Fernando Villanea
@fervillanea.bsky.social
He/Him. Assistant Professor of Anthropology at CU Boulder. March Mammal Madness Genetics Team. Population genetics of Neanderthals and other people. Latino in STEM 🇨🇷
Each one of my lectures starts with a meme, and rarely do my 18-20yo students get the reference, but today I feel like I have driven that generational wedge even deeper 😅
November 11, 2025 at 4:10 PM
Each one of my lectures starts with a meme, and rarely do my 18-20yo students get the reference, but today I feel like I have driven that generational wedge even deeper 😅
In honor of the theatrical re-release of Jurassic Park tomorrow.
November 4, 2025 at 6:06 PM
In honor of the theatrical re-release of Jurassic Park tomorrow.
I'm re-teaching an R class from four years ago and found out today qplot was deprecated to encourage me to learn ggplot, which like, fair point since I've had four years to improve the class and clearly didn't.
September 10, 2025 at 12:04 AM
I'm re-teaching an R class from four years ago and found out today qplot was deprecated to encourage me to learn ggplot, which like, fair point since I've had four years to improve the class and clearly didn't.
This originally showed up an an excess of heterozygous sites in these Neanderthals, similar to humans who are also heterozygous. We then phased these Neanderthals at this site, and yes, they carry the "Denisovan" variant too. This is intriguing, because Neanderthal genomes are largely homozygous.
August 21, 2025 at 7:36 PM
This originally showed up an an excess of heterozygous sites in these Neanderthals, similar to humans who are also heterozygous. We then phased these Neanderthals at this site, and yes, they carry the "Denisovan" variant too. This is intriguing, because Neanderthal genomes are largely homozygous.
But also, surprise! The Vindija and Chagysrkaya Neanderthals carry this MUC19 variant in heterozygous form. They each carry exactly one variant that looks like the Altai Neanderthal but also one variant that looks like introgressed humans and similar to the single Denisovan genome.
August 21, 2025 at 7:36 PM
But also, surprise! The Vindija and Chagysrkaya Neanderthals carry this MUC19 variant in heterozygous form. They each carry exactly one variant that looks like the Altai Neanderthal but also one variant that looks like introgressed humans and similar to the single Denisovan genome.
We also identified "Denisovan-specific" SNPs that are nonsynonimous, the archaic MUC19 has a few amino acid differences. Moreso, we used these SNPs as identifiers for population abundance of the archaic MUC19. Modern Latino and ancient Indigenous individuals carry the archaic version more frequently
August 21, 2025 at 7:36 PM
We also identified "Denisovan-specific" SNPs that are nonsynonimous, the archaic MUC19 has a few amino acid differences. Moreso, we used these SNPs as identifiers for population abundance of the archaic MUC19. Modern Latino and ancient Indigenous individuals carry the archaic version more frequently
MUC19 has a Variable Number Tandem Repeat functional region, like all mucins, each unit (30bp) is a sugar binding domain. More domains, longer protein skeleton for sugars to bind. The majority of humans carry ~400 units, the outliers are many American individuals who carry up to ~800.
August 21, 2025 at 7:36 PM
MUC19 has a Variable Number Tandem Repeat functional region, like all mucins, each unit (30bp) is a sugar binding domain. More domains, longer protein skeleton for sugars to bind. The majority of humans carry ~400 units, the outliers are many American individuals who carry up to ~800.
American populations present a signature of positive selection around MUC19 and its very long haplotype (very low recombination rate). Once you partition the variants and calculate PBS, that selection is unique to Denisovan and Neanderthal variants carried by some modern humans.
August 21, 2025 at 7:36 PM
American populations present a signature of positive selection around MUC19 and its very long haplotype (very low recombination rate). Once you partition the variants and calculate PBS, that selection is unique to Denisovan and Neanderthal variants carried by some modern humans.
MUC19 in humans is:
1) Archaic, one variant was passed from Denisovans->Neanderthals->humans.
2) Under positive natural selection uniquely in Indigenous and Latino American populations.
3) MUC19 in those populations shows an expansion of the functional protein domain, a VNTR that is twice as long.
1) Archaic, one variant was passed from Denisovans->Neanderthals->humans.
2) Under positive natural selection uniquely in Indigenous and Latino American populations.
3) MUC19 in those populations shows an expansion of the functional protein domain, a VNTR that is twice as long.
August 21, 2025 at 7:36 PM
MUC19 in humans is:
1) Archaic, one variant was passed from Denisovans->Neanderthals->humans.
2) Under positive natural selection uniquely in Indigenous and Latino American populations.
3) MUC19 in those populations shows an expansion of the functional protein domain, a VNTR that is twice as long.
1) Archaic, one variant was passed from Denisovans->Neanderthals->humans.
2) Under positive natural selection uniquely in Indigenous and Latino American populations.
3) MUC19 in those populations shows an expansion of the functional protein domain, a VNTR that is twice as long.
And if you do, you might as well modify a Tinamou, since that's the sister taxa to Moas. A Dire Tinamou would sell pretty well actually.
July 9, 2025 at 10:34 PM
And if you do, you might as well modify a Tinamou, since that's the sister taxa to Moas. A Dire Tinamou would sell pretty well actually.
