Search

The effective population size (N e ) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on N e , with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between N e and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long-term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X-chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X-chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations., (© 2017 John Wiley & Sons Ltd.)

Background: Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations., Results: While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods. These changes, particularly in coding sequences, are most consistent with the operation of balancing selection and the antagonistic pleiotropy theory of aging and life history traits that tend to be intercorrelated. Genes involved in antioxidant defenses, along with multiple lncRNAs, were among those most affected by balancing selection. Despite the overwhelming genetic diversification and the paucity of selective sweep regions, two genes with functions important for central nervous system and memory, Ptp10D and Ank2, evolved under positive selection in the longevity lines., Conclusions: Overall, the 'evolve-and-resequence' experimental approach proves successful in providing unique insights into the complex evolutionary dynamics of genomic regions responsible for longevity.

Habitat loss and fragmentation represent the most serious extinction threats for many species and have been demonstrated to be especially detrimental for mammals. Particularly, highly specialized species with low dispersal abilities will encounter a high risk of extinction in fragmented landscapes. Here we studied the edible dormouse (Glis glis), a small arboreal mammal that is distributed throughout Central Europe, where forests are mostly fragmented at different spatial scales. The aim of this study was to investigate the effect of habitat fragmentation on genetic population structures using the example of edible dormouse populations inhabiting forest fragments in south western Germany. We genotyped 380 adult individuals captured between 2001 and 2009 in four different forest fragments and one large continuous forest using 14 species-specific microsatellites. We hypothesised, that populations in small forest patches have a lower genetic diversity and are more isolated compared to populations living in continuous forests. In accordance with our expectations we found that dormice inhabiting forest fragments were isolated from each other. Furthermore, their genetic population structure was more unstable over the study period than in the large continuous forest. Even though we could not detect lower genetic variability within individuals inhabiting forest fragments, strong genetic isolation and an overall high risk to mate with close relatives might be precursors to a reduced genetic variability and the onset of inbreeding depression. Results of this study highlight that connectivity among habitat fragments can already be strongly hampered before genetic erosion within small and isolated populations becomes evident.

A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1) estimating genetic relationships among individuals and 2) designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks.

A number of evolutionary mechanisms have been suggested for generating low but significant genetic structuring among marine fish populations. We used nine microsatellite loci and recently developed methods in landscape genetics and coalescence-based estimation of historical gene flow and effective population sizes to assess temporal and spatial dynamics of the population structure in European flounder (Platichthys flesus L.). We collected 1062 flounders from 13 localities in the northeast Atlantic and Baltic Seas and found temporally stable and highly significant genetic differentiation among samples covering a large part of the species' range (global F(ST) = 0.024, P < 0.0001). In addition to historical processes, a number of contemporary acting evolutionary mechanisms were associated with genetic structuring. Physical forces, such as oceanographic and bathymetric barriers, were most likely related with the extreme isolation of the island population at the Faroe Islands. A sharp genetic break was associated with a change in life history from pelagic to benthic spawners in the Baltic Sea. Partial Mantel tests showed that geographical distance per se was not related with genetic structuring among Atlantic and western Baltic Sea samples. Alternative factors, such as dispersal potential and/or environmental gradients, could be important for generating genetic divergence in this region. The results show that the magnitude and scale of structuring generated by a specific mechanism depend critically on its interplay with other evolutionary mechanisms, highlighting the importance of investigating species with wide geographical and ecological distributions to increase our understanding of evolution in the marine environment.

Clinal analysis for fitness-related traits provides a well-known approach to investigate adaptive evolution. Several fitness-related traits (developmental time, thorax length, wing length and wing loading) were measured at two laboratory generations (G7 and G33) of D. buzzatii from an altitudinal gradient from northwestern Argentina, where significant thermal differences persist. Developmental time (DT) was positively correlated with altitude of origin of population. Further, DT was negatively correlated with maximal mean temperature at the site of origin of population, and this thermal variable decreases with altitude. Wing loading tended to be larger in highland than in lowland populations, suggesting that flight performance is subject to stronger selection pressure in highland populations. Developmental time showed a significant increase with laboratory generation number. There was no significant correlation between developmental time and body size across populations along the altitudinal cline of DT. This result illustrates that developmental time and body size do not always evolve in the same direction, even though both traits are often positively and genetically correlated in a well-known tradeoff in Drosophila.

