Here is an incomplete list of things we're (I'm) reading—those that I particularly enjoyed or found useful are in bold.
Focused lab readings (Fall 2018):
Shi et al. 2018, No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster
Henry and Newton 2018, Mitochondria and Wolbachia titers are positively correlated during maternal transmission
Truitt et al. 2018, Wolbachia modifies thermal preference in Drosophila melanogaster
Rajpurohit and Schmidt 2016, Measuring thermal behavior in smaller insects: A case study in Drosophila melanogaster demonstrates effects of sex, geographic origin and rearing temperature on adult behavior
Bonneau et al. 2018, Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
Arnold et al. biorxiv, Drosophila melanogaster infected with Wolbachia strain wMelCS prefer cooler temperatures
Meany et al. biorxiv, Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana
-Megan's first paper—WOOT!
Local evogen reading group (Fall 2018):
Comeron 2017, Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Birky and Walsh 1988, Effects of linkage on rates of molecular evolution
Stankowski et al. biorxiv, The tempo of linked selection: emergence of a heterogeneous genomic landscape during a recent radiation of monkeyflowers
Elyashiv et al. 2016, A Genomic Map of the Effects of Linked Selection in Drosophila
Zhang et al. 2017, Genomic differentiation and patterns of gene flow between two long-tailed tit species (Aegithalos)
Brodie 1992, Correlational Selection for Color Pattern and Antipredator Behavior in the Garter Snake Thamnophis ordinoides
Hu et al. 2014, Evolvability of the Cichlid Jaw: New Tools Provide Insights into the Genetic Basis of Phenotypic Integration
Lovell et al. 2013, Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation
Kim et al. 2017, A sex-linked supergene controls sperm morphology and swimming speed in a songbird
Lotterhos et al. 2018, Modularity of genes involved in local adaptation to climate despite physical linkage
Other papers I'm reading (Fall 2018):
Comeault and Matute 2018, Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation
Kelleher et al. 2018, QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline
KERN!!! and Hahn 2018, The Neutral Theory in Light of Natural Selection
-Few papers have led to as much discussion as this one has!
Li and Ralph biorxiv, Local PCA shows how the effect of population structure differs along the genome
Giraldo et al. 2018, Sun Navigation Requires Compass Neurons in Drosophila
Focused lab readings (Spring 2018):
Lindsey et al. 2018, Conflict in the intracellular lives of endosymbionts and viruses: a mechanistic look at Wolbachia-mediated pathogen-blocking
Bi et al. 2018, Wolbachia affects sleep behavior of Drosophila melanogaster
Kamath et al. 2018, Polar cell fate stimulates Wolbachia intracellular growth
Hague et al. 2017, Convergent adaptation to dangerous prey proceeds through the same first-step mutation in the garter snake Thamnophis sirtalis. (Beautiful story and work here.)
Bi et al. 2018, Wolbachia affects sleep behavior in Drosophila melanogaster
Local evogen reading group (Spring 2018):
VanKuren and Long 2018, Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. (Figure 3 is a thing of beauty.)
Sloan et al. 2017, The on-again, off-again relationship between mitochondrial genomes and species boundaries. (I did not love this one—happy to elaborate if I ever get time.)
Zhang et al. 2016, Genome-wide introgression among distantly related Heliconius butterfly species
Schumer et al. 2017, Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes. (Molly's work is always so impressive.)
Huber et al. 2017, Determining the factors driving selective effects of new nonsynonymous mutations. (I really enjoyed this in terms of getting students up to speed on the DFE, but using isofemale lines in the main comparison seems problematic—humans may seem to have a higher proportion of strongly deleterious mutations than Drosophila simply because those mutations (deleterious variants in Dros.) were lost during line formation.)
Sackman et al. 2017, Mutation-driven parallel evolution during viral adaptation
Gerken et al. 2015, Constraints, independence, and evolution of thermal plasticity: probing genetic architecture of long-and short-term thermal acclimation. (I found this one confusing, and not sure what to take away.)
