1. Population genomics and genome
evolution: Do selection and recombination interact to
shape patterns of genetic variation and linkage disequilibrium -- via
genetic hitchhiking, background selection, and interference effects?
Are mutation and recombination coupled? What genomic features
facilitate or limit weak selection? What demographic processes shape
genetic variation? How do breeding system differences affect genetic
variation? How can
the complementary information of different marker types be integrated
to improve inference of demography and selection?
hyperdiversity defines populations of the nematode Caenorhabditis brenneri.
Thomas & A.D. Cutter. 2013. PNAS. 110:
We are building on our discoveries of hyperdiverse
nucleotide variation in the genomes of various Caenorhabditis
species in several exciting ways. As a specific example, C.
brenneri has the highest molecular diversity of any
animal or plant! We are exploiting this to more finely dissect the
function of genes and regulatory
elements. This includes the intriguing
genes, as well as other small RNA genes, and genomic features
like operons and repetitive DNA.
To better understand how different ongoing forces (recombination,
mutation, selection, demography) shape genetic variation in genomes, we
are sequencing entire genomes of multiple
genomics. Our recent discoveries of closely-related
divergent populations makes genome-scale divergence population genetics
analysis an exciting means of quantifying adaptation and other
evolutionary processes with unprecedented resolution. In parallel, we
are developing a platform for comparative
population genetics across the Caenorhabditis
study the causes of molecular diversity in a phylogenetic context.
of this work are in collaboration with Bret Payseur (U. Wisconsin),
Patrick Phillips (U. Oregon), and Lincoln Stein (OICR).
signatures of selection at linked sites: unifying the disparity among
species. Cutter, A.D. & B.A.
Reviews Genetics. 14: 262-274. [pdf]
*Molecular hyperdiversity and evolution in
very large populations. Cutter, A.D., R. Jovelin
& A. Dey.
Ecology. 22: 2074-2095. [pdf]
*Integrating phylogenetics, phylogeography
and population genetics through genomes and evolutionary theory.
Cutter, A.D. 2013. Molecular
Evolution. In press. [pdf]
of finite-sites mutation,
subdivision and sampling schemes on patterns of nucleotide polymorphism
for species with molecular hyperdiversity. Cutter,
A.D., G.-X. Wang,
& Y. Peng. 2012.
21: 1345-1359. [pdf]
sequence variation potentially contributes to within-species functional
divergence in the nematode Caenorhabditis
R. & A.D. Cutter. 2011. Genetics.
189: 967-976. [pdf]
2. Genetics of reproductive isolation:
What governs the strong male inviability and
sterility in inter-species hybrids (Haldane's Rule)? What causes one
species to be a
better "mom" than another in inter-species hybrids (Darwin's
Corollary)? How much genetic variation within-species is there for
between-species hybrid viability and fertility? What causes gametic
isolation? What genetic
differences are responsible for reproductive isolation between species?
Several new projects in the lab aim to
Caenorhabditis as a model
genetics. A growing number of Caenorhabditis
species pairs have been discovered to be incompletely reproductively
isolated from one another: they form viable and fertile hybrids.
This permits, for the first time, the ability to
use the power of Caenorhabditis to investigate the
genetic basis of reproductive isolation. We are exploring this at
several levels, from pre-mating
factors like the evolution of male responses to mating pheromone to post-mating pre-zygotic
factors implicating gametic
isolating barriers to post-zygotic
incompatibilities that cause inviability
and sterility in hybrids. Using powerful tools, including
inter-species NIL mapping, in
vivo sperm labeling, and gene knockdown by RNAi, we are
dissecting the mechanistic and genetic causes of these barriers to gene
depression with low genetic variation in selfing Caenorhabditis
Jovelin, S. Han, C.
Ferrari, A.D. Cutter & C. Braendle. 2013. Evolution.
67: 3087-3101. [pdf]
genetic structure of Caenorhabditis
remanei reveals incipient speciation. Dey, A.,
Wang & A.D. Cutter. 2012. Genetics. 191:
*The polymorphic prelude to
Bateson-Dobzhansky-Muller incompatibilities. Cutter,
A.D. 2012. Trends in
Evolution. 27: 209-218. [pdf]
for post-zygotic reproductive isolation between Caenorhabditis
briggsae and Caenorhabditis
sp. 9. Kozlowska,
J.L., A.R. Ahmad, E. Jahesh
& A.D. Cutter. 2012. Evolution.
66: 1180-1195. [pdf]
variation: What controls temperature-dependent fecundity
variation? What genes underlie behavioral differences among
individuals? Do identical complex phenotypes in different species
or divergent molecular mechanisms?
traits that differ between latitudinally- and
phylogeographically-distinct strains of C. briggsae.
In collaboration with the labs of Scott Baird (Wright
State U.) and William Ryu (U.
Toronto), we are now interrogating the genetic basis of
traits with recombinant inbred lines (RILs) to
determine the nucleotide changes that cause this natural phenotypic
thought to reflect local
adaptation. In particular, we are attempting
to determine the genetic underpinnings of behavior trait
and fitness differences resulting from problems in gametogenesis. In
related work, we are using inter-species NILs to genetically map traits
that have diverged between species.
We are starting to expand this work to determine a potential role for small RNAs in C. briggsae
fecundity variation (in collaboration with Julie Claycomb at U. Toronto).
and consequences of breeding
system evolution: How many sperm is the optimal number
for a hermaphrodite to produce? Has adaptive evolution or relaxed
selection generated the "selfing syndrome" in species with
hermaphrodites? Under what conditions do different Caenorhabditis
species demonstrate competitive advantages? What conditions and traits
allow males to persist in androdioecious populations?