scholarly journals Florida Drosophila melanogaster genomes sampled 13 years apart show increases in warm-associated SNP alleles

2020 ◽  
Author(s):  
Krishna R. Veeramah ◽  
Evgeny Brud ◽  
Walter F. Eanes
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Change ◽  
Whole Genome ◽  
Latitudinal Cline ◽  
Frequency Increase ◽  
Significant Frequency ◽  
Snp Data ◽  
Climate Shifts ◽  
Latitudinal Clines ◽  
Frequency Changes

ABSTRACTWe studied genetic change in Drosophila melanogaster using whole-genome SNP data from samples taken 13 years apart in Homestead, FL. This population is at the southern tip of a well-studied US latitudinal cline. On the non-inversion-carrying chromosome arms, 11-16% of SNPs show significant frequency changes. These are enriched for latitudinal clines and genic sites. For clinal SNPs each allele is either the northern- or southern-favored. Seventy-eight to 95 percent with significant frequency increase are southern-favored. Five to seven percent of SNPs also show significant seasonal change and involve increases in the northern-favored allele during the season. On the 2L and 3R chromosome arms there are significant seasonal shifts for common inversions. We identify regions and genes that are candidates for selection. These regions also show correspondence with those associated with soft sweeps in Raleigh, NC. This shift towards southern-favored alleles may be caused by climate shifts or increased African-European admixture.

scholarly journals Changes in relative fitness with temperature among second chromosome arrangements in Drosophila melanogaster.

Genetics ◽  
1991 ◽  
Vol 127 (3) ◽  
pp. 507-514
Author(s):  
W van Delden ◽  
A Kamping
Keyword(s):  
Drosophila Melanogaster ◽  
Development Time ◽  
Relative Fitness ◽  
Significant Excess ◽  
Chromosome Arrangements ◽  
Different Temperatures ◽  
Latitudinal Clines ◽  
Frequency Changes ◽  
Weight Decrease ◽  
Increasing Temperature

Abstract Development time and body weight of In(2L)t, R (a putative short inversion on the left arm of the second chromosome) and ST (standard) karyotypes of Drosophila melanogaster were measured at different temperatures. Frequency changes were followed in populations polymorphic for In(2L)t and ST and kept under different environmental conditions. These experiments were carried out in order to explain the worldwide latitudinal clines for In(2L)t and other inversions. To avoid interactions with the Adh and alpha Gpdh loci, which also have latitudinal clines, all karyotypes were homozygous AdhS alpha GpdhF. In(2L)t homokaryotypes had a longer development time and a lower weight than the other karyotypes at all temperatures. R/ST heterokaryotypes had the shortest development time and ST/ST had the smallest weight decrease with increasing temperature. The differences among the In(2L)t and ST karyotypes in development time were further analyzed in an experiment where the age at which 50% of the larvae were able to become adults, without further food ingestion, was determined. In polymorphic populations at 20 degrees and 25 degrees a significant decline of In(2L)t frequencies was observed. At 29.5 degrees and 33 degrees there was no change in In(2L)t frequencies but a significant excess of heterokaryotypes occurred. On ethanol-supplemented food the most drastic decline in In(2L)t frequency was observed. Populations transferred at 2- and 3-week intervals at 25 degrees exhibited large differences in final In(2L)t frequencies. The frequency changes could in part be attributed to the differences in development time and to previously observed differences in high temperature resistance. The experiments prove that the karyotypes are under selection. The results are discussed in relation to the geographic distribution of In(2L)t.

scholarly journals GENETIC DIFFERENTIATION BETWEEN GEOGRAPHICALLY DISTANT POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽  
1982 ◽  
Vol 101 (2) ◽  
pp. 235-256
Author(s):  
Rama S Singh ◽  
Donal A Hickey ◽  
Jean David
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Differentiation ◽  
Gene Frequency ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Clinal Variation ◽  
Significant Genetic Differentiation ◽  
African Populations ◽  
Latitudinal Clines ◽  
North And South

ABSTRACT We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and south. These differences arise mainly from seven loci that show gene-frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation is such that subtropical populations are more heterozygous than temperate populations. These results are discussed in relation to the selectionist and neutralist hypotheses of genetic variation in natural populations.

scholarly journals Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2644 ◽  
Author(s):  
William P. Gilks ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Matthew T. Webster ◽  
Edward H. Morrow
Keyword(s):  
Drosophila Melanogaster ◽  
Complex Traits ◽  
Population Sample ◽  
Genomic Variation ◽  
Genotype Data ◽  
Whole Genome ◽  
Unique Haplotype ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

scholarly journals THE ALCOHOL DEHYDROGENASE POLYMORPHISM IN POPULATIONS OF DROSOPHILA MELANOGASTER. I. SELECTION IN DIFFERENT ENVIRONMENTS

