He became famous (infamous?) for challenging the Three Domain Hypothesis of Carl Woese (and friends) and for advocating better methods of constructing gene trees. Jim Lake proposed that eukaryote nuclei arose from within the archaebacterial clade and not as a sister groups of Archaea as the Three Domain Hypothesis claimed. The sister group was the "eocytes," represented at the time by Sulfolobus solfataricus, an archaebacterium that lives in hot springs (~80°C) and uses sulfur as a source of energy.
Eukaryotic origins: progress and challenges [see The origin of eukaryotes and the ring of life].
The title of his paper is simply, "Eukaryotic origins" (Lake, 2015) and it's very fitting that it's the first paper since the current consensus is that he was right all along and the Three Domain Hypothesis is dead. Vindication. Jim Lake is a very modest man (unlike some of the proponent of the Three Domain Hypothesis) so I'm glad to see that he is getting the recognition he deserves.
Here's the abstract of his paper.
The origin of the eukaryotes is a fundamental scientific question that for over 30 years has generated a spirited debate between the competing Archaea (or three domains) tree and the eocyte tree. As eukaryotes ourselves, humans have a personal interest in our origins. Eukaryotes contain their defining organelle, the nucleus, after which they are named. They have a complex evolutionary history, over time acquiring multiple organelles, including mitochondria, chloroplasts, smooth and rough endoplasmic reticula, and other organelles all of which may hint at their origins. It is the evolutionary history of the nucleus and their other organelles that have intrigued molecular evolutionists, myself included, for the past 30 years and which continues to hold our interest as increasingly compelling evidence favours the eocyte tree. As with any orthodoxy, it takes time to embrace new concepts and techniques.
A few years later (1988), Lake published a very famous paper in Nature in which he challenged the ribosomal RNAs trees that were used to promote the Three Domain Hypothesis. Naturally there was lots of criticism from other scientists but there was also criticism from anti-evolutionists and he quotes one of them in the paper ....
"... you say humans came from an organism that lived at high temperatures and smelled of sulfur. I have news for you, that's not where we came from, that's where you're going."Lots of scientists are now talking about a ring of life as opposed to a tree because most of the genes in eukaryotes don't come from the Eocyte branch but from bacteria via endosymbiotes such as those that became mitochondria and chloroplasts. Lake's figure is complex but you get the general idea—two (or more) lineages fuse to form the first eukaryotes.
Lake, J. (2015) Eukaryotic origins. Phil. Tran. R. Soc. B 370: Published online Aug. 31, 2015 [doi: 10.1098/rstb.2014.0321]