lost in the fog of a cosmic storm floating on
whimsical wavelengths is the norm dancing through
the stars chasing spectrums of light riding the
waves that are just out So one of the things
that I've noticed is that I don't introduce myself
very often. And for all those new listeners out
there that show up from time to time, my name's
Dr. Jeffrey Zurich. I'm the host of Whimsical
Wavelengths. And today is all about the white
sturgeon. Because, you know, I've spent the vast
majority of my life living along the major rivers
in southern British Columbia, Canada. The Kootenai
and the Columbia Rivers and now the Fraser River.
These rivers have a lot in common from the ecology
standpoint with respect to salmon and the subject
of today's episode, the white sturgeon. And these
fish are amazing. I've spent a lot of time fishing
the Columbia for trout and walleye, also known
as pickerel in other parts of Canada. But I've
never interacted with a sturgeon. To me, they've
always been mysterious fish of the river. I know
they are there, but I've never seen them. The
Loch Ness of the Columbia and the Fraser River.
And I've always wanted to learn more about these
creatures. You know, this group, sturgeon, and
their family group, they first appeared in the
late Cretaceous, with the oldest seen in the
fossil record at 100 million years ago, found
in Alberta. canada in fact they look today very
similar to what they looked in the late cretaceous
they join a short list of creatures that have
not at least outwardly significantly changed
their body shapes or their large scale building
blocks in a very long time like the crocodile
whose modern body shape came together 80 to 90
million years ago or the horseshoe crab which
has been around a lot longer nearly 400 million
years Besides being what some term a living dinosaur,
they're also polyploidy, meaning they can have
different numbers of chromosomes. This whole
part of it actually makes my head hurt. Give
me the simplicity of a wave equation. Thankfully,
in a few minutes, I have a guest to help me understand
it. But let me attempt to set this up. So they,
the white sturgeon, are scientifically amazing
already. And we haven't even gotten into what
the species do. Above and beyond what the local
rivers mean to us. There are culturally important
food for First Nations of North America and harvested
for caviar in other places. The caviar can go
for $1 ,000 to $5 ,000 Canadian per pound. A
true luxury item. that starts its history almost
2500 years ago when the persians ate them in
a belief that it provided strength later becoming
a prized delicacy of european nobility sturgeon
are predators and scavengers using barbells or
whisker -like sensory organs that smell and taste
to detect on the riverbed things like salmon
carcasses eggs lamprey crayfish clams and worms
some might call them a keystone scavenger aiding
in keeping riverbeds healthy for other species
now we have the geologic time perspective and
the culture perspective and how they are important
to the river systems they inhabit what about
their population i can anecdotally attest to
these fish being rare In fact, they're threatened
as a species due to overfishing and habitat modification.
The Columbia River has many, many dams along
it due to the Columbia River Treaty. All right,
time to bring in the guest. To help us understand
about these enigmatic fish, their populations,
and their genetics, please welcome a fisheries
geneticist with the Hagerman Genetics Lab, Dr.
Stuart Willis. Hi, Jeff. Always excited to talk
about sturgeon. Yay. Before jumping into the
science, I always think it's important to like
see how someone comes by their chosen subject.
I mean, careers in STEM, we need to make them
less scary in general. And science is always
a human endeavor. I grew up living beside a river.
But what about you? Was there a river, a body
of water? Was it fishing? What brought you to
studying fish and their ecosystems? Yeah, so
I did a lot of fishing with my dad as a kid back
in Texas, except I always wanted to bring our
catch home and keep them in an aquarium to learn
more about them. So as a teenager, I did keep
a lot of aquarium, but mostly South American
river fishes, not our North American native fishes.
And so then when I went to college, I got hooked
up with a professor who had a graduate student
doing phylogenetic and evolutionary ecology work
on South American fishes, and I was hooked. And
so I did my graduate work on phylogenetics and
population genetics of South American fishes.
But in academia, as you know, you sort of have
to go where the money is. And so that eventually
led into the work that I do today for a consortium
of tribal nations for whom fish, and particularly
salmon, are an integral part of their culture.
They've taken a lead role in managing the natural
resources within their ancestral territories
in the Columbia River Basin. And as a part of
that work, I manage our genetic investigations
of white sturgeons, which are the largest freshwater
fish in North America. Okay. So, I mean... I
grew up next to the Columbia. I fully support
this sort of research and keeping those ecosystems
at least understandable, what's happening to
them, monitor them and make sure they're there
for the next generation. But are you also looking
at different opportunities to do other research
outside of those drainage catchments as well?
I mean, yes, you follow the money, but, you know,
I also want to go back one day and do some volcano
research that might take years and years and
years and years to actually come to fruition.
I mean, that's the nature. of sometimes playing
science. It's a long game. Yeah, I still do collaborate
on occasion with people from my past. I still
have a project that I'm working on looking at
photosensory evolution in shallow and deep walling
reef fishes and things like that. But for the
most part, I stay within what the tribes need
and the tribes are focused on fisheries in the
Columbia River Basin. A lot of what I do day
to day is... salmon genomics. And there's a huge
community of people, as you can imagine, that
are interested in all things salmon, everything
we find out about salmon. White sturgeon is a
little bit smaller of a community, but to me,
because there's so much less known about white
sturgeon, it sort of feels more like a voyage
of discovery, much more like the things that
I did as a graduate student, where I was going
out into the Amazon and finding things for the
first time, seeing places that no scientist had
collected fish before, at least. A lot of new
stuff. Hard, difficult, but new. Right. And I
will get into how you managed to find these fish,
hopefully eventually here. But I want to pivot
a little bit to the rivers themselves that are
kind of the focus of this study and your work
in general. The mighty Fraser and the Columbia,
two rivers here on the west coast of North America.
