Charikleia Karageorgiou (Clio)
@evobioclio.bsky.social
Postdoc at @UBuffalo | Gokcumen Lab
Evolution, structural variants and population genetics.
PhD from @uab.cat | Inversion polymorphism.
https://biolevol.github.io/
Evolution, structural variants and population genetics.
PhD from @uab.cat | Inversion polymorphism.
https://biolevol.github.io/
Starting in 30 minutes at Carrer de Perill 44! If you’re in Barcelona for #ESEB, join us for Breaking Bread, our outreach event on how mutation, recombination and selection shape the amylase locus and human evolution. Come curious (and hungry, there’s bread!)
August 16, 2025 at 4:32 PM
Starting in 30 minutes at Carrer de Perill 44! If you’re in Barcelona for #ESEB, join us for Breaking Bread, our outreach event on how mutation, recombination and selection shape the amylase locus and human evolution. Come curious (and hungry, there’s bread!)
Regulatory motifs alone don’t explain tissue specificity. FOXC1 sites appear in most paralogs. Patterns likely reflect combinatorial motif turnover plus cis-regulatory context (promoters/enhancers), chromatin accessibility and locus architecture altered by duplications.
August 15, 2025 at 11:53 AM
Regulatory motifs alone don’t explain tissue specificity. FOXC1 sites appear in most paralogs. Patterns likely reflect combinatorial motif turnover plus cis-regulatory context (promoters/enhancers), chromatin accessibility and locus architecture altered by duplications.
Ancestral AMY1′ was expressed in both pancreas and salivary glands. In great apes, duplication led to AMY1 (salivary) and AMY2A (pancreatic). In macaques and baboons, AMY1′ still shows dual expression, with a tendency toward higher salivary expression.
August 15, 2025 at 11:53 AM
Ancestral AMY1′ was expressed in both pancreas and salivary glands. In great apes, duplication led to AMY1 (salivary) and AMY2A (pancreatic). In macaques and baboons, AMY1′ still shows dual expression, with a tendency toward higher salivary expression.
In baboons, the novel AMYp2 gene shows strong positive selection, while the ancestral AMY2B carries a premature stop codon, hinting at functional compensation. Multiple paralogs contribute to salivary amylase in Old World monkeys.
August 15, 2025 at 11:53 AM
In baboons, the novel AMYp2 gene shows strong positive selection, while the ancestral AMY2B carries a premature stop codon, hinting at functional compensation. Multiple paralogs contribute to salivary amylase in Old World monkeys.
LTR retrotransposons are enriched at the amylase locus and correlate with copy number gains. Other TE types are depleted. LTRs may prime the locus for structural instability and recurrent duplications.
August 15, 2025 at 11:53 AM
LTR retrotransposons are enriched at the amylase locus and correlate with copy number gains. Other TE types are depleted. LTRs may prime the locus for structural instability and recurrent duplications.
In rhesus macaques and olive baboons, NAHR produced lineage‐specific amylase duplicates (AMYm, AMYp1, AMYp2) within the last ~5 Myr, showing structural innovation has occurred multiple times in this locus.
August 15, 2025 at 11:53 AM
In rhesus macaques and olive baboons, NAHR produced lineage‐specific amylase duplicates (AMYm, AMYp1, AMYp2) within the last ~5 Myr, showing structural innovation has occurred multiple times in this locus.
From a single ancestral AMY2B gene, a γ‐actin insertion and duplication in Catarrhini created AMY1′. In great apes, AMY1′ acquired an ERV insertion and underwent further duplications, giving rise to AMY1 (salivary) and AMY2A (pancreatic) specialization.
August 15, 2025 at 11:53 AM
From a single ancestral AMY2B gene, a γ‐actin insertion and duplication in Catarrhini created AMY1′. In great apes, AMY1′ acquired an ERV insertion and underwent further duplications, giving rise to AMY1 (salivary) and AMY2A (pancreatic) specialization.
We find repeated gains and losses of amylase copies, arising independently, revealing it as a structural hotspot in primate genomes.
August 15, 2025 at 11:53 AM
We find repeated gains and losses of amylase copies, arising independently, revealing it as a structural hotspot in primate genomes.
