Understanding population history for conservation purposes: population genetics of Saxifraga aizoides (Saxifragaceae) in the lowlands and lower mountains north of the Alps

2000 ◽  
Vol 87 (4) ◽  
pp. 583-590 ◽  
Author(s):  
Eva Lutz ◽  
J. Jakob Schneller ◽  
Rolf Holderegger
2019 ◽  
Vol 36 (8) ◽  
pp. 1701-1710 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J Balick ◽  
Christopher Cassa ◽  
Jack A Kosmicki ◽  
Mark J Daly ◽  
...  

Abstract The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation–selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation–selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.


2016 ◽  
Author(s):  
A. Mesut Erzurumluoglu ◽  
Denis Baird ◽  
Tom G. Richardson ◽  
Nicholas J. Timpson ◽  
Santiago Rodriguez

AbstractY chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits (including cardio-metabolic traits) have been reported. In apparently homogeneous populations, there is still Y-DNA haplogroup variation which will result from population history. Therefore, hidden stratification and/or differential phenotypic effects by Y-DNA haplogroups could exist. To test this, we hypothesised that stratifying individuals according to their Y-DNA haplogroups before testing associations between autosomal SNPs and phenotypes will yield difference in association. For proof of concept, we derived Y-DNA haplogroups from 6,537 males from two epidemiological cohorts, ALSPAC (N=5,080, 816 Y-DNA SNPs) and 1958 Birth Cohort (N=1,457, 1,849 Y-DNA SNPs). For illustration, we studied well-known associations between 32 SNPs and body mass index (BMI), including associations involving FTO SNPs. Overall, no association was replicated in both cohorts when Y-DNA haplogroups were considered and this suggests that, for BMI at least, there is little evidence of differences in phenotype or gene association by Y-DNA structure. Further studies using other traits, Phenome-wide association studies (PheWAS), haplogroups and/or autosomal SNPs are required to test the generalisability of this approach.


2010 ◽  
Vol 161 (6) ◽  
pp. 207-215 ◽  
Author(s):  
Felix Gugerli ◽  
Christoph Sperisen

Fossil records (pollen, macroremains) and genetic structures based on molecular markers provide complementary data sets for elucidating the (post-)glacial histories of extant plant populations. Based on comparative studies using both data sources, this article focuses on the effects of postglacial recolonization on the genetic structures in common, widespread forest tree species in the Alpine range. We recall that at least at the continental level, the three large southern European peninsulas, Iberia, Italy and the Balkans, but also the Carpathians represented important refugial areas for many European tree species during the last glacial maximum. However, these refugia had a minimal impact on the recolonization of the Alpine range. In contrast, recent studies demonstrate that refugial areas in the proximity of the Alps, e.g. at their eastern and western ends, harbored prominent source populations of current occurrences of the dominant forest trees in the Alpine range. Furthermore, there is strong evidence that several species were able to maintain populations north of the Alps, such as in the Bohemian Massif. We advocate that the Alps did not necessarily represent a barrier to northward migration, since terrain for advancement from various refugia was available along the margins of this mountain range. Such migration patterns allowed diverged genetic lineages to meet, leading to increased genetic diversity in respective contact zones. This overview underlines how paleoecological and molecular genetic studies may complement each other to develop a more comprehensive vision of the postglacial history of forest trees in the Alpine range.


2018 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J. Balick ◽  
Christopher Cassa ◽  
Jack Kosmicki ◽  
Mark J. Daly ◽  
...  

AbstractThe fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation-selection balance, as has been proposed earlier [1]. Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC dataset [2]. Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation-selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.


Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2276
Author(s):  
Elena Buzan ◽  
Urška Gerič ◽  
Sandra Potušek ◽  
Katarina Flajšman ◽  
Boštjan Pokorny

Across its pan-European distribution, the European roe deer (Capreolus capreolus) faces a wide diversity of environmental and climatic conditions; therefore, several factors, including intrinsic ones, shape life-history traits and cause significant variability in parameters of fitness. By utilizing microsatellite variations in 214 roe deer females collected throughout Slovenia, Central Europe, we determined the genetic variability and population structure of this species in the contact zone between the Alps and the Dinaric Mountains, i.e., over a wider area where data on the genetic outlook for this—the most common and widespread European wild ungulate—have been completely lacking so far. Throughout the country, we found moderate microsatellite diversity (Ho = 0.57–0.65) in relation to the observed heterozygosity reported for other roe deer populations in Europe. Spatial differences in genetic diversity of the species in Slovenia can be explained by population history linked to varying approaches to population management and/or different connectivity among subpopulations in topographically differentiated habitats. A country-wide pattern of genetic structure is clearly defined by separation of the populations into three groups present in the following regions: (i) Southern sub-Mediterranean and Karst regions, (ii) Central Slovenia, and (iii) the Sub-Pannonian Region in the north-east. This is also confirmed by evidencing a moderate isolation by distance, especially by separating southern samples (coastal Slovenia) from others. Levels of genetic differentiation vary among populations, which can be explained by the effect of natural geographical barriers or the presence of anthropogenic barriers such as urban areas and highways. In the subset of 172 yearling females, we analyzed the influence of genetic advantage (individual heterozygosity) and other genetic data (reflected in the structuring of the population) on body mass and reproductive ability. We found evidence that genetic factors influence the body mass of roe deer yearling females (explaining altogether 18.8% of body mass variance), and the level of individual heterozygosity alone also positively affected body mass, which is in accordance with the theory that heterozygosity is commonly positively correlated with fitness in wild populations. However, we did not uncover any effect of heterozygosity on two parameters of reproductive ability (fertility and potential reproductive outcome), indicating that several other factors, especially environmental ones, have a predominant effect on the parameters of fitness in roe deer.


2009 ◽  
Author(s):  
Hermann Alexander Berlepsch ◽  
Leslie Stephen
Keyword(s):  

2014 ◽  
Author(s):  
William John Law
Keyword(s):  

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