scholarly journals A Genomic Reference Panel for Drosophila serrata

2018 ◽  
Author(s):  
Adam R. Reddiex ◽  
Scott L. Allen ◽  
Stephen F. Chenoweth
Keyword(s):  
Cuticular Hydrocarbon ◽  
Mate Recognition ◽  
Inbred Lines ◽  
Population Substructure ◽  
Base Pairs ◽  
Genetic Studies ◽  
Technical Errors ◽  
Drosophila Serrata ◽  
D Values ◽  
Population Genetic Analyses

AbstractHere we describe a collection of re-sequenced inbred lines of Drosophila serrata, sampled from a natural population situated deep within the species endemic distribution in Brisbane, Australia. D. serrata is a member of the speciose montium group whose members inhabit much of south east Asia and has been well studied for aspects of climatic adaptation, sexual selection, sexual dimorphism, and mate recognition. We sequenced 110 lines that were inbred via 17-20 generations of full-sib mating at an average coverage of 23.5x with paired-end Illumina reads. 15,228,692 biallelic SNPs passed quality control after being called using the Joint Genotyper for Inbred Lines (JGIL). Inbreeding was highly effective and the average levels of residual heterozygosity (0.86%) were well below theoretical expectations. As expected, linkage disequilibrium decayed rapidly, with r2 dropping below 0.1 within 100 base pairs. With the exception of four closely related pairs of lines which may have been due to technical errors, there was no statistical support for population substructure. Consistent with other endemic populations of other Drosophila species, preliminary population genetic analyses revealed high nucleotide diversity and, on average, negative Tajima’s D values. A preliminary GWAS was performed on a cuticular hydrocarbon trait, 2-MeC28 revealing 4 SNPs passing Bonferroni significance residing in or near genes. One gene Cht9 may be involved in the transport of CHCs from the site of production (oenocytes) to the cuticle. Our panel will facilitate broader population genomic and quantitative genetic studies of this species and serve as an important complement to existing D. melanogaster panels that can be used to test for the conservation of genetic architectures across the Drosophila genus.

scholarly journals Cuticular hydrocarbons discriminate cryptic Macrolophus species (Hemiptera: Miridae)

2012 ◽  
Vol 102 (6) ◽  
pp. 624-631 ◽  
Author(s):  
C. Gemeno ◽  
N. Laserna ◽  
M. Riba ◽  
J. Valls ◽  
C. Castañé ◽  
...  
Keyword(s):  
Biological Control ◽  
Cuticular Hydrocarbons ◽  
Cross Validation ◽  
Molecular Genetic ◽  
Cuticular Hydrocarbon ◽  
Hydrocarbon Composition ◽  
Dark Spot ◽  
Prediction Errors ◽  
Control Activity ◽  
Genetic Studies

AbstractMacrolophus pygmaeus is commercially employed in the biological control of greenhouse and field vegetable pests. It is morphologically undistinguishable from the cryptic species M. melanotoma, and this interferes with the evaluation of the biological control activity of M. pygmaeus. We analysed the potential of cuticular hydrocarbon composition as a method to discriminate the two Macrolophus species. A third species, M. costalis, which is different from the other two species by having a dark spot at the tip of the scutellum, served as a control. Sex, diet and species, all had significant effects in the cuticular hydrocarbon profiles, but the variability associated to sex or diet was smaller than among species. Discriminant quadratic analysis of cuticular hydrocarbons confirmed the results of previous molecular genetic studies and showed, using cross-validation methods, that M. pygmaeus can be discriminated from M. costalis and M. melanotoma with prediction errors of 6.75% and 0%, respectively. Therefore, cuticular hydrocarbons can be used to separate M. pygmaeus from M. melanotoma reliably.