I really felt like I needed to add a little bit
Canadian content from the political past. It's
kind of a fun little tidbit. The two rivers are
separated by only about 45 meters of elevation.
Like there's a divide right near Vail Mount,
British Columbia. In the 1960s, British Columbia
actually made a public threat in taking the Columbia's
water in a negotiating tactic for the Columbia
Basin River Treaty. In a geographic sense, the
rivers are very similar. Yet today... are very
different. Perhaps let's start there. What is
kind of like the state of the two rivers? Yeah.
So both the Fraser and Columbia basins face increasing
pressure from urbanization and other intentional
and unintentional modifications, as well as changing
precipitation and temperature patterns that make
life as an aquatic organism exponentially harder.
The Fraser, fortunately, doesn't have the same
level of damming that Columbia does, particularly
the main channels. Thanks, and going back to
your... comment on Canadian politics, as I understand
it, to push back from the public about the effects
that would have on aquatic species and the people
that depend on them. Which is not to say that
Fraser is in pristine shape. Channel modification
and pollution are a big issue and anagimous fisheries
have been on the decline for a number of years.
Some of the factors for that are local and some
of them probably regional. The Columbia, on the
other hand, is strongly segmented by hydroelectric
facilities from the tributaries through the main
channel. And on top of that, as well as urbanization
and other habitat degradation, not to mention
climate change, invasive species have really
started chasing their toll. Some intentionally
introduced by well -meaning but short -sighted
state agencies like Channel Catfish and Chad.
Some introduced by well -meaning but ignorant
bucket biologists like walleye. And some completely
unintentional hitchhikers, like quagga mussels
and Siberian ponds. So the answer to your question,
the state of the rivers is probably middling
to struggling, respectively. Right. But maybe
where I was kind of wondering is like, what's
the effect of those dams? Because that's like,
all things being equal, they have, I mean, yeah,
I could say that Columbia, at least in its lower
reaches, has more population pressure. And they're
very similar in their geographic and everything
else, but the Fraser's dirty. It has a lot of
sediment. I wouldn't say dirty. Dirty is the
wrong word necessarily because it's not like
it's polluted or anything, but you have all these
dams in the Columbia that are causing all that
sediment to settle out. And that's, you know,
I've heard it said that a dam gives a river a
stroke. You can partially recover from that stroke,
but you're never going to get all the way back.
Right. So there are great diversity of dams on
the Columbia. Sort of the two main types are
run of river dams that sort of don't have a big
difference in elevation. And then dams that have
a large body of water that are held behind them.
And those in particular have major effects on
the river ecosystems because. Not only do they
slow down their water, which means that fish
now have to swim rather than just being in the
current, but they also allow the water to heat.
And that hot water is really hard for these very
cold -specific species, cold -adapted species,
because they get in hot water, their retazolums
ramp up, their parasite load is more difficult
to manage. And so they're very different, both
at a very small -scale endocrine level and then
at a major ecological level. And then, of course,
there are a number of dams that don't even have
fish passage at all. So it's hard to be an anagimous
fish when you can't even get over the dam in
the first place. Okay. I was going to move on
to the next question, but I need to check the
word. Anagimous? So anagimous is a term that
just means fish that start out in freshwater,
go and live part of their life in saltwater,
and then come back to spawn in saltwater. It's
a subset of what we call diadromous fish, so
fish that have sort of two different parts to
their life history strategy or life cycle. The
alternative is catadromous fish that live in
saltwater as adults, spawn, they're young, go
into freshwater for some period of time, and
then return back to saltwater response. I think
the American eel is a catadromous fish. They
all spawn out in the ocean. They're young, spend
most of their life in freshwater. So then what
would salmon be? Salmon are anadromous fish.
They spawn in fresh water. The young go out to
the ocean, grow up, and then come back to adults.
And this is sort of getting off on a tangent.
There are some salmon that don't, right? Like
rainbow trout. Anything we call a trout is because
they can't complete their life cycle in fresh
water. The reason that they go to the ocean is
because there are so much more nutrients in the
ocean. So there's an advantage to going out to
the ocean. to be able to grow faster or have
greater access to nutrients. And so all of that
life history differences are adaptations that
these fish sort of manage across time as environments
changed. Right. Okay, well, to pivot to the topic
of the day, the white sturgeon. Who are they
and what role do they fill in the ecosystem of
these two rivers? Yeah, sturgeon are very charismatic
fishes for those who are lucky enough to live
where they do. As you mentioned in your intro,
they look very prehistoric. And indeed, as a
group, the order as a pincer of forms, which
includes sturgeons and paddlefish, had been around
for a long time, being one of the earliest groups
of bony fishes to break off at least 300 million
years ago. So before the divergence of the dinosaurs
from other reptiles. But I personally don't like
the term. living fossil or living dinosaur that
sometimes gets applied because they are, in fact,
highly modified both from other fishes and from
their own ancestors. For example, they have a
mostly cartilaginous skeleton, like sharks, but
that's a feature that they evolved after diverging
from other fishes. It's a secondary characteristic.
Similarly, while fish recognizable as asapensirthons
have existed since at least the early Jurassic,
Modern sturgeon and paddlefish were as different
from those forms as sturgeon and paddlefish are
from each other today. But, you know, as you
say, they have been around for a long time, and
they have some neat features beyond their unique
appearance. For example, they still retain electrosensory
organs on their head called ampullae of Lorenzini.
that allow them to sense the weak electric field
emitted by other aquatic organisms, a feature
that they share with sharks and rays and one
of the group of early diverging fawny fishes.
