James A. Lake
James A. Lake (born August 10, 1941, Kearney, Nebraska) is an American evolutionary biologist and a Distinguished Professor of Molecular, Cell, and Developmental Biology and of Human Genetics at UCLA. Lake is best known for the New Animal Phylogeny and for the first three-dimensional structure of the ribosome. He has also made significant contributions to understanding genome evolution across all kingdoms of life, including discovering informational and operational genes, elucidating the complexity hypothesis for gene transfer, rooting the tree of life, and understanding the early transition from prokaryotic to eukaryotic life.
Jim Lake graduated from the University of Colorado, Boulder with a BA in physics in 1963. In 1967 he was awarded a Ph.D. in physics from the University of Wisconsin, Madison on the structure of tRNA. Following postdocs in Molecular Biology at MIT and Harvard Medical School, an Assistant Professorship of Cell Biology in George Palade’s Department at Rockefeller University (1970–73) and an Associate Professorship of Cell Biology at NYU Medical School (1973–76), he became a Professor of Molecular Biology in Biology at UCLA in 1976 and is currently a Distinguished Professor of Molecular, Cell, and Developmental Biology and of Human Genetics.
In 2011, Lake was presented the Darwin-Wallace Medal by the Linnean Society of London for elucidating the new animal phylogeny. The Medal is awarded to individuals who have made major advances in evolutionary biology. Lake has made a number of highly significant contributions toward understanding diverse aspects of genome evolution across all kingdoms of life. These include discovering informational and operational genes, developing the complexity hypothesis for horizontal/lateral gene transfer, and rooting the tree of life, topics on which he has published over 160 papers.
In the mid-1980s it was becoming clear that ribosomal RNA sequences could be used to determine metazoan relationships. Interpretation of the trees was complicated by the problem of Long branch attraction (LBA). By developing new algorithms that were less sensitive to these LBA artefacts, Lake was able to show that the Annelida-Mollusca lineage is the sister group of an arthropod subgroup. This finding was contrary to the Articulata hypothesis that grouped arthropods with annelids, and was nearly universally endorsed at that time.
With the advent of PCR and increased ease of sequencing rDNA in the 1990s, Lake focused on the bilateral animals, and recognised that there were questions over the placement of the lophophorate animals, such as bryozoans, phoronids, and brachiopods. Lake provided clear DNA-based evidence indicating that the lophophorates were not deuterostomes as had been widely believed. In fact, they were most closely related to the mollusc – annelid clade. The result of this research was the creation of a new super-phylum, the Lophotrochozoa containing molluscs, annelids, lophophorates, and other animals. Lake recognised that long branch attraction was a severe problem for the mostly rapidly evolving nematodes and was able to provide rDNA sequences from a number of slowly evolving nematodes in order to bypass this difficulty. This sampling showed that the moulting animals form a clade, called the Ecdysozoa, a second protostomian superphylum sister to the Lophotrochozoa.
Lake also explored concepts concerning the deep phylogenetic origins of the eukaryotic cell. In the eocyte hypothesis, Lake and colleagues proposed that eukaryotes (animals, fungi, plants, and protists) evolved from a specific group of thermophilic prokaryotes, the "eocyte" archaebacteria.
- "James A Lake CURRICULUM VITAE" (pdf). Retrieved 2011-07-01.
- Zimmer, C. (2009). "On the Origin of Eukaryotes". Science 325 (5941): 666–668. doi:10.1126/science.325_666. PMID 19661396.
- Lake, J. A. (2009). "Evidence for an early prokaryotic endosymbiosis". Nature 460 (7258): 967–971. doi:10.1038/nature08183. PMID 19693078.
- Lake, J. A.; Skophammer, R. G.; Herbold, C. W.; Servin, J. A. (2009). "Genome beginnings: Rooting the tree of life". Philosophical Transactions of the Royal Society B: Biological Sciences 364 (1527): 2177–2185. doi:10.1098/rstb.2009.0035. PMC 2873003. PMID 19571238.
- Rivera, M.C., Jain, R., Moore, J. E., Lake, J.A. (1998). "Genomic Evidence for two functionally distinct gene classes",95, 6239-6244, Proc. Natl. Acad. Sci. USA, .
- Lake, J.A., Servin, J.A., Herbold, C.W., and Skophammer, R.G. Evidence for a new root of the tree of life. Syst Biol (2008) 57 (6): 835-843. doi:10.1080/1063515080255593d
- Lake, J. A. (1990). "Origin of the Metazoa". Proceedings of the National Academy of Sciences of the United States of America 87 (2): 763–766. doi:10.1073/pnas.87.2.763. PMC 53346. PMID 2300560.
- Garey, J. (2001). "Ecdysozoa: The Relationship between Cycloneuralia and Panarthropoda". Zoologischer Anzeiger - A Journal of Comparative Zoology 240 (3–4): 321–330. doi:10.1078/0044-5231-00039.
- Halanych, K. M.; Bacheller, J. D.; Aguinaldo, A. M.; Liva, S. M.; Hillis, D. M.; Lake, J. A. (1995). "Evidence from 18S ribosomal DNA that the lophophorates are protostome animals". Science 267 (5204): 1641–1643. Bibcode:1995Sci...267.1641H. doi:10.1126/science.7886451. PMID 7886451.
- Aguinaldo, A. M. A.; Turbeville, J. M.; Linford, L. S.; Rivera, M. C.; Garey, J. R.; Raff, R. A.; Lake, J. A. (1997). "Evidence for a clade of nematodes, arthropods and other moulting animals". Nature 387 (6632): 489–493. doi:10.1038/387489a0. PMID 9168109.
- Cox, C. J.; Foster, P. G.; Hirt, R. P.; Harris, S. R.; Embley, T. M. (2008). "The archaebacterial origin of eukaryotes". Proceedings of the National Academy of Sciences 105 (51): 20356–20361. doi:10.1073/pnas.0810647105. PMC 2629343. PMID 19073919.
- Lake, J. A.; Henderson, E.; Oakes, M.; Clark, M. W. (1984). "Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes". Proceedings of the National Academy of Sciences of the United States of America 81 (12): 3786–3790. doi:10.1073/pnas.81.12.3786. PMC 345305. PMID 6587394.
- Lake, J. A. (1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature 331 (6152): 184–186. doi:10.1038/331184a0. PMID 3340165.
- Rivera, M. C.; Lake, J. A. (1992). "Evidence that eukaryotes and eocyte prokaryotes are immediate relatives". Science 257 (5066): 74–76. doi:10.1126/science.1621096. PMID 1621096.
- Tourasse, N.; Gouy, M. (1999). "Accounting for Evolutionary Rate Variation among Sequence Sites Consistently Changes Universal Phylogenies Deduced from rRNA and Protein-Coding Genes". Molecular Phylogenetics and Evolution 13 (1): 159–168. doi:10.1006/mpev.1999.0675. PMID 10508549.