Genetic structure of the Danish red deer ('Cervus elaphus')
The red deer ('Cervus elaphus') population in Denmark became almost extinct in recent historical times due to over-hunting. The species has subsequently recovered within remote areas, but non-Danish individuals have been introduced at several localities. To assess genetic structure, past demographic history, and the possibility of a still existing original stock, we analysed 349 specimens from 11 geographically separate areas and from three enclosed areas, genotyping 11 microsatellite loci. Moreover, an 826-bp fragment of the control region of the mitochondrial DNA was sequenced for 116 recent specimens and seven museum specimens. There was a significant difference in mean expected heterozygosity (HE) between the three enclosed areas and the 11 unenclosed areas. Significant departures from Hardy–Weinberg equilibrium were observed in the three enclosed areas and in nine of the unenclosed areas. The overall degree of genetic differentiation among all 14 areas was significant (FST = 0.09, P < 0.01), primarily because the mean pairwise FST for the three enclosed areas was significantly higher than that for the 11 unenclosed areas. A Bayesian clustering procedure detected three genetically distinct populations and indicated reduced gene flow between the enclosed and unenclosed areas. The individuals in the unenclosed areas show genotypic mixture, presumably as a result of gene flow among them. Markov Chain Monte Carlo simulations, based on the genealogical history of the microsatellite alleles, suggest a drastic decline in the effective population size of the enclosed areas some 188–474 years ago. Mitochondrial DNA analysis of the recent specimens showed seven haplotypes. Individuals from the enclosed Jægersborg Dyrehave contain haplotypes that occur all over Denmark and also are found in Western Europe. A close relationship between Scandinavian and Western European red deer is most likely. Only individuals from the unenclosed Lindenborg Estate and the enclosed Tofte Skov did not group with any other Danish individuals. As six of seven museum specimens had haplotypes also found in modern Danish samples, current population of red deer in Denmark is genetically close to the original Danish red deer.
Characterization of the 'shsp' genes in 'Drosophila buzzatii' and association between the frequency of Valine mutations in 'hsp23' and climatic variables along a longitudinal gradient in Australia
The small heat shock gene ('shsp') cluster of 'Drosophila buzzatii' was sequenced and the gene order and DNA sequence were compared with those of the 'shsps' in 'Drosophila melanogaster'. The 'D. buzzatii shsp' cluster contains an inversion and a duplication of 'hsp26'. A phylogenetic tree was constructed based on 'hsp26' genes from several 'Drosophila' species of the 'Sophophora' and 'Drosophila subgenera'. The tree shows first a separation of the 'Sophophora' and the 'Drosophila subgenera' and then the 'Drosophila' subgenus is divided into the Hawaiian 'Drosophila' and the 'repleta/virilis' groups. Only the latter contain a duplicated 'hsp26'. Comparing the gene organisation of the 'shsp' cluster shows that all the 'Drosophila' subgenus species contain the inversion. Putative heat shock elements (HSE) were found in the promoters of all the 'shsp' and putative regulator elements for tissue specific expression were found in the promoter of 'hsp23', 'hsp27' and one of the 'hsp26' genes. 'hsp23' was found to be polymorphic for four non-synonymous changes that all lead to exchange of a Valine. The duplicated 'hsp26' gene in 'D. buzzatii' '(phsp26)' was polymorphic for two non-synonymous changes. The allele frequencies of these variants were determined in nine 'D. buzzatii' populations covering most of its distribution in Australia using high-resolution melting curves. The allele frequencies of one of the 'hsp23' variants showed a significant linear regression with longitude and the pooled frequency of the four Valine changes of 'hsp23' in the nine populations showed a significant linear regression with longitude and with a composite measure of climatic variables.
Erratum - Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian 'Drosophila buzzatii'
Correction to: Heredity (2009) 102, 389-401; doi: https://doi.org/10.1038/hdy.2008.127. The authors have realized that an incorrect version of Table 3 was published. Please see the correct table below. The authors apologize for this error.
The consequences of the variance-mean rescaling effect on effective population size
The effective population size (Ne), and the ratio between Ne and census population size (N) are often used as measures of population viability. We show that using the harmonic mean of population sizes over time – a common proxy for Ne– has some important evolutionary consequences and implications for conservation management. This stems from the fact that there is no unambiguous relationship between the arithmetic and harmonic means for populations fluctuating in size. As long as the variance of population size increases moderately with increasing arithmetic mean population size, the harmonic mean also increases. However, if the variance of population size increases more rapidly, which existing data often suggest, then the harmonic mean may actually decrease with increasing arithmetic mean. Thus maximizing N may not maximize Ne, but could instead lower the adaptive potential and hence limit the evolutionary response to environmental change. Large census size has the clear advantage of lowering demographic stochasticity, and hence extinction risk, and under certain conditions large census size also minimizes the loss of genetic variation. Consequently, maximising census size has served as a useful dogma in ecology, genetics and conservation. Nonetheless, due to the intricate relationships among Ne, population viability and the properties of population fluctuations, we suggest that this dogma should be taken only as a rule of thumb.