And you can imagine that feature helps them to
find fish in the deepest, darkest parts of large
rivers where they're found. And that leads into
their ecological roles, which change depending
on their life stage. As eggs, larvae, and fry,
they are food for a lot of other creatures. But
they grow really fast in the first couple of
years of life, usually reaching 30 to 40 centimeters
in the first year and a meter within three to
five years. And after that, especially as adults
that reach three or four or even more meters
long, they don't have a lot of natural predators.
So they can sit at the top of the aquatic food
chain, eating basically anything that can hoover
up into their mouth that smells good, which could
be live or dead. And so they are both top predators
and scavengers. All right, so I guess they're
kind of like a keystone species to some extent
for these two rivers. You know, it's hard to
say keystone species because that sort of depends
on your perspective. I mean, you could say that
salmon are a keystone species for these ecosystems
because they bring all of those marine direct
nutrients. They're an apex species, right? They
sit at the top of the food chain, and certainly
they have effects on the ecosystem. You know,
Keystone is sort of an amorphous concept. So
I'd be cautious to venture out and say that for
sure. Well, how long does it take for them to
get to adulthood? Because I know that they're
long living. And generally speaking, those species
who are long living, you know, they take a long
time to reach adulthood. They take a long time
to reproduce. Is that the same for this species
as well? It is. As a survival strategy, you avoid
being prey yourself. White sturgeons grow as
fast as they can to get into a size so that they're
less likely to be eaten. But once they do, they
slow down their growth and just sort of chill.
Since prehistorically, at least, mortality amongst
sub -adults and adults was really low. While
conversely, finding food to maintain such large
bodies is a full -time job. So they are a type
of fish that exhibit what we call a periodic
life history strategy, which means that they
reproduce at regular intervals, usually in the
late spring when snow melt is high but the water
is warming. But the local conditions that help
their young to survive can be unpredictable spatially.
And so it's really advantageous to produce a
ton of eggs that get spread out across space
to mitigate risk. And for organisms like that,
for which egg number or secondity is a determining
factor in reproductive success, size at reproduction,
which generally also means age, also becomes
a determining factor, which explains why sturgeon
males, for whom size is slightly less of a constraining
factor, don't mature to around 12 to 20 years
of age, while sturgeon females don't usually
start to mature around at least 15, usually 18,
but can hit the 30 years. to mature and then
once they do because that kind of pulse reproductive
effort is so taxing females in the wild will
usually only reproduce every three to six years
or so and some of those years would be good recruitment
years and some will be bad and based on prevailing
environmental conditions so the reason why they
succeed is because they can live so long Long
enough for a few fry to survive from a few of
the 70, even 100 years that they're going to
live. But that's in natural conditions and rivers
unaltered by dams and dredging and pollution,
invasive species, et cetera, et cetera. So how
that continues to function in our modern river
ecosystems is something we are actively studying.
I have a feeling I'm about to jump the shark
here with this question because you kind of brought
it up. take decades to like humans have a couple
of years and we you know sexually mature like
it's it's it's a standard window it's not exactly
the same between individuals but it's pretty
close like it's not decades and you just gave
a range that were potentially decades long that
it takes to mature like that seems Could you
imagine being a teenager for decades? And one
person or one fish goes through that in 12 years.
The next one takes 20 years. We make jokes about
us men taking a lot longer to mature, but this
is taking it to the whole next level, right?
It is. Yeah. And so some of that is probably
environmental conditions. If you grow quickly,
you're more likely to mature quickly if your
growth rate is sort of... set at an early age
to be slow. You're going to take longer to reproduce.
But sometimes that can be an advantage. You know,
we talk about keeping it back to salmon because
that's one of the other things that I work on.
Salmon have very distinct peaks in age at maturity,
but larger fish have larger precondities. They
produce more eggs. And so it can actually be
an advantage to become sexually mature later.
And so it's entirely possible that's true for
sturgeon as well, that it can be an advantage
to wait to become sexually mature because you're
larger, you end up having a greater fecundity,
maybe you weathered out a time period of which
you wouldn't have been successful reproducing
anyway because there were cruddy conditions for
offspring. And so, yeah, that range certainly
has implications for population dynamics, but
at an individual level can actually be an advantage.
And not to get too hard, to jump too far ahead
into talking about, you know, sort of state of
the population. One of the things that we're
seeing in looking at some of these river segments,
the ones that are sectioned off by dams and that
kind of thing, is that fish are taking longer
to mature. And so basically that's probably because
the ecosystems are not as productive or the fish
don't have access to the areas where they historically
would have been able to. get enough for me to
be able to reproduce at younger ages. So let's
pivot towards the actual paper, the reason I
got you onto the show. And to be honest, I really
struggled with it to understand it. I mean, I
guess I'm a volcanologist, this to be expected,
but even the more I learned, the more I was blown
away. The paper, Genome Assembly and Diagnostic
DNA Markers for Sex of the Largest Freshwater
Fish in North America, the White Sturgeon Assenpenser
Transmountainous. I know I did the terrible job
of pronouncing that, but that's okay. So I guess
let's start with the hardest thing that I had
wrapping my head around and I made a joke. Give
me wave equations instead. What exactly is ploidy?
Yeah. So this paper is our first attempt at reconstructing
the genome of white sturgeon so that we could
develop new genomic tools for their conservation.
But we really couldn't do that without confronting
the issue of ploidy. And so hopefully I can explain
that without getting too much into the weeds
and feel free to jump in if I'm getting entirely
too nerdy and esoteric. But we fully embrace.
Don't worry about that. Esoteric. Well, to a
point, because we have to understand it, too.
