Robert L. Unckless

Evolutionary and ecological genomics

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#365 Papers – February update

I found myself behind this month, but was able to catch up due to some home days.  Arvid and Emily are machines.  A few of my favorites this month were Hamilton et al. 2016, Yamaguchi et al. 2015, Pipoly et al. 2015 and Mcdonald et al. 2016.

Here’s my entire list…

Yu et al 2016 AAC -The More The Better? Combination Effects of Antimicrobial Peptides –
Kern et al 2015 Biology Letters -Double trouble: combined action of meiotic drive and Wolbachia feminization in Eurema butterflies. –
Yamamoto-Hino and Soto 2016 Cell Structure and Function -Spätzle-processing enzyme-independent activation of the Toll pathway in Drosophila innate immunity. –
Bronkhorst et al 2012 PNAS – The DNA virus Invertebrate iridescent virus 6 is a target of the Drosophila RNAi machinery –
Carvalho et al 2015 PNAS – Birth of a new gene on the Y chromosome of Drosophila melanogaster. –
Zhao et al 2015 Dev. Bio. – The IMD innate immunity pathway of Drosophila influences somatic sex determination via regulation of the Doa locus. –
Manuscript review
Lynch et al 2016 JEB – Evolution of behavioral and cellular defenses against parasitoid wasps in the Drosophila melanogaster subgroup –
Kariithi et al 2013 – JGV – Correlation between structure, protein composition, morphogenesis and cytopathology of Glossina pallidipes salivary gland hypertrophy virus –
Strand and Burke 2015 ARV – Polydnaviruses: Nature’s Genetic Engineers –
Bezier et al 2015 Journal of Virology- The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family –
Grant Draft
Wang et al 2008 Journal of Virological Methods – Sequencing of the large dsDNA genome of Oryctes rhinoceros nudivirus using multiple displacement amplification of nanogram amounts of virus DNA –
Grimaldi et al 2015 PLoS ONE -Strange Little Flies in the Big City: Exotic Flower-Breeding Drosophilidae (Diptera) in Urban Los Angeles –
Mistry et al 2016 DCI – Exploring interactions between pathogens and the Drosophila gut.-
Brandvain and Wright. 2016. Trends Genetics. The limits of natural selection in a nonequilibrium world
Zanders and Malik 2015 Current Biology – Chromosome Segregation: Human Female Meiosis Breaks All the Rules-
Halldorsdottir and Arnason 2015 PeerJ -Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species –
Hamilton et al 2015 mBio – Infection Dynamics and Immune Response in a Newly Described Drosophila-Trypanosomatid Association-
Manuscript review
Yamauchi et al 2016 Science -Two genes substitute for the mouse Y chromosome for spermatogenesis and reproduction. -
Miller et al 2016 PNAS – Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster-
Zeng et al 2016 BMC Evolutionary Biology – Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes-
Pipoly et al 2015 Nature – The genetic sex-determination system predicts adult sex ratios in tetrapods -
Steinhauer 2015 Spermatogenesis – Separating from the pack: Molecular mechanisms of Drosophila spermatid individualization –
Zhong et al. 2016 Scientific Reports -Co-expression of Dorsal and Rel2Negatively Regulates Antimicrobial Peptide Expression in the Tobacco Hornworm Manduca sexta –
Besnard-Guerin et al 2015 PLOS One -The Cricket Paralysis Virus Suppressor Inhibits microRNA Silencing Mediated by the Drosophila Argonaute-2 Protein –
Metzger et al 2016 Evolution – The Red Queen lives: Epistasis between linked resistance loci –
McDonald et al. 2016. Nature. Sex speeds adaptation by altering the dynamics of molecular evolution

This is Arvid Agren’s list:

