Modern genomics and human evolution Dennis R. Venema

1. Modern genomics and human evolution Dennis R. Venema Department of Biology, Trinity Western University Fellow, BioLogos Foundation Michelangelo: The Creation of Adam (1511)

2. Resources: Evolution Basics: a 40 part blog series (and counting!) on evolutionary theory from a Christian perspective www.biologos.org/blog

3. Talk outline: Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation Raphael: The School of Athens (1510 - 1511)

4. Talk outline: Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation thedales.org.uk/files/ stalling_busk_ruin.jpg

5. Talk outline: Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation Titian: The Fall of Man (c. 1570)

6. Talk outline: Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation Bruegel the Elder: The Tower of Babel (1563)

7. Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation Raphael: The School of Athens (1510 - 1511)

8. The term theory has a very different meaning in science than it does in colloquial usage.

9. The term theory has a very different meaning in science than it does in colloquial usage. In science, a theory is an explanatory framework that has withstood repeated experimentation (i.e. it continues to produce hypotheses that make testable predictions).

10. The term theory has a very different meaning in science than it does in colloquial usage. In science, a theory is an explanatory framework that has withstood repeated experimentation (i.e. it continues to produce hypotheses that make testable predictions). In colloquial usage, “theory” means something closer to “guess” or “conjecture”.

11. The term theory has a very different meaning in science than it does in colloquial usage. In science, a theory is an explanatory framework that has withstood repeated experimentation (i.e. it continues to produce hypotheses that make testable predictions). In colloquial usage, “theory” means something closer to “guess” or “conjecture”. “Only a theory” is in fact quite a compliment from a scientificviewpoint.

12. The term theory has a very different meaning in science than it does in colloquial usage. In science, a theory is an explanatory framework that has withstood repeated experimentation (i.e. it continues to produce hypotheses that make testable predictions). In colloquial usage, “theory” means something closer to “guess” or “conjecture”. “Only a theory” is in fact quite a compliment from a scientificviewpoint. Theories vary in their importance to a given scientific discipline. For example, the chromosomal theory of inheritance is very important for the study of genetics, whereas the germ theory of disease is more central to microbiology.

13. Some theories in science are so well-supported that it is unlikely that they will be substantially modified by future experimentation – but they remain “only a theory”.

14. Some theories in science are so well-supported that it is unlikely that they will be substantially modified by future experimentation – but they remain “only a theory”. Heliocentrism: only a theory http://en.wikipedia.org/wiki/File:Geoz_wb_en.svg

15. Despite what you may have been told as a Christian, evolution is a theory in the scientific sense.

16. Despite what you may have been told as a Christian, evolution is a theory in the scientific sense. Evolution is a well-tested explanatory framework, supported by a large body of experimental evidence, that makes accurate predictions, that has not (yet) been falsified through experimentation.

17. - populations become genetically separated Evolution is a population-level phenomenon:

18. - populations become genetically separated - genetic changes (through mutation, recombination) are not averaged across the populations Evolution is a population-level phenomenon:

19. - populations become genetically separated - genetic changes (through mutation, recombination) are not averaged across the populations - differences accrue, average characteristics change Evolution is a population-level phenomenon:

20. - populations become genetically separated - genetic changes (through mutation, recombination) are not averaged across the populations - differences accrue, average characteristics change - these differences may lead to new species over time Evolution is a population-level phenomenon:

21. - populations become genetically separated - genetic changes (through mutation, recombination) are not averaged across the populations - differences accrue, average characteristics change - these differences may lead to new species over time Evolution is a population-level phenomenon: Related species thus once shared a genome in common.

22. As such, comparative genomics (the comparison of entire genome sequences across species) is a treasure trove of evolutionaryinformation, including for our own species.

23. As such, comparative genomics (the comparison of entire genome sequences across species) is a treasure trove of evolutionaryinformation, including for our own species. Modern comparative genomics has confirmed that 1. we share ancestry with other forms of life, such as the great apes

24. As such, comparative genomics (the comparison of entire genome sequences across species) is a treasure trove of evolutionaryinformation, including for our own species. Modern comparative genomics has confirmed that 1. we share ancestry with other forms of life, such as the great apes 2. humans became a separate species as a large population, not through a single ancestral pair

25. As such, comparative genomics (the comparison of entire genome sequences across species) is a treasure trove of evolutionaryinformation, including for our own species. Modern comparative genomics has confirmed that 1. we share ancestry with other forms of life, such as the great apes 2. humans became a separate species as a large population, not through a single ancestral pair 3. the lineage leading to some modern humans interbred with other hominid groups in the recent past

26. Talk outline: Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation thedales.org.uk/files/ stalling_busk_ruin.jpg

27. 1. Humans are the product of evolution. We share common ancestors with other forms of life. The human and chimpanzee genomes are over 95% identical when compared side-by-side

28. 1. Humans are the product of evolution. We share common ancestors with other forms of life. The human and chimpanzee genomes are over 95% identical when compared side-by-side We have the same genes, and in the same order. Our two genomes are exactly what one would predict as slightly modified versions of an ancestral genome.