Well, that's my that's my wife's euphemistic
term for me. So, you know, that's just how I.
Yeah. But ploidy refers to the number of complete.
sets of chromosomes in a cell, whatever complete
is for that species. And I'm using air quotes
when I say complete. My voice does not convey
that. And I'll come back to that in a moment.
But to give you an example you're familiar with,
humans, like most multicellular organisms, are
diploid, diploid, di meaning two. That is, we
get one complete set of chromosomes from mom
and one from dad. So the final set contains pairs
of each unique or homologous. chromosome, meaning
what each mom and dad contributes, eggs and sperm,
are, in this case, monoploid, mono meaning one,
one complete cell. Now, technically, we use the
term haploid to refer to the complement of chromosome
in a gamete, an egg or a sperm, meaning half.
And what the combined gametes produce, somatic
cells, are called duploid. The root U, meaning
true or even. And then we call instances where
there are incomplete sets of chromosomes aneuploid
or not even. For example, in humans, we may be
familiar with trisomy, where there are three
copies of a chromosome. And the trisomy, three
bodies of chromatome or chromosome, which creates
uneven sets of chromosome or even. aneuploidy.
And this is usually a problem developmentally,
like trypsin via chromosome 21 in humans produces
Down syndrome, because gene regulation, as it
turns out, is frequently dosage dependent, meaning
the regulation and expression of genes has evolved
to be balanced in a copy number dependent manner,
and aneuploidy messes up the typical dosage.
But going back to the air quotes, complete...
set of chromosomes, when we look across animal
and plant species, we see wildly different numbers
of chromosomes and genome sizes. Some of these
differences are because chromosomes have expanded
or contracted individually, or some chromosomes
have split or combined. And so we see relatively
moderate changes in chromosome numbers among
related species. But those changes don't affect
the ploidy. because it's not changing how many
sets of chromosomes are in each cell, rather
just the numbers that make up each set. But sometimes
the genome sizes changes because of polypoidization,
poly meaning many, in this case many sets, where
the number of chromosomes goes up by entire sets
all at once. And there are two main ways this
can happen. In allopolypoidization, allo meaning
different, in this case different species, Two
moderately divergent species hybridize, and through
some cell developmental magic, the progeny end
up with twice the combined set of chromosomes
from both parental species. And this form of
polyploidy is fairly rare in animals, though
there's at least one group of fishes, the Catastomidae,
or suckers, that are thought to be allopolyploids.
But it's actually fairly common in plants, including
some you might know, like wheat. Wheat is an
allopolyploid. If, on the other hand, polyploidization
happens without hybridization, by the doubling
of a genome within a species, we call that autopolyploidization.
Auto meaning cell. And autopolyploidization has
happened repeatedly, not only in plants, but
also in vertebrates, especially in fishes, and
in particular in sturgeons. So based on mapping
of chromosome counts across the phylogenetic
tree of fishes, that is the relationships among
species of fish, we can estimate the ancestor
of the Acipensia reforms, that was sturgeons
and paddlefish, had a euploid or complete number
of chromosomes around 60. But all modern Acipensia
reforms have at least 120 chromosomes in their
genome. And many sturgeons, like the white sturgeon,
normally have at least 240 chromosomes in themselves.
So approximately double to quadruple the ancestral
number. So if we presume that that ancestor with
60 chromosomes was diploid, which is a reasonably
safe bet for a reason we can talk about, then
the species with around 120 chromosomes would
be evolutionary or ancestral tetraploids. That
is relative for complete sets to that ancestor
that had two. And species with 240 or so chromosomes
would be ancestral octoploids, the eight complete
sets. And so the haploid number for those organisms,
what's found in an egg or a sperm, and what's
half the euploid number, and all of that, is
multiple complete sets relative to the ancestors.
And big jumps like that from 60 to 120 to 240
as the euploid number are the hallmark of...
polyp organization. Okay. To be honest, I had
a hard time following. I think it's just because
it's like, there's not enough numbers. No. And
I also couldn't spell any of those words. Like,
I just come back to like the human idea here.
And we talk about human genetics when we end
up with, like, it seems like the more you have,
the more things that can go wrong. Or is it the
more you have, the more Fail safes you have like
Yeah, how does that work? So it's what's really
interesting is that in most of the ancestor polyploids
we know in both plants and animals the genome
actually acts as functional diploids made the
same two pairs of chromosomes Pair up and split
for distribution in gametes rather than in sets
of multiples on random parable the original multiple
We call this process redeploytization. And although
the reasons for why this seemed to inevitably
happen are an active area of research, we think
that it's some combination of fixing what dosage
problems were created by polypoidization, particularly
around sex regeneration, and the redeployment
of what duplicated genes are retained for distinct
purposes. And indeed, in an ancestral tetrapoid
European sturgeon called the sterlet, for which
we have a pretty good genome sequence, there's
pretty clear evidence that most of the genome
has at least redeployed that. But white sturgeon,
the subject of our paper, to get to be an ancestral
octopoid has probably undergone two polyphoretization
events. The first prior to its split its sterlet,
so a shared one, and then one that's more recent
and exclusive to Pacific sturgeon. But if sterlet
are ancestral tetraploids, functional diploids,
what does that make white sturgeon? So what we've
gained from our genome assembly from white sturgeon
is that there's evidence both that the majority
of the genome seems to exist in four copies or
relative to the sterlet sturgeon, that's a template,
your diploid number, which makes white sturgeon
technically tetraploid. There's also evidence
that four ancestral chromosomes don't recombine
much during meiosis, suggesting that enough of
the genome has rediploidized for the machinery
of cell division to treat them as two pair rather
than four of a kind. So notwithstanding that
there's ambiguity in our results, because shockingly,
it's really hard to assemble an octoploid genome.
