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.

Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia

Background

Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region's reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well.

Methods

During the annual monitoring that was performed in the period from 2013-2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers.

Results

The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn't demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.

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.

Further Evidence of Population Admixture in the Serbian Honey Bee Population

Simple Summary

The western honey bee is one of the most ecologically and economically important pollinator species. Due to human interference, it faces serious challenges, not only in number decline and habitat loss, but also in natural subspecies diversity and distribution. The conservation of genetic diversity and perseverance of locally adapted populations and subspecies becomes a crucial task in the face of rapid environmental changes. In order to further assess present genetic variability in Serbian honey bee populations, we analyzed 14 microsatellite loci and then compared nine of them with previously published data. Our results suggest that Serbia now harbors a distinct, relatively homogenous honey bee population, although some local differences are still preserved.

Abstract

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.

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

Simple Summary

Does variation in the mitochondrial DNA sequence influence the survival and reproduction of an individual? What is the purpose of genetic variation of the mitochondrial DNA between individuals from the same population? As a simple laboratory model, Drosophila species can give us the answer to this question. Creating experimental lines with different combinations of mitochondrial and nuclear genomic DNA and testing how successful these lines were in surviving in different experimental set-ups enables us to deduce the effect that both genomes have on fitness. This study on D. obscura experimentally validates theoretical models that explain the persistence of mitochondrial DNA variation within populations. Our results shed light on the various mechanisms that maintain this type of variation. Finally, by conducting the experiments on two experimental temperatures, we have shown that environmental variations can support mitochondrial DNA variation within populations.

Abstract

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.

Genetic Diversity Analysis of Mitochondrial Cytb Gene, Phylogeny and Phylogeography of Protected Griffon Vulture (Gyps fulvus) from Serbia

Once a widespread and common species across the region of southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia with 290 couples represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction or recolonization programs. To estimate the level of genetic diversity, the mitochondrial Cytb gene from 58 unrelated birds sampled during the marking in the nests was sequenced and compared to the homologous Griffon vulture sequences available in publicly accessible online databases. Phylogeographic analysis based on Cytb sequences showed that the most frequent haplotype is found in all Griffon vulture populations and that each population possesses private haplotypes. Our data suggest that the Griffon vulture population from Serbia should be used as a source population for restocking and reintroduction programs in the region. The observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds from remote populations should be avoided and that birds from indigenous or neighboring populations, if available, should be used instead.

Unprecedented Density and Persistence of Feral Honey Bees in Urban Environments of a Large SE-European City (Belgrade, Serbia)

It is assumed that wild honey bees have become largely extinct across Europe since the 1980s, following the introduction of exotic ectoparasitic mite (Varroa) and the associated spillover of various pathogens. However, several recent studies reported on unmanaged colonies that survived the Varroa mite infestation. Herewith, we present another case of unmanaged, free-living population of honey bees in SE Europe, a rare case of feral bees inhabiting a large and highly populated urban area: Belgrade, the capital of Serbia. We compiled a massive data-set derived from opportunistic citizen science (>1300 records) during the 2011-2017 period and investigated whether these honey bee colonies and the high incidence of swarms could be a result of a stable, self-sustaining feral population (i.e., not of regular inflow of swarms escaping from local managed apiaries), and discussed various explanations for its existence. We also present the possibilities and challenges associated with the detection and effective monitoring of feral/wild honey bees in urban settings, and the role of citizen science in such endeavors. Our results will underpin ongoing initiatives to better understand and support naturally selected resistance mechanisms against the Varroa mite, which should contribute to alleviating current threats and risks to global apiculture and food production security.

Life History Traits in Two Drosophila Species Differently Affected by Microbiota Diversity under Lead Exposure

Simple Summary

Microbiota have a significant functional role in the life of the host, including immunity, lifespan and reproduction. Drosophila species are attractive model organisms for investigating microbiota diversity from different aspects due to their simple gut microbiota, short generation time and high fertility. Considering such an important role of the microbiota in the life of Drosophila, we investigated the extent to which lead (Pb), as one of the most abundant heavy metals in the environment, affects the microbiota and the fitness of this insect host. The results indicate that different factors, such as population origin and sex, may affect individual traits differently and this could be species-specific. In addition, there are members of microbiota that help the host to overcome environmental stress and they could play a key role in reducing the fitness cost in such situations. Studying the influence of microbiota on the adaptive response to heavy metals and the potential implications on overall host fitness is of great pertinence.

Abstract

Life history traits determine the persistence and reproduction of each species. Factors that can affect life history traits are numerous and can be of different origin. We investigated the influence of population origin and heavy metal exposure on microbiota diversity and two life history traits, egg-to-adult viability and developmental time, in Drosophila melanogaster and Drosophila subobscura, grown in the laboratory on a lead (II) acetate-saturated substrate. We used 24 samples, 8 larval and 16 adult samples (two species × two substrates × two populations × two sexes). The composition of microbiota was determined by sequencing (NGS) of the V3–V4 variable regions of the 16S rRNA gene. The population origin showed a significant influence on life history traits, though each trait in the two species was affected differentially. Reduced viability in D. melanogaster could be a cost of fast development, decrease in Lactobacillus abundance and the presence of Wolbachia. The heavy metal exposure in D. subobscura caused shifts in developmental time but maintained the egg-to-adult viability at a similar level. Microbiota diversity indicated that the Komagataeibacter could be a valuable member of D. subobscura microbiota in overcoming the environmental stress. Research on the impact of microbiota on the adaptive response to heavy metals and consequently the potential tradeoffs among different life history traits is of great importance in evolutionary research.

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

Simple Summary

The western honey bee is one of the most economically and ecologically important species currently facing serious challenges in its whole area of distribution. The honey bee is a highly diverse species with about 30 subspecies that are adapted to regional climate factors, vegetation, pests and pathogens. The local populations of honey bees are rapidly changing and their diversity is constantly manipulated by beekeepers through the import of foreign queens, selection and migratory beekeeping. This manipulation may lead to such changes that honey bees lose their ability to thrive in the areas that were previously suitable for their wellbeing. To see how this human interference changed the genetic variability of native honey bee populations from Serbia, we sequenced part of the mitochondrial genome and compared them with published sequences. Our results suggest that human influence significantly changes the natural composition of honey bees in Serbia and that the presence of some previously reported subspecies could not be confirmed.

Abstract

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 tRNA^leu-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 F_ST 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.

Sex-specific effects of sympatric mitonuclear variation on fitness in Drosophila subobscura

Background

A number of recent studies have shown that the pattern of mitochondrial DNA variation and evolution is at odds with a neutral equilibrium model. Theory has suggested that selection on mitonuclear genotypes can act to maintain stable mitonuclear polymorphism within populations. However, this effect largely relies upon selection being either sex-specific or frequency dependent. Here, we use mitonuclear introgression lines to assess differences in a series of key life-history traits (egg-to-adult developmental time, viability, offspring sex-ratio, adult longevity and resistance to desiccation) in Drosophila subobscura fruit flies carrying one of three different sympatric mtDNA haplotypes.

Results

We found functional differences between these sympatric mtDNA haplotypes, but these effects were contingent upon the nuclear genome with which they were co-expressed. Further, we demonstrate a significant mitonuclear genetic effect on adult sex ratio, as well as a sex × mtDNA × nuDNA interaction for adult longevity.

Conclusions

The observed effects suggest that sex specific mitonuclear selection contributes to the maintenance of mtDNA polymorphism and to mitonuclear linkage disequilibrium in this model system.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0421-2) contains supplementary material, which is available to authorized users.