[MUSIC]
We are the paradoxical ape,
bipedal, naked, large brain,
long the master of fire, tools,
and language but still trying to understand ourselves.
Aware that death is inevitable yet filled with optimism.
We grow up slowly.
We hand down knowledge.
We empathize and deceive.
We shape the future from
our shared understanding of the past.
CARTA brings together experts from diverse disciplines to
exchange insights on who we are and how we got here.
An exploration made possible by
the generosity of humans like you.
[MUSIC]
I'm glad for the opportunity to
discuss the emerging impact of
comparative genomics on understanding
evolutionary processes including extinction.
This new capacity to understand
the evolution of life to the evolution of genomes
can be used to better assess threats to
biodiversity and even help restore biodiversity.
This knowledge along with the ability to
save living cells from which animals and plants
can be produced offers a new role for
human intervention and a novel development
in life on the planet.
As we've heard, we are experiencing
an accelerated extinction rate
largely due to human causes.
Extinction is an endpoint.
There are many species that
are declining and we are losing
biodiversity even without having an extinction event.
It's estimated that 1/3 of vertebrate species are in
decline and the International Union for the Conservation
of Nature that assemble
the Red List for the species that they have analyzed,
28 percent are recognized as threatened or endangered.
We are in a very challenging time for biodiversity.
But knowledge of extinction can be
gathered from fossil evidence,
from studying extant species genomes
and back through time,
and also of ancient extinct species with DNA methods.
I want to focus for a moment
on the wrangle island mammoth.
This is the last population surviving population of
mammoths and because of preservation of specimens,
good genome assemblies have been produced
from wrangle island mammoths.
This has allowed an evaluation
of their genetic status as they were declining in
comparison to other mammoth populations
and the closest living relative
of mammoths which is the Asian elephant.
In the central figure there,
in the blue column on
the right is the wrangle island
mammoth and the color is coming
from the bottom up to the darker purple at
the top represents the severity of
deleterious impact of mutations
across the genomes that are represented there.
The wrangle island mammoth has more mutations in
the deleterious categories than the other mammoths,
the Siberian mammoths and it's been
suggested that the wrangle island
mammoth was in a mutational meltdown.
By comparison of wrangle island
mammoth mutations with similar locations
in the human genome,
this word cloud has been produced to
show what the impacts of these mutations might be,
which are indeed quite severe.
It's possible to use genome information to
infer historical aspects of population size,
especially the effective population size.
This is the number of individuals that
actually contribute genetically across
generations and the Hawaiian monk seal
is a critically endangered US species.
This is information from
a preprint depicting this population size through time.
The scale goes from
hundreds of thousands of years ago
back to 1,000 years ago and
you can see that
the wrangle island mammoth population declined rapidly.
But it was 50,000 years ago
and then the last 30,000 years or so,
the wrangle island population
of mammoths has stayed small.
For them to have survived,
they must have purged some of
their genetically deleterious mutations.
By studying genomes of other species,
we're gathering more information about this,
two species I'll mention are the vaquita,
the most endangered citation in the world,
critically endangered population and it's only found in
the northern Gulf of California
and there may be only a dozen individuals that survive.
In the lower-left figure,
you can see the genetic variation
across the vaquita genome.
The horizontal red line represents the level
of genetic diversity in the human genome and
across the blue shades of
blues chromosomes scaffolds of
the vaquita genome assembly,
you can see that there's much lower genetic variation,
but that variation is not in large blocks of uniformity.
It's consistent with there not
being a high degree of recent inbreeding
even though the population is small so the vaquita
may have purged a lot of its genetic variation.
Mountain gorillas are another example.
There's two populations of mountain gorillas.
Together they comprise something
approximately 1,200 individuals
and in comparison to
their much more numerous Western lowland gorillas,
these are the gorillas you see in zoos.
Western lowland gorillas have
more severe deleterious mutations.
They have a much larger population size
and they have more mutational differences,
but they also have a larger proportion
of severe deleterious mutations
as estimated by mutations that are
believed to cause loss of function of a gene.
On the other hand, the mountain gorillas have
proportionately higher number of missense mutations,
mutations which alter
the amino acid sequence of a protein,
but may not be highly
deleterious and in small populations,
mildly deleterious mutations can accumulate and
that's because this is a deterministic process involved.
It's been called the extinction vortex.
In a small population,
it's more likely that individuals will reproduce with
other individuals to whom they're closely
related and in small populations,
there won't be a lot of offspring and
there will be less likelihood to
transmit the entire gene pool from
generation to generation so that
these combined effects of inbreeding and
genetic drift cause a loss of genetic variation,
which causes a reduction in individual fitness,
less resilience to disease,
less fecundity, lower reproduction rate.
These factors combined to produce
a smaller population and we're
in a positive feedback loop.
What can we learn about extinction from
a more comprehensive survey
of mammalian genome assemblies?
This is work that's been underway,
at the end of 2020, the tsunami,
a consortium published the alignment
of over 240 mammalian genomes,
many of which were provided by samples from
the San Diego Zoo Wildlife Alliance and
this analysis is being continued now.
Specifically, in a study that
emphasizes the application of comparative genomics to
evaluation of extinction risk
as categorizing species with respect
to their threatened status
as produced by the Red List of IUCN.
This is work of Aryn Wilder at
the San Diego Zoo Wildlife Alliance and Megan
Supple in the Shapiro's lab at UC Santa Cruz.
Using the genomic data from Zoonomia and the alignments,
they're able to find some correlates
with extinction risk across
this much larger number of species.
They find that overall,
the lower genome-wide heterozygosity
is associated with increased risk
of being in threatened status.
Heterozygosity refers to variation in the genome.