It looks like the white sturgeon genome is in
sort of an intermediate phase of rediploidizing
from being functionally petroploid to the most
recent autopletoplasmic event. So I guess what
I'm trying to say in answering your question
is that it's hard and it creates problems, but
it seems that most of the time genomes go back
to being diploid across time. polyploidy is an
important factor. Evolutionary is sort of a different
question, but in terms of how it sort of rejiggers
the machinery, it does that by becoming rediploid,
going back to being diploid over time. So it
tries to simplify over time genetically. Right,
yeah. In the, what's the word, I guess the background
research that I tried to do in I don't pretend
to understand it. They made the case that perhaps
this sort of branching ploidy is to deal with
evolutionary or environmental conditions. So
I guess the argument is plants began that process
when they came onto land. Is that kind of where
we're going here? The environment changes so
much that the genetics had to change really quickly.
And one way to do that is to have more chromosomes
that can drift and change with the environment?
Yeah. And I, the broad answer to your question
is maybe, um, I don't want to get into what one
might call, um, an adaptationist or selection
paradigm, um, because not every trait that an
organism has is necessarily adaptive. Sometimes
it's just neutral. Um, or maybe even disadvantageous,
but developmentally connected to a trait that
is advantageous. In addition, for any trait to
actually being adapted, it has to be advantageous
at an individual level. That is, it has to give
that individual an edge over competitors within
its own species. So that trait can't just appear
to be beneficial for the population as a whole.
And the same here goes with coity. It's likely
that in most cases, these kinds of genomic changes
are ultimately lethal. And it's only when the
stars align that a polycoidization event happens.
That genome is developmentally viable. The phenotype
it creates is relatively neutral or even has
some advantage in some environments. And then
that that individual is fertile and able to reproduce
either with normal coity individuals or that
there are enough. other polypoids around that
tend to reproduce. And those are pretty exceptional
circumstances. But the answer to the broader
question of why would this ever possibly work
out is really the same answer to why we have
sexual reproduction in the first place, which
I think is part of what you're talking about.
And the answer to that is novelty. The most salient
theory for why we have sexual reproduction, which
creates generally diploid offspring using material
from two parents, Why it evolved in the first
place is because of a race between organisms
and their generally clonally reproducing parasites
and pathogens. Combining DNA from two individuals
creates new variants a lot faster than having
to mutate them from scratch. And the same is
true for polypoids. When we look across environments,
polypoids are associated with two things. As
you say, extreme environments and also humans.
Humans, and this is mostly true for agricultural
species like the wheat that I mentioned, because
when we find weirdos that have traits that we
like, even if those traits would have put them
at a disadvantage out in the wild, we baby them
and we breed them a bunch. So like with wheat,
most grasses have tiny dinky little seeds, and
most of what's adaptive about them is their ability
to delay germination, to resist being eaten or
resist digestion if they are eaten, or to spread
as far as possible. But wheat, on the other hand,
has these giant honking brains that we love,
but are pretty terrible for avoiding being eaten
or dispersed. And it turns out the same goes
in extreme environments. A lot of polypoids,
where they are viable, have exaggerated characteristics
compared to those normal voiding individuals
in their next seasons. So think like wheat with
the giant seeds. They're often what Stephen Jay
Gould once called hopeful monsters, obvious mutants
that are just looking for the right environment.
And in places where you're competing with normal
-point individuals in an ancestral environment,
you may be at a disadvantage. But if you happen
to disperse into an extreme environment, extreme
here simply meaning beyond the normal environmental
tolerances for that species, immediately you've
got less competition than the normal -point individuals.
And if those exaggerated characteristics make
you better suited for that environment than normal
-point individuals, then you're off to the races.
Ecologists would say you're exploiting a new
niche. But to bring it home to Sturgeon, why
Sturgeon specifically exhibit this kind of ploidy
variation, my guess is that this is genomic flexibility.
It has more to do with a slow mutation rate and
a compound history of polyploidy than an adaptively
retained ability to tolerate or utilize changes.
Though, sort of to your broader point, whether
that has given them an advantage to weather the
many changes that they have seen over 300 million
years, that's an open question. Yeah, I don't
think we really have the answer for that yet.
Okay, I'm going to go on a short tangent because
I don't know if you have the answer. You mentioned
extreme environments and environments where you
can change quickly, where you have less, you
know, other animals and plants being in competition
with you. What about things like ocean islands
that, you know, volcanic, they're wiped clean.
Is this another type of environment where Ploody
can take it? So I'm thinking Galapagos, I'm thinking
Hawaii, I'm thinking those sorts of really extreme
but yet isolated environments. Yeah, so islands
have always been sort of a natural laboratory
for evolutionary diversification and adaptation.
And there are a number of reasons for that. Islands,
as you say... They often have less competition
because there are so many fewer species, which
means that there are a lot of unoccupied niches.
They tend to be very isolated, so there's not
a lot of input from other populations that would
prevent you from adapting to those new environments.
And they often have very small population sizes.