Aerodynamics of Gliding Flight in a Falcon and Other Birds

1970 ◽  
Vol 52 (2) ◽  
pp. 345-367 ◽  
Author(s):  
VANCE A. TUCKER ◽  
G. CHRISTIAN PARROTT
Keyword(s):  
Wind Tunnel ◽  
High Performance ◽  
Lift Coefficient ◽  
Aerodynamic Characteristics ◽  
Wing Span ◽  
Technical Errors ◽  
Gliding Flight ◽  
Air Speed ◽  
D Values ◽  
D Value

1. A live laggar falcon (Falco jugger) glided in a wind tunnel at speeds between 6.6 and 15.9 m./sec. The bird had a maximum lift to drag ratio (L/D) of 10 at a speed of 12.5 m./sec. As the falcon increased its air speed at a given glide angle, it reduced its wing span, wing area and lift coefficient. 2. A model aircraft with about the same wingspan as the falcon had a maximum L/D value of 10. 3. Published measurements of the aerodynamic characteristics of gliding birds are summarized by presenting them in a diagram showing air speed, sinking speed and L/D values. Data for a high-performance sailplane are included. The soaring birds had maximum L/D values near 10, or about one quarter that of the sailplane. The birds glided more slowly than the sailplane and had about the same sinking speed. 4. The ‘equivalent parasite area’ method used by aircraft designers to estimate parasite drag was modified for use with gliding birds, and empirical data are presented to provide a means of predicting the gliding performance of a bird in the absence of wind-tunnel tests. 5. The birds in this study had conventional values for parasite drag. Technical errors seem responsible for published claims of unusually low parasite drag values in a vulture. 6. The falcon adjusted its wing span in flight to achieve nearly the maximum possible L/D value over its range of gliding speeds. 7. The maximum terminal speed of the falcon in a vertical dive is estimated to be 100 m./sec.

scholarly journals Speed and accuracy in nest-mate recognition: a hover wasp prioritizes face recognition over colony odour cues to minimize intrusion by outsiders

2015 ◽  
Vol 282 (1802) ◽  
pp. 20142750 ◽  
Author(s):  
D. Baracchi ◽  
I. Petrocelli ◽  
L. Chittka ◽  
G. Ricciardi ◽  
S. Turillazzi
Keyword(s):  
Visual Cues ◽  
Cuticular Hydrocarbon ◽  
Mate Recognition ◽  
Social Wasp ◽  
False Alarms ◽  
Nest Mate ◽  
Colony Odour ◽  
Sensory Modalities ◽  
Chemical Profiles ◽  
Serious Injury

Social insects have evolved sophisticated recognition systems enabling them to accept nest-mates but reject alien conspecifics. In the social wasp, Liostenogaster flavolineata (Stenogastrinae), individuals differ in their cuticular hydrocarbon profiles according to colony membership; each female also possesses a unique (visual) facial pattern. This species represents a unique model to understand how vision and olfaction are integrated and the extent to which wasps prioritize one channel over the other to discriminate aliens and nest-mates. Liostenogaster flavolineata females are able to discriminate between alien and nest-mate females using facial patterns or chemical cues in isolation. However, the two sensory modalities are not equally efficient in the discrimination of ‘friend’ from ‘foe’. Visual cues induce an increased number of erroneous attacks on nest-mates (false alarms), but such attacks are quickly aborted and never result in serious injury. Odour cues, presented in isolation, result in an increased number of misses: erroneous acceptances of outsiders. Interestingly, wasps take the relative efficiencies of the two sensory modalities into account when making rapid decisions about colony membership of an individual: chemical profiles are entirely ignored when the visual and chemical stimuli are presented together. Thus, wasps adopt a strategy to ‘err on the safe side’ by memorizing individual faces to recognize colony members, and disregarding odour cues to minimize the risk of intrusion from colony outsiders.

scholarly journals Time flies: time of day and social environment affect cuticular hydrocarbon sexual displays in Drosophila serrata

2014 ◽  
Vol 281 (1792) ◽  
pp. 20140821 ◽  
Author(s):  
Susan N. Gershman ◽  
Ethan Toumishey ◽  
Howard D. Rundle
Keyword(s):  
Recent Work ◽  
Social Environment ◽  
Cuticular Hydrocarbons ◽  
Cuticular Hydrocarbon ◽  
Time Of Day ◽  
Temporal Changes ◽  
Temporal Patterning ◽  
Drosophila Serrata