Molaro and Malik. 2016. Curr. Opin. Genet. Dev Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline
Stuart et al. 2014. Science. Rapid evolution of a native species following invasion by a congener
Arkhipova and Rice 2016 Mol Ecol Mobile Genetic Elements: In Silico, In Vitro, In Vivo
Theis et al. 2016. BioRxiv Getting the Hologenome Concept Right: An Eco-Evolutionary Framework for Hosts and Their Microbiomes
Journal of Evolutionary Biology – Review
Okasha. 2004. Biol Philos. The “averaging fallacy” and the levels of selection
Galbraith et al. 2016. PNAS Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera)
Poirotte et al. 2016. Current Biology. Morbid attraction to leopard urine in Toxoplasma-infected chimpanzees
Lescak et al. 2015. PNAS. Evolution of stickleback in 50 years on earthquake-uplifted islands
Carvalho et al. 2015. PNAS. Birth of a new gene on the Y chromosome of Drosophila melanogaster
Brandvain and Wright. 2016. Trends Genetics. The limits of natural selection in a nonequilibrium world
Immonen et al. 2016. JEB. Complex mitonuclear interactions and metabolic costs of mating in male seed beetles
Arnqvist et al. 2010. Evolution. Genetic architecture of metabolic rate: environment specific epistasis between mitochondrial and nuclear genes in an insect
Immonen et al. 2016. Heredity. Direct and indirect genetic effects of sex-specific mitonuclear epistasis on reproductive ageing
Dobler et al. 2014. JEB. A meta-analysis of the strength and nature of cytoplasmic genetic effects
Traverse et al. 2012. PNAS. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections
Cotner et al. 2014. Reports of the National Center for Science Education. Science and society. Evolution and student voting patterns
Maumus and Quesneville. 2016. Curr Opin Plant Biol Impact and insights from ancient repetitive elements in plant genomes
Buzzoni. 2015. J Gen Philos Sci Causality, teleology, and thought experiments in biology
Korb and Heinze. 2016. Ann Rev Entomol. Major hurdles in the evolution of sociality
Beerenwinkel et al. 2016. PLoS Comput Biol. Computational cancer biology: An evolutionary perspective
Wit et al. 2013. Exp Geront. Longevity for free? Increased reproduction with limited trade-offs in Drosophila melanogaster selected for increased life span
Soria-Carrasco et al. 2014. Science. Stick insect genomes reveal natural selection’s role in parallel speciation
Yanai and DeLisli. 2002. Genome Biol. The society of genes: networks of functional links between genes from comparative genomics
Lindholm et al. 2016. TREE. The ecology and evolutionary dynamics of meiotic drive
McDonald et al. 2016. Nature. Sex speeds adaptation by altering the dynamics of molecular evolution
Rainey and De Monte. 2014. Annu. Rev. Ecol. Evol. Syst. Resolving conflicts during the evolutionary transition to multicellular life
Kirkpatrick and Guerrero. 2014. Genetics. Signatures of sex-antagonistic selection on recombining sex chromosomes
van Doorn and Kirkpatrick. 2007. Nature. Turnover of sex chromosomes induced by sexual conflict

Here’s Emily Davenport’s list:

Theis et al. BioRxiv 2016; Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes
Hu et al. Nature Communications 2016; GWAS of 89,283 individuals identifies genetic variants associated with self-reporting ob being a morning person
Morton et al. PLoS Genetics 2015; Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence
Dominguez-Bello et al. Nature Medicine 2016; Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
Milani et al. Applied and Environmental Microbiology 2016; Genomics of the genus Bifidobacterium reveals species-specific adaptation to the glycan-rich gut environment
Gamazon et al. Nature Genetics 2015; A gene-based association method for mapping traits using reference transcriptome data
Loose et al. BioRxiv 2016; Real time selective sequencing using nanopore technology
Terrell et al. PeerJ Preprints 2016; Gender bias in open source: Pull request acceptance of women versus men
Minica et al. Molecular Psychiatry 2014; MZ twin pairs of MZ singletons in population family-based GWAS? More power in pairs
Thornton et al. PLoS Genetics 2013; Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in gene of large effect
Sanjak et al. G3 2016; Efficient software for multi-marker, region-based analysis of GWAS data
Simonti et al. Science 2016; The phenotypic legacy of admixture between modern humans and Neandertals
Gibson et al. PLoS Computational Biology 2016; On the origins and control of community types in the human microbiome
Clooney et al. PLoS One 2016; Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysis
Gage et al. PLoS Genetics 2016; G = E: What GWAS can tell us about the environment
Denny et al. Nature Biotechnology 2013; Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data
Manuscript review
Lanan et al. ISME 2016; A bacterial filter protects and structures the gut microbiome of an insect
Blanton et al. Science 2016; Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
McGeachie et al. Scientific Reports 2016; Longitudinal prediction of the infant gut microbiome with dynamic bayesian networks
Schweizer Burguete et al. eLife 2015; GGGGCC micrsatellite RNA is neuritically localized, induces branching defects, and perturbs transport granule function
Sveinbjornsson et al. Nature Genetics 2016; Weighting sequence variants based on their annotation increases power of whole-genome association studies
Paliy et al. Molecular Ecology 2016; Application of multivariate statistical techniques in microbial ecology
Ma et al. Nature Communications 2016; Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts
Fonseca-Garcia et al. Frontiers in Microbiology 2016; The cacti microbiome: Interplay between habitat-filtering and host-specificity
Gomez et al. Cell Reports 2016; Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns
Weiss et al. ISME 2016; Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
Noecker et al. mSystems 2016; Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation
Charbonneau et al. Cell 2016; Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition

