Department of Biology
A genome-wide association study (GWAS) of age at maturity in Atlantic salmon: implications for conservation and management
Author(s): Primmer, CR, Johnstone, S, Orell, P, Niemilä, E, Lien, S, Kent, M, Erkinaro, J
In wild Atlantic salmon (Salmo salar), there is variation in the age at maturity within and between populations, as individuals can spend anywhere between one and five years feeding at sea before returning, often to their natal river, to spawn. The larger, late-maturing ‘multi-sea winter’ (MSW) individuals that have spent multiple years at sea prior to maturation are highly sought after by anglers. This life-history strategy has also been shown to be important from a biodiversity perspective, thus creating a management conflict. Knowledge of the genetic basis of age at maturity would provide a foundation for developing effective management strategies for conservation of this important life-history trait. The Atlantic salmon population of the Teno River in northern Finland is arguably the most biodiverse salmon population in the world from a life history strategy perspective, with more than 100 different life history strategies (combinations of river years, years at sea and repeat spawning) being recorded. It also has immense socioeconomic importance, both due to fishing tourism (15,000 anglers visit this remote region annually) as well as local and indigenous fisheries, with up to 60,000 individuals (60% of the annual run of ascending salmon) caught annually. Alarmingly, the proportion of late-maturing MSW fish has been declining in recent decades. A long term scale archive combined with the availability of an Atlantic salmon 7K Illumina® iSelect SNP-array provided an opportunity to conduct a genome-wide association study (GWAS) to identify genomic regions associated with age at maturity. By implementing genome-wide relatedness information to account for unexpected population structure, we identified several genomic regions harbouring loci significantly associated with age at maturity. The implications of the findings for conducting GWAS in wild populations, as well as for the practical management and conservation of exploited salmon populations will be presented.
School of Biological, Earth and Environmental Sciences
A range-wide conservation genetic study of Little Penguins (Eudyptula minor): augmenting population genetics at neutral loci with an adaptive immune gene
Author(s): Vogel, S, Sinclair, JJ, Sherwin, WB
Neutral genetic markers, i.e. genes not directly targeted by selection, are frequently used to quantify genetic diversity of populations and often provide the basis for management plans. However, patterns of variation and divergence in adaptive traits such as immune competence are not always correlated with variation in neutral markers. The validity of approaches using only neutral markers for development of conservation strategies is therefore questionable. The present study of conservation genetics and demography in E. minor aims to assess connectivity between penguin colonies along the Australian coast of New South Wales (NSW). A fine-scale analysis of genetic structure is being conducted to determine the extent of dispersal among these colonies and compare their genetic variability. In addition to using neutral genetic markers (microsatellites and mitochondrial DNA), we present the first study investigating non-neutral genetic diversity in penguins. Sequencing of an immune gene of the major histocompatibility complex (MHC) showed high allelic diversity at the functionally relevant peptide binding groove of the MHC molecule in penguins from Western Australia (WA). It is thus an ideal candidate gene to augment the population genetic study in NSW. This new genetic marker will be used to facilitate the choice of management strategies for E. minor and related species with a particular focus on resilience to pathogenic threats and immunogenetic population viability.
Ecology and Genetics
Applied conservation genomics in the wolverine (Gulo gulo)
Author(s): Ekblom, R, Smeds, L, Johansson, M, Magnusson, J, Ellegren, H
Natural selection may rapidly lead to local adaptation in genetically structured populations of threatened and administrated species. Investigators trying to find specific genetic variation important for conservation of such populations in non-model organisms have previously been restricted to using a small number of anonymous genetic markers or variation in a few candidate genes. With the advent of high throughput sequencing and genotyping it has now, for the first time, become possible to identify adaptive genetic variation at a genome wide scale. We will present data from a whole genome sequencing project and large scale genetic variation profiling of a mammalian predator, the wolverine (Gulo gulo). Scandinavian wolverine populations are subjected to habitat fragmentation and high mortality from poaching due to conflicts with livestock herders. Genetic monitoring is already an important part of the national conservation programmes for this species in Sweden and Norway but the resolution and applications of genetic data have been hampered by a lack of genomic information. By assembling the complete wolverine genome and characterising genome wide genetic variation by re-sequencing of several different individuals, we now take this system to a new level. We describe how these novel genomic resources are utilised to investigate genomic signatures of population subdivision, reconstruct kin structure and to infer effects of inbreeding depression in small and partially isolated populations. We also discuss how the insights gained from this project will be applied to practical conservation efforts and monitoring of this highly charismatic species in the Scandinavian countries.
