We are currently focusing on four aspects of the evolution of eukaryotic microbes:
- Assembling the tree of life with focus on microbial lineages in SAR
- Phylogeography of Coastal Choreotrich and Oligotrich Ciliates
- Biodiversity and biogeography of testate amoebae in bogs and fens
- Genome Evolution in Ciliates
Assembling the tree of life with a focus on microbial lineages in SAR
Our lab is part of a multi-institution project entitled Open Tree of Life. The goals of this project include synthesizing taxonomic and phylogenetic information from the ~2.5 million named species on Earth, and generating a publically-accessible version of the tree of life that captures the history of major lineages. We focus on the microbial portions of biodiversity, and on the impact of lateral gene transferon the tree of life.
We also continue to work on phylogenomics of eukaryotes. Eukaryotes, cells with nuclei, existed exclusively as microorganisms for at least 500 million years before the evolution of plants and animals. These microbial eukaryotes, or protists, represent a tremendously diverse assemblage of organisms. Protists are characterized by numerous innovations in cell biology (e.g. multiple acquisitions of chloroplasts), play an essential role in ecosystems (e.g. carbon fixation in marine systems), and some are causative agents of prevalent infectious diseases (e.g. malaria) that impact the social and economic fortunes of entire countries. We are working to generate and analyze high throughput data to make inferences about the eukaryotic tree of life.
Phylogeography of Coastal Choreotrich and Oligotrich Ciliates
In collaboration with George McManus, an ecologist at the University of Connecticut, we are collecting molecular data to assess the phylogeography of Oligotrich and Choreotrich ciliates. Current ideas on protist biogeography fall into one of two camps: (1) all protists are cosmopolitan (high gene flow) and we have discovered the bulk of protist species, and (2) there are many endemic species (low gene flow) of protists yet to be discovered. Our data suggest the need to redefine this debate as we find repeated evidence of ciliate lineages with both high gene flow and high genetic diversity (e.g. Katz et al. 2005). We are now analyzing culture-independent 454 sequence data of ciliates in near-shore environments combined with DGGE gels to look at patterns of biodiversity.
Biodiversity and biogeography of testate amoebae in bogs and fens
The highest abundance of many testate (shelled) amoebae can be found in low pH Sphagnum rich bogs and fens. We are combing molecular and morphological analyses to assess the biodiversity and phylogeography of these beautiful species. Sampling species from across numerous bogs and fens in New England has revealed considerable genetic diversity within morphospecies and evidence of non-monophyly of both species and genera. We are now extending this work to look at additional sampling of both species and genes.
Genome evolution in ciliates
Ciliates are defined by the presence of two distinct genomes, each contained within its own nucleus. One of these nuclei, the ‘germline’ micronucleus (MIC), undergoes meiosis and mitosis but is transcriptionally inactive. In contrast, the macronucleus (MAC) is the site of virtually all transcription within ciliates. The macronuclear genome develops from a zygotic genome through a series of sometimes-extensive chromosomal rearrangements, including fragmentation of chromosomes, elimination of specific sequences and amplification of the remaining chromosomes.
The Katz lab has focused on exploring patterns of chromosomal rearrangements among diverse ciliate lineages. We demonstrated that extensively fragmented genomes occur in three classes of ciliates: in addition to the well-studied class Spirotrichea, the Armophorea and Phyllopharyngea extensively fragment their MAC genome to generate ‘gene-sized’ chromosomes. For example, in these lineages the ~1.6kb a-tubulin gene resides on a chromosome 1.8-2.2 kb in length. The appearance of several lineages containing extensively fragmented genomes suggests multiple origins of gene-sized MAC chromosomes.
Having established that extensively processed genomes evolved multiple times in ciliates, we are now characterizing the mechanisms of genome rearrangements from diverse ciliates. Moset recently, we have demonstrated that alternative processing of germline regions underlies gene family evolutoin in ciliates. Our analyses suggest that the dimorphic nature of ciliate genomes enables ciliates to cross the ‘valleys’ in the adaptive landscape of protein evolution — ciliates may be able to maintain deleterious copies of paralogs in their MICs while ‘hiding’ them from selection in their MACs. Processed MAC genomes: (1) break up linkage groups (fate of paralogs less affected by fate of other polymorphisms on linked chromosomes); (2) allow assortment of paralogs in the MAC but not in the MIC (deleterious mutations may be hidden in the MAC even though they are present in the MIC); and (3) redefine ‘genetic load’ through differential amplification of MAC chromosomes (may make it relatively inexpensive for ciliates to carry duplicated genes).
Katz, L. A. 2001. Evolution of nuclear dualism in ciliates: a reanalysis in light of recent molecular data. Int. J. Syst. Evol. Microbiol. 51:1587-1592.
Katz, L. A., J. Bornstein, E. Lasek-Nesselquist, and S. V. Muse. 2004. Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes. Mol Biol Evol. 21:555-562.
Katz, L. A., E. Lasek-Nesselquist, and O. L. O. Snoeyenbos-West. 2003. Structure of the micronuclear a-tubulin gene in the phyllopharyngean ciliate Chilodonella uncinata: implications for the evolution of chromosomal processing. Gene 315:15-19.
Katz, L. a., G. B. McManus, O. L. O. Snoeyenbos-West, A. Griffin, K. Pirog, B. Costas, and W. Foissner. 2005. Reframing the ‘Everything is everywhere’ debate: evidence for high gene flow and diversity in ciliate morphospecies. Aquatic Microbial Ecology 41:55-65.
Lasek-Nesselquist, E., and L. A. Katz. 2001. Phylogenetic position of Sorogena stoianovitchae and relationships within the class Colpodea (Ciliophora) based on SSU rDNA sequences. Journal of Eukaryotic Microbiology 48:604-607.
McGrath, C., R. A. Zufall, and L. A. Katz. 2006. Genome evolution in ciliates in L. A. Katz and D. Bhattacharya, eds. Genomics and Evolution of Eukaryotic Microbes. Oxford University Press.
Olive, L. S. 1978. Sorocarp development by a newly discovered ciliate. Science 202:530-532.
Parfrey, L. W., E. Barbero, E. Lasser, M. Dunthorn, D. Bhattacharya, D. J. Patterson, and L. A. Katz. 2006. Evaluating support for the current classification of eukaryotic diversity. Plos Genetics 2:2062-2073.
Riley, J. L., and L. A. Katz. 2001. Widespread distribution of extensive genome fragmentation in ciliates. Mol. Biol. Evol. 18:1372-1377.
Snoeyenbos-West, O. L. O., J. Cole, A. Campbell, D. W. Coats, and L. A. Katz. 2004. Molecular phylogeny of phyllopharyngean ciliates and their group I introns. Journal of Eukaryotic Microbiology 51:441-450.
Snoeyenbos-West, O. L. O., T. Salcedo, G. B. McManus, and L. A. Katz. 2002. Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci. International Journal of Systematic and Evolutionary Microbiology 52:1901-1913.
Zufall, R. A., C. McGrath, S. V. Muse, and L. A. Katz. 2006. Genome architecture drives protein evolution in ciliates. Mol. Biol. Evol. 23:1681-1687.