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New Meiotic Drive Review in TREE

Last summer I was lucky enough to participate in a meiotic drive meeting in Arolla, Switzerland.  The organizers, Tom Price and Anna Lindholm, told us that we would spend the first two days presenting our recent findings, the next day brainstorming and outlining an invited review for Trends in Ecology and Evolution and the final two days writing a first draft.  I think the general consensus was that they were crazy and that such a plan was way too ambitious.  Amazingly, their plan is exactly how it happened.  The group was wonderful to work with and we finished the meeting with a rough but full draft. The paper was published online today and can be found here.  In case you are feeling bad for us for having to work so hard for those five days, check out the view from our hike.


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#365Papers – month #1

There’s a Clark lab effort to improve the amount that we read by participating in the #365Papers challenge.  I didn’t really want to tweet each one out as I go, but publishing a monthly update here helps keeps me honest.  So this is the list for January 2016…

Hamilton et al 2015 PNAS –
Helenius et al. 2015 J Immunol –
Kutch and Fedorka 2015 Proc Biol Sci –
Evolution – Review
Palopoli et al 2015 PNAS –
Vanha-aho et al 2016 Immun. Letters –
Leshchinsky and Klasing 2001 DCI –
Nguyen et al 1998 Aust Vet J –
Chae et al 2014 Cell –
Lambiable et al 2016 PNAS –
Chakraborty et al 2015 BioRxiv –
Chakraborty and Fry 2016 Current Biology –
Zug and Hammerstein 2015 Frontiers in Microbiology –
Avadhanula et al 2009 PLoS Pathogens –
Boettiger et al 2016 Nature –
Costa et al 2009 PLOS ONE –
Grant proposal
Dideon et al 2015 BioRxiv –
Malone et al 2015 Curr Op Gen Dev
Allen et al 2015 Current Biology –
Lack et al 2016 PNAS –
Yassin et al 2016 Nature Communication –
Faria et al 2015 Evolution – Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs –
Cao et al 2016 PLOS Pathogens -A Polymorphism in the Processing Body Component Ge-1 Controls Resistance to a Naturally Occurring Rhabdovirus in Drosophila –
Sedghifar et al 2016 Genetics – Genomic patterns of geographic differentiation in Drosophila simulans –
Erkosar et al 2015 Cell Host Microbe – Pathogen Virulence Impedes Mutualist-Mediated Enhancement of Host Juvenile Growth via Inhibition of Protein Digestion –
Wang et al 2015 Databases -FlyVar: a database for genetic variation in Drosophila melanogaster –
Wang et al 2015 Science Advances – Drosophila Dicer-2 has an RNA interference–independent function that modulates Toll immune signaling –
Carrillo et al 2013 Plant Pathology – Lateral transfer of a phytopathogenic symbiont among native and exotic ambrosia beetles –
Dudzic et al 2015 BMC Biology – Drosophila innate immunity: regional and functional specialization of prophenoloxidases –
Faye et al 2014 PLOS NTD – Molecular Evolution of Zika Virus during Its Emergence in the 20th Century –


Below is Arvid Agren’s (@arvidagren) list.  He’s read some very interesting looking stuff….