Other papers I'm reading (Spring 2018):
Ohm et al. 2016, Fitness consequences of altered feeding behavior in immune-challenged mosquitoes
Smith et al. 2018, Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans
Focused lab readings (Fall 2017):
Conner et al. 2017, Genome comparisons indicate recent transfer of wRi-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella
LePage et al. 2017, Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility
Beckmann et al. 2017, A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility
The amazing Bill Sullivan 2017, Wolbachia, bottled water, and the dark side of symbiosis
Simhadri et al. 2017, The gut commensal microbiome of Drosophila melanogaster is modified by the endosymbiont Wolbachia
Geoghegan et al. 2017, Perturbed cholesterol and vesicular trafficking associated with dengue blocking in Wolbachia-infected Aedes aegypti cells
Gill et al. 2014, Iron necessity: The secret of Wolbachia's success?
Duneau et al. 2017, Stochastic variation in the initial phase of bacterial infection predicts the probability of survival in D. melanogaster
Turissini and Matute 2017, Fine scale mapping of genomic introgressions within the Drosophila yakuba clade
Kent and Bordenstein 2010, Phage WO of Wolbachia: lambda of the endosymbiont world
Ballard 2004, Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans
Local evogen reading group (Fall 2017):
Martinson et al. 2017, The Evolution of Venom by Co-option of Single-Copy Genes
Botero-Castro et al. 2017, Avian genomes revisited: hidden genes uncovered and the rates vs. traits paradox in birds
Yang et al. 2017, Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral
Tarvin et al. 2017, Interacting amino acid replacements allow poison frogs to evolve epibatidine resistance
Pfeifer et al. bioaXiv, The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow
Passow et al. 2017, The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish
Schumer et al. 2017, Assortative mating and persistent reproductive isolation in hybrids
Good et al. 2017, The dynamics of molecular evolution over 60,000 generations
Milot et al. 2017, Mother's curse neutralizes natural selection against a human genetic disease over three centuries
Copetti et al. 2017, Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
Didion et al. 2016, R2d2 drives selfish sweeps in the house mouse
Mossman et al. 2016, Mitonuclear interactions mediate transcriptional responses to hypoxia in Drosophila
Bosse et al. 2017, Recent natural selection causes adaptive evolution of an avian polygenic trait
Other papers I'm reading (Fall 2017):
Gomes et al. 2017, Effect of naturally occurring Wolbachia in Anopheles gambiae s.l. mosquitoes from Mali on Plasmodium falciparum malaria transmission
Bordenstein and Bordenstein 2016, Eukaryotic association module in phage WO genomes from Wolbachia
Avise and Robinson 2008, Hemiplasy: A new term in the lexicon of phylogenetics
Mallet et al. 2016, How reticulated are species?
Turelli 2017, Fisher's infinitesimal model: A story for the ages
Fredericksen et al. 2017, Three-dimensional visualization and a deep-learning model reveal complex fungal parasite networks in behaviorally manipulated ants
Turissini et al. 2017, The ability of Drosophila hybrids to locate food declines with parental divergence
Sharon et al. 2010, Commensal bacteria play a role (THEY DON'T) in mating preference of Drosophila melanogaster
Leftwich et al. 2017, Gut microbiomes and reproductive isolation in Drosophila. (Be sure to read this paper if you read the Sharon et al. paper above. Hint: this is the good one—don't believe in magic!)
Vanderpool et al. 2017, Know Your Farmer: Ancient Origins and Multiple Independent Domestications of Ambrosia Beetle Fungal Cultivars
Gompert et al. 2017, Analysis of population genomic data from hybrid zones
Lamichhaney et al. 2017, Rapid hybrid speciation in Darwin's finches
Lee and Coop 2017, Distinguishing among modes of convergent adaptation using population genomic data
Hill 2017, The mitonuclear combatibility species concept (This should not be considered a viable species concept).
