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Genomes as the Hub of Biology

Genomes as the Hub of Biology. UNIT 2. The hub of biology. As biologists, we seek not only to understand how a single organism works, but how organisms interact. The same is true for genomes. To see life clearly, we must understand how genomes relate to one another.

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Genomes as the Hub of Biology

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  1. Genomes as the Hub of Biology UNIT 2

  2. The hub of biology • As biologists, we seek not only to understand how a single organism works, but how organisms interact. • The same is true for genomes. • To see life clearly, we must understand how genomes relate to one another. • Within an individual (cell to cell, developmental changes in gene expression) • Within/among populations (variation and change) • Among species (evolutionary relationships; understanding how genomes evolve; genome interactions via disease, predation, etc.)

  3. Genomics and development • Donut analogy • Monodelphisdomestica • Divergence from humans ~180 mya • ~18-20k genes • Only eightlack human homologs • The differences between us is primarily due to differences in regulation of the same suite of genes. • Example = HOX genes – responsible for anterior/posterior patterning in flies, humans, C. elegans.

  4. Genomics and behavior • C. elegansdining behavior: • Wild-type Australian taxa congregate to eat • British wild-type eat separately • Traces to a single AA mutation in a transmembrane protein, NPR-1 • Changes in CREB (cyclic AMP response element binding protein) impact learning and memory in flies and mouse. • Multiple genes are associated with schizophrenia • Severe, prolonged depression is associated with being homozygous for the short allele of the serotonin transporter, 5-HTT

  5. Genomics and populations • Phenotypic variation in populations is the raw material of evolution • Genomic variation is the raw material for phenotypic variation • Founder effects and bottlenecks can reduce variation and impact evolutionary processes in populations • Genomic variation can be measured in multiple ways

  6. Genomics and populations • SNPs – Single Nucleotide Polymorphisms • Single base variations among genomes • STRs – Short Tandem Repeats aka microsatellites • Populations with long evolutionary histories tend to have higher variation • An African origin for humans • 22 divergent lineages in Africa, three outside of Africa

  7. Genomics and populations • Mitochondrial haplotypes

  8. Genomics and populations • SNPs tell a story of admixture in human history

  9. Genomics and populations • SNPs tell the story of admixture in human history • Comparison of the Neanderthal and modern human genomes reveal an influx of novel alleles in non-African modern humans • Those novel alleles are similar to Neanderthal alleles

  10. Genomics and populations • SNPs tell the story of admixture in human history • Four possible scenarios • 1 - hybridization between ancient ancestor and Neanderthals • 2 – hybridization of ancient European and Asian populations with Neanderthals • 3 – hybridization between Neanderthals and a common non-African ancestor • 4 – persistent population substructure shared between Neanderthals and modern humans

  11. Genomics and populations • SNPs tell the story of population sizes in human history • PSMC (pairwise sequential Markovian coalescent) analysis • A diploid genome sequence harbors hundreds of thousands of independent loci, each with its own TMRCA. • Use local densities of heterozygous sites to reconstruct the TMRCA distribution across the autosomes and chromosome X • Parameters include the scaled mutation rateand recombination rate, and piecewise constant ancestral population sizes • If you know two, you can estimate the third. The population sizes inferred from autosomes of six individuals ~10-60 kya Severe bottleneck in Eurasian populations Less severe in African populations

  12. Genomics and species • Species are a fundamental unit of evolution • Despite the fact that no one can truly define what a species is. • Genomics can influence our understanding of species by: • Providing large scale data sets to determine species relationships • Buddenbrockiaplumatellae • 129 protein alignments nematodes

  13. Genomics and species • Species are a fundamental unit of evolution • Despite the fact that no one can truly define what a species is. • Genomics can influence our understanding of species by: • Providing large scale data sets to determine species relationships • Buddenbrockiaplumatellae • 129 protein alignments • Quantitative measurements of the divergences between species • Crocodile vs. alligator whole genome pairwise alignment • 93.3% identity (assuming G = 20 yrs, TMRCA = 100 my) • μ(Crocodylia) = ~6.7 x 10 -9

  14. Genomics and species • Reversing extinctions? • http://www.livescience.com/40264-how-to-bring-back-the-woolly-mammoth-infographic.html

  15. Genomics and species • How big are genomes?

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