June 25, 2025 at 12:07 AM
Come say hi at the Evolutionary Theory I session tomorrow at 10:15am in Athena AB!
I’ll be presenting our latest findings on the structural, mutational and functional dynamics of the amylase locus across primates.
#Evol2025
I’ll be presenting our latest findings on the structural, mutational and functional dynamics of the amylase locus across primates.
#Evol2025
June 21, 2025 at 10:27 AM
Come say hi at the Evolutionary Theory I session tomorrow at 10:15am in Athena AB!
I’ll be presenting our latest findings on the structural, mutational and functional dynamics of the amylase locus across primates.
#Evol2025
I’ll be presenting our latest findings on the structural, mutational and functional dynamics of the amylase locus across primates.
#Evol2025
You can still submit an abstract for the 2025 Ecological & Evolutionary Genomics GRS to be considered for a poster. If you’ve been accepted for a talk or poster, don’t forget to register via the GRC website. We look forward to seeing many of you in Lucca this summer.
@jcbnunez.bsky.social
@jcbnunez.bsky.social
May 8, 2025 at 1:50 PM
You can still submit an abstract for the 2025 Ecological & Evolutionary Genomics GRS to be considered for a poster. If you’ve been accepted for a talk or poster, don’t forget to register via the GRC website. We look forward to seeing many of you in Lucca this summer.
@jcbnunez.bsky.social
@jcbnunez.bsky.social
Join us at the Gordon Research Seminar on Ecological and Evolutionary Genomics in Tuscany, co-chaired by
@jcbnunez.bsky.social and me. If you’d like to present your research and be considered for a talk, make sure to submit your application before April 6th! www.grc.org/ecological-a...
@jcbnunez.bsky.social and me. If you’d like to present your research and be considered for a talk, make sure to submit your application before April 6th! www.grc.org/ecological-a...
February 11, 2025 at 2:12 AM
Join us at the Gordon Research Seminar on Ecological and Evolutionary Genomics in Tuscany, co-chaired by
@jcbnunez.bsky.social and me. If you’d like to present your research and be considered for a talk, make sure to submit your application before April 6th! www.grc.org/ecological-a...
@jcbnunez.bsky.social and me. If you’d like to present your research and be considered for a talk, make sure to submit your application before April 6th! www.grc.org/ecological-a...
Join us at the Gordon Research Seminar on Ecological and Evolutionary Genomics in Tuscany, co-chaired by @jcbnunez.bsky.social and me. If you’d like to present your research and be considered for a talk, make sure to submit your application before April 6th! www.grc.org/ecological-a...
February 4, 2025 at 12:06 AM
Join us at the Gordon Research Seminar on Ecological and Evolutionary Genomics in Tuscany, co-chaired by @jcbnunez.bsky.social and me. If you’d like to present your research and be considered for a talk, make sure to submit your application before April 6th! www.grc.org/ecological-a...
Bonus Post: For those interested in mechanisms, check out our mutational network, where we connect all distinct structural haplotypes, tracing the most parsimonious scenarios and inferring duplications, deletions, and inversions.
November 22, 2024 at 2:11 PM
Bonus Post: For those interested in mechanisms, check out our mutational network, where we connect all distinct structural haplotypes, tracing the most parsimonious scenarios and inferring duplications, deletions, and inversions.
Thank you for following along! A huge thanks to everyone who made this project possible, with special thanks to Omer! The polished version of the paper is now available in Science: www.science.org/doi/epdf/10....
November 22, 2024 at 2:07 PM
Thank you for following along! A huge thanks to everyone who made this project possible, with special thanks to Omer! The polished version of the paper is now available in Science: www.science.org/doi/epdf/10....
The significant increase in AMY1 copy numbers in European farmers over the last 4,000 years may reflect an adaptive response to changes in diet, particularly the increased consumption of starch. However, the pre-existing variation laid the groundwork for this shift.
November 22, 2024 at 2:07 PM
The significant increase in AMY1 copy numbers in European farmers over the last 4,000 years may reflect an adaptive response to changes in diet, particularly the increased consumption of starch. However, the pre-existing variation laid the groundwork for this shift.
