Julius B. Lucks/Meetings and Notes/SMBE2007/eukaryotic prokaryotic genome beginnings

= Doug Erwin : Are bilaterian animals overdesigned? The early origins of the bilaterian developmental toolkit. = Tue Jun 26 09:58:49 EDT 2007
 * Smithsonian - curator of the Burgess Shale - one of 2 keys to the room (director has other)

Words to Look Up

 * Ediacran - period preceeding Cambrian
 * Hox genes

Talk

 * Metazoan Diversification: Fossil Record
 * evol in animals prolonged historical event
 * 1st sponge biomarkers 635 mya
 * increase in num taxa - 2 stages
 * book - Wonderful Life (Steven Jay Gould - 1989)
 * diff between taxonomic divers and disparity (morphological diver)
 * major radiation of morpho forms in Cambrian followed by winnowing
 * constrained diversification
 * rapid increases in morpho disparity
 * look quantitatively at the morpho

Questions
= Peter Gogarten : Gene transfer, symbiosis, and most recent common ancestors = Tue Jun 26 09:59:30 EDT 2007
 * UConn

Words to Look Up

 * plastid

Talk

 * tracing characteris through tree/net of life
 * Darwin's coral of life, coalescence, radiation, Adam and Eve
 * coral of life since the core is dead
 * Origin of the Primary Plastids
 * Chlamidya - a third partner?
 * Cenancestor - last universal common ancestor (LUCA)
 * at the point of its existence, many organisms living at same time - long time away from origin of life
 * Coalescence - process of tracing lineages backwards in time to their common ancest. Every 2 extant leniages coalesce to most recent common ances. Even all lineages coalesce to cenancestor
 * Y chromosome Adam - lived 50,000 years ago - Thomson PNAS 2000, 97, 7280
 * Mitochondrial Eve - 166,000-249,000 years ago - Cann, R. L., 1987, Nature, 326, 31
 * adam and eve never met
 * same is true for ancestral rRNAs, EF, SRP, ATPases

Questions
= James Lake : Genome beginnings - rooting the tree of life = Tue Jun 26 10:00:02 EDT 2007
 * very good speaker

Words to Look Up

 * mevalonate pathway

Talk

 * bioinformatics
 * work in the present - decide differences between groups
 * clustering algorithms, PCA - 4 major groups
 * phylogenomics
 * going from starting 4 groups (present) to topological relationships that get to the past
 * 27 diff sorts of patterns
 * starting point is unrooted trees
 * how can we root these
 * gene transfer
 * imposes limitations or rooting the tree
 * rampant, but not random
 * informational genes
 * DNA to protein genes
 * came to eukaryotes from achaebacterio
 * operational genes
 * household work - AA, lipid biosynthesis, etc.
 * come to eukaryotes from eubacteria
 * M. Embly, W. Martin, Nature - News and Views
 * diff views on tree of life
 * Doolittle - gene transfer so extensive, can't know how groups form
 * another idea - eukaryotes so diff from prokaryotes - group into 2 classes and move on
 * ring of life - fusion of archea and bacteria to form 1st eukaryote
 * genome sequences - now can look at absences and presences
 * many ways that an absence abscence can appear
 * conditioned reconstruction - take a 3rd genome (conditioning) to identify presences - only analyze these
 * parsimony-like analysis that roots the tree
 * if fusion event, must have been present in same space-time point
 * everything after this fusion is later in the tree of life

Prokarytic Evol becomes pop driven sim to Euk evol

 * find groups that minimize gene exchange between groups
 * 4 groups
 * actinobacteria - diverse clade including many pathogens like Mycobacterium TB
 * archea
 * firmicutes (gram positive) - bacillus (anthrax)
 * double membrane prokaryotes
 * directed indels to make these determinations
 * same technique as rooting tree of life with sequences
 * parsimony arguments - see where changes ocurred wrt conditioning group - where changes occurred cannot be part of the group
 * root of TOL not within archaebacteria and eubacteria

Ubiquitous genes not needed for indel rooting

 * top-down rooting analyzes both indel presence and absence and gene p and a
 * can analyze incomplete gene sets
 * root not within double-membrane prokaryotes
 * beta-alpha-8 barrels (Tim Barrels)
 * structural motif characterized by 8 beta sheets in center, 8 alpha helices on outside
 * alpha-6: region between this and beta sheet - indel
 * 'PyrD' - pyrimidine biosynthesis - housekeeping gene

Questions

 * what is ecological basis of ring of life?
 * hydrogen hypothesis