Modern genomics and human evolution

Dennis R. VenemaDepartment of Biology, Trinity Western UniversityFellow, BioLogos Foundation

Michelangelo: The Creation of Adam (1511)

Resources:

Evolution Basics: a 40 part blog series (and counting!) onevolutionary theory from a Christian perspective

www.biologos.org/blog

Talk outline:

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

Raphael: The School of Athens (1510 - 1511)

Talk outline:

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

thedales.org.uk/files/ stalling_busk_ruin.jpg

Titian: The Fall of Man (c. 1570)

Talk outline:

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

Bruegel the Elder: The Tower of Babel (1563)

Talk outline:

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

Raphael: The School of Athens (1510 - 1511)

The term theory has a very different meaning in sciencethan it does in colloquial usage.

The term theory has a very different meaning in sciencethan it does in colloquial usage.

In science, a theory is an explanatory framework that haswithstood repeated experimentation (i.e. it continues to produce hypotheses that make testable predictions).

The term theory has a very different meaning in sciencethan it does in colloquial usage.

In science, a theory is an explanatory framework that haswithstood repeated experimentation (i.e. it continues to produce hypotheses that make testable predictions).

In colloquial usage, “theory” means something closer to“guess” or “conjecture”.

The term theory has a very different meaning in sciencethan it does in colloquial usage.

In science, a theory is an explanatory framework that haswithstood 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 scientific viewpoint.

The term theory has a very different meaning in sciencethan it does in colloquial usage.

In science, a theory is an explanatory framework that haswithstood 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 scientific viewpoint.

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.

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

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

http://en.wikipedia.org/wiki/File:Geoz_wb_en.svg

Heliocentrism:only a theory

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

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.

Evolution is a population-level phenomenon:

- populationsbecome genetically separated

Evolution is a population-level phenomenon:

- populationsbecome genetically separated

- genetic changes(through mutation,recombination) arenot averaged acrossthe populations

Evolution is a population-level phenomenon:

- populationsbecome genetically separated

- genetic changes(through mutation,recombination) arenot averaged acrossthe populations

- differences accrue,average characteristicschange

Evolution is a population-level phenomenon:

- populationsbecome genetically separated

- genetic changes(through mutation,recombination) arenot averaged acrossthe populations

- differences accrue,average characteristicschange

- these differencesmay lead to new species over time

Evolution is a population-level phenomenon:

- populationsbecome genetically separated

- genetic changes(through mutation,recombination) arenot averaged acrossthe populations

- differences accrue,average characteristicschange

- these differencesmay lead to new species over time

Related species thus once shared a genome in common.

As such, comparative genomics (the comparison of entiregenome sequences across species) is a treasure trove of evolutionary information, including for our own species.

As such, comparative genomics (the comparison of entiregenome sequences across species) is a treasure trove of evolutionary information, including for our own species.

Modern comparative genomics has confirmed that

1. we share ancestry with other forms of life, suchas the great apes

As such, comparative genomics (the comparison of entiregenome sequences across species) is a treasure trove of evolutionary information, including for our own species.

Modern comparative genomics has confirmed that

1. we share ancestry with other forms of life, suchas the great apes

2. humans became a separate species as a large population, not through a single ancestral pair

As such, comparative genomics (the comparison of entiregenome sequences across species) is a treasure trove of evolutionary information, including for our own species.

Modern comparative genomics has confirmed that

1. we share ancestry with other forms of life, suchas 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

Talk outline:

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

thedales.org.uk/files/ stalling_busk_ruin.jpg

1. Humans are the product of evolution. We share common ancestors with other forms of life.

The human andchimpanzee genomesare over 95% identicalwhen compared side-by-side

1. Humans are the product of evolution. We share common ancestors with other forms of life.

The human andchimpanzee genomesare over 95% identicalwhen 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.

Human : chimpanzee genetic synteny at the chromosome level

Unitary pseudogenes are sequences recognizable as once having been a functional gene, but now are inactivateddue to mutation.Psuedogenes can remain recognizable for millions ofyears after gene mutation.

thedales.org.uk/files/ stalling_busk_ruin.jpg

Unitary pseudogenes are sequences recognizable as once having been a functional gene, but now are inactivateddue to mutation.Psuedogenes can remain recognizable for millions ofyears after gene mutation.We share many pseudogenes in commonwith chimpanzees andother primates – withidentical mutations:

thedales.org.uk/files/ stalling_busk_ruin.jpg

The primate olfactory receptorsubgenome reveals numerouspseudogenes shared betweenhumans and great apes (withidentical inactivating mutations),as well as human-specific pseudogenized loci.

