Modern genomics and human evolution
Dennis R. Venema
Department of Biology, Trinity Western University
Fellow, BioLogos Foundation
Michelangelo: The Creation of Adam (1511)
Resources:
Evolution Basics: a 40 part blog series (and counting!) on
evolutionary theory from a Christian perspective
www.biologos.org/blog
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)
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
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)
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)
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)
The term theory has a very different meaning in science
than it does in colloquial usage.
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).
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”.
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
scientific viewpoint.
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
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 future
experimentation – 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 future
experimentation – but they remain “only a theory”.
Heliocentrism:
only a theory
http://en.wikipedia.org/wiki/File:Geoz_wb_en.svg
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:
- populations
become genetically
separated
Evolution is a population-level
phenomenon:
- populations
become genetically
separated
- genetic changes
(through mutation,
recombination) are
not averaged across
the populations
Evolution is a population-level
phenomenon:
- 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:
- 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:
- populations
become genetically
separated
- genetic changes
(through mutation,
recombination) are
not averaged across
the populations
- differences accrue,
average characteristics
change
Related species thus once
shared a genome in common.
- these differences
may lead to new
species over time
As such, comparative genomics (the comparison of entire
genome sequences across species) is a treasure trove of
evolutionary information, including for our own species.
As such, comparative genomics (the comparison of entire
genome 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, such
as the great apes
As such, comparative genomics (the comparison of entire
genome 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, such
as 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 entire
genome 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, 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
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
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
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.
Human : chimpanzee genetic synteny at the chromosome level
Unitary pseudogenes are 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
Unitary pseudogenes are 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
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.
Relatedness based on shared errors within the olfactory
receptor pseudogene subgenome matches the relatedness
predicted from gene
homology studies,
with no “out of place”
shared pseudogenes:
Vitellogenin is a protein required for egg yolk formation in
egg-laying (amniotic) organisms, such as birds.
Placental mammals, such as humans, shared a common
ancestor with birds approximately 310 million years ago:
In modern birds, the vitellogenin gene is flanked by two
other genes:
In modern birds, the vitellogenin gene is flanked by two
other genes: these genes are present side-by-side in
mammals.
Examination of this region in the human genome reveals
the heavily-mutated remains of the vitellogenin gene that
persists as a pseudogene in all humans:
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
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)
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.
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
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.
One method of estimating ancestral population
sizes employs genetic markers that are closely linked
together on chromosomes.
Such pairs of markers are seldom separated by
recombination, and stay together as pairs in lineages
for long periods of time.
These marker pairs
are distributed among
known human groups
in the predicted pattern:
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 – species
more 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 match
either species, indicating it was something different:
Later work allowed for complete genome sequencing of
this hominin (now named the “Denisovan hominid”):
Whole-genome phylogenetic analysis places the Denisovan
hominids as a group more closely related to Neanderthals
than humans:
Despite this divergence,
certain modern human
populations share genetic
marker pairs with
Neanderthals
and Denisovans:
Non-african populations
derive 1.5 - 2.1% of their
genome from Neanderthals
Melanesian / Oceanic
populations derive an
additional 3 – 6% of
their genome from
Denisovans
When modern humans migrated out of Africa ~50,000 years
ago, they encountered Neanderthals and Denisovans in
the Middle East / Asia
wikipedia/commons/2/25/Range_of_Homo_neanderthalensis.png
Some of the diversity acquired from these hominid
groups 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 human
evolution and population dynamics, many Christian
groups 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 modern
humans are fuzzy. There is not an easy point of demarcation
between “human” and “non-human”.
Christian responses to these data are varied. Many
Christians simply reject the evidence for evolution and
favor an anti-evolutionary approach (YEC, OEC, ID).
These approaches require rejection of a large swath of
modern 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 and
non-concordist approaches, each with their strengths
and weaknesses.
These same approaches were in play when heliocentrism
was a theological issue for the church – and revisiting
this time in our history may prove informative for our
times.
Questions and discussion
Michelangelo: The Creation of Adam (1511)
But don’t we all come from Mitochondrial Eve and Ychromosome 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 these
types of DNA to estimate population sizes.
Population sizes should be estimated by methods examining
regular chromosomal DNA (such as heterozygosity, discordant
trees, linkage disequilibrium, and others).