Insect Genomics Exam 3: Big Picture Stuff

Front 1

Describe maximum parsimony, including strengths and weaknesses

Back 1

Looks at the most simple explanation/least mutations needed to make the tree. Strengths: Fits well with school of Cladistics (shared derived states count). Weaknesses: DNA only has 4 characters which can flip, resulting in homoplasy, long branches attract artifacts.

Front 2

Describe maximum likelihood, including strengths and weaknesses

Back 2

Sequences in datasets evolve in unique ways, which is used as model. Model used to compare possible trees. Strengths: More statistically robust. Problems: Hard to apply to protein sequences, computationally intensive.

Front 3

Describe distance methods, including strengths and weaknesses

Back 3

Overall estimate of similarities/differences of sequences in dataset, use as criterion for building tree (neighbor-joining). Strengths: Speed, distances can be corrected for multiple changes in distant past so good for divergent proteins. Weaknesses: throws out much of detail of data

Front 4

What data are used for phylogeny at the species, genus, family, order, class, and phylum level?

Back 4

Non-coding regions, ADH/3rd codon position/mitochondrial, rRNA, rRNA plus morphology, rRNA/multiple-protein coding genes, rRNA/ESTs

Front 5

Name five effects of Wolbachia in arthropods

Back 5

Cytoplasmic incompatibility, feminization in isopods, facilitative parthenogenesis in parasitoid wasps, male/son killing in ladybirds and leps, obligate endosymbiont in bedbugs, neuro-degeneration in Drosophila

Front 6

Anopheles gambiae genome project

Back 6

International Consortium, Collins/Besansky, Celera sequenced, used PEST strain (mixture of subspecies), 2x as large as Dros but ~same # genes, lots of SNPs, big expansion of fibrogen gene family/ORs/GRs

Front 7

Compare Anopheles gambiae, Aedes aegypti, Culix quinquefasciatus, and Drosophila genomes

Back 7

Anopheles is 2x as large as drosophila, Aedes 5x larger than Anopheles due to huge number of transposons/long introns, Culix has intermediate genome with many gene expansions likely due to exposure to many pathogens/multiple hosts

Front 8

Bombyx genome project

Back 8

Chinese and Japanese groups eventually worked together to get 10x assembly, large genome with many transposons (such as mariner and 1 kind of LTR retrotransposon), longer introns than Dros, big difference in silk gland with divergent fibroin proteins, fragmentation of genome into 28 chromos

Front 9

Tribolium genome project

Back 9

Beeman/Denell/Brown, 10 chromos, lots of retrotransposons, telomeres are TCAGG repeats interspersed with retrotransposons, P450 expansion, support for Tribolium as model organism because they have many genes lost in Drosophila

Front 10

Apis genome project

Back 10

Robinson, hard to put into BACs so had to make AT-rich 1kb plasmid library, few transposons (mostly mariner), very AT-rich genome with homologous genes in AT-rich regions, only chromo 1 is metacentric, telomeres are simple and on long arm with TTAGG repeat, p450s/immune genes greatly reduced

Front 11

What are the competing processes that determine insect genome?

Back 11

Larger: High tolerance of junk DNA (transposons and pseudogenes), genetic drift not allowing selection away from large genomes, gene duplication events. Smaller: Large deletions. Drosophila has had many such deletions and losses of genes, pseudogenes, and old copies of transposons.

Front 12

Describe a proposed method for spreading novel genetically engineered traits through insect populations including difficulties.

Back 12

Use bacteria/insect pathogenic fungi to express the genes. Alter the bacteria/fungi, then they make the useful proteins in the midgut, protein prevents infection of plasmodium, spread by spraying ponds. Sustainability could be problematic.