Analysis of microsatellite variation in Pinus radiata reveals effects of genetic drift but no recent bottlenecks

Abstract

Most conifer species occur in large continuous populations, but radiata pine, Pinus radiata, occurs only in five disjunctive natural populations in California and Mexico. The Mexican island populations were presumably colonized from the mainland millions of years ago. According to Axelrod (1981), the mainland populations are relicts of an earlier much wider distribution, reduced some 8000 years ago, whereas according to Millar (1997, 2000), the patchy metapopulation‐like structure is typical of the long‐term population demography of the species. We used 19 highly polymorphic microsatellite loci to describe population structure and to search for signs of the dynamics of population demography over space and time. Frequencies of null alleles at microsatellite loci were estimated using an approach based on the probability of identity by descent. Microsatellite genetic diversities were high in all populations [expected heterozygosity (He) = 0.68–0.77], but the island populations had significantly lower estimates. Variation between loci in genetic differentiation (FST) was high, but no locus deviated statistically significantly from the rest at an experiment wide level of 0.05. Thus, all loci were included in subsequent analysis. The average differentiation was measured as FST = 0.14 (SD 0.012), comparable with earlier allozyme results. The island populations were more diverged from the other populations and from an inferred common ancestral gene pool than the mainland ones. All populations showed a deficiency of expected heterozygosity given the number of alleles, the mainland populations more so than the island ones. The results thus do not support a recent important contraction in the mainland range of radiata pine.

On the origin of the invasive olives (Olea europaea L., Oleaceae)

“…This program uses the fact that recently bottlenecked populations exhibit an excess of gene diversity among polymorphic loci. The observed gene diversity (H e ) is compared to the gene diversity expected at mutation-drift equilibrium (H eq ) given the number of alleles and the sample size (see Piry et al (1999) and Kahru et al (2006) for more detailed descriptions of the method). Several statistical tests have been proposed to evaluate the significance of such differences (Cornuet and Luikart, 1996), and we applied the Wilcoxon signedrank test, as it does not require a large number of polymorphic loci and is statistically more powerful than the other tests in detecting bottlenecks (Maudet et al, 2002).…”

Genetic Variation Amongst and Within the Native Provenances of Pinus radiata D. Don in South-eastern Australia. 3. Molecular and Quantitative Structure

“…Missing data do not appear to significantly affect the result of clustering, if the misses are not too frequent or systematic. The average amount of missing data in the data from KARHU et al (2006) across all loci is 8.3 %, with the maximum missing data being 19.2 % for locus Pr-048 and the lowest 1.3 % for Pr-001 so missing data are unlikely to cause any major anomalies in this re-analysis. Inbreeding and the presence of genotyping errors (including incorrectly assigned null alleles) can lead to overestimation of K especially for models that allow admixture within individuals and also assume correlated allele frequencies between clusters (PRITCHARD et al, 2002).…”

“…The microsatellite data from KARHU et al (2006) was reanalysed using the Bayesian models implemented in STRUCTURE (PRITCHARD et al, 2000) to estimate the number of genetic groupings (K). Unlike prior analyses of this data, individual trees are not assigned to populations a priori and the optimal number of genetic groups (K) is estimated based purely on co-ancestory.…”

“…Seed from this collection has also been assayed for isozyme variation (MORAN et al, 1988), and microsatellites were used (KARHU et al, 2006) to study variation amongst 20 year old trees in one of the provenance bulk seedlot trials (without family identity maintained). Similar to the quantitative studies, the molecular studies have indicated large, significant differences between the provenances, particularly between the island and mainland groups.…”

“…Violation of the assumption that geographic origin is a strong surrogate for genetic group affiliation would undermine interpretation of both molecular and quantitative studies. To counter-act this potential problem the microsatellite data from KARHU et al (2006) was reanalysed using the Bayesian models implemented in STRUCTURE (PRITCHARD et al, 2000). In this analysis we aim to estimate the number of genetic groupings (K) and to determine if these correspond to the number of observed geographic populations.…”