Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica

MethodsGenetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis.ConclusionsThe combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis.     

Genetic differentiation of Rubus chamaemorus populations in the Czech Republic and Norway after the last glacial period

The population structure of cloudberry (Rubus chamaemorus L.), collected from Krkonose Mountains (the Czech Republic), continental Norway and Spitsbergen, was examined using microsatellite analyses (SSR). Among 184 individuals, 162 different genotypes were identified. The overall unbiased gene diversity was high (). A high level of genetic differentiation among populations (F_ST = 0.45; p < .01) indicated restricted gene flow between populations. Using a Bayesian approach, six clusters were found which represented the genetic structure of the studied cloudberry populations. The value of correlation index between genetic and geographical distances (r = .44) indicates that gene flow, even over a long distance, could exist. An exact test of population differentiation showed that Rubus chamaemorus populations from regions (Krkonose Mountains, continental Norway and Spitsbergen) are differentiated although some individuals within populations share common alleles even among regions. These results were confirmed by AMOVA, where the highest level of diversity was found within populations (70.8%). There was no difference between 87 pairs of populations (18.7%) mostly within cloudberry populations from continental Norway and from Spitsbergen. Based on obtained results, it is possible to conclude that Czech and Norwegian cloudberry populations are undergoing differentiation, which preserves unique allele compositions most likely from original populations during the last glaciation period. This knowledge will be important for the creation and continuation of in situ and ex situ conservation of cloudberry populations within these areas.     

Microsatellite variation in simulated and natural founder populations of the Laysan finch (Telespiza cantans)

Historical and demographic data were used in a computer model tosimulate neutral genetic change in populations of the Laysanfinch (Telespiza cantans), an insular passerine bird that hasundergone documented founder events at Pearl and Hermes reef(PHR). Measures of genetic variation in the natural PHRpopulations generally matched those in the simulated populations,except that heterozygosity on Southeast Island was lower than themodel predicted, and the heterozygote excess in the naturalpopulations had a low probability of occurrence in the simulatedpopulations. The estimate of effective population size (N _e) fromthe stochastic demographic model matched the estimate fromgenetic data for two populations, but the demographic estimatewas higher than the genetic estimate for Southeast Island. Smallfounder number was rejected as a possible explanation for thereduced genetic variation on Southeast. We suggest that N _e wasoverestimated in part because we assumed seasonal variance inreproductive success. Additional variance components need to bemeasured in the field and incorporated into the model. Accounting for the heterozygote excess also requires furthertheoretical and field investigations. Possible explanations forthe excess include inbreeding depression, incest avoidance, andthe effect of polygyny on heterozygote excess in smallpopulations. We concluded that the Pearl and Hermes reefpopulation will continue to lose genetic variation at a highrate, and translocations from the native population on Laysan maybe required to maintain a viable population on the reef.     

Genetic variation in North Amerindian populations: the geography of gene frequencies

Ten-level synthetic gene frequency maps derived from a principal component analysis of seven polymorphic loci are displayed for a large sample of North Amerindian populations. These maps are useful for assessing population affinities over broad geographical regions and perhaps, as others have argued, for inferring recent migrations. The influence of European admixture is investigated by deleting highly admixed populations and regenerating the maps. In broad outline the resultant geographic patterning, while appearing more homogeneous, preserves many features of the maps that include the highly admixed samples--especially with respect to the Eskimo/non-Eskimo dichotomy. Further, in an effort to evaluate how varying the number of display levels affects patterning as well as interpretation, the maps were replotted at 5 and 20 levels. The 5-level maps are found to accentuate differences between the full data set and the less admixed data set, while the 20-level maps tend to obscure these differences.     

Vegetation history since the last glacial period in the Mikata lowland,the Sea of Japan area,western Japan

Local and regional vegetation since the last glacial period was reconstructed on the basis of a palynological study of sediment at Iwaya, in the Sea of Japan area, western Japan. During the interstade (before about 30 000 years BP), forests were composed predominantly ofCryptomeria japonica withTsuga sieboldii and cool-temperate deciduous broad-leaved trees. In the pre-full-glacial, the full-glacial and the early late-glacial (30 000-12 000 years BP), forests were dominated by temperate (montane) and boreal (subalpine) Pinaceae andBetula. During the early full-glacial, the pinaceous forests were mixed with cool-temperate trees such asFagus crenata. In the late full-glacial (18 000-16 000 years BP), the maximum development of pinaceous conifer forests was recognized. Cool-temperate broad-leaved forests composed mainly ofF. crenata andQuercus (Lepidobalanus) replaced the pinaceous forests at about 12 000 years BP and were maintained to the early postglacial.Cryptomeria japonica was distributed around the Mikata lowland during the last glacial.Cryptomeria japonica, which began to increase at 16 000 years BP, increased abruptly in the early postglacial and spread throughout the postglacial in the lowlands. After 6300 years BP, lucidophyllous forests composed mainly ofQuercus (Cyclobalanopsis) andCastanopsis were established in the Mikata district; this was later than in the inland and the Pacific Ocean areas in the Kinki region, western Japan. In historic times (afterca 2000 years BP), secondary forest ofPinus densiflora, which can grow as a pioneer in disturbed habitats, spread.     