Recent work on Drosophila cuticular hydrocarbons (CHCs) challenges a historical assumption that CHCs in flies are largely invariant. Here, we examine the effect of time of day and social environment on a suite of sexually selected CHCs in Drosophila serrata . We demonstrate that males become more attractive to females during the time of day that flies are most active and when most matings occur, but females become less attractive to males during the same time of day. These opposing temporal changes may reflect differences in selection among the sexes. To evaluate the effect of social environment on male CHC attractiveness, we manipulated male opportunity for mating: male flies were housed either alone, with five females, with five males or with five males and five females. We found that males had the most attractive CHCs when with females, and less attractive CHCs when with competitor males. Social environment mediated how male CHC attractiveness cycled: males housed with females and/or other males showed temporal changes in CHC attractiveness, whereas males housed alone did not. In total, our results demonstrate temporal patterning of male CHCs that is dependent on social environment, and suggest that such changes may be beneficial to males.

scholarly journals The transposable elements of the Drosophila serrata reference panel

2020 ◽  
Author(s):  
Zachary Tiedeman ◽  
Sarah Signor
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Copy Number ◽  
Genetic Background ◽  
Natural Populations ◽  
Inbred Lines ◽  
Transposable Element Insertion ◽  
Defense Systems ◽  
Drosophila Serrata ◽  
Transposable Element Copy

AbstractTransposable elements are an important element of the complex genomic ecosystem, proving to be both adaptive and deleterious - repressed by the piRNA system and fixed by selection. Transposable element insertion also appears to be bursty – either due to invasion of new transposable elements that are not yet repressed, de-repression due to instability of organismal defense systems, stress, or genetic variation in hosts. Here, we characterize the transposable element landscape in an important model Drosophila, D. serrata, and investigate variation in transposable element copy number between genotypes and in the population at large. We find that a subset of transposable elements are clearly related to elements annotated in D. melanogaster and D. simulans, suggesting they spread between species more recently than other transposable elements. We also find that transposable elements do proliferate in particular genotypes, and that often if an individual is host to a proliferating transposable element, it is host to more than one proliferating transposable element. In addition, if a transposable element is active in a genotype, it is often active in more than one genotype. This suggests that there is an interaction between the host and the transposable element, such as a permissive genetic background and the presence of potentially active transposable element copies. In natural populations an active transposable element and a permissive background would not be held in association as in inbred lines, suggesting the magnitude of the burst would be much lower. Yet many of the inbred lines have actively proliferating transposable elements suggesting this is an important mechanism by which transposable elements maintain themselves in populations.

scholarly journals admixr—R package for reproducible analyses using ADMIXTOOLS

2019 ◽  
Vol 35 (17) ◽  
pp. 3194-3195 ◽  
Author(s):  
Martin Petr ◽  
Benjamin Vernot ◽  
Janet Kelso
Keyword(s):  
Population Genetic ◽  
R Package ◽  
Supplementary Information ◽  
Command Line ◽  
Software Suite ◽  
Genetic Studies ◽  
Convenient Interface ◽  
Reference Manual ◽  
Population Genetic Analyses ◽  
R Functions

Abstract Summary We present a new R package admixr, which provides a convenient interface for performing reproducible population genetic analyses (f3, D, f4, f4-ratio, qpWave and qpAdm), as implemented by command-line programs in the ADMIXTOOLS software suite. In a traditional ADMIXTOOLS workflow, the user must first generate a set of text configuration files tailored to each individual analysis, often using a combination of shell scripting and manual text editing. The non-tabular output files then need to be parsed to extract values of interest prior to further analyses. Our package simplifies this process by automating all low-level configuration and parsing steps, making analyses as simple as running a single R command. Furthermore, we provide a set of R functions for processing, filtering and manipulating datasets in the EIGENSTRAT format. By unifying all steps of the workflow under a single R framework, this package enables the automation of analytic pipelines, significantly improving the reproducibility of population genetic studies. Availability and implementation The source code of the R package is available under the MIT license. Installation instructions, reference manual and a tutorial can be found on the package website at https://bioinf.eva.mpg.de/admixr. Supplementary information Supplementary data are available at Bioinformatics online.

