Jeremiah D Hackett
Associate Department Head, Ecology and Evolutionary Biology
Associate Professor, BIO5 Institute
Associate Professor, Ecology and Evolutionary Biology
Associate Professor, Genetics - GIDP
Primary Department
(520) 621-7514
Work Summary
Jeremiah Hackett’s research interests are in the areas of genome evolution, the evolution of photosynthesis and the physiology of harmful algae. Part of his research investigates how eukaryotes acquire plastids through endosymbiosis and how this process influences genome evolution through gene transfer. Another main area of research is the ecology and physiology of harmful algae. His lab is using microarrays to determine global gene expression patterns of harmful algae under various growth conditions. These gene expression profiles will be used to determine the factors that lead to harmful algal blooms in the oceans.
Research Interest
Dr. Jeremiah Hackett, Ph.D., is Associate Professor and Department Head of Ecology and Evolutionary Biology. He received his undergraduate degree in Biology from the University of Wisconsin-Milwaukee and a Ph.D. in Genetics, University of Iowa. Dr. Hackett’s research interests are in the areas of genome evolution, evolution of photosynthesis and the physiology of harmful algae. His research investigates how eukaryotes acquire plastids through endosymbiosis and how this process influences genome evolution through gene transfer. Another main area of research is the ecology and physiology of harmful algae. Dr. Hackett uses microarrays to determine global gene expression patterns of harmful algae under various growth conditions. These gene expression profiles will be used to determine the factors that lead to harmful algal blooms in the oceans.

Publications

Yoon, H. S., Hackett, J. D., Pinto, G., & Bhattacharya, D. (2002). The single, ancient origin of chromist plastids. Proceedings of the National Academy of Sciences of the United States of America, 99(24), 15507-12.

Algae include a diverse array of photosynthetic eukaryotes excluding land plants. Explaining the origin of algal plastids continues to be a major challenge in evolutionary biology. Current knowledge suggests that plastid primary endosymbiosis, in which a single-celled protist engulfs and "enslaves" a cyanobacterium, likely occurred once and resulted in the primordial alga. This eukaryote then gave rise through vertical evolution to the red, green, and glaucophyte algae. However, some modern algal lineages have a more complicated evolutionary history involving a secondary endosymbiotic event, in which a protist engulfed an existing eukaryotic alga (rather than a cyanobacterium), which was then reduced to a secondary plastid. Secondary endosymbiosis explains the majority of algal biodiversity, yet the number and timing of these events is unresolved. Here we analyzed a five-gene plastid data set to show that a taxonomically diverse group of chlorophyll c(2)-containing protists comprising cryptophyte, haptophyte, and stramenopiles algae (Chromista) share a common plastid that most likely arose from a single, ancient ( approximately 1,260 million years ago) secondary endosymbiosis involving a red alga. This finding is consistent with Chromista monophyly and implicates secondary endosymbiosis as an important force in generating eukaryotic biodiversity.

Reed, K. M., Hackett, J. D., & Phillips, R. B. (2000). Comparative analysis of intra-individual and inter-species DNA sequence variation in salmonid ribosomal DNA cistrons. Gene, 249(1-2), 115-125.

PMID: 10831845;Abstract:

This study examines sequence divergence in three spacer regions of the ribosomal DNA (rDNA) cistron, to test the hypothesis of unequal mutation rates. Portions of two transcribed spacers (ITS-1 and 5' ETS) and the non-transcribed spacer (NTS) or intergenic spacer (IGS) formed the basis of comparative analyses. Sequence divergence was measured both within an individual lake trout (Salvelinus namaycush) and among several related salmonid species ( lake trout; brook trout, Salvelinus fontinalis; Arctic char, Salvelinus alpinus; Atlantic salmon, Salmo salar; and brown trout, Salmo trutta). Despite major differences in the length of the rDNA cistron within individual lake trout, minimal sequence difference was detected among cistrons. Interspecies comparisons found that molecular variation in the rDNA spacers did not conform to the predicted pattern of evolution (ITS spacers

Hackett, J. D., Yoon, H. S., Li, S., Reyes-Prieto, A., Rümmele, S. E., & Bhattacharya, D. (2007). Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Molecular biology and evolution, 24(8), 1702-13.

Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup Chromalveolata (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multigene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and, surprisingly, two members of the Rhizaria, Reticulomyxa filosa and Bigelowiella natans. The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.

Chan, C. X., Soares, M. B., Bonaldo, M. F., Wisecaver, J. H., Hackett, J. D., Anderson, D. M., Erdner, D. L., & Bhattacharya, D. (2012). ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE(). Journal of phycology, 48(5), 1130-1142.

Microbial eukaryotes may extinguish much of their nuclear phylogenetic history due to endosymbiotic/horizontal gene transfer (E/HGT). We studied E/HGT in 32,110 contigs of expressed sequence tags (ESTs) from the dinoflagellate Alexandrium tamarense (Dinophyceae) using a conservative phylogenomic approach. The vast majority of predicted proteins (86.4%) in this alga are novel or dinoflagellate-specific. We searched for putative homologs of these predicted proteins against a taxonomically broadly sampled protein database that includes all currently available data from algae and protists and reconstructed a phylogeny from each of the putative homologous protein sets. Of the 2,523 resulting phylogenies, 14-17% are potentially impacted by E/HGT involving both prokaryote and eukaryote lineages, with 2-4% showing clear evidence of reticulate evolution. The complex evolutionary histories of the remaining proteins, many of which may also have been affected by E/HGT, cannot be interpreted using our approach with currently available gene data. We present empirical evidence of reticulate genome evolution that combined with inadequate or highly complex phylogenetic signal in many proteins may impede genome-wide approaches to infer the tree of microbial eukaryotes.

Yoon, H. S., Hackett, J. D., & Bhattacharya, D. (2002). A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proceedings of the National Academy of Sciences of the United States of America, 99(18), 11724-11729.

PMID: 12172008;PMCID: PMC129336;Abstract:

The most widely distributed dinoflagellate plastid contains chlorophyll c2 and peridinin as the major carotenoid. A second plastid type, found in taxa such as Karlodinium micrum and Karenia spp., contains chlorophylls c1 + c2 and 19′-hexanoyloxy-fucoxanthin and/or 19′-butanoyloxy-fucoxanthin but lacks peridinin. Because the presence of chlorophylls c1 + c2 and fucoxanthin is typical of haptophyte algae, the second plastid type is believed to have originated from a haptophyte tertiary endosymbiosis in an ancestral peridinin-containing dinoflagellate. This hypothesis has, however, never been thoroughly tested in plastid trees that contain genes from both peridinin- and fucoxanthin-containing dinoflagellates. To address this issue, we sequenced the plastid-encoded psaA (photosystem I P700 chlorophyll a apoprotein A1), psbA (photosystem II reaction center protein D1), and "Form I" rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) genes from various red and dinoflagellate algae. The combined psaA + psbA tree shows significant support for the monophyly of peridinin- and fucoxanthin-containing dinoflagellates as sister to the haptophytes. The monophyly with haptophytes is robustly recovered in the psbA phylogeny in which we increased the sampling of dinoflagellates to 14 species. As expected from previous analyses, the fucoxanthin-containing dinoflagellates formed a well-supported sister group with haptophytes in the rbcL tree. Based on these analyses, we postulate that the plastid of peridinin- and fucoxanthin-containing dinoflagellates originated from a haptophyte tertiary endosymbiosis that occurred before the split of these lineages. Our findings imply that the presence of chlorophylls c1 + c2 and fucoxanthin, and the Form I rbcL gene are in fact the primitive (not derived, as widely believed) condition in dinoflagellates.