My own research interests are focused on two main areas: the evolutionary consequences of polyploidy and the evolutionary genetics of interactions among organisms (including mating systems and host-pathogen interactions). My recent research has combined classical Mendelian genetics with more advanced technologies, including: comparative sequence analysis (PCR, cloning, sequencing), rtPCR-based gene expression studies, genomic-scale expression studies using microarrays, genome content analysis using flow cytometry, cytogenetics using image analysis, and inheritance and diversity studies using microsatellite DNA.  We are also embarking on new projects incorporating next generation sequencing methods, such as 454 tagged amplicon sequencing, RAD sequencing and bulked segregant analysis using Solexa sequencing.

Evolutionary Consequences of Polyploids

 Polyploidy, the presence of more than two copies of each chromosome in the cells of an individual organism, has undoubtedly been a significant force driving genetic diversity and speciation in the evolutionary history of plants, and recent evidence suggests that it is more important in animal evolution than was previously thought. In fact, evidence from genome sequencing projects suggests that even in organisms with small genomes (the yeast Saccharomyces cerevisiae and the plant Arabidopsis thaliana) there is evidence of ancient genome duplication events. This has lead to a dramatic increase in study of the potential fate of duplicate genes, and has brought polyploidy from a somewhat peripheral plant-only perspective to the main stream of comparative genomics, bioinformatics, and evolutionary research in plants and interest in the role that it might play in animals is increasing (reviewed by Mable et al. 2011. Journal of Zoology). . Recent technological advances have greatly enhanced the potential to elucidate both the origins and consequences of polyploidy (and gene duplication in general) in a wide array of organisms.

Currently, we are investigating genetic diversity and gene copy number at the MHC in a 40-year old feral population of Xenopus laevis from Wales (in collaboration with Mark Viney and Richard Tinsley, at the University of Bristol). 

I have studied the evolution of polyploidy in animals (frogs in the genera Hyla and Neobatrachus and salamanders in the genus Ambystoma), plants (flowering plants in the genus Arabidopsis), and fungi (yeast in the genus Saccharomyces)(Figure 1). My current research combines classical Mendelian genetics with more advanced technologies, including: comparative sequence analysis (PCR, cloning, sequencing), rtPCR-based gene expression studies, genomic-scale expression studies using microarrays, genome content analysis using flow cytometry, cytogenetics using image analysis, and inheritance and diversity studies using microsatellite DNA.

 Figure 1. Techniques used to assess ploidy level. (a) Flow cytometry; (b) chromosome counts (Based on Dart, Kron & Mable, 2004. Can J. Bot.).

Current Projects

Evolutionary Genetics of Plant Mating Systems

i) Evolutionary dynamics of genes controlling self-incompatibility in natural populations
Sporophytic self-incompatibility (SSI), which is controlled by genes that belong to large gene families, has been extensively studied in cultivated plants in the genus Brassica. In collaborative project with the research groups of Deborah Charlesworth (University of Edinburgh, Scotland) and Mikkel Schierup (University of Aarhus, Denmark) we characterized the system in naturally occurring populations of Arabidopsis lyrata, which is related both to Brassica and to the self-compatible genetic model, Arabidopsis thaliana, as well as extending it to other species in the Brassicaceae (in collaboration with Xavier Vekemans, University of Lille; Steve Ansell, Natural History Museum London; Detlef Weigel, Max Planck Institute for Developmental Biology, Tübingen).  This work  This work involved a combination of controlled hybridisation experiments in the greenhouse to establish the genetics of SSI and extensive molecular characterization (through PCR, cloning and sequencing studies) of the number of S-alleles present in natural populations, their relative age, and divergence levels compared to alleles at loci that are members of the same gene family but that are not involved in SI, and differences in expression and dominance of alleles of different types. We identified a large number of S-alleles from the stigma-expressed SRK allele (the female S-gene) and an additional 7 paralogous loci that do not appear to be directly involved in the SI reaction (Figure 2).  Recently we have been developing methods to more rapidly genotype these highly polymorphic gene families using 454 tagged amplicon sequencing (in collaboration the NERC Biomolecular Analysis Facility in Liverpool and the Centre for Ecological and Evolutionary Synthesis in Oslo).

 Figure 2. Gene tree showing relationships among a subset of alleles at the self-incompatibility locus of A. lyrata. Sequences can be divided roughly into two major groups (A and B). (Based on Prigoda, Nassuth & Mable, 2005. Mol. Biol. Evol.).

ii) Break-down of SI in natural diploid populations.
Despite reports that A. lyrata is an exclusively self-compatible species, we unexpectedly discovered that this is not true for all populations. We have identified diploid and tetraploid populations that appear to be completely self-compatible, whereas others consist of completely self-incompatible individuals or a mixture of self-compatible and self-incompatible individuals. We have established that loss of SI has resulted in a substantial loss of genetic diversity and that there has been a shift to inbreeding in some populations (Mable et al. 2005 Evolution Mable & Adam 2007 Molecular Ecology). These populations are found on threatened habitats (sand dunes, cliff edges, and limestone pavements: Figure 3) and results from this work may have conservation implications for the effects of habitat fragmentation on plant mating systems. 

