Disentangling Types of Linked Selection Using Patterns of Nucleotide Variation in Drosophila pseudoobscura

2021 ◽  
Author(s):  
Katharine L. Korunes ◽  
Kieran Samuk ◽  
Mohamed A. F. Noor
Keyword(s):  
Drosophila Pseudoobscura ◽  
Nucleotide Variation ◽  
Linked Selection

scholarly journals Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila

2021 ◽  
Author(s):  
Alison Nguyen ◽  
Doris Bachtrog
Keyword(s):  
Transposable Element ◽  
Y Chromosome ◽  
Structural Diversity ◽  
Size Difference ◽  
Drosophila Pseudoobscura ◽  
Nucleotide Variation ◽  
Y Chromosomes ◽  
Long Read ◽  
Low Levels ◽  
Element Accumulation

Y chromosomes of many species are gene poor and show low levels of nucleotide variation, yet often display high amounts of structural diversity. Dobzhansky cataloged several morphologically distinct Y chromosomes in Drosophila pseudoobscura that differ in size and shape, but the molecular causes of their dramatic size differences are unclear. Here we use cytogenetics and long-read sequencing to study the sequence content of polymorphic Y chromosomes in D. pseudoobscura. We show that Y chromosomes differ by almost 2-fold in size, ranging from 30 to 60 Mb. Most of this size difference is caused by a handful of active transposable elements (TEs) that have recently expanded on the largest Y chromosome, with different elements being responsible for Y expansion on differently sized D. pseudoobscura Ys. We show that Y chromosomes differ in their heterochromatin enrichment, expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. Intriguingly, the same helitron element that showed the most drastic amplification on the largest Y in D. pseudoobscura independently amplified on a polymorphic large Y chromosome in D. affinis, suggesting that some TEs are inherently more prone to become deregulated on Y chromosomes.

Genetic Loads and Cold Temperature Resistance in Drosophila pseudoobscura

1969 ◽  
Vol 103 (931) ◽  
pp. 235-246 ◽  
Author(s):  
Dragoslav Marinkovic ◽  
David W. Crumpacker ◽  
Victor M. Salceda
Keyword(s):  
Cold Temperature ◽  
Drosophila Pseudoobscura ◽  
Temperature Resistance

Longevity and Male Mating Success in Drosophila pseudoobscura

1981 ◽  
Vol 117 (6) ◽  
pp. 1035-1039 ◽  
Author(s):  
Charles E. Taylor ◽  
Cindra Condra ◽  
Michael Conconi ◽  
Mary Prout
Keyword(s):  
Mating Success ◽  
Drosophila Pseudoobscura ◽  
Male Mating ◽  
Male Mating Success

scholarly journals VARIATION IN BIOCHEMICAL PROPERTIES OF ALLOZYMES OF XANTHINE DEHYDROGENASE IN DROSOPHILA PSEUDOOBSCURA

Genetics ◽  
1980 ◽  
Vol 96 (4) ◽  
pp. 927-938
Author(s):  
David R Wilcox ◽  
Satya Prakash
Keyword(s):  
Substrate Specificity ◽  
Binding Affinity ◽  
Electrophoretic Mobility ◽  
Significant Variation ◽  
Xanthine Dehydrogenase ◽  
Biochemical Properties ◽  
Variant Allele ◽  
Drosophila Pseudoobscura ◽  
Mesa Verde

ABSTRACT Twenty-six D. pseudoobscura strains isogenic for xanthine dehydrogenase alleles from Mesa Verde, Colorado, were tested for differences in the biochemical properties of different allelic forms of xanthine dehydrogenase. No significant differences in binding affinity (Km) or substrate specificity of the enzyme were found. Significant variation among strains, in activity (V  max) and among electromorphs, as well as among strains, in thermolability was found. For the few strains tested, the activity and thermolability differences were shown to co-segregate with the electrophoretic mobility of the variant allele.

scholarly journals Balancing Selection on Electrophoretic Variation of Phosphoglucose Isomerase in Two Species of Field Cricket: Gryllus veletis and G. pennsylvanicus

Genetics ◽  
1997 ◽  
Vol 147 (2) ◽  
pp. 609-621
Author(s):  
Laura A Katz ◽  
Richard G Harrison
Keyword(s):  
Balancing Selection ◽  
Emergent Property ◽  
Phosphoglucose Isomerase ◽  
Field Cricket ◽  
Nucleotide Variation ◽  
Eastern United States ◽  
Electrophoretic Variation ◽  
Sympatric Populations ◽  
Field Crickets ◽  
Gryllus Veletis

Two species of crickets, Gryllus veletis and G. pennsylvanicus, share six electrophoretic mobility classes for the enzyme phosphoglucose isomerase (PGI), despite evidence from other genetic markers that the two species are not closely related within eastern North American field crickets. Moreover, the frequencies of the two most common PGI electrophoretic classes (PGI-100 and PGI-65) covary in sympatric populations of these species in the eastern United States, suggesting that PGI may be subject to trans-specific balancing selection. To determine the molecular basis of the electrophoretic variation, we characterized the DNA sequence of the Pgi gene from 29 crickets (15 G. veletis and 14 G. pennsylvanicus). Amino acid substitutions that distinguish the electrophoretic classes are not the same in the two species, and there is no evidence that specific replacement substitutions represent trans-specific polymorphism. In particular, the amino acids that diagnose the PGI-65 allele relative to the PGI-100 allele differ both between G. veletis and G. pennsylvanicus and within G. pennsylvanicus. The heterogeneity among electrophoretic classes that covary in sympatric populations coupled with analysis of patterns of nucleotide variation suggest that Pgi is not evolving neutrally. Instead, the data are consistent with balancing selection operating on an emergent property of the PGI protein.

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

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