Oligogenic Adaptation, Soft Sweeps, and Parallel Melanic Evolution in Drosophila melanogaster

2016 ◽  
Author(s):  
Héloïse Bastide ◽  
Jeremy D. Lange ◽  
Justin B. Lack ◽  
Yassin Amir ◽  
John E. Pool
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Simulation Analysis ◽  
Mapping Method ◽  
Sub Saharan Africa ◽  
Mountain Ranges ◽  
Sub Saharan

AbstractUnraveling the genetic architecture of adaptive phenotypic divergence is a fundamental quest in evolutionary biology. In Drosophila melanogaster, high-altitude melanism has evolved in separate mountain ranges in sub-Saharan Africa, potentially as an adaptation to UV intensity. We investigated the genetic basis of this melanism in three populations using a new bulk segregant analysis mapping method. Although hundreds of genes are known to affect cuticular pigmentation in D. melanogaster, we identified only 19 distinct QTLs from 9 mapping crosses, with several QTL peaks being shared among two or all populations. Surprisingly, we did not find wide signals of genetic differentiation (Fst) between lightly and darkly pigmented populations at these QTLs, in spite of the pronounced phenotypic difference in pigmentation. Instead, we found small numbers of highly differentiated SNPs at the probable causative genes. A simulation analysis showed that these patterns of polymorphism are consistent with selection on standing genetic variation (leading to “soft sweeps“). Our results thus support a role for oligogenic selection on standing genetic variation in driving parallel ecological adaptation.

scholarly journals Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila

2021 ◽  
Author(s):  
Jason A Tarkington ◽  
Hao Zhang ◽  
Ricardo Azevedo ◽  
Rebecca Zufall
Keyword(s):  
Genetic Variation ◽  
Experimental Evolution ◽  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Nuclear Division ◽  
Tetrahymena Thermophila ◽  
Laboratory Populations ◽  
Evolutionary Success ◽  
Sexual Progeny ◽  
Open Question

Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional processes that may also generate substantial genetic variation in some populations and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. Tetrahymena thermophila is a ciliate with an unusual mechanism of nuclear division, called amitosis, which can generate genetic variation among the asexual descendants of a newly produced sexual progeny. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.

scholarly journals Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

2019 ◽  
Vol 37 (3) ◽  
pp. 627-638 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Suzan Mansourian ◽  
Jeremy D Lange ◽  
Daniel R Matute ◽  
Brandon S Cooper ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Central Africa ◽  
Model Organism ◽  
Sub Saharan Africa ◽  
Wilderness Areas ◽  
Southern Central ◽  
History Of ◽  
Sub Saharan ◽  
Improved Model

Abstract A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species’ geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼13,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,800 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.

scholarly journals Homozygosity for TYK2 P1104A underlies tuberculosis in about 1% of patients in a cohort of European ancestry

2019 ◽  
Vol 116 (21) ◽  
pp. 10430-10434 ◽  
Author(s):  
Gaspard Kerner ◽  
Noe Ramirez-Alejo ◽  
Yoann Seeleuthner ◽  
Rui Yang ◽  
Masato Ogishi ◽  
...  
Keyword(s):  
Odds Ratio ◽  
Genetic Basis ◽  
Sub Saharan Africa ◽  
European Ancestry ◽  
Uk Biobank ◽  
The United Kingdom ◽  
The Common ◽  
Sub Saharan ◽  
The Uk ◽  
High Level

The human genetic basis of tuberculosis (TB) has long remained elusive. We recently reported a high level of enrichment in homozygosity for the common TYK2 P1104A variant in a heterogeneous cohort of patients with TB from non-European countries in which TB is endemic. This variant is homozygous in ∼1/600 Europeans and ∼1/5,000 people from other countries outside East Asia and sub-Saharan Africa. We report a study of this variant in the UK Biobank cohort. The frequency of P1104A homozygotes was much higher in patients with TB (6/620, 1%) than in controls (228/114,473, 0.2%), with an odds ratio (OR) adjusted for ancestry of 5.0 [95% confidence interval (CI): 1.96–10.31, P = 2 × 10−3]. Conversely, we did not observe enrichment for P1104A heterozygosity, or for TYK2 I684S or V362F homozygosity or heterozygosity. Moreover, it is unlikely that more than 10% of controls were infected with Mycobacterium tuberculosis, as 97% were of European genetic ancestry, born between 1939 and 1970, and resided in the United Kingdom. Had all of them been infected, the OR for developing TB upon infection would be higher. These findings suggest that homozygosity for TYK2 P1104A may account for ∼1% of TB cases in Europeans.

