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

Biotic interactions are believed to play a role in the origin and maintenance of species diversity, and multiple hypotheses link the latitudinal diversity gradient to a presumed gradient in the importance of biotic interactions. Here we address whether biotic interactions are more important at low latitudes, finding support for this hypothesis from a wide range of interactions. Some of the best-supported examples are higher herbivory and insect predation in the tropics, and predominantly tropical mutualisms such as cleaning symbioses and ant-plant interactions. For studies that included tropical regions, biotic interactions were never more important at high latitudes. Although our results support the hypothesis that biotic interactions are more important in the tropics, additional research is needed, including latitudinal comparisons of rates of molecular evolution for genes involved in biotic interactions, estimates of gradients in interaction strength, and phylogenetic comparisons of the traits that med...

Is There a Latitudinal Gradient in the Importance of Biotic Interactions

Biotic interactions are believed to play a role in the origin and maintenance of species diversity, and multiple hypotheses link the latitudinal diversity gradient to a presumed gradient in the importance of biotic interactions. Here we address whether biotic interactions are more important at low latitudes, finding support for this hypothesis from a wide range of interactions. Some of the best-supported examples are higher herbivory and insect predation in the tropics, and predominantly tropical mutualisms such as cleaning symbioses and ant-plant interactions. For studies that included tropical regions, biotic interactions were never more important at high latitudes. Although our results support the hypothesis that biotic interactions are more important in the tropics, additional research is needed, including latitudinal comparisons of rates of molecular evolution for genes involved in biotic interactions, estimates of gradients in interaction strength, and phylogenetic comparisons of the traits that mediate biotic interactions.

Is There a Latitudinal Gradient in the Importance of

Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2010.04691.x

Landscape genetics: where are we now?

Infectious diseases are common in marine environments, but the effects of a changing climate on marine pathogens are not well understood. Here we review current knowledge about how the climate drives host-pathogen interactions and infectious disease outbreaks. Climate-related impacts on marine diseases are being documented in corals, shellfish, finfish, and humans; these impacts are less clearly linked for other organisms. Oceans and people are inextricably linked, and marine diseases can both directly and indirectly affect human health, livelihoods, and well-being. We recommend an adaptive management approach to better increase the resilience of ocean systems vulnerable to marine diseases in a changing climate. Land-based management methods of quarantining, culling, and vaccinating are not successful in the ocean; therefore, forecasting conditions that lead to outbreaks and designing tools/approaches to influence these conditions may be the best way to manage marine disease.

Climate Change Influences on Marine Infectious Diseases: Implications for Management and Society

Habitat use patterns of 3 species of temperate eels, Anguilla anguilla, A. japonica and A. rostrata, were investigated using otolith strontium:calcium ratio life history transects. Published and unpublished data from 6 sites (Canada, United States, Sweden, France, Taiwan and Japan) sam- pled across the geographical range of each eel species were compiled. Sr:Ca patterns indicated that the 3 species displayed similar patterns of habitat use. In all sites, patterns of habitat use consisted of either residency in one habitat (fresh, brackish, or marine) or movements between habitats. One movement pattern consisted of either a single change or 2 changes of habitat from fresh to brackish waters, or from brackish water to freshwater. Seasonal movements between fresh and brackish waters were observed for all 3 species. When only a single habitat switch event was detected, it occurred between 3 and 5 yr of age. Occurrence of eels with no freshwater experience was demon- strated, but such eels accounted for a smaller proportion of the overall sample than eels with some (even brief) freshwater experience. Contrary to the common convention that these are obligate catadromous species, we must now consider them as facultative catadromous, with far more flexibil- ity in habitat use. The most variable parameter among study sites was the relative proportion, rather than the diversity, of lifetime spent in the various habitat use patterns. Eels found at higher latitudes exhibited a greater probability of remaining in the lower reaches of watersheds in brackish water. Diversity of habitat use appears to be a common strategy of temperate eel species, and, as a life his- tory tactic, is under environmental control.

/pdf/phenotypic-plasticity-of-habitat-use-by-three-temperate-eel-13xv662lzx.pdf

Phenotypic plasticity of habitat use by three temperate eel species, Anguilla anguilla, A. japonica and A. rostrata

Disentangling evolutionary forces that may interact to determine the patterns of genetic differentiation within and among wild populations is a major challenge in evolutionary biology. The objective of this study was to assess the genetic structure and the potential influence of several ecological variables on the extent of genetic differentiation at multiple spatial scales in a widely distributed species, the Atlantic salmon, Salmo salar. A total of 2775 anadromous fish were sampled from 51 rivers along the North American Atlantic coast and were genotyped using 13 microsatellites. A Bayesian analysis clustered these populations into seven genetically and geographically distinct groups, characterized by different environmental and ecological factors, mainly temperature. These groups were also characterized by different extent of genetic differentiation among populations. Dispersal was relatively high and of the same magnitude within compared to among regional groups, which contrasted with the maintenance of a regional genetic structure. However, genetic differentiation was lower among populations exchanging similar rates of local as opposed to inter-regional migrants, over the same geographical scale. This raised the hypothesis that gene flow could be constrained by local adaptation at the regional scale. Both coastal distance and temperature regime were found to influence the observed genetic structure according to landscape genetic analyses. The influence of other factors such as latitude, river length and altitude, migration tactic, and stocking was not significant at any spatial scale. Overall, these results suggested that the interaction between gene flow and thermal regime adaptation mainly explained the hierarchical genetic structure observed among Atlantic salmon populations.