And so you have, it's technically inbreeding,
but essentially what's happening in populations,
you always have a balance between. Things that
are happening because of genetic drift. So these
are just numerical things that gene frequencies
change because they're just a limited number
of individuals and natural selection. Natural
selection is creating adaptation. And so those
factors are often in conflict with one another
because a drift will often sort of accidentally
take you away from the adaptive. field that you're
looking for. I don't want to anthropomorphize
it. That is optimal. And so in large populations,
natural selection is less opposed by drift, and
therefore it can be more effective. And in small
populations, drift is a much bigger force. And
what that can sometimes mean is you can drift
over into different phenotypes that are actually
better for niches, unoccupied niches that you
wouldn't have been able to exploit before. And
that can be true for polyploidy as well. Think
of polyploidy as being sort of the oddballs that
normally they would get selected out. But when
you're in these isolated environments where you're
not getting input from a lot of nomoploidy individuals,
it doesn't take that many polyploid individuals
to start an entire new population. So that combined
with the unoccupied niches, with the isolation,
all those kinds of things, gives them an opportunity
that they wouldn't normally have in mainland
environments. Cool. All right. So we know they
have complex genetics and I don't really want
to get into it, but I will just kind of drop
it. We have a society that has gotten confused
when talking about the rare cases in human genetics
when it comes to sex. But with four or six different
pairs or chromosome groups like. Can they switch
sexes like other species? Is there some combination
of chromosomes that kind of try to determine
this? Like, it's got to be way more complicated
for them than it is for us. It is. I mean, it's
also in some ways sort of fundamentally different
because, as I alluded to, sex is one of the primary
reasons that genomes are forced to restructure
after a polyploidization event. So, for example,
in mammal species, which have an XY sex chromosome
system like humans, females, which of course
have two X chromosomes, one of them is generally
completely turned off during development or silent
to maintain the same dosage as in males, which
only have a single act, right? And an interesting
manifestation of this, if you've ever seen a
tortoiseshell cat, which have that attractive
black and orange spotting. It's because of that
gene or colors on the X chromosome in cats. And
which X chromosome is silenced can vary across
the body in early development in females, which
leads to different versions of the gene being
expressed in different patches of skin. But to
your question, part of the reason why it's very
different in sturgeons to a degree is because
they show a ZW sex determination system. Birds
generally have a ZW sex determination system,
and that's where the female is the sex with the
two different sex chromosomes rather than the
male. And so just to be obvious about that, we
say ZW instead of XY in these female heterogametic
species. And we know that that's true, that sturgeons
have a ZW sex determination system because you
can actually feminize or masculinize fish using
hormones. So when feminized males are used, so
this would be a fish that only has the ZZ chromosome,
they produce all male offspring because there
are no W chromosomes amongst them. Whereas if
you masculinize females and make ZW females be
male, they produce both male and female offspring,
although the ratio is messed up because there
are now more W chromosomes than there would usually
be. And indeed, in the sterlet sturgeon, that
diploid European sturgeon that I may have mentioned
before, there is a region on one chromosome that's
only present in females, as expected. And it
happens to be a gene that's strongly expressed
in the sex organs of some other fishes. And then
we found the same region present in white sturgeon,
too. And it seems to predict sex pretty well,
depending on which population you're looking
at. But all of that being said... It's true.
We don't know how much environment may play a
role in determining sex of sturgeon. It is possible
that this genomic region that we found, both
in these two seasons of sturgeon, can be mediated
or completely overridden in certain environments.
And that could cause some noise around what the
markers that we develop from this predict in
terms of sex. Interesting. All that to say is
it's possible, but we don't know. It is possible.
So as I thought this earlier and didn't get a
chance, the other wonky thing about sturgeon
is that not only are they probably functional
tetraploids themselves, they also show spontaneous
autopolyploids. So these are the fish with the
six N chromosomes that you were talking about.
And these spontaneous autopoly, what we know
is that they have one and a half times. the normal
amount of dna normal for white turkish which
is of course a sort of a more of this concept
but these individuals then one and a half times
would either be um hexaploid the six in you mentioned
or if you're talking ancestrally they could be
dodecaploid 12n or if you consider that white
spirits are normally diploid they are triploid
but and i can i can talk about how we think that
actually happens is spontaneous auto polyploidy
but the weirder part is as a rule triploid fish
are sterile right in fact triploid fish you may
have heard of these rainbow trout brass carp
atlantic salmon are often stocked in the wild
specifically because they're sterile because
they won't invade habitats or interbreed with
wild fish and they're sterile because having
three sets of chromosomes when they go to make
their haploid gametes the chromosomes get all
shuffled up in unpredictable ways and their gametes
end up having uneven set that is their aneuploid
But I guess nobody told white sturgeon, because
while we've found that these one and a half times
variants are rare in the wild, they're still
present, but they're rare. They're pretty common
in hatcheries, common enough that they've been
unintentionally crossed with normal ploidy sturgeon.
And lo and behold, they produce five offspring
with an intermediate ploidy, which is probably
safest to call pentaploid, I guess, which is
five sets of chromosome. And we don't really
know a lot about these pentaploids except that
they're viable. So it's sort of an open question
as to whether or not they could be important
evolutionarily if they were created out in the
wild and half the population. But the point,
you know, to your point is that those spontaneous
autopolyploids, the one and a half times fish,
that are hexaploid, dodecaploid, triploid, whatever
you call them. are at least viable and partly
fertile. And you can sort of imagine that there
are situations where enough of them were accumulating
out there in sort of an isolated environment
that they actually could create an entirely new
population. And so that sort of gives you a bridge
or a window to how these higher ploidies could
have formed in the first place. And you have
these sort of strange cellular developmental
things going on that result from sort of... breakdowns
in environmental conditions and just create this
sort of convergence of conditions where new set
of OED variants happen to start reproducing and
diverge from the original population. Okay, so
let's go back to the paper. You're using DNA
markers to figure out whether or not individuals
are male or female. And according to this, you're
like, you can't. see, I would imagine, a fish,
whether it's male or female, just by looking
at it. And so you're using genetics and you're
96 % accurate for females, but only 81 % for
males. Why is it easier to spot the female genetically?
