Pacific rockfish and the trade-offs of a long life
Genome comparison of 88 rockfish species pinpoints genes associated with
a long lifespan

Date:
November 11, 2021
Source:
University of California - Berkeley
Summary:
Pacific rockfish are among the longest-lived vertebrates -- some
species live 200+ years. Yet others live barely 10. Their varied
lifespans make rockfish a unique genus in which to pinpoint genes
associated with long lifespan. Biologists sequenced and compared the
genomes of 88 species and found longevity-related genes involved
in living at depth and growing larger, but also an increase in
some types of regulatory genes. Longer life also correlates with
decreased population sizes.



FULL STORY ========================================================================== Rockfish is on the menu around the Pacific Rim, for the most part with
little regard for the fish's origin or which of the 137 species is on the
plate - - it's typically identified simply as rockfish or, incorrectly,
as rock cod or red snapper.


==========================================================================
But this seemingly anonymous fish -- among the longest-lived vertebrates
on Earth -- holds clues to the genes that determine lifespan and the
pluses and minuses of living longer.

In a study appearing this week in the journal Science, biologists at
the University of California, Berkeley, compare the genomes of nearly two-thirds of the known species of rockfish that inhabit coastal waters
around the Pacific Ocean and uncover some of the genetic differences
that underlie their widely varying lifespans.

Some rockfish, like the colorful calico rockfish (Sebastes dallii),
live for little more than a decade, while the most long-lived of the
genus Sebastes - - the rougheye rockfish (Sebastes aleutianus), which
can be found from Japan to the Aleutian Islands -- can hang out on the
seabed in cold, deep coastal waters for more than 200 years.

Their wide range of lifespans, not to mention differences in size,
lifestyle and ecological niche, which scientists call their phenotypes,
evolved over a mere 10 million years -- one of the most rapid radiations
among all fishes.

To uncover the genetic determinants of lifespan in rockfish, the
researchers obtained tissue samples -- and occasionally tasting
samples -- from 88 species and sequenced their complete genomes with a state-of-the-art technique known as Pacbio, or SMRT, sequencing.



==========================================================================
They found a variety of genes associated with longer lifespan, though some
of these genes involve adaptions to living at greater depth and growing
larger, both of which are associated with increased lifespan. Among
mammals, for example, elephants live longer than rats.

The findings also highlight the trade-offs of a long lifespan, which
include smaller populations -- something also seen in mammals, with
short-lived rats vastly outnumbering long-lived elephants.

"In this study, we identified both the genetic causes and consequences
of adaptation to extreme lifespan," said senior author Peter Sudmant,
UC Berkeley assistant professor of integrative biology. "It's very
exciting to be able to look at a group of species and see how their
phenotype has been shaped through time and the genetic changes that
drive that phenotype, and simultaneously, how that phenotype then
feeds back and influences the genetic diversity of that population."
Sudmant acknowledges that many of the biological pathways he and his
team found to be associated with lifespan have been identified before in genetic studies of variation within a single animal species, though this
study does implicate several new genes in these pathways. Nevertheless,
the natural variation within this one genus of fish that has radiated throughout the Pacific Ocean uniquely encapsulates most of the many
genetic factors that influence lifespan.

"You could think of rockfish as sort of the perfect storm. in some ways,
both on an individual level -- having individual fish able to live for
a really long time because of size and depth adaptations -- but also
just having all these different species that are showing these different trends," he said. "They're a perfect set of individuals to look at, where
other people just had a single species to look at." The study also has implications for understanding human lifespan. Sudmant and his colleagues
found that longer-lived species had more immune modulating genes --
in particular, a group called butyrophilins -- than shorter-lived species.

Because the immune system is involved in regulating inflammation, and
increased inflammation has been implicated in human aging, the findings
point to genes that could be targets of therapeutics to slow age-related
damage in the body.



========================================================================== "There is an opportunity here to look in nature and see how natural
adaptations have shaped lifespan and to think about how those same sorts
of genes are acting in our own bodies," he said.

Size and habitat explain a lot of lifespan variation in fishes The
researchers looked for DNA variations that were more common in fish with
longer lives and found 137 longevity-associated gene variations.

