24 June 2014

evolution

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Evolution 2014 notes

Evolution 2014 notes

My helter-skelter and probably inaccurate notes from various talks I attended in various states of awakefullness. Apologies to the presenters for any errors.

Full program here

2014-06-21

How to train your symbionts: antagonistic coevolution and the evolution of transmission mode

• Devin Drown

Examining the presence of a geographic mosaic of coevolution in the walnut aphid biological control system

• Jeremy Andersen

How Nonadditivity of Finess Impacts Alters Selection for Resistance in a Multiple-Herbivore Community

• Michael Wise

Evolving virulence and defense in a symbiotic community

-Paul Nelson

Is it time to abandon the holey fitness landscape metar

• Bjorn Ostman
• Yes!

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii

• David Lowry
• many plant species have different dry and wet habitat ecotypres
  • shared gene networks
  • plant hormones?
• Panicum hallii
  • diploid, small genome, fast generation time
  • var. halii
  • var. filipies
• QTL analyis
  • RAD sequencing - Wang et al. 2012 Nature Methods
  • 1 major QTL for (divergence?)
  • 5 major QTL for seed size
  • two locus hybrid-incompatability
• Evolution of gene expression
  • dry-down experiment
  • about 10k genes differ in expression btwn varieties
  • 3k differ btwn treatments
  • effect of time of day
  • mapping expression QTLs (eQTL) before and after rainfall event

The evolution of bet-hedging and phenotypic plasticity

• Jeremy Van Cleve
• stochastic switching
• bet hedging can increase geometric fitness by reducing fitness variance
• whether bet-hedging or plasticity evolve depends on whether costs of plasticity accelerate or decelerate

Mechanistic overlap between plastic and evolved responses to heat stress, revealed through RNAseq

• Morgan Kelly
• ecology and evolution of marine organimsms
• isopod Tigriopus californicus
• experiences variable environment
• relationship between plastic and evolved response to heat stress
• crossed northern and southern populations
• selected F2 lines for increased heat tolerance
• 1895 differentially-expressed genes (6 heat shock proteins) for plastic response to heat shock
• 204 DE genes for increased heat tolerance.
• 170 shared between selected and plastic response!
• suggests selection for constitutive expression of plastically-expressed genes for heat tolerance
• genetic assimilation

Genetic basis of life history plasticity in D. melanogaster

• Katherine O’Brien
• plasticity of diapause phenotype

Breaking G: variable pleiotropy and environmentally induced changes in the correlated response to selection

• Kristin Sikkink
• multiple correlated traits can constrain evolutionary trajectories
• are covariances stable?
• Caenorhabditis remanei
• stress response pathways; Insulin/IGF-1 signaling
• DAF-16 responds (signals?) to heat and oxidative stress
• experimental evolution
  • resistance to acute heat shock
  • resistance to acute oxidative shock
  • same in oxidative environment
• results
  • no differences in control line
  • heat shock selection increases heat shock resistance, but no correlated response for oxidative stress. same for the inverse with oxidative stress
  • in oxidative environment, correlated negative resistance to oxidative resistance under selection for heat shock resistance
  • in oxidative environment, positive correlated heat resistance when selecting for increased oxidative resistance
• correlated responses dependent on environment of selection

The molecular basis of gene by environment interaction in Arabidopsis thaliana

• David Des Marais
• gene expression variation is relevant in traits affecting fitness
  • strong correlations of expression and traits (Des Marais et al 2012 Plant Cell)
  • gene expression associated with local climate (Lasky et al 2014 MBE)
• structural variants in transcription factor drive differential expression of about 700 genes
• variation in cis-regulatory motif
  • many genes have expression that differs by “treatment” (E)
  • about 1000 genes have GxE expression pattern in wet/dry environments in panel of 80 Arabidopsis accessions
  • “treatment” plants have more ABRE motifs

Life history effects and demographic consequences of interacting QTL for flowering and seed dormancy in Arabidopsis thaliana

• Johanna Schmitt
• life history traits depend on alleles at earlier stages

The genetic architecture of local adaptation at fine spatial scales – a case study of three montane conifer species

• Andrew Eckert
• local adaptation via genetic approaches at fine scales in conifers
• Lake Tahoe Basin, 15km scale
• Fst - Qst comparisons show differentiation
  
• genotype - phenotype associations and genotype - environment associations show almost complete overlap!