Genetic variation in natural populations of the aphid Rhopalosiphum padi as revealed by maternally inherited markers

A survey on 148 clones of the aphid Rhopalosiphum padi from 11 widespread localities has been carried out to study the genetic structure of populations of this species as revealed by mitochondrial DNA restriction site and length polymorphisms as well as by restriction site analysis of a maternally inherited plasmid carried by the aphid eubacterial endosymbiont Buchnera aphidicola. Our results support the existence in the area under study of two main aphid maternal lineages strikingly coincidental with the two main reproductive categories displayed by this species. Those aphid clones possessing an incomplete life cycle that lacks the sexual phase (anholocyclic or androcyclic clones) show mitochondrial DNA (mtDNA) haplotype I and plasmid haplotype I, whereas those clones displaying the complete life cycle (holocyclic clones) posses some other distinct mtDNA haplotypes closely related to each other and plasmid haplotype II. While restriction-site analysis of maternally inherited markers points to a relatively ancient origin of anholocycly/androcycly (between 460 000 and 1 400 000 years) followed by interrupted gene flow with respect to the ancestral holocyclic population, mtDNA size variation also suggests that historical stochastic processes have a different effect on the evolution of both main aphid lineages. Evidence of occasional nuclear gene flow between lineages and its consequences on the correspondence between maternally inherited haplotypes and life cycle are also presented and discussed.     

A note on the application of diallel crosses for the analysis of genetic variation in natural populations

Summary The complete diallel cross among homozygous lines can be a useful tool to analyze the genetic architecture of natural populations. However, it represents the natural population only approximately, in particular if the number of lines is small and the analyzed traits exhibit inbreeding depression or other forms of directional dominance. Some incorrect expected mean squares that can be found in the literature suggest tests for genetic variance components that can be misleading under such circumstances. Expected mean squares for a factorial analysis and for a modified Hayman analysis are presented and the effect of the number of lines and directional dominance is discussed.     

On the neutrality of molecular genetic markers: pedigree analysis of genetic variation in fragmented populations

Many studies employ molecular markers to infer ecological and evolutionary processes, assuming that variation found at genetic loci offers a reliable representation of stochastic events in natural populations. Increasingly, evidence emerges that molecular markers might not always be selectively neutral. However, only a few studies have analysed how deviations from neutrality could affect estimates of genetic variation, using populations with known genealogy. We monitored changes in allozyme variation over eight generations in captive metapopulations of the butterfly Bicyclus anynana. Population demography was recorded by individually marking 35 000 butterflies and constructing pedigrees. We designed a computer program that simulated the inheritance of founder allozyme alleles in butterfly pedigrees. We thus tested whether the observed transmission of allozyme alleles could be explained by random genetic drift alone, or whether there was evidence for positive or negative selection. This analysis showed that in the smallest metapopulations the loss of allozyme variation exceeded the neutral rate. Possibly, linkage disequilibria between deleterious mutations and marker alleles resulted in background selection and a faster erosion of allozyme variation. In larger metapopulations, one locus (MDH) showed a significant heterozygote excess and smaller than expected loss in heterozygosity, observations consistent with (associative) overdominance. This study demonstrates that the neutrality of molecular markers cannot always be assumed, particularly in small populations with a high mutation load.     

Novel genetic sex markers reveal high frequency of sex reversal in wild populations of the agile frog (Rana dalmatina) associated with anthropogenic land use

Populations of ectothermic vertebrates are vulnerable to environmental pollution and climate change because certain chemicals and extreme temperatures can cause sex reversal during early ontogeny (i.e. genetically female individuals develop male phenotype or vice versa), which may distort population sex ratios. However, we have troublingly little information on sex reversals in natural populations, due to unavailability of genetic sex markers. Here, we developed a genetic sexing method based on sex‐linked single nucleotide polymorphism loci to study the prevalence and fitness consequences of sex reversal in agile frogs (Rana dalmatina). Out of 125 juveniles raised in laboratory without exposure to sex‐reversing stimuli, 6 showed male phenotype but female genotype according to our markers. These individuals exhibited several signs of poor physiological condition, suggesting stress‐induced sex reversal and inferior fitness prospects. Among 162 adults from 11 wild populations in North‐Central Hungary, 20% of phenotypic males had female genotype according to our markers. These individuals occurred more frequently in areas of anthropogenic land use; this association was attributable to agriculture and less strongly to urban land use. Female‐to‐male sex‐reversed adults had similar body mass as normal males. We recorded no events of male‐to‐female sex reversal either in the laboratory or in the wild. These results support recent suspicions that sex reversal is widespread in nature, and suggest that human‐induced environmental changes may contribute to its pervasiveness. Furthermore, our findings indicate that sex reversal is associated with stress and poor health in early life, but sex‐reversed individuals surviving to adulthood may participate in breeding.     

Phylogeography of the high alpine plant Senecio halleri (Asteraceae) in the European Alps: in situ glacial survival with postglacial stepwise dispersal into peripheral areas

Whether alpine plant species survived Pleistocene glaciations in situ on high alpine nunatak mountains is still under debate. To test this hypothesis, Senecio halleri, a high alpine and endemic species with a narrow distribution range in the European Alps, was chosen as a model organism. Polymerase chain reaction-restriction fragment length polymorphisms of chloroplast DNA (cpDNA PCR-RFLPs) were used in a phylogeographic analysis of 14 populations of S. halleri, covering its total distribution area. The results of haplotype diversity and distribution gave evidence of in situ glacial survival on siliceous central-alpine nunatak mountains in two areas, southwest and northeast of the Aosta valley. According to the absence of genetic differentiation between these two nunatak areas (based on amova), nested clade analysis implied a history of preglacial gene flow, in situ survival and extinction of intermediate populations during glaciation and postglacial stepwise recolonization of peripheral and intermediate areas.