Akçay and Van Cleve 2016 Proc B There is no fitness but fitness, and the lineage is its bearer
Mascagni et al 2015 GBE Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes
O’Malley and Powell 2016 Biol Philos Major problems in evolutionary transitions: how a metabolic perspective can enrich our understanding of macroevolution
Kovaka 2015 Philos. Sci. Biological Individuality and Scientific Practice
Ewing 2015 Mobile DNA Transposable element detection from whole genome sequence data
Rahman et al. 2015. Nucl. Acids. Res Unique transposon landscapes are pervasive across Drosophila melanogaster genomes
Mallet et al. 2015. BioEssays. How reticulated are species?
Okasha and Martens 2016 JEB Hamilton’s Rule, Inclusive Fitness Maximization, and the Goal of Individual Behaviour in Symmetric Two-Player Games
Hartfield et al. 2016. Genetics. Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity
Brunet and Doolittle. 2015. GBE. Multilevel selection theory and the evolutionary functions of transposable elements
Sterelny and Kitcher. 1988. J Phil The return of the gene
Kapheim et al. 2015. Science. Genomic signatures of evolutionary transitions from solitary to group living
Maynard Smith. 1987. How to model evolution. In “The Latest on the Best” (J Dupre ed.)
Manuscript draft
Rollins et al. 2016. MBE Selection on mitochondrial variants occurs between and within individuals in an expanding invasion
Lander. 20116. Cell The Heroes of CRISPR
Rosenberg 1993 Midwest Stud Phil Genic slection, molecular biology and biological instrumentalism
Griffin et al. 2015. JEB Within-population Y-linked genetic variation for lifespan in Drosophila melanogaster
Camus et al. Curr Biol 2012 Mitochondria, maternal inheritance, and male aging
Beekman et al. 2014 Proc B The costs of being male: are there sex-specific effects of uniparental mitochondrial inheritance?
Yee et al. 2015 Evolution Intergenomic interactions between mitochondrial and Y‐linked genes shape male mating patterns and fertility in Drosophila melanogaster
Dean et al. 2015 JEB Context-dependent effects of Y chromosome and mitochondrial haplotype on male locomotive activity in Drosophila melanogaster
Waters. 1990. Biol and Philos Rosenberg’s rebellion
Felsenstein. 2001. Syst. Biol. The troubled growth of statistical phylogenetics
Kofler et al. 2015. PLoS Genetics Tempo and mode of transposable element activity in Drosophila
Haig. 1996. PNAS Gestational drive and the green-bearded placenta
Foster. 2006. JEB. Balancing synthesis with pluralism in sociobiology
Current Zoology – Review
Krupp. 2016. TREE Causality and the levels of selection
Herron. 2015. Mol Ecol. Origins of Multicellular Complexity: Volvox and the Volvocine Algae
Manuscript draft

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New paper on convergent balancing selection in Drosophila

A paper I wrote with Ginny Howick and Brian Lazzaro was published in Current Biology today.  The link is here: Convergent Balancing Selection on an Antimicrobial Peptide in Drosophila It was a lot of fun and started as a questionable GWAS hit for a completely different project.  What we find is that the same amino acid polymorphism in the antimicrobial peptide, Diptericin, segregates in D. melanogaster and D. simulans and that the two alleles have very different effects in terms of immune defense.  Null alleles also segregate in both species at relatively high frequencies and are associated with very poor immune defense.  In D. simulans, a tandem duplication of Diptericin is segregating.

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The Unckless lab at the University of Kansas

438px-university_of_kansas_jayhawk_logo-svgIn August, I will be starting a lab at the University of Kansas in the Department of Molecular Biosciences.  I’m thrilled for this opportunity and will be looking to take graduate students and hire technicians and postdocs.  Please send me a message if you are interested.  Check out my amazing colleagues at and  More to come as we get closer to the date…