Genome Evolution

Question	Answer
Evolution over Ecological (short) Time Frames 4	Alterations in allele frq. than in generation of new alleles Alterations in level of heterozygosity Some alleles completely lost Eg colour morphs of star spider
Evolution over Long Time Frames 2	Mutation driving force Includes substantial changes on both genome size and content
How is Adaptation Constrained 3	Mutation determines rate of adaptation Small number of ways adaptation works at molecular level Number of ways is <1
Human Lactose Tolerance 6	Pokot Kenya people have 3 mutations to allow the digestion of milk Most recent mutation only took place a few 1000yrs ago Same time cattle domesticated Evolution found 3 solutions to same problem All on the same gene Venom-toxins evolve back into non-toxic compounds
Co-evolution of Genomes 4	Host - symbiotic bacteria Bobtail squid and Vibrio fisheri - luminescent bacterium Can develop statis - no longer evolve rapidly The endosymbiotic bacteria of aphids stopped rapid evolution
Pleitropy 4	ONE GENE INFLUENCES MANY TRAITS Limits types of genetic changes that can occur Melanocortin system determines colour patterns as well as immunity Dark owls = more aggressive or sexually active and more resistant to stress than lighter individuals
Development Limits Genome Evolution 4	DNA per cell varies between closely related species C-VALUE = total amount of DNA per cell nucleus HIGH C-VALUE - develop more slowly than species with low C-value Salamanders Plethodon vehiculum has x2 C-value that P. cinerus
Comparative Genomics 2	Comparison between dolphins, primates and other mammals Dolphins have similar changes in brain and metabolism with primate lineage
Gene Conversion 4	Can be due to repair Allele on one chromo is'repaired' by copying a homologus allele Repair doesn't always result in original - could be further mutated Biased direction of repair - concerted evo. and one one allele dominates
Gene Conversion Example 4	Saccharomyes cerevisiae Each individual has 'master copy' of each mating type (2) Working copy can be removed and replaced with other type using master copy as template MATING TYPE SWITCHING
Homogenisation through gene conversion 4	Repair (gene conversion) is not always random Repair biased to one allele = eventually all alleles the same Ribo DNA genes repeated in tandem Concerted evo through gene conversion and unequal crossing over = all end up the same
Exogenous DNA 7	Horizontal gene transfer - Plasmid in bacteria - mobilisation of transposable (P) elements in Drosphilia Hybridisation - alleles from one spp to another - closely related species et mice - relies on recombination
Transposable Elements 4	Genetic elements capable of moving from one location to next = leave copy behind = increase in overall number Usually encode own -transposase' enzyme
Transposable Elements Example Class 1 4	Class 1 Reterotransposons Leave copy behind when transpose LINE elements in humans Chromo 22 >14,000 of them
Transposable Elements Example 2 5	Class 2 SOME leave copy behind when transpose, some do not Most concern type in bacteria IS elements in E. coli P elements in Drosphilia
Transposable Elements 'Selfish DNA' 7	Can 'knock-out' genes by landing in the middle Causes white eye mutation in Drosphilia Recombination of transposons On different chromos/ different sites on same choromor = inversions/translocations/deletions Relies on matching eye regions These provided by transposable elements
Horizontal Gene Transfer Virogene 3	Strain in baboons similar to cats Not closely related = HGT Gene transferred from ancient primate ancestor to ancient cat ancestor after lion, cheetah and leopard lineages diverged
Horizontal Gene Transfer Mito and chloro into the nucleus 5	Endosymbiont bacteria into euk. cells Bacterial evolve into mito and chloro Some required genes for the organelles are now in the nuclues Ribulose bisphosphate carboxylase (fixation of CO2) Small subunit of protein in nucleus, large subunit in chloro.
Studying Patterns of Diversification and Adaptation 9	Comparision of colourful spiders Gasteracantha cancriforms - from America Has 3 same colours morphs in any population Males and females have the same colours (not sex.sel) Gasteracantha kuhli -similar species Has 2 colour morphs Ancestor shared millions of years ago Limit to the colour morphs? Evo. not had enough time to make more?