/pdf/landscape-genetics-and-hierarchical-genetic-structure-in-17unfbu0m3.pdf

Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation

In vertebrates, variability at genes of the Major Histocompatibility Complex (MHC) represents an important adaptation for pathogen resistance, whereby high allelic diversity confers resistance to a greater number of pathogens. Pathogens can maintain diversifying selection pressure on their host's immune system that can vary in intensity based on pathogen richness, pathogen virulence, and length of the cohabitation period, which tend to increase with temperature. In this study, we tested the hypothesis that genetic diversity of MHC increases with temperature along a latitudinal gradient in response to pathogen selective pressure in the wild. A total of 1549 Atlantic salmon from 34 rivers were sampled between 46°N and 58°N in Eastern Canada. The results supported our working hypothesis. In contrast to the overall pattern observed at microsatellites, MHC class II allelic diversity increased with temperature, thus creating a latitudinal gradient. The observed temperature gradient was more pronounced for MHC amino acids of the peptide-binding region (PBR), a region that specifically binds to pathogens, than for the non-PBR. For the subset of rivers analyzed for bacterial diversity, MHC amino acid diversity of the PBR also increased significantly with bacterial diversity in each river. A comparison of the relative influence of temperature and bacterial diversity revealed that the latter could have a predominant role on MHC PBR variability. However, temperature was also identified as an important selective agent maintaining MHC diversity in the wild. Based on the bacteria results and given the putative role of temperature in shaping large-scale patterns of pathogen diversity and virulence, bacterial diversity is a plausible selection mechanism explaining the observed association between temperature and MHC variability. Therefore, we propose that genetic diversity at MHC class II represents local adaptation to cope with pathogen diversity in rivers associated with different thermal regimes. This study illuminates the link between selection pressure from the environment, host immune adaptation, and the large-scale genetic population structure for a nonmodel vertebrate in the wild.

/pdf/clinal-variation-in-mhc-diversity-with-temperature-evidence-1lgvg2ri82.pdf

Clinal variation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in Atlantic salmon.

Analyses of otolith strontium:calcium (Sr:Ca) ratios in 162 American eels Anguilla ros- trata of the St. Jean River watershed in eastern Canada demonstrated the co-existence of 6 migratory patterns, including freshwater and brackish water residence, and the predominance of an amphidro- mous migratory behavior. We tested the hypothesis that the choice of a particular life-history tactic may be controlled by a conditional strategy with status-dependent selection. This prediction was not supported because migratory patterns did not vary as a function of individual size, age and/or sex of eels prior to migration. However, we demonstrated that the utilisation of the estuarine brackish envi- ronment, more productive than the freshwater river and lake, resulted in a higher growth rate. Fresh- water yellow eels, the typical catadromous tactic, were rare and experienced lower growth rates. Moreover, we suggest that freshwater overwintering periods are not recorded in otoliths owing to the cold winter climate that occurs at northern latitudes. Thus, Sr:Ca ratio patterns that show brackish residence may in some cases hide a seasonal migration between fresh and brackish habitats.

/pdf/facultative-catadromy-in-american-eels-testing-the-520sbavsl1.pdf

Facultative catadromy in American eels: testing the conditional strategy hypothesis

Hedger, R. D., Martin, F., Dodson, J, J., Hatin, D., Caron, F., and Whoriskey, F. G. 2008. The optimized interpolation of fish positions and speeds in an array of fixed acoustic receivers. - ICES Journal of Marine Science, 65: 1248-1259.The principal method for interpolating the positions and speeds of tagged fish within an array of fixed acoustic receivers is the weighted-mean method, which uses a box-kernel estimator, one of the simplest smoothing options available. This study aimed to determine the relative error of alternative, non-parametric regression methods for estimating these parameters. It was achieved by predicting the positions and speeds of three paths made through a dense array of fixed acoustic receivers within a coastal embayment (Gaspe Bay, Quebec, Canada) by a boat with a GPS trailing an ultrasonic transmitter. Transmitter positions and speeds were estimated from the receiver data using kernel estimators, with box and normal kernels and the kernel size determined arbitrarily, and by several non-parametric methods, i.e. a kernel estimator, a smoothing spline, and local polynomial regression, with the kernel size or smoothing span determined by cross-validation. Prediction error of the kernel estimator was highly dependent upon kernel size, and a normal kernel produced less error than the box kernel. Of the methods using cross-validation, local polynomial regression produced least error, suggesting it as the optimal method for interpolation. Prediction error was also strongly dependent on array density. The local polynomial regression method was used to determine the movement patterns of a sample of tagged Atlantic salmon (Salmo salar) smolt and kelt, and American eel (Anguilla rostrata). Analysis of the estimates from local polynomial regression suggested that this was a suitable method for monitoring patterns of fish movement.

https://www.bio.ulaval.ca/cirsa/Publications/Hedgeretal2008%20ICES.pdf

François Caron

Papers

Phenotypic plasticity of habitat use by three temperate eel species, Anguilla anguilla, A. japonica and A. rostrata

Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation

Clinal variation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in Atlantic salmon.

Facultative catadromy in American eels: testing the conditional strategy hypothesis

The optimized interpolation of fish positions and speeds in an array of fixed acoustic receivers