Not all of these have a direct effect on lifespan, however. The
researchers took care to separate out the genetic variations that
allowed rockfish to adapt to deeper depths and grow to larger size,
since those adaptations themselves have the side-effect of increasing
lifespan. Deeper, cooler waters slow metabolism, for example, which is associated with a longer lifespan in many animals.

"We can explain 60% of the variation in lifespan just by looking at
the size at maturity and the depth at which a fish lives," Sudmant
said. "So, you can predict lifespan with pretty high accuracy just from
these factors. This allowed us to identify the genes that allow them to
do those things." The remainder of the longevity-associated variation primarily involved three types of genes: an enrichment in the number of
genes for repairing DNA; variations in many genes that regulate insulin,
which has long been known to influence lifespan; and an enrichment for
genes that modulate the immune system. More DNA repair genes could help
protect against cancer, while more immune genes could help ward off
infections, as well as cancer.

"Six different members of the insulin signaling pathway are under
selection in these fish," Sudmant said. "If you look at the textbooks,
there's about nine or 10 core members of the pathway, so the majority
of them are under selection in rockfish." Essentially, Sudmant said,
some rockfish species extended their lifespan simply by adapting to live
in deeper, colder waters and increasing their size. The longest-lived
species, however, boosted their lifespan even further by tweaking their
DNA repair, insulin signaling and immune-modulation genes.

From the 88 rockfish genomes, the researchers also were able to infer what
the ancestral rockfish genome looked like and how species evolved from
that common ancestor 10 million years ago. With increased lifespan, they
found, also came decreased population levels. Some of the longest-lived
species survive today in small numbers that rely on very old, but very
fertile, females to replenish the population. These big, old, fat, fecund female fish, or BOFFFF, as they are known in fish conservation circles,
produce the majority of offspring - - sometimes in the millions per year, though with a low survival rate -- that seed the next generation.

"In these rockfish, we can actually watch this evolution happening over
this 10-million-year time period, and we observe that when some species
evolve a short lifespan, their population sizes expand, and when they
evolve a long lifespan, their population sizes contract," he said. "We
can see a signature of that in their genomes, in the genetic variation
that exists in these species.

So, there is a consequence to adapting to long and short life." One
intriguing finding, he said, is that long-lived species have an excess
of certain kinds of DNA mutations -- specifically, the conversion of the nucleotide pair CG (cytosine-guanine) to TG (thymine-guanine) -- known
to accumulate in tumors with aging. Because the oldest females of these long-lived species produce most of the offspring, these unusual genetic alterations are passed along to the rest of the long-lived population.

Sudmant and his lab colleagues are currently involved in similar genome comparisons among bats, primates and other organisms, looking at the
genes correlated with lifespan, aging, stress and other phenotypic
differences. But the rockfish project was something special, he said.

"Often, in genetics, we're derided for doing experiments that are fishing expeditions," he said. "This was both literally and figuratively a fishing expedition." UC Berkeley postdoctoral researchers Sree Rohit Raj Kolora
and Gregory Owens, now at the University of Victoria in British Columbia, Canada, are co-first authors of the paper. Other co-authors are Juan
Manuel Vazquez, Alexander Stubbs, Kamalakar Chatla and professor Doris
Bachtrog of UC Berkeley; Conner Jainese, Katelin Seeto, Merit McCrea
and Milton Love of UC Santa Barbara; Michael Sandel of the University
of West Alabama; Juliana Vianna of the Pontificia Universidad Cato'lica
de Chile; and Katherine Maslenikov and James Orr of the University of Washington. The work was funded by an award from the National Institute
of General Medical Sciences of the National Institutes of Health
(R35GM142916).

Video of rockfish with 200 year lifespan:
https://www.youtube.com/ watch?v=xYQPy5Rmz7g ========================================================================== Story Source: Materials provided by
University_of_California_-_Berkeley. Original written by Robert
Sanders. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Sree Rohit Raj Kolora, Gregory L. Owens, Juan Manuel Vazquez,
Alexander
Stubbs, Kamalakar Chatla, Conner Jainese, Katelin Seeto,
Merit McCrea, Michael W. Sandel, Juliana A. Vianna, Katherine
Maslenikov, Doris Bachtrog, James W. Orr, Milton Love, Peter
H. Sudmant. Origins and evolution of extreme life span in
Pacific Ocean rockfishes. Science, 2021; 374 (6569): 842 DOI:
10.1126/science.abg5332 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/11/211111154221.htm

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