Genetics ◽  
1978 ◽  
Vol 90 (1) ◽  
pp. 161-191
Author(s):  
W van Delden ◽  
A C Boerema ◽  
A Kamping
Keyword(s):  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Experimental Evidence ◽  
Balancing Selection ◽  
Adult Survival ◽  
High Survival ◽  
High Humidity ◽  
Allozyme Polymorphism ◽  
Degree Of Dominance ◽  
Frequency Changes

ABSTRACT The allozyme polymorphism at the alcohol dehydrogenase locus in Drosophila melanogaster was studied in order to obtain experimental evidence about the maintenance of this polymorphism. Populations started with different initial allele frequencies from homozygous F and S lines showed a convergence of frequencies on regular food at 25°, leading to values equal to those in the base populations. These results were interpreted as due to some kind of balancing selection. In populations kept at 29.8°, a lower equilibrium F frequency was attained. Addition of ethanol and some other alcohols to the food gave a rapid increase in F frequency, and high humidity decreased the F frequency slightly. Combination or alternation of ethanol and high humidity had variable effects in the populations tested. For a further analysis of the allele-frequency changes, estimates were obtained for egg-to-adult survival under different conditions and for adult survival on ethanol-supplemented food. On ethanol food (both at regular and high humidity), egg-to-adult survival of SS homozygotes was considerably lower than that of the FF and FS genotypes. Under regular conditions of food, temperature and humidity, a tendency to heterozygote superiority was observed, while at high humidity a relative high survival of SS was noticed in some tests. Adult survival of SS was lower than that of FF, but FS was generally intermediate, though the degree of dominance differed between populations. The results are consistent with the hypothesis of the occurrence of selection at the Adh locus.

scholarly journals Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2644 ◽  
Author(s):  
William P. Gilks ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Matthew T. Webster ◽  
Edward H. Morrow
Keyword(s):  
Drosophila Melanogaster ◽  
Complex Traits ◽  
High Throughput Sequencing ◽  
Population Sample ◽  
Genomic Variation ◽  
Genotype Data ◽  
Whole Genome ◽  
Short Read ◽  
Short Read Archive ◽  
Ncbi Short Read Archive

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics (https://zenodo.org/communities/sussex_drosophila_sequencing/).

scholarly journals Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Hélène Muranty ◽  
Caroline Denancé ◽  
Laurence Feugey ◽  
Jean-Luc Crépin ◽  
Yves Barbier ◽  
...  
Keyword(s):  
Middle Ages ◽  
Whole Genome ◽  
Large Pedigree ◽  
Snp Data ◽  
Plant Collections ◽  
French And English ◽  
History Of ◽  
Speed Up ◽  
Apple Cultivars ◽  
Seven Generations

Abstract Background Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees. Results Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as ‘Ribston Pippin’, ‘White Transparent’ and ‘Braeburn’ were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely ‘Reinette Franche’ and ‘Margil’, and one North-Eastern Europe cultivar from the 1700s, ‘Alexander’. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. Conclusions The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.

Molecular analysis of the P-M gonadal dysgenesis cline in eastern Australian Drosophila melanogaster.

Genetics ◽  
1988 ◽  
Vol 119 (4) ◽  
pp. 889-902
Author(s):  
I A Boussy ◽  
M J Healy ◽  
J G Oakeshott ◽  
M G Kidwell
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Gonadal Dysgenesis ◽  
Molecular Techniques ◽  
P Element ◽  
Latitudinal Cline ◽  
Deletion Derivative ◽  
P Elements ◽  
Regulatory Ability ◽  
Eastern Australia

Abstract The latitudinal cline in P-M gonadal dysgenesis potential in eastern Australia has been shown to comprise three regions which are, from north to south respectively, P, Q, and M, with the P-to-Q and Q-to-M transitions occurring over relatively short distances. The P element complements of 30 lines from different regions of the cline were determined by molecular techniques. The total amount of P element-hybridizing DNA was high in all lines, and it did not correlate in any obvious way with the P-M phenotypes of individual lines. The number of potentially full-sized P elements per genome was high in lines from the P regions, but variable or low among lines from the Q and M regions, and thus declined overall from north to south. A particular P element deletion-derivative, the KP element, occurred in all the tested lines. The number of KP elements was low in lines from the P region, much higher in lines from the Q region, and highest among lines from the M region, thus forming a cline reciprocal to that of the full-sized P elements. Another transposable element, hobo, which has been described as causing dysgenic traits similar to those of P-M hybrid dysgenesis, was shown to be present in all lines and to vary among them in number, but not in any latitudinal pattern. The P-M cline in gonadal dysgenesis potential can be inferred to be based on underlying clinal patterns of genomic P element complements. P activity of a line was positively correlated with the number of full-sized P elements in the line, and negatively correlated with the number of KP elements. Among Q and M lines, regulatory ability was not correlated with numbers of KP elements.

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