VARIATIONS IN GENETIC ARCHITECTURE AT DIFFERENT DOSES OF γ-RADIATION AS MEASURED BY LONGEVITY IN DROSOPHILA MELANOGASTER

1973 ◽  
Vol 15 (2) ◽  
pp. 289-298 ◽  
Author(s):  
Jane M. Westerman ◽  
P. A. Parsons
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Architecture ◽  
Inbred Lines ◽  
Additive Effects ◽  
Control Data ◽  
Genetic Studies ◽  
Γ Radiation ◽  
Γ Rays ◽  
High Doses ◽  
Different Doses

Longevity (as a measure of resistance to irradiation) has been examined after different doses of 60Co γ-rays, in four inbred lines and their hybrids in D. melanogaster. The control data showed some additive and non-additive effects. At 40, 60, 80, 100 and 120 krads, non-additive effects were highly significant, but additive effects were significant only at 100 and 120 krads, in particular the latter. Thus the genetic architecture varies with dose. Detailed genetic studies probably are simplest to carry out at high doses, because of the importance of additive effects.

scholarly journals Genetic polymorphism of fifteen microsatellite loci in Brazilian (blue-egg Caipira) chickens

2014 ◽  
Vol 34 (1) ◽  
pp. 98-102 ◽  
Author(s):  
Graziela Vieira Fonteque ◽  
Jaqueline Battilana ◽  
Ediane Paludo ◽  
Carlos André da Veiga Lima-Rosa
Keyword(s):  
Genetic Polymorphism ◽  
Polymorphic Information Content ◽  
Marker Locus ◽  
Chain Reaction ◽  
Base Pairs ◽  
Breeding Programs ◽  
Genetic Studies ◽  
Hardy Weinberg Equilibrium ◽  
Polymerase Chain ◽  
The City

The purpose of this study was to investigate the genetic polymorphism of fifteen microsatellites loci in Brazilian (blue-egg Caipira) chickens. Samples were collected from 100 blue eggs of Caipira chickens from rural properties in the city of Dois Lajeados, RS. After DNA extraction, the fragments related to molecular markers LEI0248, LEI0221, LEI0214, LEI0192, LEI0217, LEI0254, LEI0194, LEI0212, MCW0371, ADL0278, LEI0234, MCW0183, MCW0216, MCW0330 and MCW0081 were obtained by polymerase chain reaction (PCR). The statistical analysis were carried out with the softwares ARLEQUIN 3.5 version and CERVUS 3.0.3 version. The allelic and genotypic frequencies, deviations from Hardy-Weinberg equilibrium, estimates of observed (HO) and expected (HE) heterozygosity and polymorphic information content (PIC) were obtained for each marker locus. A total of 186 alleles from 15 loci were obtained, with sizes ranging of 83 to 490 base pairs. The medium number of alleles was 12.4, the HE was 0.76±0.14 and HO was 0.49±0.21 and PIC was 0.706. The first conclusion is that the microsatellites used are polymorphic and can be used to genetic studies in chickens. The second is that the "Caipira" chicken (blue eggs) population investigated has a great genic variability, which makes than an important source of genetic resources for future animal breeding programs.

scholarly journals Learning and discrimination of cuticular hydrocarbons in a social insect

2011 ◽  
Vol 8 (1) ◽  
pp. 17-20 ◽  
Author(s):  
Ellen van Wilgenburg ◽  
Antoine Felden ◽  
Dong-Hwan Choe ◽  
Robert Sulc ◽  
Jun Luo ◽  
...  
Keyword(s):  
Chain Length ◽  
Social Insect ◽  
Species Recognition ◽  
Cuticular Hydrocarbon ◽  
Mate Recognition ◽  
Olfactory Conditioning ◽  
Argentine Ants ◽  
Nest Mate ◽  
Chemical Signalling ◽  
Branching Patterns

Social insect cuticular hydrocarbon (CHC) mixtures are among the most complex chemical cues known and are important in nest-mate, caste and species recognition. Despite our growing knowledge of the nature of these cues, we have very little insight into how social insects actually perceive and discriminate among these chemicals. In this study, we use the newly developed technique of differential olfactory conditioning to pure, custom-designed synthetic colony odours to analyse signal discrimination in Argentine ants, Linepithema humile . Our results show that tri-methyl alkanes are more easily learned than single-methyl or straight-chain alkanes. In addition, we reveal that Argentine ants can discriminate between hydrocarbons with different branching patterns and the same chain length, but not always between hydrocarbons with the same branching patterns but different chain length. Our data thus show that biochemical characteristics influence those compounds that ants can discriminate between, and which thus potentially play a role in chemical signalling and nest-mate recognition.

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