Hill 2015, Mitonuclear ecology
Elya et al., bioRxiv, A fungal pathogen that robustly manipulates the behavior of Drosophila melanogaster in the laboratory
Schiffman and Ralph 2017, System drift and speciation
Blumenstiel et al. 2016, What drives positive selection in the Drosophila piRNA machinery? The genomic autoimmunity hypothesis
Guerrero and Hahn 2017, Speciation as a sieve for ancestral polymorphism
Shi et al. 2018, No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster
Henry and Newton 2018, Mitochondria and Wolbachia titers are positively correlated during maternal transmission
Truitt et al. 2018, Wolbachia modifies thermal preference in Drosophila melanogaster
Rajpurohit and Schmidt 2016, Measuring thermal behavior in smaller insects: A case study in Drosophila melanogaster demonstrates effects of sex, geographic origin and rearing temperature on adult behavior
Bonneau et al. 2018, Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
Arnold et al. biorxiv, Drosophila melanogaster infected with Wolbachia strain wMelCS prefer cooler temperatures
Meany et al. biorxiv, Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana
-Megan's first paper—WOOT!
Local evogen reading group (Fall 2018):
Comeron 2017, Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Birky and Walsh 1988, Effects of linkage on rates of molecular evolution
Stankowski et al. biorxiv, The tempo of linked selection: emergence of a heterogeneous genomic landscape during a recent radiation of monkeyflowers
Elyashiv et al. 2016, A Genomic Map of the Effects of Linked Selection in Drosophila
Zhang et al. 2017, Genomic differentiation and patterns of gene flow between two long-tailed tit species (Aegithalos)
Brodie 1992, Correlational Selection for Color Pattern and Antipredator Behavior in the Garter Snake Thamnophis ordinoides
Hu et al. 2014, Evolvability of the Cichlid Jaw: New Tools Provide Insights into the Genetic Basis of Phenotypic Integration
Lovell et al. 2013, Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation
Kim et al. 2017, A sex-linked supergene controls sperm morphology and swimming speed in a songbird
Lotterhos et al. 2018, Modularity of genes involved in local adaptation to climate despite physical linkage
Other papers I'm reading (Fall 2018):
Comeault and Matute 2018, Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation
Kelleher et al. 2018, QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline
KERN!!! and Hahn 2018, The Neutral Theory in Light of Natural Selection
-Few papers have led to as much discussion as this one has!
Li and Ralph biorxiv, Local PCA shows how the effect of population structure differs along the genome
Giraldo et al. 2018, Sun Navigation Requires Compass Neurons in Drosophila
Focused lab readings (Spring 2018):
Lindsey et al. 2018, Conflict in the intracellular lives of endosymbionts and viruses: a mechanistic look at Wolbachia-mediated pathogen-blocking
Bi et al. 2018, Wolbachia affects sleep behavior of Drosophila melanogaster
Kamath et al. 2018, Polar cell fate stimulates Wolbachia intracellular growth
Hague et al. 2017, Convergent adaptation to dangerous prey proceeds through the same first-step mutation in the garter snake Thamnophis sirtalis. (Beautiful story and work here.)
Bi et al. 2018, Wolbachia affects sleep behavior in Drosophila melanogaster
Local evogen reading group (Spring 2018):
VanKuren and Long 2018, Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. (Figure 3 is a thing of beauty.)
Sloan et al. 2017, The on-again, off-again relationship between mitochondrial genomes and species boundaries. (I did not love this one—happy to elaborate if I ever get time.)
Zhang et al. 2016, Genome-wide introgression among distantly related Heliconius butterfly species
Schumer et al. 2017, Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes. (Molly's work is always so impressive.)
Huber et al. 2017, Determining the factors driving selective effects of new nonsynonymous mutations. (I really enjoyed this in terms of getting students up to speed on the DFE, but using isofemale lines in the main comparison seems problematic—humans may seem to have a higher proportion of strongly deleterious mutations than Drosophila simply because those mutations (deleterious variants in Dros.) were lost during line formation.)
Sackman et al. 2017, Mutation-driven parallel evolution during viral adaptation
Gerken et al. 2015, Constraints, independence, and evolution of thermal plasticity: probing genetic architecture of long-and short-term thermal acclimation. (I found this one confusing, and not sure what to take away.)
