We are currently focusing on four aspects of the evolution of eukaryotic microbes:

  1. Assembling the tree of life with focus on microbial lineages in SAR
  2. Phylogeography of Coastal Choreotrich and Oligotrich Ciliates
  3. Biodiversity and biogeography of testate amoebae in bogs and fens
  4. Genome Evolution in Ciliates

Assembling the tree of life with a focus on microbial lineages in SAR
The Katzlab focuses 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. Recent papers focus on phylogeny, lateral gene transfer, and genome evolution (see below0.

Biodiversity of SAR, with focus on ciliates
In collaboration with George McManus, an ecologist at the University of Connecticut, we are collecting molecular data to assess the phylogeography of marine 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 HTS data generated using primers designed to characterize SAR (Stramenopila, Alveolata, Rhizaria)

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).