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.
Centro de Biologia Ambiental / Departamento de Biologia Animal
Can reproductive barriers maintain differentiation in face of global changes? A case study in Drosophila subobscura
Author(s): Matos, M, Bárbaro, M, Mira, M, Fragata, I, Simões, P, Lima, M, Lopes-Cunha, M, Kellen, B, Santos, J, Magalhães, S
Species with wide distributions may be highly differentiated across contrasting environments. While gene flow may help maintain similarities among populations, local adaptation may lead to their divergence, as well as promote reproductive isolation, further fostering evolutionary diversification. The interplay between these two processes is of major importance for Conservation, as it will determine if populations differentiate or become more similar in the long run, as a result of environmental changes such as those imposed by man. In Drosophila subobscura, populations are differentiated along a latitudinal gradient, but recent evidence indicates that northern populations are becoming more similar to southern ones. An important issue is how much populations from the extremes of the cline differ in mating preferences, as this might contribute to reduce genetic introgression when populations meet. To address this, we analyzed the evolutionary dynamics of reproductive isolation of D. subobscura populations derived from the extremes of the European cline, while adapting to a common, laboratorial environment. We show that mating performance increased during laboratory adaptation. In general northern populations had a better performance than southern ones, and this difference was sustained across generations. Moreover northern females preferred mates from their own populations while southern females preferred males from the north. The assortative mating of the northern populations was stable through time, while disassortative mating of the southern populations faded away during laboratory evolution. Overall this study suggests that reproductive barriers may slow down the genetic introgression due to migration to the north, an important finding in evolutionary and conservation terms.
School of Biological Sciences
Can we use molecular techniques to measure inbreeding in wild populations of highly inbred, bottlenecked species?
Author(s): Taylor, H, Ramstad, K, Kardos, M
Understanding the effects of inbreeding depression is important for viability assessment and effective management of rare and endangered species, but accurately measuring inbreeding in such species remains challenging. Highly inbred species that have experienced severe bottleneck events typically lack the behavioural pedigree information, high levels of genetic diversity and large population sizes (and thus sample sizes) required to accurately estimate individual inbreeding. This raises the question of whether investing resources into research in this area is worthwhile for conservation managers and, if so, what the best approach might be. We modeled the accuracy of pedigrees constructed using varying numbers of simulated microsatellite markers for the little spotted kiwi (Apteryx owenii), a species that has experienced a recent, severe bottleneck and that exhibits extremely low genetic variation. We found that the number of microsatellite markers required to reconstruct precise pedigrees and provide accurate inbreeding coefficients will be cost prohibitive for the majority of conservation studies. Alternative approaches, such as heterozygosity fitness correlations, would also require a prohibitively large number of neutral markers. Pairwise relatedness measures show promise for estimating inbreeding in this species and those with similar histories, but genomic measures such as runs of homozygosity (ROH) currently provide the most effective alternative for measuring inbreeding. We acknowledge that genomic methods may also prove too costly currently for many conservation programmes and emphasise that conservation managers should weigh the costs and benefits of alternative strategies prior to investing in genetic measures as part of their rescue strategies.
Institute of Biosciences
Characterization of MHC-class II DRB diversity in the lesser anteater (Tamandua tetradactyla)
Author(s): Clozato, CL, Moraes-Barros, N, Morgante, JS, Sommer, S
Studies of immune gene variation in the Major Histocompatibility Complex (MHC) provide a powerful tool to investigate patterns of adaptative genetic diversity shaped by natural selection. The use of MHC makers in population genetics has grown to a great extant in the past few years. However, studies with non-model species are still challenging due to the lack of a references and information of loci number. The lesser anteater is a medium sized mammal of the order Pilosa. The species is geographically widespread, found throughout South America in several types of habitats such as grasslands, savannas, forests and wetlands. Such flexibility on habitat use may lead to local adaptations reflected in the species’ MHC gene diversity, accounting for different parasite pressures in the environment. To understand the contribution of natural selection to Tamandua tetradactyla populations we described the diversity of the MHC Class II DRB exon 2 gene. At first, Single Strand Conformation Polymorphism (SSCP) was used to screen diversity in order to develop the optimal primer pair for sequential amplification (i.e., the one that catches most diversity and shows less null alleles). DRB exon 2 was amplified in ten gDNA samples from individuals trapped at different geographical locations using three primer sets. PCR products were run twice on SSCP gels and sequenced. A fragment of 198 base pairs (66 aminoacids) was obtained, and no indels were found. After choosing the best primer set, a total of 22 alleles were detected on the aminoacid level (TateDRB01 to TateDRB22), and 26 on the nucleotide level. Between four and eight alleles were found per individual (average of 4.7), indicating the presence of at least two DRB loci. Secondly, 50 samples derived from four different biomes of the species occurrence are currently analysed through Next Generation Sequencing (NGS) on a 454 Junior platform. This will allow the analyses of the genetic structure of MHC DRB gene in the species.