DNA from archived otoliths was used to explore the temporal stability of the genetic composition of two cod populations, the Moray Firth (North Sea) sampled in 1965 and 2002, and the Bornholm Basin (Baltic Sea) sampled in 1928 and 1997. We found no significant changes in the allele frequencies for the Moray Firth population, while subtle but significant genetic changes over time were detected for the Bornholm Basin population. Estimates of the effective population size (Ne) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and Ne's most likely range in the thousands. There was no apparent loss of genetic variability and no evidence of a genetic bottleneck for either of the populations. Calculations of the expected levels of genetic variability under different scenarios of Ne showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by Ne's exceeding thousand. Recent fishery-induced bottlenecks can, however, not be ruled out as an explanation for the apparent discrepancy between high levels of variability and recently reported estimates of Ne << 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species' biology and extremely low Ne/N ratios. Our data suggest that very small Ne's are not likely to be of general concern for cod populations and, accordingly, most populations do not face any severe threat of losing evolutionary potential due to genetic drift.

The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.

Biodiversity is increasingly subjected to human-induced changes of the environment. To persist, populations continually have to adapt to these often stressful changes including pollution and climate change. Genetic erosion in small populations, owing to fragmentation of natural habitats, is expected to obstruct such adaptive responses: (i) genetic drift will cause a decrease in the level of adaptive genetic variation, thereby limiting evolutionary responses; (ii) inbreeding and the concomitant inbreeding depression will reduce individual fitness and, consequently, the tolerance of populations to environmental stress. Importantly, inbreeding generally increases the sensitivity of a population to stress, thereby increasing the amount of inbreeding depression. As adaptation to stress is most often accompanied by increased mortality (cost of selection), the increase in the 'cost of inbreeding' under stress is expected to severely hamper evolutionary adaptive processes. Inbreeding thus plays a pivotal role in this process and is expected to limit the probability of genetically eroded populations to successfully adapt to stressful environmental conditions. Consequently, the dynamics of small fragmented populations may differ considerably from large nonfragmented populations. The resilience of fragmented populations to changing and deteriorating environments is expected to be greatly decreased. Alleviating inbreeding depression, therefore, is crucial to ensure population persistence. [ABSTRACT FROM AUTHOR]

Abstract: Molecular genetic markers can be used to identify quantitative trait loci (QTL) for thermal resistance and this has allowed characterization of a major QTL for knockdown resistance to high temperature in Drosophila melanogaster. The QTL showed trade-off associations with cold resistance under laboratory conditions. However, assays of thermal tolerance conducted in the laboratory may not necessarily reflect performance at varying temperatures in the field. Here we tested if lines with different genotypes in this QTL show different thermal performance under high and low temperatures in the field using a release recapture assay. We found that lines carrying the QTL genotype for high thermal tolerance were significantly better at locating resources in the field releases under hot temperatures while the QTL line carrying the contrasting genotype were superior at cold temperatures. Further, we studied copulatory success between the different QTL genotypes at different temperatures. We found higher copulatory success in males of the high tolerance QTL genotype under hot temperature conditions, while there was no difference in females at cold temperatures. The results allow relating components of field fitness at different environmental temperatures with genotypic variation in a QTL for thermal tolerance. [Copyright &y& Elsevier]

