Population History Shapes Responses to Different Temperature Regimes in Drosophila subobscura.

Drosophila subobscura is considered a good model species for investigation of a population's ability to adapt and cope with climate changes. Decade long research has shown that inversion frequencies change in response to environmental factors indicating their role in adaptation to novel environments. The mechanisms behind organisms' responses to temperature are complex, involving changes in physiology, behavior, gene expression and regulation. On the other hand, a population's ability to respond to suboptimal conditions depends on standing genetic variation and population history. In order to elucidate the role of local adaptation in population response to the changing temperature, we investigated the response to temperature in D. subobscura individuals originating from two different altitudes by combining traditional cytogenetic techniques with assessing the levels of Hsp70 protein expression. Inversion polymorphism was assessed in the flies sampled from natural populations and in flies reared in laboratory conditions at three different temperatures after five and sixteen generations and Hsp70 protein expression profile in 12th generation flies at the basal level and after heat shock induction. Our results indicate that local adaptation and population history influence population response to the changing temperature.

Urban ecosystem drives genetic diversity in feral honey bee.

Urbanization can change biodiversity in both directions, positive and negative, and despite the rising global trend of urban beekeeping, little is known about the impact of urbanization on the genetic diversity of honey bees. We investigate how urbanization affects the genetic variability of feral and managed honey bee colonies that are spread throughout the entire city, even in highly urban areas, through genetic analysis of 82 worker bees. We found convincing evidence of high genetic differentiation between these two groups. Additionally, by comparing city samples with 241 samples from 46 apiaries in rural parts of the country, variations in mitochondrial tRNAleu-cox2 intergenic region and microsatellite loci indicated that feral colonies have distinct patterns of genetic diversity. These results, with evidence that feral honey bees find niches within highly modified and human-dominated urban landscapes, lead us to conclude that urbanization is a driver of the genetic diversity of feral honey bees in the city.

Stress Resistance Traits under Different Thermal Conditions in Drosophila subobscura from Two Altitudes.

Global warming and climate change are affecting many insect species in numerous ways. These species can develop diverse mechanisms as a response to variable environmental conditions. The rise in mean and extreme temperatures due to global warming and the importance of the population's ability to adapt to temperature stress will further increase. In this study, we investigated thermal stress response, which is considered to be one of the crucial elements of population fitness and survival in fast-changing environments. The dynamics and variation of thermal stress resistance traits in D. subobscura flies originating from two natural populations sampled from different altitudes were analysed. Three different temperature regimes (25 °C, 19 °C, and 16 °C) were used for the F1 progeny from both localities to establish six experimental groups and investigate stress resistance traits: desiccation resistance, heat knock-down resistance, starvation resistance, and chill-coma recovery time. We detected that laboratory thermal conditions and population origin may have an effect on the analysed traits, and that sex also significantly influences stress resistance. Individuals from the lower altitude reared at higher temperatures show inferior resistance to thermal shock.

Temperature-Specific and Sex-Specific Fitness Effects of Sympatric Mitochondrial and Mito-Nuclear Variation in Drosophila obscura.

The adaptive significance of sympatric mitochondrial (mtDNA) variation and the role of selective mechanisms that maintain it are debated to this day. Isofemale lines of Drosophila obscura collected from four populations were backcrossed within populations to construct experimental lines, with all combinations of mtDNA Cyt b haplotypes and nuclear genetic backgrounds (nuDNA). Individuals of both sexes from these lines were then subjected to four fitness assays (desiccation resistance, developmental time, egg-to-adult viability and sex ratio) on two experimental temperatures to examine the role of temperature fluctuations and sex-specific selection, as well as the part that interactions between the two genomes play in shaping mtDNA variation. The results varied across populations and fitness components. In the majority of comparisons, they show that sympatric mitochondrial variants affect fitness. However, their effect should be examined in light of interactions with nuDNA, as mito-nuclear genotype was even more influential on fitness across all components. We found both sex-specific and temperature-specific differences in mitochondrial and mito-nuclear genotype ranks in all fitness components. The effect of temperature-specific selection was found to be more prominent, especially in desiccation resistance. From the results of different components tested, we can also infer that temperature-specific mito-nuclear interactions rather than sex-specific selection on mito-nuclear genotypes have a more substantial role in preserving mtDNA variation in this model species.

Further Evidence of Population Admixture in the Serbian Honey Bee Population.

Socioeconomic interests and beekeeper preferences have often taken precedence over the conservation of locally native honey bee subspecies, leading to the predominance of admixture populations in human-dominated areas. To assess the genetic diversity of contemporary managed Serbian honey bee colonies, we used 14 microsatellite loci and analyzed 237 worker bees from 46 apiaries in eight localities of northern and southern Serbia. Furthermore, we compared data for nine microsatellite loci with 338 individuals from Italy, Hungary, Poland, and Spain. The standard parameters of genetic diversity in Serbian honey bee populations were in line with other analyses, although somewhat smaller. STRUCTURE analysis showed the existence of two equally distributed genetic clusters and Analysis of molecular variances could not confirm the presence of a geographically discrete population but showed local differences. Discriminant analysis of principal components showed overlapping of worker bees from different parts of Serbia. Clear genetic differentiation can be observed when comparing all populations between geographical regions and their corresponding subspecies. The absence of the A. m. macedonica subspecies from its historical distribution range in southern Serbia as well as the lack of distinctive geographical groups suggest that selective breeding, queen import, and migratory beekeeping practices strongly influence the genetic structure and diversity of honey bees, leading to the genetic uniformization and creation of the admixture population.

MtDNA Analysis Indicates Human-Induced Temporal Changes of Serbian Honey Bees Diversity.

Local populations of Apis mellifera are rapidly changing by modern beekeeping through the introduction of nonnative queens, selection and migratory beekeeping. To assess the genetic diversity of contemporary managed honey bees in Serbia, we sequenced mitochondrial tRNAleu-cox2 intergenic region of 241 worker bees from 46 apiaries at eight localities. Nine haplotypes were observed in our samples, with C2d being the most common and widespread. To evaluate genetic diversity patterns, we compared our data with 1696 sequences from the NCBI GenBank from neighbouring countries and Serbia. All 32 detected haplotypes belonged to the Southeast Europe lineage C, with two newly described haplotypes from our sample. The most frequent haplotype was C2d, followed by C2c and C1a. To distinguish A. m. carnica from A. m. macedonica, both previously reported in Serbia, PCR-RFLP analysis on the COI gene segment of mtDNA was used, and the result showed only the presence of A.m. carnica subspecies. An MDS plot constructed on pairwise FST values showed significant geographical stratification. Our samples are grouped together, but distant from the Serbian dataset from the GenBank. This, with the absence of A. m. macedonica subspecies from its historic range of distribution in southern Serbia, indicates that honey bee populations are changing rapidly due to the anthropogenic influence.

Highly contiguous assemblies of 101 drosophilid genomes.

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.