Genome Maintenance, Evolution, and Molecular Ecology

The source of all genetic variation is mutation.  As such, the mechanisms dedicated to maintaining the fidelity of genome replication are fundamental to biology. Genome instability is a common aspect of many diseases such as cancer, as DNA is continually altered by an array of mutagenic agents from the environment and cellular metabolism. The mechanisms that monitor and repair DNA damage are very complex, yet surprisingly very well-conserved, from single-celled microorganisms (such as yeasts), to plants, to humans.

Just as mutation is essential to evolution of new traits, and ultimately new species, variation in mutation shapes genome evolution.  Molecular ecology surveys genetic variation that may underlie adaptation to new or changing habitats, mapping the patterns of variation across landscapes.


Kevin Culligan -- Molecular and cellular responses to DNA damage

Kevin Culligan's research is focused on the molecular and cellular response to DNA damage in the model plant Arabidopsis thaliana.  DNA damage occurs from both exogenous (environmental) sources such as UV light, and endogenous sources such as reactive oxygen produced during metabolism. Detected cellular DNA damage initiates a cascade of signaling events within the cell to determine the most appropriate response.  For example, is it better for the cell to induce repair of the DNA damage and risk mutation, or simply induce programmed cell death if damage is too great.  Kevin’s research group studies the molecular pathways of these cellular life-and-death decisions, including the protein kinases ATR and ATM, which are master regulators of the DNA damage response in eukaryotic cells.  Both genetic and genomic approaches are currently being used in the lab to study these pathways.

Kevin Culligan – Rudman Hall, Room 310
Phone: (603) 862-2430

foci dna damage


Thomas M. Davis -- Genome Structure and Evolution in Crop Plant

We aim to understand how genome structure evolves as a consequence of  hybridization and polyploidization in crop plants (with current emphasis on strawberry), and to establish knowledge and resources needed to enable marker-assisted selection by plant breeders. Approaches include whole genome sequence, bioinformatics, site-specific resequencing and phylogenetic analysis, molecular cytogenetics, germplasm exploration and development, transmission genetics, and linkage mapping.

Thomas M. Davis - Rudman Hall, Room 104
Phone: (603) 862-3217


davis genome structure


Anita Klein --Molecular ecology of marine organisms

DNA-based methods provide a high-resolution understanding of evolution and population structure. The Klein lab is using phylogeography to understand the spread of invasive algal species. In collaboration the Mathieson lab (Jackson Estuarine Lab, UNH) we are tracking the origins and diversity of the oyster thief (Codium fragile) in New England and the Canadian Maritimes. Populations of this macroalga have explosively expanded, displacing native algae and disrupting shellfish beds. The Klein lab is part of the Porphyra community genome sequencing and annotation projectThese algae are components of integrated aquaculture systems where algae are grown in the effluent water from finfish tanks.  At UNH, common garden experiments and quantitative trait mapping or association genetics will be used to identify natural variation for traits that will improve Porphyra. A third research area is the conservation genetics of eelgrass, whose populations in estuarine environments are being threatened by the effects of pollution and by climate change. Our lab is collaborating with Drs. Short, Burdick, and Moore (Jackson Estuarine Lab, UNH) to examine the population structure of eelgrass beds from Southern New England and Long Island Sound to better understand eelgrass metapopulation dynamics in order to improve conservation efforts.

Anita Klein - Rudman Hall, Room 383
Phone: (603) 862-2455

Molecular ecology of marine organisms


Adrienne Kovach-- Molecular ecology and conservation genetics of vertebrates

Research in the Kovach lab is focused on the application of genetic approaches to the population ecology, evolution and conservation of vertebrates. We address questions about population and stock structure, dispersal, source-sink dynamics, interspecific hybridization, landscape genetics and conservation genetics in a variety of vertebrate species, including black bears, New England cottontails, Saltmarsh Sparrows, vernal pool-breeding amphibians, and marine and anadromous fish. We typically combine field studies of behavior and ecology with genetic approaches, including microsatellite or SNP genotyping and DNA sequencing. A primary current focus is in elucidating anthropogenic influences on population structure and dispersal, for example, the effects of habitat fragmentation and suburban development on animal dispersal and metapopulation dynamics. Some projects also employ a population genomics approach, whereby next generation genomic sequencing technologies facilitate studies of adaptive variation in natural populations

Adrienne Kovach – Rudman Hall, Room G87
Phone: (603) 862-1603

kovach molecular ecology


Matthew MacManes -- Functional genomics in non-model organisms

Work in the MacManes lab centers around the basic theme of adaptation. The systems we use to better understand the eco-evolutionary forces driving pattern are varied, but 2 main systems form the core of the lab.

I am studying this phenomenon in captive animals. I house these animals in desert conditions, understand their physiology by analysis of blood and urine. I measure gene expression via high throughput sequencing experiments.

  1. Adaptation to Deserts: Deserts are extremely hot and dry. Animals living there must be able to endure such harsh condition. Short lived animals– e.g. mice– may live their entire live without ever drinking water, yet they thrive! Understanding how they do it is a main focus of the lab.
  2. Color Polymorphism in Dendrobatid frogs: With collaborators (Rasmus Nielsen, Kyle Summers, Cori Richards) we are attempting to understand (1) the development and of color, and (2) its maintenance in populations.

Matthew MacManes – Rudman Hall, Room 189
Phone: (603) 862-4052


Sandra Rehan - Comparative genomics and molecular ecology of social insects


The lab research focus is social evolution and genetics.  We have a special interest in the origin and evolution of social behavior in bees.  The lab has three main foci: molecular phylogeny, behavioral ecology and comparative genomics.  We employ these three levels of biological integration to study social complexity at multiple evolutionary scales.

The goal is to understand the genetic underpinnings of social behavior. We ask questions on the origin and maintenance of social behavior and how social experience affects gene regulation and behavioral plasticity in bees. We also ask questions on biodiversity and use molecular phylogenetics and historical biogeography to better understand speciation, dispersal and coevolution of native pollinators.

Sandra Rehan - Rudman Hall, Room 191
Phone: (603) 862-5310

foci rehan social insects


Kelley Thomas -- Genome-wide mutation analysis 

The Thomas Group focuses on understanding the baseline rate and pattern of mutation.  The work uses diverse organisms including Yeast, Nematodes and Paramecium that have been raised for many generations in the laboratory in the near absence of natural selection.  In this approach many lineages are derived from a single progenitor and grown for hundreds of generations in parallel.  In each lineage the organisms accumulate mutations that might otherwise be weeded out by natural selection.  By sequencing the genomes of the descendants and comparing their genomes we can identify virtually all the mutations across the genome and describe their rates and patterns.  

W. Kelley Thomas – Gregg Hall, Room 448
Phone: (603) 862-2470

Genome foci desert mice