And is it a null result sometimes instead of
like, say, a false positive or false negative?
Yeah, it's certainly possible that some cases
where our sex markers aren't 100 % accurate could
be. because of the failure of the molecular assay,
something that we call a null allele, where the
genomic region is there in that individual, but
our assay simply fails to pick it up. And that
would explain why some females were predicted
to be males, but not why males would be predicted
to be females. In those cases, it's not the assay
that's failing, since we can clearly see that
the genomic region is present. but rather a failed
association of the genomic region with phenotypic
sex. And I think what's actually going on is
any or all of three things. One, it's possible
that the sex data for our samples are wrong for
some populations. That is, which are males and
which are females was just misrecorded. As a
scientist, you have to be upfront about the fact
that your data may just be flawed in some cases.
And the fact that our markers are... 100 % accurate
for fish whose sex I have personally confirmed,
not by looking under the hood, but through offspring
of known crosses, sort of indicates that in some
cases. But two, as we said earlier, it's possible
that in some cases environment may play more
of a role in determining sex than we understand.
But three, and this is my preferred hypothesis,
or at least the one I'm most interested in pursuing,
that how far down the process of re -diploidization
and specifically how much exchange between those
ancestral sex chromosomes there still is, varies
from one population to another. And so the association
of our markers and perhaps even how that genomic
region mediates sex may vary from one sturgeon
population to another. And indeed, some of the
data that we use to make our genome assembly
indicate that at least in the Middle Snake River
in Idaho, which is one of the places where our
sex markers aren't 100 % accurate. There is still
some recombination between those ancestral sex
chromosomes. Okay, well, let's try to give this
a little bit more real world heft to it now.
How does this, I guess I'm going to add something
to my original question is like, how does this
further our understanding of genetics in the
animal kingdom? And how do we use this to like
help? conservation of the species like how do
we how do we use this information in practice
yeah it's you know been a few decades now since
we sequenced the human genome and we know a lot
more than we did then but every day we sort of
find out that our understanding of what genomes
are how they work what's wrong and that's science
that's how that's supposed to work you know so
for example these days we're interested in structural
variation. So structural variation of genomes
is entire sections of the genome that are present
in one individual or missing in another, or regions
that are, you know, reversed so that they're
in the opposite direction from one individual
to another. We sort of originally thought that
genomes were basically the same, except, you
know, I've got an A and you've got a T, and over
here you've got a G and I've got a C, that they're
very small differences. It turns out that even
among individuals of some species, there can
be huge, very big differences in the chromosomes
between individuals. And so that is particularly
true for polypoids, where not only is that happening
between just very small homologous chromosomes,
but chromosomes that have a much larger ancestral
relationship. And so the way the genomes evolve
or redepoidize following polypoidization provides
a good window into understanding that. But as
to the conservation of this species, which, of
course, is what I'm interested in on behalf of
the tribe, it's easier to imagine that folks
running commercial caviar farms would like to
know which fish are female as early as possible
so they can maximize their root hormone on investment.
But that's not really our target audience. On
behalf of the tribes, we're focused on trying
to maintain or rebuild the fisheries of these
species and understanding. Population dynamics
is a critical part of that, like the sex ratio
of wild populations or how many females reproduce
in a year and with how many males. And being
able to take a thin clip and predict sex rather
than having to do an abdominal biopsy makes that
data a lot more accessible. But beyond that,
because there are a lot of populations that are
slowly declining because of a lack of consistent
recruitment and reproduction, a number of conservation
aquaculture programs. hatcheries that are specifically
focused on rebuilding wild populations have been
developed to supplement those wild populations.
And while they have become very adept at producing
many young sturgeons, they're very effective.
We don't know whether those aquaculture practices
bias the resulting offspring towards one sex
or another. For example, it's possible that male
sturgeon grow faster than female. And at high
densities, like there are atrophied males, may
out -compete females and produce, therefore,
a male -biased population. You don't want to
dump a whole bunch of males back into the wild
because that screws up the population. So since
you can't sex young sturgeon until they're basically
begun to mature, having a molecular assay, like
we've developed from this marker, is a much more
effective way of doing that at earlier life stages.
Okay, so you're providing the information needed
for those that are making the policy decisions
about how to do the conservation. You're giving
them the tools to make those decisions. Yeah,
we're much more focused on sort of the state
agencies that are putting into action policies,
something that we need to be people who have,
you know, in a higher pay grade. Right. But you're
giving them the information to make those policy
decisions. I mean, in a volcanology sense, a
volcanologist isn't the one telling people to
evacuate. The volcanologist is telling them,
OK, this is what's happening. This is the likely
outcome. And then the policy people who make
a lot more money typically, not always, but typically
make the decision whether or not you need to
get out of town. Yes, yes, exactly. We provide
as much information as we can, and what they
choose to do with it is beyond our purview, unfortunately.
Exactly, exactly. Okay, so I'm kind of glad to
see that it's working similarly in two completely
different disciplines, actually. That's science,
yes. For better or worse. It goes both ways.
Sometimes you really don't want the scientists
making the decision for people sometimes, and
sometimes it would actually be better. I'm biased
there, I guess. Yeah, no, having everybody at
the table is not the right way to do it. It's
just being able to respect everyone's opinions
is sometimes the challenge. Yeah. On that note,
I'm going to skip one of my questions because
I think it's kind of wrapped up here in the same.
So the Fraser River, it's a river that connects
my home turf and more broadly for my local river.
