Molecular analysis of an allozyme cline: alcohol dehydrogenase in Drosophila melanogaster on the east coast of North America.

Abstract Clines may either be selectively maintained or be the by-product of nonadaptive processes related to population structure and history. Drosophila melanogaster populations on the east coast of North America show a latitudinal cline in the frequencies of two common electrophoretically distinguishable alleles at the alcohol dehydrogenase locus (Adh), designated Adh-S and Adh-F. This cline may either be adaptive or an artifact of a possible recent dual founding of North American D. melanogaster populations in which frequencies of Adh alleles differed between founder populations. By means of a high resolution restriction-mapping technique, we studied the distribution of 113 haplotypes derived from 44 polymorphic DNA markers within the Adh region in 1533 individuals from 25 populations throughout the cline. We found significant clinal differentiation at the polymorphism determining the mobility-difference causing amino acid replacement between Adh-F and Adh-S alleles. Hitchhiking was limited, despite extensive linkage disequilibrium, and other sites did not vary clinally. Such a pattern of differentiation implies that selection is responsible for the cline. To investigate whether selection acts only on the Adh-F/S site, we performed a "selective equivalence" test under the assumption that all variability within the specified allelic class is selectively neutral. This revealed selective equivalence among Adh-S-bearing haplotypes, whose frequencies showed no differentiation throughout the cline, implying high levels of frequency-homogenizing gene flow. Geographical heterogeneity among Adh-F-bearing haplotypes implied the action of selection on one or more additional variants in linkage disequilibrium with Adh-F. In a further study of a subset of the data (n = 1076 from 18 populations), we found a combined insertion/deletion polymorphism, designated delta 1, located in the 5' adult intron and in linkage disequilibrium with Adh-F, to show more marked clinal variation than Adh-F/S. Although the unequivocal identification of the precise target(s) of selection requires further study, we suggest that clinal selection may be acting epistatically on the Adh-F/S and delta 1 polymorphisms.

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Molecular Evolution of Two Linked Genes, Est-6 and Sod, in Drosophila melanogaster

Genetics ◽

10.1093/genetics/153.3.1357 ◽

1999 ◽

Vol 153 (3) ◽

pp. 1357-1369 ◽

Cited By ~ 3

Author(s):

Evgeniy S Balakirev ◽

Elena I Balakirev ◽

Francisco Rodríguez-Trelles ◽

Francisco J Ayala

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Early Experiment ◽

Amino Acid Replacement ◽

Allozyme Polymorphism ◽

Nucleotide Polymorphism ◽

Significant Linkage Disequilibrium ◽

Nucleotide Level ◽

S Alleles ◽

Significant Linkage

Abstract We have obtained 15 sequences of Est-6 from a natural population of Drosophila melanogaster to test whether linkage disequilibrium exists between Est-6 and the closely linked Sod, and whether natural selection may be involved. An early experiment with allozymes had shown linkage disequilibrium between these two loci, while none was detected between other gene pairs. The Sod sequences for the same 15 haplotypes were obtained previously. The two genes exhibit similar levels of nucleotide polymorphism, but the patterns are different. In Est-6, there are nine amino acid replacement polymorphisms, one of which accounts for the S-F allozyme polymorphism. In Sod, there is only one replacement polymorphism, which corresponds to the S-F allozyme polymorphism. The transversion/transition ratio is more than five times larger in Sod than in Est-6. At the nucleotide level, the S and F alleles of Est-6 make up two allele families that are quite different from each other, while there is relatively little variation within each of them. There are also two families of alleles in Sod, one consisting of a subset of F alleles, and the other consisting of another subset of F alleles, designed F(A), plus all the S alleles. The Sod F(A) and S alleles are completely or nearly identical in nucleotide sequence, except for the replacement mutation that accounts for the allozyme difference. The two allele families have independent evolutionary histories in the two genes. There are traces of statistically significant linkage disequilibrium between the two genes that, we suggest, may have arisen as a consequence of selection favoring one particular sequence at each locus.

