It is increasingly important to improve our understanding of the genetic basis of local adaptation because of its relevance to climate change, crop and animal production, and conservation of genetic resources Phenotypic patterns that are generated by spatially varying selection have long been observed, and both genetic mapping and field experiments provided initial insights into the genetic architecture of adaptive traits Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation These advances are also allowing research in non-model species, the adaptation patterns of which may differ from those of traditional model species

Ecological genomics of local adaptation

Twenty-four articles by biologists, ecologists, and other scientists represent a year's progress in the field. Among the topics addressed: the effects of introduced species, paleobiogeography, genetics and geographic structure, marine fisheries management, time as an ecological resource, genetic var

Annual Review of Ecology, Evolution and Systematics

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, ...

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced-representation sequencing, candidate-gene approaches, linearity of allele-environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13322

A practical guide to environmental association analysis in landscape genomics

FST outlier tests are a potentially powerful way to detect genetic loci under spatially divergent selection. Unfortunately, the extent to which these tests are robust to nonequilibrium demographic histories has been understudied. We developed a landscape genetics simulator to test the effects of isolation by distance (IBD) and range expansion on FST outlier methods. We evaluated the two most commonly used methods for the identification of FST outliers (FDIST2 and BayeScan, which assume samples are evolutionarily independent) and two recent methods (FLK and Bayenv2, which estimate and account for evolutionary nonindependence). Parameterization with a set of neutral loci (‘neutral parameterization’) always improved the performance of FLK and Bayenv2, while neutral parameterization caused FDIST2 to actually perform worse in the cases of IBD or range expansion. BayeScan was improved when the prior odds on neutrality was increased, regardless of the true odds in the data. On their best performance, however, the widely used methods had high false-positive rates for IBD and range expansion and were outperformed by methods that accounted for evolutionary nonindependence. In addition, default settings in FDIST2 and BayeScan resulted in many false positives suggesting balancing selection. However, all methods did very well if a large set of neutral loci is available to create empirical P-values. We conclude that in species that exhibit IBD or have undergone range expansion, many of the published FST outliers based on FDIST2 and BayeScan are probably false positives, but FLK and Bayenv2 show great promise for accurately identifying loci under spatially divergent selection.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12725

Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests.

Thanks to genome-scale diversity data, present-day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up-to-date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self-fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype-environment correlations and five designed to detect adaptive differentiation (based on F(ST) or similar measures). We show that genotype-environment correlation methods have substantially more power to detect selection than differentiation-based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype-environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations. (Texte integral)

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations : [W633]

Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion.

https://hal.umontpellier.fr/hal-01808409/document

Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda

Testar se e como populacoes naturais sao adaptadas ao seu ambiente local e prever suas respostas em funcao das alteracoes futuras do habitat e de importância fundamental diante do cenario de mudancas climaticas. Este e o caso dos cafeeiros, em que o ritmo das alteracoes climaticas pode ser rapido e drastico para a adaptacao das populacoes. Usando a distribuicao geografica de populacoes selvagens com habitats contrastantes, o objetivo do presente estudo foi identificar polimorfismos de nucleotideo unico (SNPs) em genes candidatos (GCs) identificados como estando envolvidos na adaptacao de populacoes de Coffea canephora da Uganda ao seu ambiente local. Em particular, modificacoes que ocorrem proximos e/ou em genes relacionados a tolerância aos estresses abioticos tornam esses GCs alvos, potenciais determinantes adaptativos das plantas em funcao das mudancas climaticas. Ao identificar os fatores ambientais que impulsionam esses processos, poderiamos prever a adaptabilidade esperada das populacoes para o clima local futuro.

/pdf/potencial-adaptativo-de-coffea-canephora-para-projecoes-das-1pl7u54k4z.pdf

Potencial adaptativo de Coffea canephora para projeções das alterações climáticas

A captura direcionada de sequencias acoplada ao sequenciamento de alto rendimento tornou-se um metodo poderoso para o estudo da variacao de sequencias genomicas. Usando o genoma disponivel de C. canephora (tamanho estimado de 710 Mb/haploide) como referencia, projetamos sondas para 323 genes candidatos selecionados (CGs) visando capturar seus homeologos em 293 acessos de C. canephora da Uganda, 12 clones do Brasil e um subconjunto de 19 individuos cobrindo todos os grupos de diversidade de C. canephora . Para um total de 324 individuos de C. canephora , projetamos, com sucesso, cerca de 19.000 sondas e identificamos mais de 16.000 polimorfismos de nucleotideo unico (SNPs) de qualidade, localizados dentro ou proximo a 318 genes anotados, gerando dados genotipicos para populacoes que estao localizadas em regioes que abrangem diferentes condicoes climaticas. Nos investigamos questoes como desenho das sondas, cobertura do sequenciamento, eficiencia da hibridizacao e captura, e estrategias de analise dos dados por bioinformatica.

/pdf/genotipagem-por-enriquecimento-e-captura-direcionada-de-2st6yfjr3k.pdf

Stéphanie Manel

Papers

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations : [W633]

Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda

Potencial adaptativo de Coffea canephora para projeções das alterações climáticas

GENOTIPAGEM POR ENRIQUECIMENTO E CAPTURA DIRECIONADA DE GENES CANDIDATOS EM Coffea canephora