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Raphaël Bouchard

@raphaelbouchard.bsky.social
167 followers 383 following 11 posts

NSERC Postdoctoral Fellow | @ualberta.ca (Venney Lab). Investigating epigenomic & genomic mechanisms of resistance to whirling disease in at-risk Rocky Mountain Salmonids. 🐟🧬

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Reposted by Raphaël Bouchard
Dr. Paige Duffin @paigeduffin.bsky.social · 14/09/2026
I’m excited to share the 🌷🪻 "meadow plot" 🌻🌷, a new pop genomics visualization tool I created to ID putative selective sweeps across the genome using windowed π & FST estimates from pixy. User-friendly tutorial here: paigeduffin.github.io/meadow_plot_... Please help spread the word by sharing! 🧬
paigeduffin.github.io
Meadow Plot Tutorial
A step-by-step tutorial for creating meadow plots and candidate peak summaries from pixy output.
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Reposted by Raphaël Bouchard
Darrin T. Schultz @dts.bsky.social · 19/08/2026
Our new paper in Science Advances asks how animals' genomes have changed since their origin from a common ancestor over 600 million years ago, and what patterns in their DNA have arisen in the churn of speciation and extinction. www.science.org/doi/10.1126/...
Five-panel diagram explaining fusion-with-mixing in chromosome evolution. Red and blue represent two different ancestral chromosomes throughout.

A, Fusion-with-mixing: a red chromosome and a blue chromosome fuse into one half-red, half-blue bar. Down the page, successive rows show inversions, drawn as X-shaped crossings between rows, progressively interleaving the two colors until the bottom bar is finely striped. A widening gray wedge labeled Entropy runs alongside an arrow marked Time plus evolution, pointing down.

B, Independent regulation: two separate chromosomes, one red and one blue. In each, a regulatory element, drawn as an oval, acts by an arrow on a gene within its own chromosome only.

C, FWM and novel regulation: on a fused, mixed chromosome, a red gene and a blue gene now sit next to each other across an inversion breakpoint. Red and blue arrows show regulatory elements reaching across it to act on the other chromosome's gene.

D, Regulatory entanglement: an extensively mixed chromosome, finely striped. Below it, a row of alternating red and blue genes is linked by a dense web of crossing curved arrows, so many overlapping regulatory connections that unmixing the chromosome would break them.

E, Emergence of entangled loci: a five-species phylogeny. A red and a blue chromosome fuse at an ancestral node, and helical icons on later branches mark continued mixing. Colored boxes mark four new red-blue regulatory interactions arising after inversions. Species A keeps its two chromosomes separate. In species B through E, the two earliest interactions, cyan boxes 1 and 2, are present in every descendant lineage, while later ones, yellow 3 and magenta 4, appear in fewer.
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Reposted by Raphaël Bouchard
David Lowry @davidlowry.bsky.social · 19/08/2026
A new Primer on QTL mapping. academic.oup.com/genetics/adv...
academic.oup.com
QTL mapping
Abstract. Most biologically relevant traits are quantitative, controlled by multiple genes, and can be influenced by the environment. The multiple genes, c
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Reposted by Raphaël Bouchard
Laura Bertola @lauradbertola.bsky.social · 18/08/2026
Putatively Adaptive and Genome-Wide Genetic Variation Often Rank Populations as Similarly Distinctive onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Putatively Adaptive and Genome‐Wide Genetic Variation Often Rank Populations as Similarly Distinctive
Identifying which populations within species to prioritize to maintain genetic diversity is challenging. Due to its direct connection to current patterns of adaptation and presumed connection to adap....
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Reposted by Raphaël Bouchard
ProfColinBean @profcolinbean.bsky.social · 02/08/2026
Phylogeny of Cutthroat Trout (Oncorhynchus clarkii) Based on Full Mitochondrial Genomes With Comments on Species Delimitation and Taxonomy. Evolutionary Applications 19, no. 7: e70304. doi.org/10.1111/eva.....
doi.org
Phylogeny of Cutthroat Trout (<fi>Oncorhynchus clarkii</fi>) Based on Full Mitochondrial Genomes With Comments on Species Delimitation and Taxonomy
Despite the important role that species concepts and taxonomy play in understanding the evolution of species, taxonomists have struggled to describe the relationship between many organisms. Here, usi...