Taken together: Our findings suggest that the initial AMY1 duplication event occurred far before the rise of agriculture, possibly even before the human-Neanderthal split around 800KYA. This highlights how structural variation at the amylase locus has deep evolutionary roots.
November 22, 2024 at 2:07 PM
Taken together: Our findings suggest that the initial AMY1 duplication event occurred far before the rise of agriculture, possibly even before the human-Neanderthal split around 800KYA. This highlights how structural variation at the amylase locus has deep evolutionary roots.
We also examined the evolution of the AMY2 gene. Although AMY2 shows less variation in copy number compared to AMY1, our findings suggest that its duplications occur primarily through non-recurrent mechanisms, specifically microhomology-mediated break-induced replication (MMBIR).
November 22, 2024 at 2:07 PM
We also examined the evolution of the AMY2 gene. Although AMY2 shows less variation in copy number compared to AMY1, our findings suggest that its duplications occur primarily through non-recurrent mechanisms, specifically microhomology-mediated break-induced replication (MMBIR).
Duplications at the AMY locus are primarily driven by non-allelic homologous recombination (NAHR). This mechanism has been key to generating the structural and copy number variation seen across different human populations today.
November 22, 2024 at 2:07 PM
Duplications at the AMY locus are primarily driven by non-allelic homologous recombination (NAHR). This mechanism has been key to generating the structural and copy number variation seen across different human populations today.
The oldest anatomically modern human genome analyzed, Ust'-Ishim from Siberia (~45KYA), had six AMY1 copies per diploid cell. Similarly, the oldest modern human from Europe, Peştera Muierii (~34KYA), had eight AMY1 copies.
November 22, 2024 at 2:07 PM
The oldest anatomically modern human genome analyzed, Ust'-Ishim from Siberia (~45KYA), had six AMY1 copies per diploid cell. Similarly, the oldest modern human from Europe, Peştera Muierii (~34KYA), had eight AMY1 copies.
Over the past 4,000 years, an increase in AMY1 copy number is observed in European populations. This increase coincides with the spread of agriculture, possibly reflecting changes in diet during this period, but the exact pressures driving this increase remain uncertain.
November 22, 2024 at 2:07 PM
Over the past 4,000 years, an increase in AMY1 copy number is observed in European populations. This increase coincides with the spread of agriculture, possibly reflecting changes in diet during this period, but the exact pressures driving this increase remain uncertain.
Our findings suggest that archaic hominins had increased AMY1 copy numbers, potentially dating the duplication as far back as 800KYA. However, several possible scenarios could explain these findings, and more research is needed to understand the origins of these duplications.
November 22, 2024 at 2:07 PM
Our findings suggest that archaic hominins had increased AMY1 copy numbers, potentially dating the duplication as far back as 800KYA. However, several possible scenarios could explain these findings, and more research is needed to understand the origins of these duplications.
Strong negative selection limits functional variation among amylase gene copies. Despite the extensive variation in copy number, the coding sequences of all AMY genes remain highly conserved due to strong negative selection operating in the locus.
November 22, 2024 at 2:07 PM
Strong negative selection limits functional variation among amylase gene copies. Despite the extensive variation in copy number, the coding sequences of all AMY genes remain highly conserved due to strong negative selection operating in the locus.
The amylase locus exhibits a high mutation rate, far exceeding most other regions of the genome. This elevated rate has likely contributed to the extensive copy number variation seen in AMY1, making it a key locus for studying human SVs.
November 22, 2024 at 2:07 PM
The amylase locus exhibits a high mutation rate, far exceeding most other regions of the genome. This elevated rate has likely contributed to the extensive copy number variation seen in AMY1, making it a key locus for studying human SVs.
The AMY1 gene shows wide diversity across human populations, with no clear geographic specificity. We observe the three-copy haplotypes of the AMY1 gene across almost all populations in Africa.
November 22, 2024 at 2:07 PM
The AMY1 gene shows wide diversity across human populations, with no clear geographic specificity. We observe the three-copy haplotypes of the AMY1 gene across almost all populations in Africa.