Genetic variability in the mitochondrial DNA of the Danish Pine marten
Here we study genetic differentiation and changes over time in genetic variability in the rare pine marten 'Martes martes'. Samples from three isolated geographic regions: Jutland and Sealand (Denmark) and southern Scania (southernmost Sweden), were genotyped by sequencing the hypervariable domain of the mitochondria control region. Both recent and museum samples were analysed in order to evaluate any temporal loss of genetic variability. Eight haplotypes were found. Two were main haplotypes shared by individuals from all three regions, and in all localities unique haplotypes were found. When comparing the data with previous haplotype analysis, our results suggest that at least three different haplotype groups exist in central and Northern Europe, with the samples from southern Scania being differentiated from samples previously analysed from central Sweden, and the genotypic data for Jutland and Sealand suggest a recent independent evolutionary history for the Danish pine marten.
Spatio-temporal population genetics of the Danish pine marten ('Martes martes')
Jutland peninsula and from the island of Sealand was performed using 11 microsatellite markers. Samples obtained from 1892 to 2003 were subdivided into historical (prior to 1970) and recent (from 1970) groups. As compared with the historical samples, there was a significant loss of genetic variation in the recent Jutland population, but not in Sealand. Effective population sizes were estimated using Bayesian-based software (TMVP). Historical effective population sizes were 5897 (90% highest probability density, HPD, limits: 1502–6849) in Jutland and 1300 (90% HPD limits: 224–5929) in Sealand, whereas recent effective population sizes were 14.7 (90% HPD limits: 10.9–23.5) in Jutland and 802 (90% HPD limits: 51.8–5510) in Sealand. Significant genetic differentiation (FST) was found between the two historical samples, between the two recent samples, and between the historical and the recent sample in Jutland; whereas the FST value between the historical and the recent sample in Sealand was not significant. The significant genetic differentiation between the historical and the recent samples indicates changes in the genetic compositions over time, and the higher FST values between the two recent samples, as compared with the two historical samples, indicates that the populations in Sealand and Jutland have drifted apart within a short time span. No deviation from Hardy–Weinberg equilibrium was found within populations, indicating no further substructuring.
Climatic adaptation of 'Drosophila buzzatii' populations in southeast Australia
Variation in 19 traits possibly relevant for thermal adaptation was studied in 11 populations of 'Drosophila buzzatii' collected in southeast Australia. Using stepwise multiple regression, the variation was compared to variation in geographic coordinates and to a set of climatic variables estimated for each collection site. For 13 of the traits, a significant part of the variation was explained by climatic variables and/or geographic coordinates, suggesting directional selection for adaptation to the environment in the majority of traits studied. In 10 of the traits, both geographic coordinates and climatic variables explained significant proportions of the variation, with R² ranging from 0.075 to 0.58. Although larvae, pupae and adults of 'D. buzzatii' share a common habitat, the measured traits were not correlated across life stages and gender. Also, there seemed to be special conditions in marginal populations near species borders, giving rise to nonlinear relations with latitude. Climate apparently does influence the adaptive evolution of the traits studied, but they also are affected by other factors that vary with latitude, longitude and distance to coast. These results highlight the complex challenges imposed by the environment on the adaptive process.
Extreme temperatures increase the deleterious consequences of inbreeding under laboratory and semi-natural conditions
The majority of experimental studies of the effects of population bottlenecks on fitness are performed under laboratory conditions, which do not account for the environmental complexity that populations face in nature. In this study, we test inbreeding depression in multiple replicates of inbred when compared with non-inbred lines of Drosophila melanogaster under different temperature conditions. Egg-to-adult viability, developmental time and sex ratio of emerging adults are studied under low, intermediate and high temperatures under laboratory as well as semi-natural conditions. The results show inbreeding depression for egg-to-adult viability. The level of inbreeding depression is highly dependent on test temperature and is observed only at low and high temperatures. Inbreeding did not affect the developmental time or the sex ratio of emerging adults. However, temperature affected the sex ratio with more females relative to males emerging at low temperatures, suggesting that selection against males in pre-adult life stages is stronger at low temperatures. The coefficient of variation (CV) of egg-to-adult viability within and among lines is higher for inbred flies and generally increases at stressful temperatures. Our results contribute to knowledge on the environmental dependency of inbreeding under different environmental conditions and emphasize that climate change may impact negatively on fitness through synergistic interactions with the genotype.
Altitudinal and seasonal variation in microsatellite allele frequencies of 'Drosophila buzzatii'
Variation in climate, particularly temperature, is known to affect the genetic composition of populations. Although there have been many studies of latitudinal variation, comparisons of populations across altitudes or seasons, particularly for animal species, are less common. Here, we study genetic variation (microsatellite markers) in populations of 'Drosophila buzzatii' collected along altitudinal gradients and in different seasons. We found no differences in genetic variation between 2 years or between seasons within years. However, there were numerous cases of significant associations between allele frequencies or expected heterozygosities and altitude, with more than half showing nonlinear relationships. While these associations indicate possible selection and local altitudinal adaptation, direct tests gave strong evidence for selection affecting two loci and weaker evidence for five other loci. Two loci that are located within an inversion (including the one with strongest evidence for selection) show a linear increase in genetic diversity with altitude, likely due to thermal selection. Parallel associations with altitude here and with latitude in Australian populations indicate that selection is operating on chromosomal regions marked by some of the loci.