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Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

10.1101/009084 ◽

2014 ◽

Cited By ~ 2

Author(s):

Alan O. Bergland ◽

Ray Tobler ◽

Josefa Gonzalez ◽

Paul Schmidt ◽

Dmitri Petrov

Keyword(s):

Drosophila Melanogaster ◽

North America ◽

Local Adaptation ◽

Latitudinal Gradients ◽

Secondary Contact ◽

Clinal Variation ◽

Evolutionary Forces ◽

Genome Wide ◽

Spatially Varying ◽

Spatially Varying Selection

Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and, moreover, can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations ofDrosophila melanogastersampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this admixture event contributed to genome-wide patterns of parallel clinal variation. The pervasive effects of admixture meant that only a handful of loci could be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation inD. melanogasterand provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as some temperate endemics.

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The Identification and Study of Indian Shell Middens in Eastern North America: 1643–1861

North American Archaeologist ◽

10.2190/e9u1-2nh4-d6lj-jwqa ◽

1986 ◽

Vol 6 (3) ◽

pp. 227-243 ◽

Cited By ~ 4

Author(s):

Andrew L. Christenson

Keyword(s):

Nineteenth Century ◽

Civil War ◽

North America ◽

East Coast ◽

Eastern North America ◽

Shell Midden ◽

Shell Middens ◽

Work Done

Although the interest in shell middens in North America is often traced to reports of the discoveries in Danish kjoekkenmoeddings in the mid-nineteenth century, extensive shell midden studies were already occurring on the East Coast by that time. This article reviews selected examples of this early work done by geologists and naturalists, which served as a foundation for shell midden studies by archaeologists after the Civil War.

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SEA LEVEL BUDGET ALONG THE EAST COAST OF NORTH AMERICA

10.1130/abs/2017ne-289898 ◽

2017 ◽

Author(s):

Allison Pease ◽

◽

James Davis

Keyword(s):

North America ◽

Sea Level ◽

East Coast

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REDESCRIPTION OF A LARGE PALEOCENE GAVIALOID FROM THE EAST COAST OF NORTH AMERICA

10.1130/abs/2019se-327611 ◽

2019 ◽

Author(s):

Donald Joseph Morgan ◽

Keyword(s):

North America ◽

East Coast

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The Alcohol Dehydrogenase Gene Is Nested in the outspread Locus of Drosophila melanogaster

Genetics ◽

10.1093/genetics/143.2.897 ◽

1996 ◽

Vol 143 (2) ◽

pp. 897-911 ◽

Cited By ~ 1

Author(s):

S McNabb ◽

S Greig ◽

T Davis

Keyword(s):

Drosophila Melanogaster ◽

Alcohol Dehydrogenase ◽

Pcr Amplification ◽

Transcription Unit ◽

Adjacent Gene ◽

Dehydrogenase Gene ◽

Chromosomal Breakpoints ◽

Splicing Patterns ◽

Somatic Musculature

Abstract This report describes the structure and expression of the outspread (osp) gene of Drosophila melanogaster. Previous work showed that chromosomal breakpoints associated with mutations of the osp locus map to both sides of the alcohol dehydrogenase gene (Adh), suggesting that Adh and the adjacent gene Adh' are nested in osp. We extended a chromosomal walk and mapped additional osp mutations to define the maximum molecular limit of osp as 119 kb. We identified a 6-kb transcript that hybridizes to osp region DNA and is altered or absent in osp mutants. Accumulation of this RNA peaks during embryonic and pupal periods. The osp cDNAs comprise two distinct classes based on alternative splicing patterns. The 5′ end of the longest cDNA was extended by PCR amplification. When hybridized to the osp walk, the 5′ extension verifies that Adh and Adh' are nested in osp and shows that osp has a transcription unit of ≥74 kb. In situ hybridization shows that osp is expressed both maternally and zygotically. In the ovary, osp is transcribed in nurse cells and localized in the oocyte. In embryos, expression is most abundant in the developing visceral and somatic musculature.