Characterizing and tracking MHC variation of chyrtridiomycosis affected Chiricahua leopard frogs over time in natural populations
Author(s): Mulder, KP, Savage, AE
The amphibian disease chytridiomycosis caused by the fungus Batrachochytrium dendrobatidis (Bd) has contributed to the decline and extirpation of numerous populations of Chiricahua leopard frogs (Lithobates chiricahuensis), an endangered species native to the Southwestern United States and Northern Mexico. Conservation efforts have focused on captive rearing of wild-caught egg masses and subsequent release following metamorphosis (called head-starting) to increase population sizes across the species range. The survival rate of released individuals is, however, heavily dependent on their ability to combat chytridiomycosis. In captivity, populations of other species of leopard frogs show differential survival to experimental Bd infections dependent on their genetic variation in the major histocompatability complex (MHC), a highly variable gene family in vertebrates known to be important in pathogen resistance. We used single locus 454 pyrosequencing to characterize MHC genetic variation in head-started Chiricahua leopard frogs that will be released and monitored for one year to determine survival rates and identify alleles that confer an advantage against Bd in a natural environment. This information will be used to identify candidate resistance alleles and add MHC-based marker assisted selection to captive breeding efforts, with the goal of increasing the success rate of head-starting efforts and mitigating the impact of Bd on natural populations of both Chiricahua leopard frogs as well as other amphibian species affected by chrytridiomycosis. This is a case study of how evolutionary genetic analyses of adaptive markers can assist conservation efforts in captive breeding.
Comparison of estimators of effective population size: variation and bias in the methods
Author(s): Jimenez-Mena, B, Hospital, F, Verrier, E
The effective population size (Ne) is a parameter of paramount importance in population genetics. Many estimators of Ne have been developed in the literature and each one uses different kinds of data (pedigree, molecular markers). But the various methods give very different estimates of Ne for the same population. Therefore, there is a need for an assessment of the consistency and reliability of the methods. The aim of our study is to analyze a few of them, making a comparison by using simulation data. A forward-in-time simulation of a multi-allelic population subjected to genetic drift was developed. We modelled a diploid population which reproduced randomly in discrete generations, with constant population size N. Self-fertilization was allowed. Selection, migration, and new mutations were assumed to not happen across generations. At each generation, Ne was estimated with various methods. We performed 700 replicates. We used the classical estimator 1/(2 x rate of Inbreeding). The coefficients of inbreeding were obtained by several ways: (i) the average pairwise coancestry derived from pedigree, (ii) the heterozygosity (He) computed from the observed allele frequencies. We also included in the comparison two estimators based on temporal changes in the allele frequency taken from the population at two points in time. We performed the comparisons varying different conditions: number of generations between sampled populations (d), initial allele configuration, and N. The results showed that the use of (ii) resulted in a huge range of Ne values, in some cases with extreme values as large as 1e+06. This is due to the large variation of the estimated values of He, which can lead to a bias in Ne. Increasing d reduced this variability of results and increased the accuracy of Ne estimation, but not very much. Estimations based on (i) resulted in very accurate estimates of Ne.
Department of Biological Sciences
Consistent patterns of return cross-species application of SNP chips
Author(s): Miller, JM, Kijas, JW, Heaton, MP, McEwan, JC, Coltman, DW
Recent advances in technology facilitated development of large sets of genetic markers for many taxa, though most often model or domestic organisms. Cross-species application of genomic technologies may allow for rapid marker discovery in wild relatives of taxa with well developed resources. We investigated cross-species application of three commercially available SNP chips (the OvineSNP50, BovineSNP50, and EquineSNP50 BeadChips) as a function of divergence time between the domestic source species and wild target species. Across all three chips we observed a consistent linear decrease in call rate (~1.5% per million years), while retention of polymorphisms showed an exponential decay. These results will allow researchers to predict the expected amplification rate and polymorphism of cross-species application for their taxa of interest, as well as provide a resource for estimating divergence times.