What is the future for this species? Because
you've mentioned the Snake River already being
already quite different. But I know you're focused
more on the Columbia and its tributaries. But
what can you say about the Fraser and what needs
to happen to protect it? Yeah. So as we said,
the Columbia has a major challenge of having
all of these dams. And you can imagine that.
prehistorically a five meter fish could go basically
anywhere it wanted in in the basin you know if
there are different sections of the river basin
that are better for reproduction for growth or
you know hanging out in hot summer temperatures
that kind of thing you could choose that and
you put in dams in the way well now you just
got to deal with whatever is available and unfortunately
in many of these sections there's not enough
good habitat for rearing in the early life stages,
that they're getting a lot of recruitment. And
so what is there is getting older and older,
and as a result, the populations diminish over
time. The Frasier does not have that problem
of damming. From my understanding, the biggest
threats to the Frasier white sturgeon are habitat
degradation and the diminishing runs of the naturalist
fish, particularly chum, phantom, and eucalon.
It may be strange to think of a freshwater fish
as being dependent on marine species, but these
interior Pacific ecosystems have evolved with
that regular influx of marine -derived nutrients.
And that's especially true for white sturgeon,
which depend on those returning fish, their carcasses,
their eggs, their offspring for food. And as
those runs diminish, it's likely that sturgeon
will continue to do so too, unfortunately. And
we're already hearing reports of, and I should
say, that's not something that conservation aquaculture
can overcome. You can dump a bunch of young fish
in the river, but if there's nothing for them
to eat, then you're just spinning your wheels.
And we're already hearing reports this year of
another warm water blob developing off of California
and the prediction of a super El Nino later this
year. So it seems to be that while there are
things that we can do to give the Fraser River
or the Columbia River sturgeon the best chance
we can, their fate, like the fate of so many
other species, is going to depend on whether
we humans can get our act together as a species
and realize that we're not entitled to be the
center of the universe and start acting like
good stewards, like we should be. So we could
sum it up with essentially climate change. Yeah.
I mean, that's certainly the train coming down
the tracks, right? It's how long do we need to
see the train before we decide that we're going
to get off of it, off the tracks. And I'm actually
more of an optimist than a doomsayer because
I think being a doomsayer paralyzes action. We
are doing stuff. Things are changing. It's just
changing too slowly, to be fair. Yeah. Well,
I mean, the science is there and it's really
just a matter of political will when it comes
down to it, which is both. promising and depressing.
Yeah, it's both simultaneously. One of these
days, actually, as a plug, I don't know if it'll
be my last episode of the season, but because
of just the nature of when things need to be
published, because we're going to I have another
one that I have to record that I don't know what
I can get out. It's going to be all about volcanoes
and climate change and how we know that volcanoes
do not put out. nearly as much co2 as humans
i'm going to go through the the nerdy math and
the melt inclusions and the whole nine yards
so that that i don't know if it'll help but you
know what i mean yeah no dispelling any alternative
then we're doing it to ourselves is definitely
part of the puzzle okay so we're nearing the
end and it's time for call outs this is your
chance to flag cool projects something you're
working on something completely random it's whatever
you want Yeah, I mean, really, I just want to
acknowledge all the people that have contributed
to this. What we do with sturgeon is a team effort,
and we have a number of irons in the fire. You
know, we're looking at spontaneous autopolycoiding
in wild fish because it seems to be happening
in the wild as well in really hot weather years.
We're continuing to look at how things like shad,
which are the big thing in the Columbia River
Basin now, huge, huge runs of shad that turn
out to have a lot of something called thiaminase
in their tissue. And that thiaminase causes the
eggs to be thiamin deficient and for these fish
to die or grow weird. So we have a number of
projects that we're working on, and all of them
depend on our collaborations with state agencies
and universities to work. And in particular,
I want to acknowledge the leadership of Janella
Miller, who's now a manager with Pritvik, but
was formerly with the Yakima Nation Fisheries
when they developed their conservation aquaculture
program. And she has been... Just a huge, steadfast
champion for understanding and rebuilding white
surgeon populations. I'm really glad to be able
to work with her. Awesome. You know what that
means. It's time for the infamous question. The
one that I warn every single guest is coming.
I warn it before they even see what kind of topics
I'm going to ask them or anything else. It is
the traditional last question. What is your favorite
science joke? Yeah. I don't know if I would call
it a joke or a lament, but I have always enjoyed
the description of the kind of work that I do
by a guy named John Shepard, who's sort of a
famous fishery professor. He said that studying
fish populations is exactly like studying forests,
except you can't see them and they move, which
I guess makes white sturgeon like the giant sequoias
of the freshwater fish world. So I'm glad to
be working on that. Perfect. Well, thank you
so much for taking the time to come on and teaching
me a lot about white surgeon. Yep. I'm always
happy to talk about surgeon and genetics. My
favorite things. And that brings the second to
last episode of season two to an end. Okay. So
that means that next episode is the last of season
two and it's going to be a solo episode. All
about volcanoes and CO2 and climate change. A
little bit of a historical romp, I guess, through
how we can prove that volcanoes do not put out
anywhere near the amount of CO2 that humans do.
A fitting way to end Season 2. At any rate, just
remember that over the summer there will be encore
editions to kind of fill the feed to make sure
that the... Computer overlords are still happy
with whimsical wavelengths. And then we'll be
back in September. There are a few things that
could get into the mix, and I'll repeat these
next time, because I'm also expecting a surgery
somewhere over summer, and I really don't know
when that'll happen. So hopefully everything
lines up, and I'll be able to start Season 3
on time September 14th. All right. I'll see you
again in two weeks. so chaotic so misbehaved
echoes of melodies remind us it's always colors
weave stories painting the sky swaying to rhythms
as the galaxies fly by deep in our bones through
this melodic maze our minds explore change