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Reposted by Raphaël Bouchard
ProfColinBean @profcolinbean.bsky.social · 01/08/2026
Biogeography of Atlantic Salmon in the Cape Breton Highlands, Canada. Fisheries Management and Ecology 1–13. doi.org/10.1111/fme.....
doi.org
Biogeography of Atlantic Salmon in the Cape Breton Highlands, Canada
Atlantic Salmon (Salmo salar) populations have experienced significant declines in recent decades. In Canada, conservation efforts are divided into 16 designatable units (DUs) to address unique regio...
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Reposted by Raphaël Bouchard
Matthew Hahn @3rdreviewer.bsky.social · 31/07/2026
Very cool pair of papers demonstrating little link between amount of additive genetic variation and amount of nucleotide variation within species: journals.plos.org/plosbiology/... www.pnas.org/doi/10.1073/...
journals.plos.org
Levels of additive genetic variation vary substantially between species
Adaptive potential determines how populations respond to environmental change. This study compiles evolvability estimates from over 170 multicellular species, revealing substantial variation across th...
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Reposted by Raphaël Bouchard
Marty Kardos @martykardos.bsky.social · 20/07/2026
This looks super cool: www.cell.com/current-biol...
cell.com
Florida scrub-jay genomes across space and time reveal impacts of population decline and reduced gene flow
By analyzing genomes from 241 Florida scrub-jays across five populations and two time points, Nguyen et al. reveal substantial losses of genetic diversity and increased inbreeding following population...
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Reposted by Raphaël Bouchard
Proceedings of the National Academy of Sciences @pnas.org · 08/07/2026
One of the most-discussed PNAS Nexus articles on Reddit last month was “Follow the money: A startup-based measure of AI exposure across occupations, industries, and regions.” Read now: ow.ly/jsQR50Zl7oP Learn more about submitting to PNAS Nexus: ow.ly/vFgz50Zl7nz
Occupation-level AISE versus AIOE scatter plot. Each dot represents a SOC occupation and is color-coded according to corresponding education and training level as described by O*NET job zones. The left column of points not available shows occupations for which no AIOE value is provided. Both indicators are normalized to range from 0 to 1, where lower values indicate lower levels of AI exposure.
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Reposted by Raphaël Bouchard
Pat Thomson @patthomson.bsky.social · 07/07/2026
I’ve got a bit tired of hearing that nobody at all will read your thesis. patthomson.net/2026/07/07/p...
patthomson.net
people do read your thesis
That tweet is back. You know the one. A PhD thesis, it says, is the only book in the world read cover to cover by exactly three people: the author, the proofreader, and the examiner. The screenshot…
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Reposted by Raphaël Bouchard
Luís M. Silva @luismsilva.bsky.social · 06/07/2026
1/🧵 With this paper finally published, I want to talk about the worst peer review experience of my career as a non-native English speaker, early-career researcher, and solo author, and why I think it matters. #AcademicSky #AcademicPublishing #EvoSky
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ProfColinBean @profcolinbean.bsky.social · 05/07/2026
Do Habitat Restoration Efforts and the Associated Releases of Hatchery-Reared Fish Affect the Genetic Diversity and Integrity of Native Brown Trout Populations?. Fisheries Management and Ecology1–14. doi.org/10.1111/fme.....
doi.org
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Laura Bertola @lauradbertola.bsky.social · 02/07/2026
Allele Frequency Spectra as a General Tool for Modeling Genetic Diversity link.springer.com/article/10.1...
link.springer.com
Allele Frequency Spectra as a General Tool for Modeling Genetic Diversity - Acta Biotheoretica
In this paper we study genetic variation at a highly polymorphic locus of a monoecious or dioecious population whose census and effective sizes differ and possibly vary independently over time. More s...
