So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Statistics for Spatial Data.

In this book, Andrew Harvey sets out to provide a unified and comprehensive theory of structural time series models. Unlike the traditional ARIMA models, structural time series models consist explicitly of unobserved components, such as trends and seasonals, which have a direct interpretation. As a result the model selection methodology associated with structural models is much closer to econometric methodology. The link with econometrics is made even closer by the natural way in which the models can be extended to include explanatory variables and to cope with multivariate time series. From the technical point of view, state space models and the Kalman filter play a key role in the statistical treatment of structural time series models. The book includes a detailed treatment of the Kalman filter. This technique was originally developed in control engineering, but is becoming increasingly important in fields such as economics and operations research. This book is concerned primarily with modelling economic and social time series, and with addressing the special problems which the treatment of such series poses. The properties of the models and the methodological techniques used to select them are illustrated with various applications. These range from the modellling of trends and cycles in US macroeconomic time series to to an evaluation of the effects of seat belt legislation in the UK.

Forecasting, Structural Time Series Models and the Kalman Filter

Genetics and analysis of quantitative traits

Microplastics in freshwater systems: A review of the emerging threats, identification of knowledge gaps and prioritisation of research needs

Lakes are complex ecosystems composed of distinct habitats coupled by biological, physical and chemical processes. While the ecological and evolutionary characteristics of aquatic organisms reflect habitat coupling in lakes, aquatic ecology has largely studied pelagic, benthic and riparian habitats in isolation from each other. Here, we summarize several ecological and evolutionary patterns that highlight the importance of habitat coupling and discuss their implications for understanding ecosystem processes in lakes. We pay special attention to fishes because they play particularly important roles as habitat couplers as a result of their high mobility and flexible foraging tactics that lead to inter-habitat omnivory. Habitat coupling has important consequences for nutrient cycling, predator-prey interactions, and food web structure and stability. For example, nutrient excretion by benthivorous consumers can account for a substantial fraction of inputs to pelagic nutrient cycles. Benthic resources also subsidize carnivore populations that have important predatory effects on plankton communities. These benthic subsidies stabilize population dynamics of pelagic carnivores and intensify the strength of their interactions with planktonic food webs. Furthermore, anthropogenic disturbances such as eutrophication, habitat modification, and exotic species introductions may severely alter habitat connections and, therefore, the fundamental flows of nutrients and energy in lake ecosystems.

/pdf/habitat-coupling-in-lake-ecosystems-4a85r6qxn4.pdf

Habitat coupling in lake ecosystems

One of the most spectacular phenomena in nature is the annual return of millions of salmon to spawn in their natal streams and lakes along the Pacific coast of North America The salmon die after spawning, and the nutrients and energy in their bodies, derived almost entirely from marine sources, are deposited in the freshwater ecosystems This represents a vital input to the ecosystems used as spawning grounds Salmon-derived nutrients make up a substantial fraction of the plants and animals in aquatic and terrestrial habitats associated with healthy salmon populations The decline of salmon numbers throughout much of their southern range in North America has prompted concern that the elimination of this “conveyor belt” of nutrients and energy may fundamentally change the productivity of these coastal freshwater and terrestrial ecosystems, and consequently their ability to support wildlife, including salmon If progress is to be made towards understanding and conserving the connection between migratory sa

Pacific salmon and the ecology of coastal ecosystems

Diel vertical migration (DVM) is a widespread phenomenon in aquatic organisms, yet the adaptive significance of this behavior is still unclear. In particular, diel vertical migration by juvenile sockeye salmon (Oncorhynchus nerka) has received considerable attention. We studied how changes in the light environment affect juvenile sockeye DVM in Alaskan lakes through changes in foraging rates and predation risk. Using hydroacoustics to track temporal changes in fish distribution, we found clear patterns of DVM and a strong, significant correlation between the mean depth of the sockeye and the amount of light at the lake surface. However, we could not detect diel changes in the depth distribution of fish large enough to be sockeye predators. Given a lack of diel vertical migration in the zooplankton community, it appears that juvenile sockeye were not simply tracking their food supply. Calculations of the in situ light experienced by individual juvenile sockeye suggested that they migrate to maintain a constant light environment. This light environment allowed the sockeye to exploit an antipredation window whereby they could forage on zooplankton while reducing the odds of visual detection by their predators. Furthermore, this antipredation window was continuous in early summer, but was split into two discrete time periods during the crepuscular hours in late summer. These data support the hypothesis that changes in habitat use by juvenile sockeye salmon reflect a dynamic strategy to minimize the ratio of predation risk to foraging gain that changes dramatically over the course of diel cycles in pelagic ecosystems.