The aim of this study was to examine genetic variation in desiccation tolerance in cocoons of the parthenogenetically reproducing earthworm Dendrobaena octaedra by comparing populations originating from different geographic regions (Denmark, Norway and Finland), representing large differences in precipitation and temperature. In one experiment, the tolerance of the three populations to increasing desiccation stress in the range from 100 to 91.6% relative humidity (RH) was examined, aiming to represent ecologically relevant RH values. In a second experiment, the effect of cocoon size on desiccation tolerance was investigated at 92.3% RH in the same three populations. There were highly significant differences in desiccation tolerance between populations, indicating a high genetic differentiation of this trait in D. octaedra. Cocoons from Denmark were much more sensitive (71±14% mortality at 91.6% RH) than cocoons from Norway (21±4% mortality) and Finland (4±5% mortality). Cocoons of worms from Finland and Norway were significantly larger than cocoons produced by worms from Denmark suggesting that cocoons from Denmark lost water at a higher rate when subjected to low humidity. Assuming that slow dehydration is necessary for physiologically based protection mechanisms it may be expected that desiccation tolerance is positively correlated with cocoon size. However, within each of the populations cocoon fresh weight did not have any significant impact on desiccation tolerance. When all populations were pooled there was a significant positive effect of cocoon fresh weight on desiccation tolerance, explaining about 20% of the total variation (linear regression). It seems therefore that genetic variation of desiccation tolerance in D. octaedra cocoons is related to variation in both cocoon size and other, physiologically based tolerance mechanisms. [Copyright &y& Elsevier]

Variation of three morphological traits (thorax length, wing length and sternopleural bristle number) was examined in Drosophila melanogaster reared on a medium with low yeast content and on a standard medium using the isofemale line analysis and offspring–parent regression. The aim was to test whether these experimental approaches give different patterns of changes in genetic variability estimates when stressful and nonstressful environments are compared. Heritabilities and genetic and phenotypic variances were generally higher in the isofemale line design than in the offspring–parent regression design under both standard and poor nutritional conditions. For each trait, the response of heritability to stress was similar in both designs: wing length exhibited lower heritability under poor nutrition, whereas heritabilities of thorax length and sternopleural bristle number did not differ between nutritional regimes. Statistically significant differences in the genetic variances and the environmental variances between stressful and nonstressful environments were recorded only in isofemale lines: the genetic variance of thorax length and the environmental variances of thorax length and wing length were higher under poor nutrition. The results are compared to literature data and possible reasons of increased genetic variability estimates in isofemale lines are briefly discussed. [ABSTRACT FROM AUTHOR]

Although adaptation of Drosophila to thermal extremes has been investigated for many years, only recently has much progress been made in identifying the genetic and physiological basis of evolutionary shifts in thermoresistance. Here we examine the way the Drosophila research has been used to understand the evolution of plastic responses, tradeoffs and limits to selection, and to develop links between laboratory studies and adaptive shifts leading to population and species differences.Several methods have been devised to rapidly measure heat and cold resistance, but the relevance of these measures to selection pressures in nature remains largely unknown. Plastic responses to thermal extremes are usually divided into short-term exposures to sub-lethal conditions or into longer-term exposures (often referred to as hardening and acclimation respectively). Hardening responses appear to have costs associated with the expression of a heat shock protein (Hsp70). Costs of acclimation are more difficult to identify because exposing Drosophila to suboptimal conditions for a long time can have deleterious effects unrelated to the acclimation response.Quantitative genetic analyses have revealed genetic variation for thermoresistance under laboratory conditions, but variation under natural conditions has rarely been identified. In a few cases selection responses within laboratory populations have been linked to specific candidate genes and physiological mechanisms.Population comparisons have provided evidence for clinal variation in thermoresistance traits, although many studies lack power because only a few populations have been considered. Clinal patterns in candidate genes have also been demonstrated. However evidence for direct selection for thermoresistance and for the involvement of specific genes under natural conditions is mostly lacking. Clinal responses to cold extremes can involve changes in diapause strategies and altered patterns of reproduction. Inbreeding influences thermoresistance and acclimation responses, but inbreeding effects may be environment-specific.Species differences in heat or in cold resistance commonly match the geographical (climatic) distributions of species. Interspecific differences for heat resistance are usually smaller than for cold resistance. Drosophila species from the same location can differ markedly for stress resistance, and this may allow species to occupy different niches.Rapid progress is likely in the next few years in identifying genes and traits underlying variation in stress resistance among populations and species of Drosophila, and in comparing these findings to those from other taxa. [Copyright &y& Elsevier]