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Reposted by Raphaël Bouchard
Evolution Letters @evolletters.bsky.social · 29/06/2026
Comparing reproductive isolation across species has been harder than it should be. The new Reproductive Isolation Ontology (RIO) provides a common framework to standardize RI estimates across the tree of life. academic.oup.com/evlett/advan...
academic.oup.com
A standardised framework for classifying estimates of reproductive isolation
Abstract. Understanding reproductive isolation (RI) between lineages is a central goal of speciation research. While the strength of RI has been estimated
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Reposted by Raphaël Bouchard
Alan Rogers @alanrogers.bsky.social · 22/06/2026
PSMC estimates of Ne now reach back not merely 2 My but more like 8. Estimates from humans, chimps, and bonobos share a peak between 3 and 6 Mya, which may reflect a complex speciation event separating hominins and panins. mcb.peercommunityin.org/articles/rec...
mcb.peercommunityin.org
Genetic Estimates of Population History Reach Even Farther into ...
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ProfColinBean @profcolinbean.bsky.social · 20/06/2026
Atlantic Salmon post-smolt migration from Canadian rivers to the Labrador Sea: routes, timing, and influence of sea surface temperature. Canadian Journal of Fisheries and Aquatic Sciences. 83: 1-31. doi.org/10.1139/cjfa...
doi.org
Atlantic Salmon post-smolt migration from Canadian rivers to the Labrador Sea: routes, timing, and influence of sea surface temperature
Atlantic Salmon (Salmo salar) populations are at historic lows, primarily due to poor marine survival, and knowledge gaps regarding their migration limit our ability to identify population-specific st...
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Raphaël Bouchard @raphaelbouchard.bsky.social · 18/06/2026
Thesis defence today. Wish me luck! Or don’t, depending on how superstitious you are 🤪
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Marty Kardos @martykardos.bsky.social · 16/06/2026
Genetic rescue increases long-term fitness despite elevating putative genetic load in a male-dimorphic mite www-nature-com.weblib.lib.umt.edu:2443/articles/s41...
www-nature-com.weblib.lib.umt.edu
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
🧵 New paper! We’re excited to release OPTICS: software that immediately predicts color sensitivity from any opsin protein sequence. In other words: give OPTICS any opsin sequence, and it predicts the wavelength of light the pigment is most sensitive to 🌈👁️ academic.oup.com/mbe/advance-...
academic.oup.com
Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map
Abstract. Predicting phenotypes from genetic variation is a central challenge in biology. Here, machine learning (ML) offers great promise, but its use is
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Reposted by Raphaël Bouchard
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 15/06/2026
People. @ksamuk.bsky.social and others have made this argument before. There’s good software to do this right. Here’s the argument again: Invariant sites matter! They’re not in your standard vcf and many programs pretend they are anyway. academic.oup.com/gbe/article/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
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Reposted by Raphaël Bouchard
Amanda Ackiss @fin-gen.bsky.social · 15/06/2026
New preprint! We built a GT-seq panel to help us distinguish the ciscoes of the Great Lakes. Its flexibility has blown us away, and many exciting papers are coming soon from its use with historic and contemporary samples. 🐟🧬 @wes-larsonak.bsky.social @fishgenomes.bsky.social #ciscoinferno🔥
doi.org
A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels
A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic va...
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Reposted by Raphaël Bouchard
David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 14/06/2026
Comparison of metrics for identifying Key Biodiversity Areas doi.org/10.1016/j.bi...
doi.org
Comparison of metrics for identifying Key Biodiversity Areas
Achieving global biodiversity targets requires reliable identification of Key Biodiversity Areas (KBAs). The KBA Standard defines six metrics to ident…
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Reposted by Raphaël Bouchard
David Tian @david-tian.bsky.social · 11/06/2026
New preprint from the last portion of my PhD! Despite low masked load, we found evidence for strong inbreeding depression in Devils Hole pupfish. The reason? A recessive lethal haplotype that causes a heart defect among developing embryos. www.biorxiv.org/content/10.6...
biorxiv.org
Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (Cyprinodon diabolis)
As anthropogenic habitat fragmentation and population decline accelerate globally, growing numbers of species face compounding demographic and genetic threats to long-term survival. Many populations a...
