Comparison of genetic differentiation at marker loci and quantitative traits

Merilä, Juha; Crnokrak, Peter

doi:10.1046/j.1420-9101.2001.00348.x

Cited by 1,125 publications

(1,014 citation statements)

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“…Underprediction on short timescales suggests that diversifying selection has produced departures from neutrality. This result is common in studies of divergence among local populations, for example, when assessed by F ST -Q ST comparisons (Merilä and Crnokrak 2001;McKay and Latta 2002). On such short timescales, adaptation to spatially varying selection is often rapid, so that phenotypic divergence exceeds neutral rates.…”

Section: Interpretation Of Resultsmentioning

confidence: 93%

“…These approaches assess the statistical significance of departures from neutral rates of evolution. Enough empirical tests have been performed to provide general conclusions: on short timescales, rates are typically faster than expected under neutrality (Merilä and Crnokrak 2001;McKay and Latta 2002), but on long timescales, they are usually slower-often much slower (Lynch 1990;Hansen and Houle 2004;Estes and Arnold 2007). We can with confidence reject the general hypothesis that rates of trait evolution at all timescales conform to neutral expectations.…”

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confidence: 87%

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MIPoD: A Hypothesis‐Testing Framework for Microevolutionary Inference from Patterns of Divergence

Hohenlohe¹,

Arnold²

2008

The American Naturalist

119

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Despite the many triumphs of comparative biology during the past few decades, the field has remained strangely divorced from evolutionary genetics. In particular, comparative methods have failed to incorporate multivariate process models of microevolution that include genetic constraint in the form of the G matrix. Here we explore the insights that might be gained by such an analysis. A neutral model of evolution by genetic drift that depends on effective population size and the G matrix predicts a probability distribution for divergence of population trait means on a phylogeny. Use of a maximum likelihood (ML) framework then allows us to compare independent direct estimates of G with the ML estimates based on the observed pattern of trait divergence among taxa. We assess the departure from neutrality, and thus the role of different types of selection and other forces, in a stepwise hypothesis-testing procedure based on parameters for the size, shape, and orientation of G. We illustrate our approach with a test case of data on vertebral number evolution in garter snakes. KeywordsG matrix; genetic line of least resistance; maximum likelihood; selective line of least resistance; Thamnophis; vertebral number A large literature on the comparative analysis of evolving traits has blossomed during the past 25 years (Felsenstein 1985;Harvey and Pagel 1991;Lynch 1991;Martins and Garland 1991;Martins 1994Martins , 2000Rohlf 2001;Steppan 2004;Carvalho et al. 2005). Interest in tracing trait evolution on independently estimated phylogenies has been responsible for putting a new face on comparative biology. New methodologies have allowed investigators to assay statistical associations between trait values and putative selective pressures (e.g., Darst et al. 2005;Ord and Martins 2006;Strmberg 2006) and to test alternative models of evolutionary process (Hansen 1997;Butler and King 2004). Despite success on these and other fronts, the new comparative biology has been strangely divorced from evolutionary genetics. Process models have been adopted from evolutionary genetics to provide the substructure for statistical inference (Martins and Hansen 1997), but estimates of genetic parameters usually play no role in comparative biology. The divorce between comparative biology and evolutionary genetics is especially vivid in the case of continuously distributed phenotypic traits. For these kinds of traits, which are often polygenic, quantitative genetic models promise deep understanding of

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Section: Interpretation Of Resultsmentioning

confidence: 93%

mentioning

confidence: 87%

MIPoD: A Hypothesis‐Testing Framework for Microevolutionary Inference from Patterns of Divergence

Hohenlohe¹,

Arnold²

2008

The American Naturalist

119

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“…The magnitude of selection in natural populations can be approached by complementing spatial studies of neutral variability with distribution patterns of traits. A popular approach has been to compare population structure at neutral markers versus selected traits, the so-called F ST versus Q ST approach (review in Merilä and Crnokrak, 2001; see Chapuis et al, 2007 for a recent reference). This approach may help unraveling the nature of selection.…”

Section: Introductionmentioning

confidence: 99%

Contrasting the distribution of phenotypic and molecular variation in the freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni

et al. 2013

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Population differentiation was investigated by confronting phenotypic and molecular variation in the highly selfing freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni. We sampled seven natural populations separated by a few kilometers, and characterized by different habitat regimes (permanent/temporary) and openness (open/closed). A genetic analysis based on five microsatellite markers confirms that B. pfeifferi is a selfer (sE0.9) and exhibits limited variation within populations. Most pairwise F ST were significant indicating marked population structure, though no isolation by distance was detected. Families from the seven populations were monitored under laboratory conditions over two generations (G 1 and G 2 ), allowing to record several life-history traits, including growth, fecundity and survival, over 25 weeks. Marked differences were detected among populations for traits expressed early in the life cycle (up to sexual maturity). Age and size at first reproduction had high heritability values, but such a trend was not found for early reproductive traits. In most populations, G 1 snails matured later and at a larger size than G 2 individuals. Individuals from permanent habitats matured at a smaller size and were more fecund than those from temporary habitats. The mean phenotypic differentiation over all populations (Q ST ) was lower than the mean genetic differentiation (F ST ), suggesting stabilizing selection. However, no difference was detected between Q ST and F ST for both habitat regime and habitat openness.

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“…resistance to chloroquine in Plasmodium falciparum [189] and to benzimadazole in Haemonchus contortus [190]), most of the parasite traits which interest us from an epidemiological viewpoint are likely to be polygenic, quantitative traits [19]. A number of studies over a wide range of taxa have shown that there is a poor correlation between the among-group genetic variance in neutral, single gene markers (typically measured by F ST ) and the among-group genetic variance in complex, quantitative traits (as measured by Q ST ) [191][192][193].…”

Section: Markers For Traits Of Epidemiological Importancementioning

confidence: 99%

The molecular epidemiology of parasite infections: Tools and applications

Lymbery

Thompson

2012

Molecular and Biochemical Parasitology

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Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilise genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.

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Comparison of genetic differentiation at marker loci and quantitative traits

Cited by 1,125 publications

References 103 publications

MIPoD: A Hypothesis‐Testing Framework for Microevolutionary Inference from Patterns of Divergence

MIPoD: A Hypothesis‐Testing Framework for Microevolutionary Inference from Patterns of Divergence

Contrasting the distribution of phenotypic and molecular variation in the freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni

The molecular epidemiology of parasite infections: Tools and applications

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