Other papers I'm reading (Spring 2018):
Ohm et al. 2016, Fitness consequences of altered feeding behavior in immune-challenged mosquitoes
Smith et al. 2018, Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans
Focused lab readings (Fall 2017):
Conner et al. 2017, Genome comparisons indicate recent transfer of wRi-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella
LePage et al. 2017, Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility
Beckmann et al. 2017, A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility
The amazing Bill Sullivan 2017, Wolbachia, bottled water, and the dark side of symbiosis
Simhadri et al. 2017, The gut commensal microbiome of Drosophila melanogaster is modified by the endosymbiont Wolbachia
Geoghegan et al. 2017, Perturbed cholesterol and vesicular trafficking associated with dengue blocking in Wolbachia-infected Aedes aegypti cells
Gill et al. 2014, Iron necessity: The secret of Wolbachia's success?
Duneau et al. 2017, Stochastic variation in the initial phase of bacterial infection predicts the probability of survival in D. melanogaster
Turissini and Matute 2017, Fine scale mapping of genomic introgressions within the Drosophila yakuba clade
Kent and Bordenstein 2010, Phage WO of Wolbachia: lambda of the endosymbiont world
Ballard 2004, Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans
Local evogen reading group (Fall 2017):
Martinson et al. 2017, The Evolution of Venom by Co-option of Single-Copy Genes
Botero-Castro et al. 2017, Avian genomes revisited: hidden genes uncovered and the rates vs. traits paradox in birds
Yang et al. 2017, Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral
Tarvin et al. 2017, Interacting amino acid replacements allow poison frogs to evolve epibatidine resistance
Pfeifer et al. bioaXiv, The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow
Passow et al. 2017, The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish
Schumer et al. 2017, Assortative mating and persistent reproductive isolation in hybrids
Good et al. 2017, The dynamics of molecular evolution over 60,000 generations
Milot et al. 2017, Mother's curse neutralizes natural selection against a human genetic disease over three centuries
Copetti et al. 2017, Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
Didion et al. 2016, R2d2 drives selfish sweeps in the house mouse
Mossman et al. 2016, Mitonuclear interactions mediate transcriptional responses to hypoxia in Drosophila
Bosse et al. 2017, Recent natural selection causes adaptive evolution of an avian polygenic trait
Other papers I'm reading (Fall 2017):
Gomes et al. 2017, Effect of naturally occurring Wolbachia in Anopheles gambiae s.l. mosquitoes from Mali on Plasmodium falciparum malaria transmission
Bordenstein and Bordenstein 2016, Eukaryotic association module in phage WO genomes from Wolbachia
Avise and Robinson 2008, Hemiplasy: A new term in the lexicon of phylogenetics
Mallet et al. 2016, How reticulated are species?
Turelli 2017, Fisher's infinitesimal model: A story for the ages
Fredericksen et al. 2017, Three-dimensional visualization and a deep-learning model reveal complex fungal parasite networks in behaviorally manipulated ants
Turissini et al. 2017, The ability of Drosophila hybrids to locate food declines with parental divergence
Sharon et al. 2010, Commensal bacteria play a role (THEY DON'T) in mating preference of Drosophila melanogaster
Leftwich et al. 2017, Gut microbiomes and reproductive isolation in Drosophila. (Be sure to read this paper if you read the Sharon et al. paper above. Hint: this is the good one—don't believe in magic!)
Vanderpool et al. 2017, Know Your Farmer: Ancient Origins and Multiple Independent Domestications of Ambrosia Beetle Fungal Cultivars
Gompert et al. 2017, Analysis of population genomic data from hybrid zones
Lamichhaney et al. 2017, Rapid hybrid speciation in Darwin's finches
Lee and Coop 2017, Distinguishing among modes of convergent adaptation using population genomic data
Hill 2017, The mitonuclear combatibility species concept (This should not be considered a viable species concept).
Hill 2015, Mitonuclear ecology
Elya et al., bioRxiv, A fungal pathogen that robustly manipulates the behavior of Drosophila melanogaster in the laboratory
Schiffman and Ralph 2017, System drift and speciation
Blumenstiel et al. 2016, What drives positive selection in the Drosophila piRNA machinery? The genomic autoimmunity hypothesis
Guerrero and Hahn 2017, Speciation as a sieve for ancestral polymorphism