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ProfColinBean @profcolinbean.bsky.social · 12/06/2026
eRNA Reveals Real-Time Signals of Freshwater Fish Population Biomass and Total Abundance. Molecular Ecology35, no. 11: e70419. doi.org/10.1111/mec.....
doi.org
eRNA Reveals Real‐Time Signals of Freshwater Fish Population Biomass and Total Abundance
Biomass and abundance data are critical for ecosystem monitoring and management of fish populations, yet their acquisition represents a growing challenge as anthropogenic pressures intensify the need....
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Rishi De-Kayne @rishidekayne.bsky.social · 12/06/2026
🚨 We're hiring computational evolutionary biologists! 🚨 Boosting this - industry evolutionary biology jobs don't come along often, so if you're excited to apply your computational evolutionary biology skills to cutting-edge problems, let's talk! 🧪🧬💻
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John Stinchcombe @johnstinchcombe.bsky.social · 11/06/2026
How do you turn a purple flower white? Another from lab, led by @damianmicroeco.bsky.social and Emily Glasgow, with big contributions from Martin Henry, Margaret Li, and Amanda Peake. Mendelian Polymorphisms for the Win! #evolbio #plantscience
White-flowered Ipomoea hederacea, lacking anthocyanins in the flowers and throughout the plant
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Hanna Kokko @kokkonut.bsky.social · 11/06/2026
Polymorphisms are fun to study, here is a butterfly one. Negative freq.dependence works to maintain things but where does it come from? Temporal variation works but not always! @koraklein.bsky.social and @chriswheat.bsky.social looked into this in detail. royalsocietypublishing.org/rstb/article...
royalsocietypublishing.org
Emergence time difference can create negative frequency dependence and maintain a colour polymorphism in Colias butterflies
Abstract. Many species of Colias butterflies show a female-limited colour polymorphism where the dominant Alba allele leads to white wings, faster developm
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Reposted by Raphaël Bouchard
Ichiro Matsuzaki @ichirolake.bsky.social · 08/06/2026
Input from new study Jeffrey R. Baldock et al. 2026. Riverscape heterogeneity shapes population diversity for a migratory fish. Ecological Applications esajournals.onlinelibrary.wiley.com/doi/10.1002/...
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Nature Portfolio @natureportfolio.nature.com · 11/06/2026
🧪
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Laura Bertola @lauradbertola.bsky.social · 11/06/2026
Genetic Estimates of Relatedness: Established Practices and New Opportunities Through Low Coverage Whole-Genome Sequencing onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Genetic Estimates of Relatedness: Established Practices and New Opportunities Through Low Coverage Whole‐Genome Sequencing
Identifying close relatives in wild animal populations is fundamental across many research fields. Genetic estimates of relatedness have expanded rapidly in recent decades, drawing on a range of gene....
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UBC Oceans @ubcoceans.bsky.social · 10/06/2026
RESEARCH: A Bayesian approach to include Indigenous Knowledge and satellite telemetry data in habitat selection functions . 1st author: @rowennagryba.bsky.social Last author: Dr. @marieaugermethe.bsky.social #OPENACESS besjournals.onlinelibrary.wiley.com/doi/10.1111/...
besjournals.onlinelibrary.wiley.com
A Bayesian approach to include Indigenous Knowledge and satellite telemetry data in habitat selection functions
Our work points to the importance of both Western science and IK data sources in models used for conservation and management decisions. We show how the models that include the IK result in more infor...
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Marcela Uliano-Silva @marcelauliano.bsky.social · 10/06/2026
High quality genomes for sloths and anteaters and great mammalian biology findings alert! 🦥🧬 @sangerinstitute.bsky.social @ebpgenome.bsky.social @vertebrategenomes.bsky.social link.springer.com/article/10.1...
link.springer.com
Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution - BMC Biology
Background Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialized mammalian clades, yet the genomic basis of their adaptat...