The evolutionary interplay between dispersal traits and habitat specialization

• Nancy Emery
• how dispersal evolves in association with adaptation and differentiation
• study system: Lasthenia in California vernal pools
• which seed traits function to influence wind dispersal distance?
  • seed mass, size and pappus length influence distance
• how have wind dispersal traits evolved in association with vernal pool habitat specialization in Lasthenia?
  • vernal pool species tend to have lighter and more compact seeds

Local adaptation to climate within a tree species range: the case of sugar pine, Pinus lambertiana

• Aurore Bontemps
• 17-yr old provenance study
• at Sierra low site, trade-off between growth and survival
• populations from wet environments have greater height
• " from dry environments have greater survival

Using pooled sequencing and whole-genome environmental association analyses to study local adaptation in three Alpine Brassicaceae species

• Christian Rellstab
• detecting genetic footprints of positive selection
  • outlier analyses
  • environmental association analyses
  • identified common set of candidate genes in all three species; parallel evolution
  • large differences among species

2014-06-22

Gene expression explains patterns of evolution in tRNA synthetase genes interacting with mitochondrial and cytosolic tRNAs

• Jeffrey Adrion Gene expression alterations trigger adaptve diffusion after recurrent allopolyploidization in Dactylorhiza (Orchidaceae)

• Ovidiu Paun

Detecting relationships between integrated thermal environments & current gene expression profiles in corals

• Megan Morikawa

Thermal reactionome of the temperate forest ants Aphaenogaster rudis and A. picea

• my talk! went very well! nice comments after.
• Lev Yampolsky commented that he has seen a similar reduction of metabolism in southern vs. northern populations of Daphnia!

Gene expression dynamics in a hibernating primate

• Sheena Faherty

RNA-seq Reveals Regional Differences in Transcriptome Response to Heat Stress in the Marine Snail Chlorostoma funebralis

• Lani Gleason, Ron Burton
• nice study. quite similar to our work but in standard differential expression framework. focus on Hsps

The role of gene expression variation on climatic adaptation in Drosophila melanogaster

• Vinayak Mathur

In what types of environments is inbreeding depression strongest?

• Aneil Agrawal, Li Yun
• not a gene expression study…nice experiment. inbreeding depression greatest in the environment where the effect of density on fitness is the greatest

Some (do not) Like It Hot: The Role of Tumor Necrosis

• Nikki Traylor-Knowles
• 46 tumor necrosis factor receptors (NCFR) in coral, more than any other species

It all adds up: The genetics of thermal reaction norm variation for antibiotic resistance

• Jennifer Knies

Genome-wide rates of molecular evolution are higher in mutualistic plant-nesting ants

• Benjamin Rubin, Corrie Moreau
• 7 ant genomes, outgroup and 3 sets of mutualist/non-mutualists
• identified 7 genes in all mutualist species that show positive selection. 4 are nervous system genes

Rate of resistance evolution in long- and short-lived hosts

• Emily Bruns, Michael Hood, Janis Antonovics

Genomic Variations Associated with Gonococcal Antimicrobial Resistance

• Jeanine Abrams McLean

Elevational disease distribution in a natural plant pathogen system: Insights from genetic variation in resistance and morphology.

• Jessie Abbate
  
• limited distribution of anther smut on Silene in mountains
• evidence for resistance within range
• recovery under low-elevation conditions
• ecotype-specific morphological conditions and recovery

Population genetic and genomic identification of locally adapted loci

• Jeremy Yoder
• genotype-environment association methods
  • one sample per site
• SNPs associated with climate differ in basic population genetic measures
• consequence of association being there, or reflective of how association comes to be
• simulations with QuantiNEMO
  • stabilizing selection with varying optimum
  • soft sweep
  • MLM has fewest false positive, fewest true positives

The geographical and community context of mutualism dynamics: fig-pollinator-parasite interactions in the Sonoran Desert

• John Nason
• mutualsim persistence in extreme environments, populations typically small and spatially-isolated
• Hypotheses:
  • increase within-crown reproductive asynchrony
  • no evidence for selfing or inbreeding
  • within-crown asynchrony to support between-tree reproduction
  • increase the time period during which fig synconia are receptive to pollinators
  • diminishing benefits of waiting for pollinators

Genome-wide evidence of genetic associations in eclosion timing in Rhagoletis

• Peter Meyers
• RAD-seq of early vs. late ecolosing flies from hawthorn and apple
• correlation between early/late alleles between host races

Genomic differences reflect fitness over a small-scale thermal gradient in reef-building corals

