Julius B. Lucks/Meetings and Notes/SMBE2007/eukaryotic prokaryotic genome beginnings
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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
- rapid increases in morpho disparity
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
Red Algal and Green Plant Genes of Chlamydial Origin
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
- genome sequences - now can look at absences and presences
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