scholarly journals Genetic architecture of natural variation in visual senescence in Drosophila

2016 ◽  
Vol 113 (43) ◽  
pp. E6620-E6629 ◽  
Author(s):  
Mary Anna Carbone ◽  
Akihiko Yamamoto ◽  
Wen Huang ◽  
Rachel A. Lyman ◽  
Tess Brune Meadors ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Life Span ◽  
Candidate Genes ◽  
Natural Variation ◽  
Genetic Basis ◽  
Nervous System Development ◽  
Interindividual Variation ◽  
Human Populations ◽  
Age Dependent

Senescence, i.e., functional decline with age, is a major determinant of health span in a rapidly aging population, but the genetic basis of interindividual variation in senescence remains largely unknown. Visual decline and age-related eye disorders are common manifestations of senescence, but disentangling age-dependent visual decline in human populations is challenging due to inability to control genetic background and variation in histories of environmental exposures. We assessed the genetic basis of natural variation in visual senescence by measuring age-dependent decline in phototaxis using Drosophila melanogaster as a genetic model system. We quantified phototaxis at 1, 2, and 4 wk of age in the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and found an average decline in phototaxis with age. We observed significant genetic variation for phototaxis at each age and significant genetic variation in senescence of phototaxis that is only partly correlated with phototaxis. Genome-wide association analyses in the DGRP and a DGRP-derived outbred, advanced intercross population identified candidate genes and genetic networks associated with eye and nervous system development and function, including seven genes with human orthologs previously associated with eye diseases. Ninety percent of candidate genes were functionally validated with targeted RNAi-mediated suppression of gene expression. Absence of candidate genes previously implicated with longevity indicates physiological systems may undergo senescence independent of organismal life span. Furthermore, we show that genes that shape early developmental processes also contribute to senescence, demonstrating that senescence is part of a genetic continuum that acts throughout the life span.

scholarly journals Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

2015 ◽  
Vol 28 (4) ◽  
pp. 826-840 ◽  
Author(s):  
D. K. Fabian ◽  
J. B. Lack ◽  
V. Mathur ◽  
C. Schlötterer ◽  
P. S. Schmidt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Life History ◽  
Sub Saharan Africa ◽  
Sub Saharan ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals Interaction between M. tuberculosis Lineage and Human Genetic Variants Reveals Novel Pathway Associations with Severity of TB

Pathogens ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1487
Author(s):  
Michael L. McHenry ◽  
Eddie M. Wampande ◽  
Moses L. Joloba ◽  
LaShaunda L. Malone ◽  
Harriet Mayanja-Kizza ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Clinical Presentation ◽  
Sub Saharan Africa ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Genomes ◽  
Genome Wide ◽  
Sub Saharan ◽  
Cellular Replication

Tuberculosis (TB) remains a major public health threat globally, especially in sub-Saharan Africa. Both human and Mycobacterium tuberculosis (MTBC) genetic variation affect TB outcomes, but few studies have examined if and how the two genomes interact to affect disease. We hypothesize that long-term coexistence between human genomes and MTBC lineages modulates disease to affect its severity. We examined this hypothesis in our TB household contact study in Kampala, Uganda, in which we identified three MTBC lineages, of which one, L4.6-Uganda, is clearly derived and hence recent. We quantified TB severity using the Bandim TBscore and examined the interaction between MTBC lineage and human single-nucleotide polymorphisms (SNPs) genome-wide, in two independent cohorts of TB cases (n = 149 and n = 127). We found a significant interaction between an SNP in PPIAP2 and the Uganda lineage (combined p = 4 × 10−8). PPIAP2 is a pseudogene that is highly expressed in immune cells. Pathway and eQTL analyses indicated potential roles between coevolving SNPs and cellular replication and metabolism as well as platelet aggregation and coagulation. This finding provides further evidence that host–pathogen interactions affect clinical presentation differently than host and pathogen genetic variation independently, and that human–MTBC coevolution is likely to explain patterns of disease severity.

