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Daniel Ortiz-Barrientos

@dortizba.bsky.social

630 followers 760 following 41 posts

Evolutionary Geneticist at UQ, Australia. Speciation, adaptation, future resilience. #senecio

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Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

We’ve just published a paper on Senecio showing that ecological speciation and mutation-order speciation can act together rather than as an either/or. Congratulations, Maddie James and MC Melo!

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Reposted by Daniel Ortiz-Barrientos

Megan Frayer @hybridzones.bsky.social · Aug 9

This collaboration was so much fun!! I’m excited to see it online! www.cell.com/trends/genet...

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Reposted by Daniel Ortiz-Barrientos

The American Journal of Human Genetics @ajhgnews.bsky.social · Aug 13

📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑‍🤝‍🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social

Estimation of demography and mutation rates from one million haploid genomes

Samples of millions of genomes provide substantial information about recent demography and mutation, but standard population-genetic methods make assumptions not met in these data. We introduce DR EVI...

www.cell.com

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Reposted by Daniel Ortiz-Barrientos

Patrick McKenzie @patrickmckenzie.bsky.social · 27d

alignments are mosaics of autocorrelated genealogies... nearby bases share ancestry until recombination alters the local tree. We derived the distributions of waiting distances for tree-change and topology-change events, extending prior single-population results to arbitrary species tree models.

figure illustrating the concept of an ARG, including recombination events that create no-change, vs. tree-change, vs. topology-change

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Reposted by Daniel Ortiz-Barrientos

Camille Roux @crouxevo.bsky.social · 26d

Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants

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Reposted by Daniel Ortiz-Barrientos

Jenn Coughlan @jenncoughlan.bsky.social · 13d

I'm so proud of this work!!! It was an incredible amount of effort that started when I was trapped in a greenhouse during the pandemic and is only now seeing the light of day. Kudos to Megan, Hagar, & Pia!

We'd love to hear your thoughts!
www.biorxiv.org/content/10.1...

Introgression and Parental Conflict Underlie Repeated Occurrences of Postzygotic Isolation

Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet, it frequently evolves rapidly, in line with non-neutral evolution. A major driver of intrin...

www.biorxiv.org

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

Read the full open-access paper to learn more. A huge thank you to Charles for his brilliant work, and to
Maddie James and Jan Engelstädter for making a great team! We also thank the reviewers for their valuable feedback. #Genomics #Bioinformatics #Imputation #Genetics

Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

The impact: Retriever provides an accessible, cost-effective, and accurate solution for any researcher, especially those working on ecologically and evolutionarily important non-model species. It broadens the scope of what's possible in genomics.

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

The results are excellent. When the Retriever-constructed panel is used with standard imputation software (Beagle), it consistently achieves >95% accuracy. We tested this across a diverse range of organisms, including plants, animals, and fungi.

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

How it works: Retriever uses a sliding window approach across the genome. In each window, it identifies and retrieves segments from samples that have complete data. By stitching these complete segments together, it assembles a powerful, localized reference panel.

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

Our solution: We created Retriever to build a "chimeric" reference panel directly from the target samples. It cleverly leverages the data you already have, eliminating the need for any external resources.

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

The bottleneck: Standard imputation methods rely on a large, high-quality "reference panel" of completely sequenced genomes. Creating these panels is costly and time-consuming, making them unavailable for the vast majority of species (i.e., non-model organisms).

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

The problem: Genomic datasets, especially from next-gen sequencing, are often full of holes (missing genotypes). We can "impute" or infer this missing information, which is crucial for downstream analyses like GWAS. This process dramatically increases statistical power.

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Daniel Ortiz-Barrientos @dortizba.bsky.social · 6d

Excited to share our new paper in
@GeneticsGSA
! We developed "Retriever," a novel method that enables high-quality genotype imputation in non-model organisms. 🧬 Congratulations to Charles on his first PhD paper!

Paper: doi.org/10.1093/gene...

A thread 🧵👇

Chimeric Reference Panels for Genomic Imputation

Abstract. Despite transformative advances in genomic technologies, missing data remains a fundamental constraint that limits the full potential of genomic

doi.org

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Reposted by Daniel Ortiz-Barrientos

Matthew Cobb @matthewcobb.bsky.social · Sep 8

News in the history of molecular biology. The Science History Institute in Philadelphia has acquired a huge archive of correspondence and other scientific material from the pioneers of molecular biology (Franklin, Klug, Perutz, Delbrück etc, with items from Crick and Watson, too). 1/n

History of Molecular Biology Collection

This unparalleled collection includes Rosalind Franklin's historic 'Photo 51,' which revealed the double-helix structure of DNA.

www.sciencehistory.org

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Reposted by Daniel Ortiz-Barrientos

David Pollock @genomesevolve.bsky.social · Sep 3

onlinelibrary.wiley.com/doi/epdf/10....

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Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Teenagers who received fecal microbiota transplants (FMT) didn't lose more weight than controls, but showed better body composition, reduced inflammation, and improved metabolic health markers. Donor gut bacteria remained detectable 4 years later. Small study: needs replication before clinical use.

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Reposted by Daniel Ortiz-Barrientos

Josh Luke Davis 🏳️‍🌈 @joshlukedavis.com · Sep 3

woah this is genuinely, utterly WILD

Ant queens of one species produce males of another species, so she can then mate with them and produce hybrid workers!

This is so gloriously weird I can't quite compute it 🤯🧪🐜
www.nature.com/articles/d41...

‘Almost unimaginable’: these ants are different species but share a mother

Ant queens of one species clone ants of another to create hybrid workers that do their bidding.

www.nature.com

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Reposted by Daniel Ortiz-Barrientos

Merriam-Webster @merriam-webster.com · Sep 3

enshittification | noun | when a digital platform is made worse for users, in order to increase profits

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Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Paper: open access in Molecular Ecology (onlinelibrary.wiley.com/doi/epdf/10....

Ecological and Mutation‐Order Speciation in Senecio

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onlinelibrary.wiley.com

Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Methods in brief: controlled crosses (F1 seed set, germination), reciprocal transplants, phylogeny anchored by prior genomics, and a transparent model linking environment, genetic architecture, and DMI probability.

Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Take-home: convergent form does not guarantee genetic interchangeability. In heterogeneous landscapes, parallel solutions can be reproductively incompatible when combined.

Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Interpretation: divergent selection drives Dune–Headland barriers; heterogeneous Headlands plus polygenic adaptation yield alternative genetic solutions that sometimes clash.

Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Predictions: as φ decreases (environments diverge), the probability of incompatibilities rises; and as the number of interacting loci grows, incompatibilities accumulate faster. This provides one continuum linking ecological and mutation-order speciation.

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Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Theory: we extend Unckless–Orr with (i) an environmental symmetry parameter φ (how similarly selection acts across sites) and (ii) polygenic architectures with interacting loci.

Daniel Ortiz-Barrientos @dortizba.bsky.social · Sep 3

Field transplant reanalysis: in Dunes, non-locals perform much like locals (aligned selection). In Headlands, locals outperform non-locals (fine-scale heterogeneity). Together, these patterns explain compatibility in Dunes and idiosyncratic barriers among Headlands.