Characterization of Demographic Expansions From Pairwise Comparisons of Linked Microsatellite Haplotypes

Navascués, Miguel; Hardy, Olivier J.; Burgarella, Concetta

doi:10.1534/genetics.108.098194

Cited by 14 publications

(14 citation statements)

References 36 publications

(32 reference statements)

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“…, 2001). We used their new maximum pseudo‐likelihood estimation procedure for population growth parameters that takes homoplasy into account, implemented in the program lmse (Navascués et al. , 2009).…”

Section: Methodsmentioning

confidence: 99%

“…Navascués et al (2006) have shown that the accuracy of parameter estimates decreases if there is homoplasy in the data, as is common for cpSSRs (Provan et al, 2001). We used their new maximum pseudo-likelihood estimation procedure for population growth parameters that takes homoplasy into account, implemented in the program lmse (Navascués et al, 2009).…”

Section: Demographic Inferences From Genetic Datamentioning

confidence: 99%

“…only in the Alps and in the Czech Republic, differentiated Table 3 Tests for population expansion and estimation of demographic parameters in populations of the Pinus mugo species complex in western Europe. BAPS group: cluster assigned in the Bayesian analysis of population structure (see text); Fu's test: test of population expansion (Fu, 1997); Population growth parameters (with homoplasy): maximum pseudo-likelihood method of Navascués et al (2009) *A, Alpine cluster (cluster 8 in Fig. 1); P, Pyrenean cluster (cluster 12 in Fig.…”

Section: Phylogeographic Structurementioning

confidence: 99%

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Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in western Europe

Heuertz

Teufel

González‐Martínez³

et al. 2010

Journal of Biogeography

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Aim Our aims were to test whether morphological species of mountain pines were genetically supported in the western part of the distribution range of the Pinus mugo species complex (Pinus mugo Turra sensu lato), to resolve genetically homogeneous clusters of populations, to determine historical demographic processes, and to assess the potential hybridization of mountain pines with Scots pine, Pinus sylvestris L.Location Populations were sampled in the Iberian System, the Pyrenees, the French Mont Ventoux, Vosges and Jura mountains, the Germán Black Forest and throughout the Alps. This corresponded to a range-wide sampling for mountain pine sensu stricto (Pinus uncinata Ram.) and to a sampling of the western parts of the ranges of dwarf mountain pine (Pinus mugo Turra sensu stricto) and bog pine/peatbog pine [Pinus rotundata Lmk/Pinus X pseudopumilio (Willk.) Beck].Methods In total, 786 individuáis of P. mugo sensu lato from 29 natural populations, and 85 individuáis of P. sylvestris from four natural populations were genotyped at three chloroplast microsatellites (cpSSRs). Populations were characterized for standard genetic diversity statistics and signs of demographic expansión. Genetic structure was explored using analysis of molecular variance, differentiation statistics and Bayesian analysis of population structure (BAPS).ResuIts One hundred haplotypes were identified in P. mugo sensu lato. There was a strongerdifferentiationbetweengeographicalregionsthanbetweenmorphologically identified taxa (P. mugo sensu stricto, P. uncinata and P. rotundata/P. X pseudopumilio). Overall genetic differentiation was weak (G S T = 0.070) and displayed a clear phylogeographic structure [N S r = 0.263, N S r > N S r (permuted), P < 0.001 ]. BAPS identified a Pyrenean and an Alpine gene pool, along with several smaller genetic clusters corresponding to peripheral populations. Main conclusionsThe core regions of the Pyrenees and Alps were probably recolonized, respectivelybyP. uncinata and P. uncinatalP. mugo sensu stricto, from múltiple glacial refugia that were well connected by pollen flow within the mountain chains. Pinus rotundata/P. X pseudopumilio populations from the Black Forest, Vosges and Jura mountains were probably recolonized from various glacial populations that kept their genetic distinctiveness despite late glacial and early Holocene expansión. Marginal P. uncinata populations from the Iberian System are compatible with elevational shifts and long-term isolation. The causes of haplotype sharing between P. mugo sensu lato and P. sylvestris require further research.