Département de biologie
Applied evolutionary genomics in fish conservation: some success stories and challenges for the future
Author(s): Bernatchez, L
Conservation genetics has been defined as the application of genetics to preserve species as dynamic entities capable of coping with environmental change. Towards this end, molecular data can play two fundamental roles. The first one, inventorial, pertains to documenting patterns and has driven much of what we have accomplished until now. The second, mechanistic, refers to deciphering evolutionary processes underlying those patterns, is still in its infancy and this is where most of us put big hopes in the use of modern, high throughput genomics methods. Ultimately, we aim at finding causal relationships between genetic variation, phenotypes and the environment to predict future dynamics of selectively important variation and potential for adaptation to new conditions. In this presentation, I will illustrate some of the progress that we have made towards this end from our own research on fish conservation and management, and will comment on the main challenges that remains to be circumvented, no matter the power and resolution of the current genomics methods at hands.
Centre for Ecology and Conservation
Declining pollinator populations – do viruses hold the smoking gun?
Author(s): Wilfert, L
The pollinating insects – a diverse group comprising honeybees, bumblebees, hoverflies and many more – form a key group that is both crucial for guaranteeing our food security and for maintaining natural biodiversity. Many pollinator populations have been in decline over recent years and decades. Besides the obvious factors of habitat loss and change of land usage, infectious diseases and parasites have increasingly come into the limelight as potential causes of these declines. Rapidly evolving RNA viruses may be of particular importance, as they have been shown to be at the highest risk of causing emerging diseases. At the same time, such viruses can also be seen as a population genetic tool for studying the history of pollinator populations: quickly evolving viruses that are closely associated with their hosts allow host demographics to be reconstructed in the past. Here, I have used Acute Bee Paralysis Virus to study the pathogen transmission dynamics within bumblebee species communities consisting of rare and common species. Phylodynamic analyses reveal that this virus is commonly transmitted between species and that past epidemics may have contributed to range contractions. Rare and isolated species showed a high pathogen load whereas common species where relatively unaffected. This illustrates how non-specific pathogens may be able to shape species communities and how such coevolving pathogens may be used as monitoring tools to infer the history of species communities.
Faculté des Sciences
Decoupling population size, effective population size and pathogen prevalence in a periphery-core system in a migratory bird, the Corncrake
Author(s): Fourcade, Y, Richardson, DS, Keišs, O, Secondi, J
Inbreeding and reduced genetic diversity are known to affect the capacity of an individual to resist pathogen infection so that a negative relationship between pathogen prevalence and heterozygosity is expected. Thus, a high susceptibility to pathogens may contribute to shorten extinction time in populations with low genetic diversity. At the range scale, peripheral populations tend to be smaller and more isolated than core populations and are generally more prone to incur the costs of reduced genetic diversity. Elevated extinction risk in peripheral populations is of particular concern for species with unfavourable conservation status. However, the relationships between census size, effective size (genetic diversity) and parasite prevalence is not straightforward because gene flow from the core may maintain genetic diversity and the ability to resist pathogens at the range periphery, even in declining populations. The Corncrake Crex crex, a short live migratory bird distributed across the Palearctic has shown rapid declines in Western Europe over recent decades while Eastern populations remained large. We analysed the relationship between genetic diversity, gene flow and avian malaria prevalence across a large part of the species range. We found a very low level of population structure and no evidence of reduced diversity in peripheral populations which was likely caused by a high dispersal across the breeding range. Furthermore, contrary to expectations, the parasite prevalence was 10 times higher in core populations compared to peripheral ones, even in areas of high bird density. Our results clearly show that decouplings may occur in periphery-core systems between census and effective population size, and between genetic diversity and pathogen prevalence. Species dispersal characteristics, population densities and the ecology of pathogen community are likely to strongly affect these relationships precluding the quick and easy forecasting of a populations fate.
Institute of Zoology
Does reintroduction affect the mating systems of threatened species? The impact of inbreeding in reintroduced populations of the hihi (Notiomystis cincta)
Author(s): Brekke, P
An ever increasing number of animal and plant species are becoming rare or extinct in the wild. Reintroduction is one of the most commonly used tools for the management of these threatened species. However, this technique has a number of genetic, demographic and behavioural repercussions for which we have relatively limited understanding. In this study, of the endemic and endangered New Zealand hihi (Notiomystis cincta), our aim is to elucidate the impact of reintroduction on their mating system and reproductive success. We show the effects of inbreeding on individual reproductive tactics, extra-pair paternity and reproductive success and how it shapes the maintenance and evolution of these traits in wild small populations.