Recent work has focused on determining:
1) the causes and fitness consequences of these mating system changes (Hoebe 2009; Ph.D. Thesis; Stift et. al. unpublished );
2) the relationship between outcrossing rates, variation in strength of SI and genetic diversity in a larger population surveys; (Hoebe et al. 2009 Molecular Ecology; Tedder et al. 2010 Diversity; Foxe et al. 2010 Evolution)
3) the genome-wide causes and consequences of mating system shifts. These populations are found on threatened habitats (sand dunes, cliff edges, and limestone pavements: Figure 3) and results from this work may have conservation implications for the effects of habitat fragmentation on plant mating systems. This work is a collaborative project involving 3 postdocs: Hong-Guang Zha, Marc Stift, and Annabelle Haudry; 3 PhD students: Peter Hoebe, Andy Tedder, and Paul Foxe (York University, Toronto); as well as two main collaborators: Dr. Stephen Wright (University of Toronto) and Steve Ansell (Natural History Museum, London).  An important outcome of this research is demonstration that loss of SI does not always lead to a shift in matign system and so this should be considered a two-step process that could be subject to different selection pressures (Foxe et al. 2010; Haudry et al., unpublished).  We have been exploring the genetic basis of loss of SI via bulked segregant analysis (Solexa sequencing), in collaboration with Detlef Weigel, Sang-Tae Kim, Christa Lanz, Jörg Hagmann, and Jun Cao at the Max Planck Institute for Developmental Biology, Tübingen.  We have also investigated SRK diversity in relation to variation in outcrossing rates and mating system in Arabis alpina (Tedder et al. 2011 American Journal of Botany).

Figure 3. A. lyrata habitats. (a) Rocky ridge, Ise of Skye, Scotland; (b) Cliff edge, Tobermory, Ontario; (c) Alvar, Tobermory, Ontario; (d) Sand dune, Rondeau Provincial Park, Ontario.

iii) Polyploidy and Self-incompatibility
Some of the intriguing aspects of self-incompatibility systems are i) the spectacular polymorphisms maintained in populations over long evolutionary times and ii) the complex dominance systems that appear to operate in sporophytic systems. These phenomenon have not been described for polyploids. In some systems of SI, polyploidy is often accompanied by increased levels of self-compatibility but this pattern does not seem to be very strong in SSI systems (Mable 2004. New Phyt.). We have found both strongly SI (Europe) and completely selfing (Asia) populations of A. lyrata. Ploidy of individuals has been determined using flow cytometry and confirmed by chromosome counts for representatives from each population that we have sampled. We have already established that similar dominance of S-alleles is found in SI tetraploids, compared to that in SI diploids (Mable et al. 2004 Heredity) but we would like to look at this in more detail, using both diallele crosses and rtPCR to examine allelic expression patterns in diploids and tetraploids that share the same alleles in order to determine how increased copy number influences relative compatibility.  We are currently investigating the evolutionary dynamics of S-alleles in relation to polyploidy and hybridization in European populations of A. lyrata and Arabidopsis arenosa.  Ploidy of individuals has been determined using flow cytometry and confirmed by chromosome counts for representatives from each population that we have sampled.  Part of this work is in collaboration with Anne Brysting & Marte Jørgensen (University of Oslo) and Marcus Koch & Paola Ruiz (University of Heidelberg). 

Figure 4. Morphological differences between diploid and tetraploid A. lyrata. (a) Diploid plant (2x=16) from Iceland; (b) tetraploid plant (4x=32) from Austria; (c) comparison between diploid (upper) and tetraploid (lower) flower sizes; (d) comparison between diploid (upper) and tetraploid (lower) leaf rosettes.

Planned Projects

In addition to these currently funded projects, there are two new areas that I plan to expand research into:

1) the consequences of polyploidy on pathogen response systems in animals, using Xenopus as a model (in collaboration with Trent Garner, Institute of Zoology; Mat Fisher, Queen Mary University; and Jacques Robert, University of Rochester); and

2) the consequences of polyploidy and mating system shifts on pathogen response systems in plants, using Arabidopsis lyrata infected with Albugo candida as a model system (in collaboration with Eric Holub, University of Warwick).

Evolutionary Genetics of Host-Pathogen Interactions

Although there are a wide variety of factors that can affect host-pathogen interactions, few studies have explicitly assessed the effects of host mating system and ploidy level. In collaboration with Eric Holub (University of Warwick), we are currently using a wild host species that varies in these traits (Arabidopsis lyrata: Brassicaceae) and an important pathogen of crop plants in the Brassicaceae (oomycetes in the genus Albugo) as a model to investigate these types of interactions. Using inbred and outbred plants sampled from some of the same populations as used in Foxe et al. (2010), a pilot study (Hoebe et al. 2011 Journal of Evolutionary Biology) suggested that mating system per se was not related to observed variation in responses to a generalist strain of Albugo (Figure 5) but that genetic drift in inbred populations might make responses more variable among individuals than in outcrossing populations.

Formerly considered as one species, it is now known that there are multiple species of Albugo that infect both wild and domesticated plants in the Brassicaceae. We are currently using the Arabidopsis-Albugo system to: 1) evaluate whether response to infection with Albugo varies by mating system, ploidy or geographic distribution of the host; 2) evaluate the extent to which wild populations of A. lyrata are naturally infected with the various species of Albugo; 3) assess levels of genomic variation between isolates of Albugo infecting various host species; 4) compare the relative performance of A. lyrata populations in response to Albugo epidemics caused by exposure to an Albugo strain carried by A. thaliana under semi-natural epidemic conditions; and 5) investigate the genetic basis for variation in resistance to Albugo in natural populations of A. lyrata. The project involves postdocs at both Warwick (Volkan Cevik) and Glasgow (James Buckley), as well as two technicians (Aileen Adam, Elizabeth Kilbride) and an undergraduate assistant (Ryan Carter).

Figure 5. Photographs of individuals from the LPT population with different infection phenotypes as inferred from the degree of Albugo candida sporulation blisters. (a) resistant: no symptoms of infection; (b) partially resistant: sporulation blisters restricted to the undersides of inoculated leaves (not visible on photo), plant development appears normal; (c) susceptible: severe blister formation on the whole plant, plant development is strongly impeded (from Hoebe et al. 2011).