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Section: Methodsmentioning

confidence: 99%

Section: Demographic Inferences From Genetic Datamentioning

confidence: 99%

Section: Phylogeographic Structurementioning

confidence: 99%

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Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in western Europe

Heuertz

Teufel

González‐Martínez³

et al. 2010

Journal of Biogeography

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“…Chloroplast microsatellites were coded in a binary fashion, following Navascués et al (2006). These authors also showed, using extensive numerical simulations, that mismatch distributions based on chloroplast microsatellites are sensitive to population growth and therefore suitable to estimate demographic parameters related to population expansion (see also Navascués et al, 2009). Then, Rogers & Harpending's (1992) demographic model was fitted on the mismatch distributions following Schneider & Excoffier (1999; but see also Excoffier et al, 2005).…”

Section: Statistical Analysesmentioning

confidence: 99%

Patterns of polymorphism resulting from long‐range colonization in the Mediterranean conifer Aleppo pine

Grivet¹,

Sebastiani

González‐Martínez³

et al. 2009

New Phytologist

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Summary• The evolutionary outcomes of range expansion ⁄ contraction depend on the biological system considered and the interactions among the evolutionary forces in place. In this study, we examined the demographic history and the local polymorphism patterns of candidate genes linked to drought tolerance of a widespread Mediterranean conifer (Pinus halepensis).• To that end, we used cpSSRs and coalescence modelling of nuclear genes to infer the demographic history of natural populations covering the species range. Ten drought-response candidate genes were then examined for their patterns of polymorphism and tested for selection considering plausible demographic scenarios.• Our results revealed a marked loss of genetic diversity from the relictual Greek population towards the western range of the species, as well as molecular signatures of intense bottlenecks. Moreover, we found an excess of derived polymorphisms in several genes sampled in the western part of the range -a potential result of the action of natural selection on populations confronted with new environments following long-range colonization.• Wide-range expansions-contractions of forest trees are accompanied by strong selective pressures, resulting in distinct evolutionary units. This knowledge is of crucial importance for the conservation and management of forests in the face of climate change.

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“…By ignoring this dependency, the composite-likelihood score can be used as a criterion to estimate the parameters of the model with faster algorithms than the coalescent samplers although with lower performance, particularly regarding confidence intervals (e.g. Navascués et al, 2009;Nikolic and Chevalet, 2014).…”

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confidence: 99%

Demographic inference through approximate-Bayesian-computation skyline plots

Navascués

Leblois

Burgarella

2017

Preprint

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11The skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of the demographic trajectory. Because of this flexibility in shape, skyline plots can, in principle, provide realistic descriptions of the complex demographic scenarios that occur in natural populations. Currently, demographic estimates needed for skyline plots are estimated using coalescent samplers or a composite likelihood approach. Here, we provide a way to estimate historical effective population sizes using an Approximate Bayesian Computation (ABC) framework. We assess its performance using simulated and actual microsatellite datasets. Our method correctly retrieves the signal of contracting, constant and expanding populations, although the graphical shape of the plot is not always an accurate representation of the true demographic trajectory, particularly for recent changes in size and contracting populations. Because of the flexibility of ABC, similar approaches can be extended to other types of data, to multiple populations, or to other parameters that can change through time, such as the migration rate. At present, most of the methods to estimate demography from genetic data are based on the coalescent. 31The coalescent (see Wakeley, 2008, for a review) is a mathematical model that describes the rate at which Alternatively, the coalescent can be used to calculate the likelihood of the number of genetic differences 40 for a pair of gene copies under a given demographic model. The likelihood for all pairs in a sample 41 can be combined to obtain a composite-likelihood (which is not a true likelihood because pairs are not 42 independent and they are related by their genealogy). The composite-likelihood score can be used as 43 a criterion to estimate the parameters of the model with faster algorithms than the coalescent samplers 44 although with lower performance, particularly regarding confidence intervals (e.g. Navascués et al

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Characterization of Demographic Expansions From Pairwise Comparisons of Linked Microsatellite Haplotypes

Cited by 14 publications

References 36 publications

Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in western Europe

Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in western Europe

Patterns of polymorphism resulting from long‐range colonization in the Mediterranean conifer Aleppo pine

Demographic inference through approximate-Bayesian-computation skyline plots

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