29. Human : chimpanzee genetic synteny at the chromosome level

30. Unitary pseudogenesare sequences recognizable as once having been a functional gene, but now are inactivated due to mutation. Psuedogenes can remain recognizable for millions of years after gene mutation. thedales.org.uk/files/ stalling_busk_ruin.jpg

31. Unitary pseudogenesare sequences recognizable as once having been a functional gene, but now are inactivated due to mutation. Psuedogenes can remain recognizable for millions of years after gene mutation. We share many pseudogenes in common with chimpanzees and other primates – with identical mutations: thedales.org.uk/files/ stalling_busk_ruin.jpg

32. The primate olfactory receptor subgenome reveals numerous pseudogenes shared between humans and great apes (with identical inactivating mutations), as well as human-specific pseudogenized loci. These pseudogenes are retained in syntenic blocks between genomes.

33. Relatedness based on shared errors within the olfactory receptor pseudogenesubgenome matches the relatedness predicted from gene homology studies, with no “out of place” shared pseudogenes:

34. Vitellogeninis a protein required for egg yolk formation in egg-laying (amniotic) organisms, such as birds.

35. Placental mammals, such as humans, shared a common ancestor with birds approximately 310 million years ago:

36. In modern birds, the vitellogeningene is flanked by two other genes:

37. In modern birds, the vitellogeningene is flanked by two other genes: these genes are present side-by-side in mammals.

38. Examination of this region in the human genome reveals the heavily-mutated remains of the vitellogeningene that persists as a pseudogene in all humans:

39. Despite numerous mutations, this sequence is clearly recognizable in placental mammals: Many of the mutations which remove Vit 1 function are shared between numerous placental mammals

40. Talk outline: Part one: evolution as theory Part two: genomics & human common ancestry Part three: genomics & ancestral population sizes Part four: genomics & human speciation Titian: The Fall of Man (c. 1570)

41. 1. Humans are the product of evolution. We share common ancestors with other forms of life. 2. Humans arose as a population – we do not descend from one ancestral couple. At no time in our evolutionary history has our ancestral population been less than about 10,000 individuals.

42. 1. Humans are the product of evolution. We share common ancestors with other forms of life. 2. Humans arose as a population – we do not descend from one ancestral couple. At no time in our evolutionary history has our ancestral population been less than about 10,000 individuals. Modern humans have a high level of genetic diversity, indicating that we descend from a large population. Large populations can maintain high genetic diversity Small populations cannot maintain high genetic diversity

43. 1. Humans are the product of evolution. We share common ancestors with other forms of life. 2. Humans arose as a population – we do not descend from one ancestral couple. At no time in our evolutionary history has our ancestral population been less than about 10,000 individuals. Modern humans have a high level of genetic diversity, indicating that we descend from a large population. There are many independent ways to estimate ancestral population sizes from current genetic diversity. All methods applied to humans do date agree that we descend from a population of about 10,000 individuals.

44. One method of estimating ancestral population sizes employs genetic markers that are closely linked together on chromosomes.

45. Such pairs of markers are seldom separated by recombination, and stay together as pairs in lineages for long periods of time.

46. These marker pairs are distributed among known human groups in the predicted pattern:

48. 1. Humans are the product of evolution. We share common ancestors with other forms of life. 2. Humans arose as a population – we do not descend from one ancestral couple. At no time in our evolutionary history has our ancestral population been less than about 10,000 individuals. 3. Human speciation was prolonged and complex. As humans emerged in Africa and spread across the planet some groups interbred with non-human hominid species they encountered. http://biologos.org/blog/understanding-evolution-neanderthals-denisovans-and-human-speciation

49. Humans are the sole surviving hominin species – species more closely related to humans than to chimpanzees.

50. In 2010, the mitochondrial DNA sequence of an unknown hominid from Siberia was determined and compared to modern human and Neanderthal mtDNA sequences: