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

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.

/pdf/trophic-downgrading-of-planet-earth-4rdowr8qqu.pdf

Trophic Downgrading of Planet Earth

Background 
Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation.


Methodology 
By accurately reflecting natural variation and uncertainty to generate robust probability estimates of source proportions, the application of Bayesian methods to stable isotope mixing models promises to enable researchers to address an array of new questions, and approach current questions with greater insight and honesty.


Conclusions 
We outline a framework that builds on recently published Bayesian isotopic mixing models and present a new open source R package, SIAR. The formulation in R will allow for continued and rapid development of this core model into an all-encompassing single analysis suite for stable isotope research.

/pdf/source-partitioning-using-stable-isotopes-coping-with-too-4qd1pzfyh0.pdf

Source partitioning using stable isotopes: coping with too much variation.

1. The use of stable isotope data to infer characteristics of community structure and niche width of community members has become increasingly common. Although these developments have provided ecologists with new perspectives, their full impact has been hampered by an inability to statistically compare individual communities using descriptive metrics. 2. We solve these issues by reformulating the metrics in a Bayesian framework. This reformulation takes account of uncertainty in the sampled data and naturally incorporates error arising from the sampling process, propagating it through to the derived metrics. 3. Furthermore, we develop novel multivariate ellipse-based metrics as an alternative to the currently employed Convex Hull methods when applied to single community members. We show that unlike Convex Hulls, the ellipses are unbiased with respect to sample size, and their estimation via Bayesian inference allows robust comparison to be made among data sets comprising different sample sizes. 4. These new metrics, which we call SIBER (Stable Isotope Bayesian Ellipses in R), open up more avenues for direct comparison of isotopic niches across communities. The computational code to calculate the new metrics is implemented in the free-to-download package Stable Isotope Analysis for the R statistical environment.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2656.2011.01806.x

Comparing isotopic niche widths among and within communities: SIBER - Stable Isotope Bayesian Ellipses in R.

Sockeye salmon that spawn downstream of rearing lakes are an important example of the challenges faced by organisms with complex life histories requiring connectivity in aquatic habitat complexes. Specifically, newly emerged juvenile sockeye salmon must migrate upstream, against the flow of water, if they are to reach lake rearing habitat. Here, we examine the spatial and temporal dynamics of the water velocity landscape and juvenile sockeye salmon movement and condition at increasing distances downstream from the lake outlet of an important sockeye salmon system, the Babine Lake of British Columbia, one of Canada’s largest and most important sockeye salmon rearing lakes. The results of this study indicate that (i) there were seasonal and spatial patterns of water velocities that exceed the ability of juveniles to swim upstream to lake rearing habitat, (ii) higher water discharge was associated with more velocity barriers and potentially with less upstream movement of juveniles, and (iii) juveniles rearing in the lake obtained larger sizes (30% longer and 150% heavier) than those in downstream river habitats. Multiple processes that may be influencing these patterns could include more abundant food resources, lower metabolic demands, or size-selective immigration, emigration, or mortality among habitats. Years and seasons with high discharge may temporarily create one-way, downstream transport routes at lake outlets. Long-term changes in hydrology, perhaps driven by climate variability or land-use change, may control the degree to which lake outlets function as bidirectional travel corridors or one-way travel routes for young sockeye salmon.

Ontogenetic habitat shifts and vulnerability: lake-outlet-spawning sockeye salmon (Oncorhynchus nerka) sensitivity to habitat connectivity and hydrologic change

Juvenile Salmonid Habitat Utilization in the Skeena River Estuary

Metapopulations are often managed as a single contiguous population despite spatial structure underlying their local and regional dynamics. Disturbances from human activities can also be spatially structured with mortality impacts concentrated to just a few local populations among the aggregate. Scale transitions between local and regional processes can generate emergent properties whereby the whole system can fail to recover as quickly as expected for an equivalent single population. Here, we draw on theory and empirical case studies to ask: what is the consequence of spatially structured ecological and disturbance processes on metapopulation recoveries? We suggest that exploring this question could help address knowledge gaps for managing metapopulations including: Why do some metapopulations recover quickly while others remain collapsed? And, what risks are unaccounted for when metapopulations are managed at aggregate scales? First, we used model simulations to examine how scale transitions among ecological and disturbance conditions interact to generate emergent metapopulation recovery outcomes. In general, we found that the spatial structure of disturbance was a strong determinant of recovery outcomes. Specifically, disturbances that unevenly impacted local populations consistently generated the slowest recoveries and highest conservation risks. Ecological conditions that dampened metapopulation recoveries included low dispersal, variable local demography, sparsely connected habitat networks, and spatially and temporally correlated stochastic processes. Second, we illustrate the unexpected challenges of managing metapopulations by examining the recoveries of three USA federally listed endangered species: Florida Everglade snail kites, California and Alaska sea otters, and Snake River Chinook salmon. Overall, our results show the pivotal role of spatial structure in metapopulation recoveries whereby the interplay between local and regional processes shape the resilience of the whole system. With this understanding, we provide guidelines for resource managers tasked with conserving and managing metapopulations and identify opportunities for research to support the application of metapopulation theory to real-world challenges. This article is protected by copyright. All rights reserved.

Jonathan W. Moore

Papers

Ontogenetic habitat shifts and vulnerability: lake-outlet-spawning sockeye salmon (Oncorhynchus nerka) sensitivity to habitat connectivity and hydrologic change

Juvenile Salmonid Habitat Utilization in the Skeena River Estuary

The role of spatial structure in at-risk metapopulation recoveries.

Phenological shifts and mismatch with marine productivity vary among Pacific salmon species and populations