Genome Structure 5	Nuclear chromosomes are linear Spiders - there is no Y chromo. Sex determined by no. of X chromo Humans - X and Y - genes present never found in females Circ. DNA in mito and chloro and female cyto
Mitochondrial DNA 3	Circular DNA in mito Doesn't recombine regularly Good indicator in evo
Examples of genomic changes 8	Single base pair changes Deletions Insertions Chromo. break and fuse Duplication of genes and entire genomes Inversions Psuedogene formation Acquisition of horizontally transferred DNA - plasmids and transposons
Single Base Pair Changes 10	SNPs - single nucleotide polymorphisms Synonymous - not alter protein sequence Lead to codon bias - not all codons are equal tRNA rare Synonymous changes accumulate at faster rate than non-synonymous Synonymous less likely to be removed from the population Synonymous changes can saturate - original change is wiped out as another changes it back to original state Chance = always lose some mutations Sm pop = more likely to have an individual with new change Big pop = unlikely for new trait to persist
Chromosome Fusions and Rearrangements 6	Uncommon in mammals, more in plants V. common in the rodent spp. Sorex See where part of chromo has broken off and stuck onto another What are their DNA repair systems like? Caused rearrangements found in primates Changes over a long period of time
Chromosomal Invasion 4	Coelpa frigida - Seaweed Fly 2 types of male - large and small Inversion of one chromo. Not repaired / severely disadvantageous
Psuedogenes Humans and Chimps 6	Genes without function Comparision of chimp and human genome Humans have remnent of gene that doesn't function Linked to sense of smell 'Past is inescapable' Non-working mito. genes stuck in nucleus
Psuedogenes Grasshopper 2	Hundreds of gene inserts so genome is huge Lots of mito. gene subtypes present (10-12)
HOX Genes 5	In zebrafish, pufferfish, mouse and Amphioxus (fish) Genes lost and found on massive origin Cone jelly - nerves have same basic structure but evolved separately Scorpion - look at arachnid ancestor to see how scorpion segments fused Why scorpion has 12 or 13 segmentrs - answer in HOX
Silk Genes 4	Double stranded fibres Amino acid sequence of protein vary, also way spun through spinnerets with different morphologies, number and arrangement Stuck with previous evolution - number of spinnerets cant change Gene cluster is too fragile
Spinneret Genes 4	Way silk spun through spinnerets with different morphologies, number and arrangement Stuck with previous evolution - number of spinnerets cant change Gene cluster is too fragile Mygalomorphs (tarantulas) differ from Araneomorphs (orbweavers) in spinneret morphology
Duplication of Entire Genomes African Toad 6	Xenopus laevis African Toad X. laevis - tetreploid (4N) X. tropiralis - diploid (2N) Unsure if bigger size related to genome Doesn't take x2 time to copy the 4N (other factors) 40% of duplicate genes in 4N still functional Does confer advantage to have extra copies under certain conditions
Duplication of Entire Genomes Chiclid 2	Become tetraploid and re-diploided over time period Has genome X - product of past
How do Changes Occur? 5	Error 1/500 when copying a nucleotide (probably higher but repaired) Natural part of DNA rep. - polymerase natural error rate Proof reading enzymes DNA seq. changes in germ cells can be driven by external factors Translation polymerase - specific to continue copying even if mismatches are formed
Errors During DNA Replication 6	Insertions/Deletions during replications Common in repetitive regions Used for DNA fingerprinting Used for diversity in evolution Essential for meiosis Jumbles up alelle combinations eg for IS genes - new ag recognition molecules
Recombination: Equal Vs Non-equal 3	Unequal recombination in different genomic content of each genome Very similar DNA sequence on different chromo = Increase chances of non-homologus (ECTOPTIC) recombination events

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