This is a good time to remember that Moas, Emus, and the other ratites diverged so long ago, they FLEW to different continents, and then lost the ability to fly and became giants independently. You can't just sprinkle a few variants to make one into the other.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
July 9, 2025 at 10:34 PM
This is a good time to remember that Moas, Emus, and the other ratites diverged so long ago, they FLEW to different continents, and then lost the ability to fly and became giants independently. You can't just sprinkle a few variants to make one into the other.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Very excited for a new book! I started Absolution this morning.
June 24, 2025 at 2:35 AM
Very excited for a new book! I started Absolution this morning.
I remember the announcement of Desert Storm on TV, and understood it being serious because of how worried my parents were. This was in Costa Rica, a country with no horse on that race. I guarantee you everyone is every other country is watching right now. Kids today will remember these days forever.
June 23, 2025 at 8:01 PM
I remember the announcement of Desert Storm on TV, and understood it being serious because of how worried my parents were. This was in Costa Rica, a country with no horse on that race. I guarantee you everyone is every other country is watching right now. Kids today will remember these days forever.
For the last assignment of the semester, I ask my Anthropological Genetics students to make a meme out of the class content for extra credit.
Here's some of them:
Here's some of them:
May 9, 2025 at 6:56 PM
For the last assignment of the semester, I ask my Anthropological Genetics students to make a meme out of the class content for extra credit.
Here's some of them:
Here's some of them:
Thank you @sarahtishkoff.bsky.social for giving a wonderful talk at the University of Colorado Museum of Natural History today!
May 8, 2025 at 1:14 AM
Thank you @sarahtishkoff.bsky.social for giving a wonderful talk at the University of Colorado Museum of Natural History today!
The average American has three friends
May 2, 2025 at 1:58 AM
The average American has three friends
But also a lesson for our trainees: never give up!
May 1, 2025 at 2:47 PM
But also a lesson for our trainees: never give up!
But geneticists also have RECEIPTS. We have detailed mutation information and a very well annotated genome. We saw mutation affect function in real time too. We can tell COVID did not start as an optimized killing machine, it's scrambling to do better in this new species it was thrusted into 12/n
April 19, 2025 at 6:11 PM
But geneticists also have RECEIPTS. We have detailed mutation information and a very well annotated genome. We saw mutation affect function in real time too. We can tell COVID did not start as an optimized killing machine, it's scrambling to do better in this new species it was thrusted into 12/n
DISCLAIMER: because we have vaccines and because medical practitioners became much better at understanding and treating the role of cytokine excess in COVID deaths, reduced mortality in newer strains is very difficult to measure.
But look at this phylogeny, evolution is doing SOMETHING 11/n
But look at this phylogeny, evolution is doing SOMETHING 11/n
April 19, 2025 at 6:11 PM
DISCLAIMER: because we have vaccines and because medical practitioners became much better at understanding and treating the role of cytokine excess in COVID deaths, reduced mortality in newer strains is very difficult to measure.
But look at this phylogeny, evolution is doing SOMETHING 11/n
But look at this phylogeny, evolution is doing SOMETHING 11/n
And we see this time and time again, new lineages outcompeting older ones. New lineages with advantages as to how to infect us but at the same time becoming less deadly. THAT WAS OUR PREDICTION!!!! A natural zoonosis is theorized to do this and now we all saw it happen in real time 10/n
April 19, 2025 at 6:11 PM
And we see this time and time again, new lineages outcompeting older ones. New lineages with advantages as to how to infect us but at the same time becoming less deadly. THAT WAS OUR PREDICTION!!!! A natural zoonosis is theorized to do this and now we all saw it happen in real time 10/n
And guess what, this is what we all saw COVID do in real time - we have real time data of all the covid strains competing in the arena of natural selection
It started with one lineage and soon newer lineages like Delta outcompete the original 9/n
nextstrain.org/ncov/gisaid/...
It started with one lineage and soon newer lineages like Delta outcompete the original 9/n
nextstrain.org/ncov/gisaid/...
April 19, 2025 at 6:11 PM
And guess what, this is what we all saw COVID do in real time - we have real time data of all the covid strains competing in the arena of natural selection
It started with one lineage and soon newer lineages like Delta outcompete the original 9/n
nextstrain.org/ncov/gisaid/...
It started with one lineage and soon newer lineages like Delta outcompete the original 9/n
nextstrain.org/ncov/gisaid/...
IF the pathogen manages to not flame out, IF it starts to infect more hosts in the new species, evolution will drive it to become less deadly so it can be more contagious. This is our PREDICTION for a natural zoonosis. Starts more deadly, evolves to become more contagious 8/m
April 19, 2025 at 6:11 PM
IF the pathogen manages to not flame out, IF it starts to infect more hosts in the new species, evolution will drive it to become less deadly so it can be more contagious. This is our PREDICTION for a natural zoonosis. Starts more deadly, evolves to become more contagious 8/m
So what about these assholes? Like Ebola and the Bird Flu?Are these bad pathogens? Those are so dangerous and in the news all the time, why did evolution not drive them to be less deadly? Well, evolution did drive them to be less deadly, in their ORIGINAL HOST ORGANISM 5/n
April 19, 2025 at 6:11 PM
So what about these assholes? Like Ebola and the Bird Flu?Are these bad pathogens? Those are so dangerous and in the news all the time, why did evolution not drive them to be less deadly? Well, evolution did drive them to be less deadly, in their ORIGINAL HOST ORGANISM 5/n