• Rachael Bay, Stephen Palumbi
• corals in highly variable (HV) pool have greater thermal tolerance than those from moderately variable (MV) pool
• transplant study. 2 years.
• corals from MV acclimate to HV
• Fst analysis and GxE association identified 114 candidate SNPs
• higher frequency of rare variants in stressful env
• reciprocal transplant of transcriptome sampled individuals
• GLMM: 12 SNPs impact survival
• candidate SNP can predict transplant survival

Genomic insights into a specialized pathogen of the fungus-growing ant symbiosis

• Nicole Gerardo
• Escovopis parasite of cultivated fungus
• arginine biosynthesis genes missing in fungus-growing ant genome
• Escovopis genome; 29.5Mbp genome, 7k genes
• specialized on particular fungus-growing ant system
• lacks ability to feed on plant material
• genes that allow parasitic life-style
• two petaibol synthases - inhibit cell-wall resynthesis during fungal attack
• seven species-specific proteins involved in virulence
• 17 secondary metabolite synthesis clusters

2014-06-23

The environmental determinants of natural selection

• Christina Caruso
• environmental manipulations can determine agents of natural selection
• relevance to natural environments?
• database of selection studies
  • 3201 records of selection
  • 87% in controlled or semi-controlled environments
  • environmental manipulations - biotic, abiotic, multiple factors, transplants
  • 48% records include estimates of mean fitness
• directional selection in experimental studies is comparable to selection in natural populations
• biotic environment does not exert stronger selection than abiotic environment
• no evidence of relationship between absolute fitness and the strength of selection
• “reasons and mechanisms…can only be determined by knowledge of the biology and ecology of the organism” Endler

Scaffolding the origin of multicellular evolvability

• William Ratcliff
• clusters: mother-daughter cell adhesion
• biggest gene change - CTS1 endochitinase
• single SNP mutation to get snowflake clusters!
• genetic uniformity solves problem of genetic conflict
• high multicellular heritability = 0.84

Natural selection maintains high diversity in candidate genes underlying local adaptation to climate: evidence from whole-transcriptome sequencing

• Paul Gugger, Shawn Cokus, Juan Manuel Peñaloza Ramírez, Victoria Sork
• Valley Oak
• transcriptomes
• 50 candidate genes using EMMAX (trait?)
• Differential expression after 10 day drought treatment
• overlap between climate candidates and DE genes

Gene expression woody sunflower

• Brook T. Moyers, Loren H. Rieseberg
• wood sunflower in California
• differentially-expressed genes

Fitness functions and distributions: the shape of things to come

• Frank Shaw, Ruth Shaw
• characterizing ability of a population to adapt
• fisher’s fundamental theorem
  • requires phenotypic fitness function
  • genetic fitness distributino
• greater distance from optimum, variance for fitness increases then decreases
• amount of change in mean fitness depends on denominator
• model with multiple fitness components
• realistic functions of a heritable trait induce considerable genetic variance for fitness
• even model levels of additive genetic variance for fitness results in appreciable adaptation when mean fitness is low

Investigation of gene expression variation within the Yellowstone National Park gray wolf population using RNA-Seq

• Pauline Charruau
• exp ~ rank + age + relatedness
• age main driver of differences in gene expression

Using NGS to investigate differentially expressed genes and SNPs between closely related tephritid fruit flies, Anastrepha fraterculus and A. obliqua

• Carlos Congrains, Reinaldo de Brito
• species are largest difference in RNAseq expression analysis of brain tissue

The combined effects of artificial warming, competition, and community composition on life history traits and patterns of natural selection

• Susana Wadgymar
• three species in warming experiment.
  • monoculture/polyculture
  • density (low/high)
  • warming (yes/no)
• effects of warming depend on community…

Assessing eco-evolutionary feedbacks among pea aphids, defensive symbionts, and natural enemies

• Jacob Russell
• 7 defensive symbionts in pea aphids
• vary in abundance by location and crop type (clover, alfalfa)
• quick turnover (3 weeks) within populations, consistent across fields suggesting selection

Climate change, phylogeography and the future of genetic diversity

• Katharine Marske, Mirnesa Rizvanovic
• Does intraspecific variation matter? Yes
  • Balint et al 2011
  • D’amen et al 2012
• conserve evolutionary theater (Moritz 2012)
• How much phylogenetic diversity will be lost?
• lose tips, but backbone of tree is conserved
• conservation gradient
• ensemble modelling in BIOMOD
• overlay future projected distribution on sampling from phylogenetic tree
  • shows lineages that may be lost
• dispersal? adaptation?