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Molly Przeworski @mollyprz.bsky.social · 09/06/2026
Now published: journals.plos.org/plosbiology/...
journals.plos.org
What sets the mutation rate of a cell type in an animal species?
Mutation rates per generation are strikingly similar across germlines of animals and across at least one somatic cell type, suggesting a key role for natural selection in shaping mutation rates. This ...
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Claus Wilke @clauswilke.com · 08/06/2026
New paper about zero-shot predictions of mutational effects. There's a lot of misunderstanding about what such predictions can and cannot do. In brief, they're good at identifying deleterious mutations but bad at predicting fitness improvements. 1/ www.biorxiv.org/content/10.6...
biorxiv.org
Overestimating zero-shot fitness prediction: Broad benchmarks mask local failures and practical limitations
Deep learning models have emerged as promising tools for navigating mutational landscapes in protein engineering. These models can be used to predict mutation fitness without the need for task-specifi...
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Genome Biology and Evolution @genomebiolevol.bsky.social · 08/06/2026
Brault et al. propose guidelines for standardized π estimation, systematic reporting of summary statistics, and the adoption of richer metadata to ensure that population genomic data remain comparable and reusable across a wide range of systems. 🔗 doi.org/10.1093/gbe/... #genome #evolution
GBE | A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
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Laura Bertola @lauradbertola.bsky.social · 06/06/2026
Halting genetic diversity loss, from local to international action and policy www.nature.com/articles/s44...
nature.com
Halting genetic diversity loss, from local to international action and policy - Nature Reviews Biodiversity
The loss of genetic diversity is a major threat to population resilience, posing a challenge for conservation efforts. This Review highlights how the integration of large-scale biodiversity monitoring...
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Reposted by Raphaël Bouchard
Gernot Segelbacher 🪶 🧬 @gsegelbacher.bsky.social · 03/06/2026
Genetic Diversity is important! And we need to monitor it to stop further loss. This should be done at local and international scale in policy and management. If you want to read more - read this review, led by the amazing Australian dream team: #consgen 🦤 www.nature.com/articles/s44...
nature.com
Halting genetic diversity loss, from local to international action and policy - Nature Reviews Biodiversity
The loss of genetic diversity is a major threat to population resilience, posing a challenge for conservation efforts. This Review highlights how the integration of large-scale biodiversity monitoring...
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Joanna Masel @joannamasel.bsky.social · 03/06/2026
Our new paper doi.org/10.1098/rspb... on long-term genetic threats to small populations finds that "mutational meltdown" (bad mutations fixing) is less of a problem than "mutational drought" (too few good new mutations) @wmawass.bsky.social @uliseshmc.bsky.social @jeremyjberg.bsky.social 1/5
doi.org
Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation
Abstract. Habitat loss contributes to extinction risk in multiple ways. Genetically, small populations can face an ‘extinction vortex’—a positive feedback
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Charles Perrier @charles-perrier.bsky.social · 03/06/2026
Emilio Egal’s first PhD paper on the effects of dispersal on fitness in wild Atlantic salmon, using a 15-year genetic pedigree comprising more than 1,100 adults and 3,400 juveniles! @inrae-france.bsky.social @inrae-ecobiop.bsky.social @cbgpmontpellier.bsky.social @ofbiodiversite.bsky.social
royalsocietypublishing.org
Selection against dispersers: sex, age and origin-dependent fitness differences in wild Atlantic salmon
Abstract. Local adaptation is often portrayed as uniform fitness disadvantages of immigrants relative to locals. Yet dispersal costs vary with origin, sex
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Svenja Marfurt @svenjamarfurt.bsky.social · 01/06/2026
🎉🐬 Very excited to share the publication of my second PhD chapter in Molecular Ecology: Check it out here: onlinelibrary.wiley.com/doi/10.1111/... (& hit me up if you wanna talk seascape genomics!) Very briefly:
onlinelibrary.wiley.com
Whole‐Genome‐Sequencing Reveals Demographic History and Patterns of Parallel Adaptive Evolution in Indo‐Pacific Bottlenose Dolphins (Tursiops aduncus) Across Coastal Australian Seascapes
Understanding how demographic dynamics interact with environmental heterogeneity is central to explaining patterns of genomic variation in the marine realm. Indo-Pacific bottlenose dolphins (Tursiops...
