-related traits decreased by up to 13 percent in response to introduced fish. Rates of evolutionary change are as high as 4,238 darwins (0.036 haldanes). CONCLUSION: Species introductions into aquatic habitats can dramatically alter the selective environment of native species leading to a rapid evolutionary response. Knowledge of the rates and limits of adaptation is an important component of understanding the long-term effects of alterations in the species composition of communities. We discuss the evolutionary consequences of species introductions and compare the rate of evolution observed in the Sierra Nevada Daphnia to published estimates of evolutionary change in ecological timescales

Endogenous ROS levels in C. elegans under exogenous stress support revision of oxidative stress theory of life-history tradeoffs

BACKGROUND: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. RESULTS: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. CONCLUSIONS: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory.Keywords: Aging, Lifespan, Fitness, Free radicals, Resource allocatio

Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities

We are grateful to David Naftz and the United States Geological Survey for access to sampling sites, Chris Garrard and Robert Baskin for geospatial images, and Ethan White for statistical input.Conceived and designed the experiments: JJP GR MEP BCW. Performed the experiments: JJP GR JDVN. Analyzed the data: JJP LCL MEP JDVN BG. Contributed reagents/materials/analysis tools: JJP GR LCL MEP JDVN ZH JZ GLA BCW. Wrote the paper: JJP MEP PC BCW.BackgroundHorizontal gene transfer (HGT) plays a major role in speciation and evolution of bacteria and archaea by controlling gene distribution within an environment. However, information that links HGT to a natural community using relevant population-genetics parameters and spatial considerations is scarce. The Great Salt Lake (Utah, USA) provides an excellent model for studying HGT in the context of biogeography because it is a contiguous system with dispersal limitations due to a strong selective salinity gradient. We hypothesize that in spite of the barrier to phylogenetic dispersal, functional characteristics—in the form of HGT—expand beyond phylogenetic limitations due to selective pressure.Methodology and ResultsTo assay the functional genes and microorganisms throughout the GSL, we used a 16S rRNA oligonucleotide microarray (Phylochip) and a functional gene array (GeoChip) to measure biogeographic patterns of nine microbial communities. We found a significant difference in biogeography based on microarray analyses when comparing Sørensen similarity values for presence/absence of function and phylogeny (Student's t-test; p = 0.005).Conclusion and SignificanceBiogeographic patterns exhibit behavior associated with horizontal gene transfer in that informational genes (16S rRNA) have a lower similarity than functional genes, and functional similarity is positively correlated with lake-wide selective pressure. Specifically, high concentrations of chromium throughout GSL correspond to an average similarity of chromium resistance genes that is 22% higher than taxonomic similarity. This suggests active HGT may be measured at the population level in microbial communities and these biogeographic patterns may serve as a model to study bacteria adaptation and speciation.Yeshttp://www.plosone.org/static/editorial#pee

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

© 2020 The Authors. Published by BMC. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1186/s12862-020-01673-wBackground Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65–62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles. Results Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations. Conclusions Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.Funding for this research was provided by two grants from the National Science Foundation (BSR 88–17453, BSR 90–24505) [funding for fieldwork and lab work], two grants from the National Geographic Society (Grants 1977: 1633, 1743) [funding for fieldwork], three grants from the University of Michigan Office of the Vice President for Research, and a Research Partnership Award from the University of Michigan to RAN [morphology work]; a joint NHM-UCL IMPACT studentship [to fund STM’s PhD, lab work and fieldwork], Mohamed Bin Zayed Species Conservation Fund [funding for fieldwork] and Systematics Research Fund [funding for fieldwork] to STM; an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under Grant #P20GM103408 to LL [funding for lab work]; a NERC/BBSRC SynTax grant [funding for fieldwork and collaboration], and Darwin Initiative (grant 19–002) [funding for fieldwork, lab work and capacity building] with partners Bristol University, Islands Conservation Society, Seychelles Islands Foundation, Seychelles Ministry of Environment, Seychelles National Parks Authority, Seychelles Natural History Museum, University of Kent, Zoological Society of London to MW, DJG, JJD. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.Published onlin

The Utility of Curcumin as a Regenerative Aid in the Invertebrate Amphioxus

The invertebrate amphioxus obtain the ability to regenerate their posterior tail end after damage or loss. To increase this rate of regeneration, the chemical compound curcumin was added to the experimental tank as it contains anti-microbial, anti-inflammatory, and wound healing properties. For 4 weeks, 6 individuals in the control tank and 6 individuals in the curcumin tank were maintained at proper salinity and temperature, fed every 3 days, and photographed every 7 days to track growth. The results indicated there was no significant difference in growth between control and experimental groups, however trends of a higher mean growth can be seen in the experimental group

Ecologically Driven Genetic Variation in \u3cem\u3eDaphnia magna\u3c/em\u3e Swimming Behavior

In recent years, interest has grown in the neurobiology of organisms. Though the nervous system of D. magna is less complex than vertebrate nervous systems, studies have revealed D. magna share several neurotransmitters, and related gene pathways, with vertebrates. The purpose of this study is to examine the individual swimming behavior of four unique D. magna genotypes from three ecologically unique environments. This study provides evidence for variation in behavior across genotypes due to ecologically driven genetic differences

The Effects of Cigarette Smoke on Lung Microbiota

Smoking is known to cause adverse effects in the lungs. At the cellular and tissue level smokers experience oxidative stress and chronic inflammation leading to mutations and cancer. While the adverse effects of smoking on tissues of the respiratory system are well documented, little is known about the effects of smoking on the microbiota associated with the respiratory system. Indeed, very little is known about the microbes that normally reside in the lungs, or how microbial communities are altered in individuals with a compromised respiratory system, such as through smoking. In this experiment, a common lung microbe, Streptococcus pneumoniae, was grown on smoke-infused tryptic soy broth along with normal tryptic soy broth. The main findings indicate that the common lung microbe S. pneumoniae grows faster on the smoke-infused media with an average r-value of 2.66, while the control media had an average r-value of 1.72 in a set of 2 trials. These findings give insight into how the lung microbiota, specifically S. pneumoniae are reacting to smoke inhalation. Looking furher, the knowledge gained by this experiment may prompt further research into why S. pneumoniae’s growth is accelerated by smoke along with other lung microbes that may have similar reactions

Interspecific Interactions Between \u3cem\u3ePasser domesticus\u3c/em\u3e and \u3cem\u3eHaemorhous mexicanus\u3c/em\u3e

We are looking at the interspecific interactions between the two bird species Passer domesticus and Haemorhous mexicanus. Previous research shows that P. domesticus and H. mexicanus are aggressive towards each other in the eastern part of the United States where they are both invasive, with H. mexicanus being the most dominant species. We are looking at the interactions over in the Western United States where P. domesticus is invasive and H. mexicanus is native, to see if their interactions differ from those of the east. This can give us a better insight into how invasive species interact with native species in the environment, and how much of an affect those invasive species can have on the environment as a whole