Local adaptation by small effect alleles

• Sam Yeaman
• how does migration-selection balance shape the architecture of local adaptation?
• quantiative genetic models: differentiation depends on migration and Vg
• population genetic models: depends on migration rate and mutation effect size
• what maintains genetic variation?
• can local adaptation occur via small alleles?
• linkage disequilibrium:
• superflous loci model: greater divergence with more loci
  • maintenance of polymorphism determined by migation-drift but loci contribute to adaptive divergence
  • substantial local adaptation at realistic mutation rates
  • limited to highly polygenic traits
  • difficult to deted (Fst is low)
• non-local maladaptation
• allelic critical migration not a hard limit to adaptation; depends on architecture

• large and/or clustered alleles have higher fitness under migration-selection balance

  AoB Plants - “..a rationale for the QTN programme” “The loci of repeated evolution…”

Role of convergent evolution and standing variation in local adaptation

• Graham Coop
• at what spatial scale should we expect local adaptation to patchy environments?
• null models to understand how often convergent adaptation should occur (from population genomic data across landscapes)
• Adaptation by mutation or by migration?
• convergent adaptation among patches should be common if alleles are delerious off the patch
• Adaptation to extreme environmental patch
• role of standing genetic variation in adaptation of Mimulus guttatus to copper
• top sweep candidate shared across populations
• similar patterns for top 10 putative sweeps
• all shared across mine populations & older than mines!
• adaptation from standing genetic variation, alleles < 1%

Clinal variation in adaptation to elevation in Boechera stricta a perennial forb native to the Rocky Mountains

• Jill Anderson
• gradient approach: many populations transplanted into common gardens (not simply reciprocal)
• can identify patterns/variation not observed in reciprocal design

2014-06-24

Evolution and transcriptional connectivity of genes underlying ant social behavior

• Tim Linksvayer
• genetic toolkit hypothesis: highly conserved genes underlie variation in social traits
  • metabolism
  • nutritional state
• systems level analyses reveal gene networks underlying social traits
• is there distinct relationship among expression levels, rates of evolution and transcriptomal network connectivity for genes underlying social behavior?
  • 2 replicate colonies of pharaoh ant
  • 5 paint-marked cohorts, followed 28 days
  • observed behavior daily
  • RNAseq
  • differential gene expression
  • WGCNA
• changes in tasks with age
  • oldest ants forage!
• highly-expressed genes have lower evolutionary rates
  • less constraint in expression for
• greater connectivity for forager and nurse-upregulated genes
• genes associated with worker behavior are rapidly evolving and not conserved across lineages
• only a subset conserved and loosely connected
• little to no overlap for genes underlying social behavior in fire ants in honey bees
• loose connectedness…may facilitate rapid social evolution

Information flow through dominance networks in social insect colonies

• Anjan Nandi
• primitively eusocial species. workers have potential to reproduce
• Ropalidia marginata - queen rarely participates in dominance interactions
  
• network analysis of dominance relationships
• feed-forward loops

Dictionary of genetic elements in Drosophila

• David Houle
• Lewontin’s G-P map
  • genotype space: genomics, population genetics
  • phenotype spae: quantitative genetics
• dictionary of genetic effects
  • phenotype - genotype. perturbe phenotype, examine phenotype
• gene activity space
  • small quantitatively controlled changes in gene activity space. what happens to phenotype?
• GAL4 to manipulate gene expression in Drosophila
• RNAi to reduce gene expression at times and places where gene is normally expressed
• phenotypes are continuous wing veins.
• 122 genes knocked down
  • 28 lethal
  • 23 lethal with some level of knockdown
• validation with GWAS associations

SNP differentiation and differential gene expression in endemic Epischura baikalensis from Lake Baikal

• Lev Yampolsky
• many differentially-expressed genes among populations from different lake basins
• consistent with SNP differentiation suggesting local adaptation

Detecting changes in gene expression by high-dimensional analysis of codon usage bias

• David McCandlish
• codon usage bias: selection for translational efficiency
• tested for non-equilibrium codon usage in S. cerevisae genome

A History of High Latitude Adaptation in Holarctic Ground Squirrels (Urocitellus)

• Bryan McLean

Evaluating the immediate capacity for ongoing adaptation - Ruth Shaw, Charles Geyer, Julie Etterson, Stuart Wagenius