Although the study involves
analysis of only one genome per species,
every individual inherits half a chromosome
from its male parent and
a chromosome from its female parents.
They won't be the same.
It's possible to analyze
the differences and use that metric to
estimate the overall heterozygosity of a population.
In this case, it's strongly
correlated negatively with extinction status.
That is, the lower the genetic variability,
the more likely a species is to be threatened.
Using these data to make
the demographic inferences as I
showed with the Hawaiian monk seal trajectory,
they looked at all of their species in their analysis
and the warmer colors represents
species in the threatened categories.
Overall, all of the mammals that were looked at,
there is this very significant correlation
with this effective population size.
Actually the harmonic mean of
the effective population size.
It's because it'd be very noisy to show them all at once.
They're broken down in here into
taxonomic groups of mammals and
in the larger figure are carnivores.
It's pretty easy to see that threatened categories
species have even had
longer periods of time with low population numbers.
Historical effective population size impacts
contemporary conservation status.
Threatened species have
smaller historical effective population size.
Threatened species have larger effective population size
to census population size ratios.
If a population is very large and declines rapidly,
the harmonic mean of its effective population size
will decrease more slowly
than the census population size.
The ratio will be greatly increased.
For species that we have data like this,
they fall into very high risk of endangered status.
Overall, Aryn and
Megan looked at all of the metrics they could derive
from the genomic analysis with regard to
the extinction risk classifications.
Over the species in the threatened categories,
there was a statistically significant association
that these species had
more deleterious mutations in coding regions,
lower estimated genome-wide heterozygosity,
and smaller effective population sizes.
They also noted that increasing
the number of annotated genome assemblies would
increase the power of these analyses and we can
look forward to seeing more work in this area being done.
We've been interested in
these kinds of risk assessments with
regard to the genetic rescue
of northern white rhinoceros,
the most critically endangered form of rhinoceros.
There's only two living individuals, both females.
But the San Diego Zoo Wildlife Alliance Frozen zoo
has cell cultures from 12 individuals.
We've sequenced their genomes and compared
them to a similar number of southern white rhinos.
We find that the cell cultures
of a dozen northern white rhinos have
more genetic variation than
the standing population of 15,000 southern white rhinos.
We can see the effects of the history of
the demographic trajectory of
southern white rhinos in
the genomes of today's southern white rhinos.
The southern white rhino went through
a genetic bottleneck a century ago
down to 30 or 50 individuals.
That's why they have lower genetic diversity now.
They also have larger segments
of their DNA that's genetically homogeneous,
we call these runs of homozygosity
that occur because through the bottleneck,
individuals who were more closely related bred with each
other and produce these
what we call runs of homozygosity.
Those blocks are significantly larger
in southern white rhinos and northern white rhinos.
The gene loss is essentially irreversible.
Once it's lost, its restoration is slow.
It's only facilitated by
greatly larger population size and many generations.
As we can see from the mountain gorillas,
selection is not as effective from
mildly deleterious genes in small populations.
Beneficial mutations can be diminished or lost
because of the genetic drift is a larger factor,
is stronger than selection.
The extinction vortex is deterministic,
but is it reversible?
Is it true that once genetic diversity
is lost it can't be regained?
Well, we know from small populations
of species that are in decline,
it's possible to rescue their fitness by
translocation of individuals back into those populations.
That's known as genetic rescue in
the Florida panther is a classic example.
But could genetic rescue be possible using
advanced cellular genetic techniques
such as artificial insemination,
cloning, and applying stem cell technology
with assisted reproduction methodologies.
In evaluation or an exploration of
that possibility in collaboration
with revive and restore,
a non-profit conservation Biotech Organization
and ViaGen Equine and Pets,
world's biggest commercial cloning company,
we produced a przewalskii horse clone from
cell cultures of an individual
that were established in 1980.
That individual is now deceased,
but his clone is
the most genetically valuable stallion for
the breeding population of this endangered species.
This clone was named Kurt,
in honor of Kurt Benirschke,
the founder of the frozen zoo
and a founding member of CARTA.
This same collaboration is also teamed up
to clone the first US endangered species,
a black-footed ferret, named Elizabeth Ann.
The cells for cloning Elizabeth Ann were
derived from an individual from
the last wild population who was brought
into the managed breeding program that saved the species,
but she left now living descendants
in the current population.
This clone black-footed ferret has
a substantial amount of
genetic variation that's lost
from the current population.
When she breeds, we hope to be able to
evaluate restoring that variation
into the wild population.
The collection of living cells in
the frozen zoo has many utilities,
and we explored awhile ago
the opportunity to make
induced pluripotent stem cells out
of these in collaboration with Jeanne Loring and
Inbar Friedrich Ben-Nun at
the Scripps Research Institute.
This work is being continued by Marisa Korody
at the San Diego Zoo Wildlife Alliance who
has induced pluripotent stem cells
from nine northern white rhino individuals.
These graphics depict the evidence that
these cell cultures are indeed markers of pluripotency.
I wanted to give a shout-out to
the team that has made this possible.
The frozen zoo team that banks the cells and
the reproductive sciences team that is banking semen and
the conservation genetics team that banks frozen tissues
and undertakes the genomics work
with part of Zoonomia and our collaborators,
and just sum up by saying,
comparative genomics offers a new tool
for extinction risk assessments.
The news is maybe we need to be more
concerned about the loss of
genetic diversity than we have been.
That cellular based genetic rescue
may be a potential option for
mitigating losses of genetic diversity
within species and preventing species extinctions.
But it will depend on
a greatly enhanced efforts to bank cells.
Because at the current time,
approximately six percent of these IUCN threatened
category species actually have individuals cryopreserved.
Thank you. [MUSIC]