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Marty Kardos @martykardos.bsky.social · 31/05/2026
Historically Small Population Size Limits Purging of Deleterious Mutations in a Conservation-Reliant Species, the Kirtland’s Warbler www.biorxiv.org/content/10.6...
biorxiv.org
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Laura Bertola @lauradbertola.bsky.social · 23/05/2026
Lag in Effective Population Size Decline Amid Demographic Collapse: A Case Study of the Delta Smelt (Hypomesus transpacificus) onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
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Iliana Bista @ilianabista.bsky.social · 30/04/2026
Drivers of cold adaptation and genome evolution in Antarctic fish, and a haplotype resolved assembly for an important model notothenioid species 🐟 🧬 Our new paper available on BioRxiv #BiodiversityGenomics #ColdAdaptation www.biorxiv.org/content/10.6...
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Global Change Biology @globalchangebio.bsky.social · 08/05/2026
Climate as the Main Driver of Large‐Scale Genetic Patterns and Connectivity in the Expanding Golden Jackal 🔗 buff.ly/v1yw5Z2
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Lucas Eckert @lucaseckert.bsky.social · 06/05/2026
How useful can #herbarium collections be for genetic monitoring? 🌿 We show that Earth’s currently digitized herbarium specimens can be clustered into HUNDREDS OF THOUSANDS of historical “populations” suitable for population genetic studies 🔗 doi.org/10.1093/bios... 🧵
doi.org
The utility of herbarium collections for genetic monitoring
Abstract. Despite growing evidence of widespread genetic responses to anthropogenic activity, data shortfalls constrain genetic monitoring efforts and prec
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Methods in Ecology and Evolution @methodsinecoevol.bsky.social · 06/05/2026
📖 Published📖 charisma: An R package to perform reproducible colour characterization of digital images for biological studies🖥️ 🌍 🧪 👇️ buff.ly/bIUBOck
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Edward R. Ivimey-Cook @eivimeycook.bsky.social · 06/05/2026
Introducing * READMEBuilder * A shiny app that helps users build a high quality README to upload along with their data and code. Just install the package and run the build_readme() function to launch the app! github.com/EIvimeyCook/... Comments and suggestions welcome!
github.com
GitHub - EIvimeyCook/READMEBuilder: Shiny application that walks researchers through building a high-quality README file for research datasets and code. Automatically describes tabular data co...
Shiny application that walks researchers through building a high-quality README file for research datasets and code. Automatically describes tabular data columns (ranges, levels, NAs), det...
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Laura Bertola @lauradbertola.bsky.social · 05/05/2026
Pangolin museum genomics reveal the dynamic genetic consequences and extinction risk of the critically endangered Chinese pangolin academic.oup.com/mbe/article/...
academic.oup.com
Pangolin museum genomics reveal the dynamic genetic consequences and extinction risk of the critically endangered Chinese pangolin
Abstract. Human-driven biodiversity loss, intensified by illegal hunting and trafficking, has caused severe wildlife population declines and extinctions, n
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Blas M. Benito @blasbenito.com · 04/05/2026
📦 My new R package {spatialData} is on CRAN! 🎉 Ecological datasets as sf data frames and their companion raster data ready for analysis and modeling. Built as example data for R packages, but great for teaching too! 🔗 blasbenito.github.io/spatialData/ ❗check the Articles section!
blasbenito.github.io
spatialData: Cool Spatial Datasets
Provides spatial datasets ready to use for ecological modelling and raster companion data for prediction: Neanderthal presence during the Last Interglacial (Benito et al. 2017 <doi:10.1111/jbi.12845>)...
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Claire Mérot @clairemerot.bsky.social · 13/04/2026
Looking forward to kicking off the seminar series of our special topic network on structural variants #SV in evolutionary biology. @eseb.bsky.social Join us in listening to Pr. Rieseberg on April 29
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