These pseudogenes are retainedin syntenic blocks between genomes.

Relatedness based on shared errors within the olfactory receptor pseudogene subgenome matches the relatednesspredicted from genehomology studies, with no “out of place” shared pseudogenes:

Vitellogenin is a protein required for egg yolk formation inegg-laying (amniotic) organisms, such as birds.

Placental mammals, such as humans, shared a commonancestor with birds approximately 310 million years ago:

In modern birds, the vitellogenin gene is flanked by twoother genes:

In modern birds, the vitellogenin gene is flanked by twoother genes: these genes are present side-by-side in mammals.

Examination of this region in the human genome revealsthe heavily-mutated remains of the vitellogenin gene thatpersists as a pseudogene in all humans:

Despite numerous mutations, this sequence is clearlyrecognizable in placental mammals:

Many of the mutations which remove Vit 1 functionare shared between numerous placental mammals

Titian: The Fall of Man (c. 1570)

Talk outline:

Part one: evolution as theory

Part two: genomics & human commonancestry

Part three: genomics & ancestral population sizes

Part four: genomics & human speciation

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.

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

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 methodsapplied to humans do date agree that we descend from a population of about 10,000 individuals.

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

Such pairs of markers are seldom separated byrecombination, and stay together as pairs in lineagesfor long periods of time.

These marker pairs are distributed amongknown human groupsin the predicted pattern:

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

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

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

Unexpectedly, this hominin’s mtDNA did not matcheither species, indicating it was something different:

Later work allowed for complete genome sequencing ofthis hominin (now named the “Denisovan hominid”):

Whole-genome phylogenetic analysis places the Denisovanhominids as a group more closely related to Neanderthalsthan humans:

Despite this divergence, certain modern human populations share geneticmarker pairs with Neanderthals and Denisovans:

Non-african populationsderive 1.5 - 2.1% of theirgenome from Neanderthals

Melanesian / Oceanic populations derive an additional 3 – 6% of their genome from Denisovans

When modern humans migrated out of Africa ~50,000 yearsago, they encountered Neanderthals and Denisovans inthe Middle East / Asia

wikipedia/commons/2/25/Range_of_Homo_neanderthalensis.png

Some of the diversity acquired from these hominidgroups is in MHC I alleles:

Recent sequencing of a high-quality Neanderthal genome has revealed input from a fourth archaic hominin into the Denisovan lineage

Recent sequencing of a high-quality Neanderthal genome has revealed input from a fourth archaic hominin into the Denisovan lineage

Despite the strength of the evidence for humanevolution and population dynamics, many Christiangroups tie the gospel to a rejection of this evidence.

The findings of evolutionary biology present a number of perceived tensions with common interpretations of Scripture:

The findings of evolutionary biology present a number of perceived tensions with common interpretations of Scripture:

1. Humans are not de novo creations, but share ancestry with other forms of life.

The findings of evolutionary biology present a number of perceived tensions with common interpretations of Scripture:

1. Humans are not de novo creations, but share ancestry with other forms of life.

2. Humans do not descend from an ancestral couple, but rather a large population.

The findings of evolutionary biology present a number of perceived tensions with common interpretations of Scripture:

1. Humans are not de novo creations, but share ancestry with other forms of life.

2. Humans do not descend from an ancestral couple, but rather a large population.

3. The boundaries of the population that led to modernhumans are fuzzy. There is not an easy point of demarcationbetween “human” and “non-human”.

Christian responses to these data are varied. ManyChristians simply reject the evidence for evolution andfavor an anti-evolutionary approach (YEC, OEC, ID). These approaches require rejection of a large swath ofmodern science.

http://www.bryan.edu/origins.html

Other Christian responses attempt to respect the science, and find a means of integrating it with orthodox Christian faith.

In general, these approaches fall into concordist andnon-concordist approaches, each with their strengthsand weaknesses.

These same approaches were in play when heliocentrismwas a theological issue for the church – and revisitingthis time in our history may prove informative for our times.

Michelangelo: The Creation of Adam (1511)

Questions and discussion

But don’t we all come from Mitochondrial Eve and Y-chromosome Adam?

Mitochondrial inheritance

Y-chromosome inheritance

Mitochondrial DNA is passed on only through females:

Y-chromosome DNA is passed on only through males:

Regular chromosomal DNA is passed on through both genders:

The unusual inheritance patterns of mitochondrial and Y-chromosome DNA means it is inappropriate to use thesetypes of DNA to estimate population sizes.

Population sizes should be estimated by methods examiningregular chromosomal DNA (such as heterozygosity, discordanttrees, linkage disequilibrium, and others).