Ecology, immunogenomics and pathogen resistance in wildlife populations
Author(s): Sommer, S
In order to protect functional biodiversity and ecosystem services we need healthy populations depending on healthy environments. Understanding the complex interactions that occur between human-induced environmental changes, pathogen pressure and transmission, the potential of host adaptive genetic diversity in host-pathogen co-evolutionary processes and disease resistance is a challenging task. It requires an interdisciplinary approach which should aim to integrate knowledge from evolutionary theory, behavioral ecology, conservation biology and conservation genomics. Next generation sequencing is revolutionizing conservation research and the new technologies are likely to replace traditional genotyping methods to a great extent in the near future. We are able to address questions in non-model organism whose answers seemed out of reach just a few years ago. In my talk, I will illustrate recent advances, challenges and pitfalls of current developments in evolutionary conservation. Specifically, I will address 1) The effects of behavioral strategies in shaping the adaptive potential and its fitness-relevance 2) The effects of human induced changes on pathogen pressure 3) The functional importance of adaptive variability of endangered species in host-pathogen co-evolutionary processes and pathogen resistance 4) The current challenges and pitfalls of next generation sequencing approaches in conservation genomics
Department of Biological and Environmental Science
Genetic changes in life history traits in response to unintentional selection in a supportive breeding
Author(s): Charge, R, Sorci, G, Saint Jalme, M, Lesobre, L, Hingrat, Y, Lacroix, F, Teplitsky, C
Supportive breeding is one of the last conservation strategies to avoid species from extinction when pressures exerted are difficult to solve. However, captive breeding may generate undesirable effects such as inbreeding depression, loss of genetic diversity or genetic adaptation to captivity that could be transferred to wild reinforced populations when a supplementation program is associated with the captive breeding. Several recommendations have been proposed to limit these deleterious effects but empirical assessments of such strategies remain scarce. Particularly, it might be difficult equalizing founders contribution in species with high reproductive skews where few individuals secure most of the copulations. We investigated potential genetic changes over generations in a supportive breeding of a lekking bird, the Houbara bustard. Using quantitative genetics based on a large pedigree dataset, we found that unintentional selection was occurring on life-history traits, particularly traits linked with reproduction leading to an increase of the breeding values. The main cause of this process might be the poor contribution of some breeders to the offspring. The situation seems difficult to avoid during the “growth phase” of the captive breeding consisting in quickly constituting a sizeable flock of adult breeders. Nevertheless, unintentional selection was decreasing over years, emphasizing the effort of managers to favour contribution of poor breeders in offspring recruited in the captive breeding. Besides, best captive-born breeders sired progeny that better survives once released in the wild, which would be expected under sexual selection. Our results shed light on very fast and strong genetic changes in a captive program that follows worldwide used recommendations. Decreasing the growth rate in the very early stages of the captive breeding should allow maximizing the contribution of poor breeders and reduce the risk of genetic changes.
Institute of Evolution and Ecology
Incorporating intraspecific variation in conservation prioritization: a multi-taxa approach
Author(s): Thomassen, HA, Fuller, T, Buermann, W, Mila, B, Kieswetter, CM, Jarrin-V., P, Modro, N, Cameron, SE, Mason, E, Schweizer, R, Schlunegger, J, Chan, J, Wang, O, Peralvo, M, Schneider, CJ, Graham, CH, Pollinger, JP, Saatchi, S, Wayne, RK, Smith, TB
Human-induced land use changes are causing rapid habitat fragmentation. Species are therefore exceedingly limited in shifting their ranges in response to climate change, and likely need to adapt in situ to changing climate conditions. A prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of standing intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. We used spatially explicit ecological modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on evolutionary process (intraspecific genetic and morphological variation) or biodiversity patterns (species-level diversity). Reserves selected using species-level data showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes, and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization. To test the general applicability of our conservation prioritization framework, we are now applying this approach to target areas with varying levels of disturbance, different environmental gradients, and at small to large scales across four continents. Preliminary analyses indicate that the approach may be particularly useful at large scales, whereas other approaches should inform small-scale prioritization efforts.