scholarly journals Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola

2020 ◽  
Author(s):  
Jonathan H. Massey ◽  
Jun Li ◽  
David L. Stern ◽  
Patricia J. Wittkopp
Keyword(s):  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Species Differences ◽  
The Body ◽  
Body Parts ◽  
Genetic Changes ◽  
Body Regions ◽  
Three Body ◽  
Male Specific

AbstractUnderstanding the genetic basis of species differences is a major goal in evolutionary biology. Pigmentation divergence between Drosophila species often involves genetic changes in pigmentation candidate genes that pattern the body and wings, but it remains unclear how these changes affect pigmentation evolution in multiple body parts between the same diverging species. Drosophila elegans and D. gunungcola show pigmentation differences in the thorax, legs, and wings, with D. elegans exhibiting male-specific wing spots and D. gunungcola lacking wing spots with intensely dark thoraces and legs. Here, we performed QTL mapping to identify the genetic architecture of these differences. We find a large effect QTL on the X chromosome for all three body parts. QTL on Muller Element E were found for thorax pigmentation in both backcrosses but were only marginally significant in one backcross for the legs and wings. Consistent with this observation, we isolated the effects of the Muller Element E QTL by introgressing D. gunungcola alleles into a D. elegans genetic background and found that D. gunungcola alleles linked near the pigmentation candidate gene ebony caused intense darkening of the thorax, minimal darkening of legs, and minimal shrinking of wing spots. D. elegans ebony mutants showed changes in pigmentation consistent with Ebony having different effects on pigmentation in different tissues. Our results suggest that multiple genes have evolved differential effects on pigmentation levels in different body regions.

scholarly journals Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Lauren M Dembeck ◽  
Katalin Böröczky ◽  
Wen Huang ◽  
Coby Schal ◽  
Robert R H Anholt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Social Interactions ◽  
Individual Variation ◽  
Genetic Architecture ◽  
Natural Variation ◽  
Genetic Basis ◽  
Acid Metabolism ◽  
Cuticular Hydrocarbon ◽  
Principal Component ◽  
Hydrocarbon Composition

Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition.

scholarly journals Genomics of recombination rate variation in temperature-evolved Drosophila melanogaster populations

2020 ◽  
Author(s):  
Ari Winbush ◽  
Nadia D Singh
Keyword(s):  
Drosophila Melanogaster ◽  
Temperature Regime ◽  
Recombination Rate ◽  
Evolutionary Biology ◽  
Genetic Basis ◽  
Rate Variation ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Meiotic recombination is a critical process that ensures proper segregation of chromosome homologues through DNA double strand break repair mechanisms. Rates of recombination are highly variable among various taxa, within species, and within genomes with far-reaching evolutionary and genomic consequences. The genetic basis of recombination rate variation is therefore crucial in the study of evolutionary biology but remains poorly understood. In this study we took advantage of a set of experimental temperature-evolved populations of Drosophila melanogaster with heritable differences in recombination rates depending on the temperature regime in which they evolved. We performed whole genome sequencing and identified several chromosomal regions that appear to be divergent depending on temperature regime. In addition, we identify a set of single nucleotide polymorphisms and associated genes with significant differences in allele frequency when the different temperature populations are compared. Further refinement of these gene candidates emphasizing those expressed in the ovary and associated with DNA binding reveals numerous potential candidate genes such as Hr38, EcR, and mamo responsible for observed differences in recombination rates in these experimental evolution lines thus providing insight into the genetic basis of recombination rate variation.

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