Inferential Evolution and the Reflection Principle

• Christopher J. Ellison, Jessca Flack, David Krakauer

Preadaptation to human environmental impacts: Deforestation filters species and facilitates geographic reshuffling in an anthropogenic world

• Luke Frishkoff
• is temperature-tolerance a pre-adaptation to deforestation?
• two species of frogs
• thermal optimum in jumping performance: very similar to ecotherms performance curves!
• habitat occupancy by each species driven by temperature
• macroclimate affiliation of 22 species: larger frogs more deforestation tolerant

Geographic mosaics of phenology, host preference, adult size and microhabitat choice predict butterfly resilience to climate warming

• Nichole Bennett, Camille Parmesan, Michael C. Singer, Paul Severns
• behavioral thermo-regulation of egg laying in butterflies may allow tolerance of warming in situ

Highly variable recombinational landscape modulates efficacy of natural selection in birds

• Toni Gossmann
• positive selection greater in recombination ‘jungles’
• relaxed selection in recombination ‘deserts’

Genome sequencing, assembly and analysis of the four cactus host populations of Drosophila mojavensis

• Luciano Matzkin, Carson Allan
• positive selection at 422 loci

Genomic signatures of selection in a classic fisheries harvest experiment

• Nina Overgaard Therkildsen, Steve Munch, David Conover, Stephen Palumbi
• artificial “fishery” selection experiment for large and small fish over 4 generations
• 425 SNPs identified by Fst as differentiated between selected lines
• few signatures of hard selective sweeps

Genome wide congealing and the dynamics of speciation

• Samuel Flaxman, Jeffrey Feder, Patrik Nosil
• what are signatures of evolutionary processes at genomic level when many loci involved?
• very low amounts of gene flow (1 per 10 generations) adequate to keep neutral loci homogenized during divergence
• key influence of population size

MACPRF: detecting intragenic selection heterogeneity based on polymorphism and divergence

• Jeff Townsend
• tests for selection operate of different time scales
  • ancient: PAML, BSREL
  • recent: selective sweep detection (Tajima’s D, iHS)
  • intermediate: McDonald-Kreitman, Poisson Random Field
• MK test assumes intragenic homogeneity of selection
  • weakens test
• PRF quantitatively estimates gene-wide selection intensity
• MACPRF more powerful than MK as allows selection to vary intragenically
• S. cerevisae vs. S. paradoxus - up to 43% of total coding sequences are subject to positive selection
  • not necessarily positively-selected, but if a mutation occurred in this region it would be
• from a question - how different than sliding window? not very! but don’t need to select window size

The rate of adaptation in a changing environment

• Leonard Nunney
• species have limited or no potential to shift their range
• what is the probability that effective long-term adaptation can occur?
• Haldane 1957 - cost of natural selection; ~1 substitution per 4300 generations
• Burger & Lynch 1995 - critical rate of environmental change
• simple eco-evolutionary model
• parameters: carrying capacity (K), beneficial mutations per generation (u/g)
• in large populations, adaptation can be rapid
• rates can be 10x faster than Haldane’s rate
• but requires carrying capacity of 50k
• linked populations can form large adaptive metapopulation given migration rates of 2 - 5 from adjacent populations

The evolution of functional trait syndromes: the ecological genetics of drought resistance in annual monkeyflowers.

• Nicholas Kooyers
• genetic correlations among functional traits
• no evidence for genetic tradeoffs between early flowering and drought-tolerance traits

The evolution of the fire ant’s Y-like social chromosome

• Rodrigo Pracana, Nichols Richard, Yannick Wurm
• genetic basis of sociality
• Gp-9 BB - single queen
• GP-9 Bb - multiple queen
• Gp-9 bb - lethal
• located within 600 gene inversion!
• compared 7 B to 7 b males
• Fst ~ 1 across inversion (suggests old divergence)
• diversity is close to zero in b inversion (suggests young) - how to reconcile?
• no evidence for strata in social chromosome

Dispersal transiently alters the expression of immune-related genes

• Noah Snyder-Mackler
• costs of dispersal
• gene expression modeled using GEMMA to account for age, weight, relatedness

Exploring genome-wide signals of selection against gene flow

• Simon Aeschbacher, Graham Coop
• selection against gene flow - negative correlation btwn ‘absolute’ genetic divergence and local recombination rate
• new method…
• can’t identify individual loci, but no false positives, robust against demography