Diel vertical migration by juvenile sockeye salmon: empirical evidence for the antipredation window

Detecting and forecasting the effects of changing climate on natural and exploited populations represent a major challenge to ecologists and resource managers. These efforts are complicated by underlying density-dependent processes and the differ- ential responses of predators and their prey to changing climate. We explored the effects of density-dependence and changing climate on growth of juvenile sockeye salmon and the densities of their zooplankton prey in the Wood River system of southwestern Alaska. We fit dynamic time-series models to data collected between 1962 and 2002 describing growth of juvenile sockeye, timing of spring ice breakup, and summer zooplankton densities. The timing of spring breakup has moved about seven days earlier now than it was in the early 1960s. Our analyses suggest that most of this shift has been a response to the warm phase of the Pacific Decadal Oscillation that persisted from the mid-1970s to the late 1990s. This progression toward earlier spring breakup dates was associated with warmer summer water temperatures and increased zooplankton (especially Daphnia) densities, which translated into increased sockeye growth during their first year of life. The number of spawning adults that produced each year class of sockeye had a strong negative effect on juvenile sockeye growth rates, so that the size of the density-dependent effect was, on average, twice as large as the effect of spring breakup date. These results highlight the complexity of eco- logical responses to changing climate and suggest that climate warming may enhance growing conditions for juvenile salmonids in large lakes of Alaska.

/pdf/effects-of-changing-climate-on-zooplankton-and-juvenile-4sk1w326hw.pdf

Effects of changing climate on zooplankton and juvenile sockeye salmon growth in southwestern alaska

Summary


1.  Migration timing in animals has important effects on life-history transitions. Human activities can alter migration timing of animals, and understanding the effects of such disruptions remains an important goal for applied ecology. Anadromous Pacific salmon (Oncorhynchus spp.) inhabit fresh water as juveniles before migrating to the ocean where they gain >90% of their biomass before returning to fresh water as adults to reproduce. Although construction of dams has delayed juvenile migration for many populations, we currently lack a synthesis of patterns in migration timing and how they relate to subsequent survival to adulthood for Pacific salmon, especially for at-risk populations.



2.  We studied two groups of Pacific salmon from the Columbia River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We examined how the proportion of juveniles surviving to return as adults varied with year of migration, date of arrival in the estuary, water temperature and coastal ocean upwelling using data from over 40 000 individually tagged Chinook salmon Oncorhynchus tshawytscha and steelhead Oncorhynchus mykiss.



3.  In general, models with year, day and day2 had much better support from the data than those with temperature and upwelling. For Chinook salmon, we also found a residual effect of temperature after controlling for day, but the effect was small for steelhead.



4.  For both species, juveniles migrating from early to mid-May survived 4–50 times greater than those migrating in mid-June. As expected, however, the estimated peak in survival varied among years, presumably reflecting interannual variation in the nearshore physical environment and trophic dynamics that affect salmon during the critical juvenile life stage.



5.  Synthesis and applications. Our results indicate a possible management objective would be to speed arrival to the estuary by increasing springtime river flows. These findings also provide some insight into the mechanisms underlying seasonal differences in survival patterns, but additional studies are needed to better resolve the issue. Future changes to river flow and water temperature associated with climate change and human activities may further alter migration timing, and thus this phenomenon deserves further attention.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2664.2009.01693.x

Mark D. Scheuerell

Papers

Habitat coupling in lake ecosystems

Pacific salmon and the ecology of coastal ecosystems

Diel vertical migration by juvenile sockeye salmon: empirical evidence for the antipredation window

Effects of changing climate on zooplankton and juvenile sockeye salmon growth in southwestern alaska

Relating juvenile migration timing and survival to adulthood in two species of threatened Pacific salmon (Oncorhynchus spp.)