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GENETIC AND BIOCHEMICAL BASIS OF ENZYME ACTIVITY VARIATION IN NATURAL POPULATIONS. I. ALCOHOL DEHYDROGENASE IN DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/89.2.371 ◽

1978 ◽

Vol 89 (2) ◽

pp. 371-388

Author(s):

John F McDonald ◽

Francisco J Ayala

Keyword(s):

Gene Regulation ◽

Drosophila Melanogaster ◽

Alcohol Dehydrogenase ◽

Natural Populations ◽

Difficult Problem ◽

Regulatory Genes ◽

Biochemical Basis ◽

Evolutionary Consequence ◽

The Third ◽

Adh Activity

ABSTRACT Recent studies by various authors suggest that variation in gene regulation may be common in nature, and might be of great evolutionary consequence; but the ascertainment of variation in gene regulation has proven to be a difficult problem. In this study, we explore this problem by measuring alcohol dehydrogenase (ADH) activity in Drosophila melanogaster strains homozygous for various combinations of given second and third chromosomes sampled from a natural population. The structural locus (Adh) coding for ADH is on the second chromosome. The results show that: (1) there are genes, other than Adh, that affect the levels of ADH activity; (2) at least some of these "regulatory" genes are located on the third chromosome, and thus are not adjacent to the Adh locus; (3) variation exists in natural populations for such regulatory genes; (4) the effect of these regulatory genes varies as they interact with different second chromosomes; (5) third chromosomes with high-activity genes are either partially or completely dominant over chromosomes with low-activity genes; (6) the effects of the regulatory genes are pervasive throughout development; and (7) the third chromosome genes regulate the levels of ADH activity by affecting the number of ADH molecules in the flies. The results are consistent with the view that the evolution of regulatory genes may play an important role in adaptation.

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Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Genetics ◽

10.1093/genetics/135.2.541 ◽

1993 ◽

Vol 135 (2) ◽

pp. 541-552 ◽

Cited By ~ 5

Author(s):

S W Schaeffer ◽

E L Miller

Keyword(s):

Linkage Disequilibrium ◽

Alcohol Dehydrogenase ◽

Distance Effect ◽

Theoretical Distribution ◽

Drosophila Pseudoobscura ◽

Significant Linkage Disequilibrium ◽

Effective Population ◽

Nucleotide Distance ◽

Significant Linkage ◽

Recombination Parameter

Abstract The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D(ij), D2, r(ij), r2 and D(ij) were compared to theoretical distributions. The observed distributions of D(ij), D2, r(ij) and r2 were consistent with the theoretical distribution given an infinite sites model. The observed distribution of D(ij) differed from the theoretical distribution because of an excess of values at -1 and 1. No spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure.

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Evidence for Selection at the fused1 Locus of Drosophila americana

Genetics ◽

10.1093/genetics/158.1.279 ◽

2001 ◽

Vol 158 (1) ◽

pp. 279-290 ◽

Cited By ~ 4

Author(s):

Jorge Vieira ◽

Bryant F McAllister ◽

Brian Charlesworth

Keyword(s):

Amino Acid ◽

Sequence Variation ◽

Amino Acid Replacement ◽

Population Subdivision ◽

Amino Acid Substitutions ◽

Clinal Variation ◽

Haplotype Structure ◽

Common Amino Acid ◽

Chromosome Arrangement ◽

Dna Sequence Variation

Abstract We analyze genetic variation at fused1, a locus that is close to the centromere of the X chromosome-autosome (X/4) fusion in Drosophila americana. In contrast to other X-linked and autosomal genes, for which a lack of population subdivision in D. americana has been observed at the DNA level, we find strong haplotype structure associated with the alternative chromosomal arrangements. There are several derived fixed differences at fused1 (including one amino acid replacement) between two haplotype classes of this locus. From these results, we obtain an estimate of an age of ∼0.61 million years for the origin of the two haplotypes of the fused1 gene. Haplotypes associated with the X/4 fusion have less DNA sequence variation at fused1 than haplotypes associated with the ancestral chromosome arrangement. The X/4 haplotypes also exhibit clinal variation for the allele frequencies of the three most common amino acid replacement polymorphisms, but not for adjacent silent polymorphisms. These patterns of variation are best explained as a result of selection acting on amino acid substitutions, with geographic variation in selection pressures.

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GENETIC DIFFERENTIATION BETWEEN GEOGRAPHICALLY DISTANT POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/101.2.235 ◽

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.

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