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Craig D. Wells

@craigdwells.bsky.social
187 followers 310 following 10 posts

PhD Candidate at University of Idaho 🧬 Studying hybridization in Pacific Trout 🐟 He/him

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Reposted by Craig D. Wells
Molecular Ecology @molecology.bsky.social · 07/10/2026
We continue our showcase of the new MEC special issue, Genomics of Speciation! Schluter et al. Coexistence in Sympatry With Gene Flow Before Speciation Has Completed Read more: buff.ly/Kdy7dTe @wileyecology.bsky.social
doi.org
Coexistence in Sympatry With Gene Flow Before Speciation Has Completed
Incipient species often coexist in sympatry before complete reproductive isolation has evolved between them. How do they persist in the face of hybridization and gene flow? The challenge is more…
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Reposted by Craig D. Wells
Alex Fraik @akfraik.bsky.social · 28/09/2026
Very cool new study led by @craigdwells.bsky.social evaluating the role of structural variants in facilitating complex hybridization dymanics between native and introduced Rainbow Trout lineages and Westslope Cutthroat trout #consgen #fishgen
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Jesper Boman @jesperboman.bsky.social · 27/09/2026
Rapid genome-wide purging following tsunami-induced hybridization in a stickleback population www.nature.com/articles/s41...
nature.com
Rapid genome-wide purging following tsunami-induced hybridization in a stickleback population - Nature Ecology & Evolution
Species persistence following hybridization in nature requires the purging of introgressed alleles. Genomic monitoring of a tsunami-induced hybrid stickleback population in Japan reveals rapid genome-...
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Laura Bertola @lauradbertola.bsky.social · 25/09/2026
Inversion Polymorphisms Carried by Introduced Rainbow Trout Disrupt Hybrid Zones Between Native Species onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Inversion Polymorphisms Carried by Introduced Rainbow Trout Disrupt Hybrid Zones Between Native Species
Genomic mechanisms explaining why some hybrid zones remain stable while others collapse into hybrid swarms are poorly understood. In Montana's Kootenai River Basin, native interior redband trout (Onc...
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Marty Kardos @martykardos.bsky.social · 24/09/2026
www.nytimes.com/2026/09/21/p...
nytimes.com
The Trump Administration Defangs the Endangered Species Act
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Marty Kardos @martykardos.bsky.social · 22/09/2026
The role of inversion polymorphisms in the dynamics of a salmonid hybrid zone. onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Inversion Polymorphisms Carried by Introduced Rainbow Trout Disrupt Hybrid Zones Between Native Species
Genomic mechanisms explaining why some hybrid zones remain stable while others collapse into hybrid swarms are poorly understood. In Montana's Kootenai River Basin, native interior redband trout (Onc...
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
This project took a large collaborative effort; from decades of field sampling to linkage mapping, sharing of samples by collaborators, and many RAD libraries. Very grateful to my coauthors, including @martykardos.bsky.social and @phohenlohe.bsky.social, and everyone else who contributed!
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
This paper includes more: IRT linkage maps, local ancestry analyses to find introgression cold spots, and tests of recombination suppression across inversions and chromosome fusions! It provides a framework for studying intra- and interspecific hybridization when genome structure is known a priori.
A collection of interior redband trout from the East Fork Yaak river. This population experiences ongoing and infrequent hybridization with westslope cutthroat that doesn't progress into collapse of parental species strongholds.
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
Additionally, the Chr05 inversion complex is a hotspot of differentiation. FST was elevated in every RBT–cutthroat comparison (even when lineages shared the same orientation) suggesting divergence here reflects more than inversion structure alone and may involve selection.
Pairwise genomic differentiation (FST) within the chromosome 5 (Chr05) double inversion region (Chr05 Complex) compared to the remainder of chromosome 5 (Chr05 Background) and the genome-wide background (excluding the Chr05 Complex). Comparisons include coastal rainbow trout (CRT) carrying homozygous ancestral (CRTAA) or derived (CRTRR) Chr05 genotypes, interior redband trout (IRT), westslope cutthroat trout (WCT), and Yellowstone cutthroat trout (YCT). The figure contains violin plots with embedded boxplots for 10 pairwise taxon/genotype comparisons. Genome-wide FST is shown in dark blue, Chr05 Background in light blue, and the Chr05 Complex in gold. Across comparisons, the gold Chr05 Complex distributions are generally shifted upward relative to both background distributions. This contrast is especially pronounced in comparisons between RBT and cutthroat trout, including comparisons where the taxa share the same ancestral Chr05 orientation. Within-RBT comparisons show lower genome-wide and Chr05-background differentiation but elevated differentiation within the Chr05 Complex. The y-axis ranges from FST = 0 to 1.
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
The most surprising result was that WCT Chr05 is collinear with the ancestral RBT form, so we expected more recombination. Instead, that pairing was almost absent (just 1 of 63 RBT × cutthroat hybrids). That suggests selection or genomic incompatibility beyond structural mismatch.
Principal component analysis of genotypic variation within the chromosome 5 (Chr05) double inversion complex. Panels display clustering based on SNPs within a. the full inversion complex (excluding Yellowstone cutthroat trout [YCT] and YCT recombinants), b. inversion 1, and c. inversion 2. Genotype labels indicate haplotype composition, with subscripts denoting ancestral (A) or rearranged (R) arrangements for westslope cutthroat trout (WCT) and rainbow trout (RBT) haplotypes (e.g., WCTA/RBTR). Recombinant genotypes within inversions are denoted with a cross (×). For partial recombinants affecting only one inversion, genotypes are separated by a semicolon in order by inversion (e.g., WCTA/RBTA;RBTAA). In panel a., hybrid genotypes are surrounded by squares and linked to cartoon representation of the possible genotypes. The collinear interspecific pairing was extremely rare in our dataset.
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
Chromosome 5 stood out for a couple of reasons. Native interior redband trout were fixed for the derived inversion arrangement, while introduced coastal rainbow trout retained a migratory-associated ancestral form. Those genotypes were strongly stratified by habitat.
Weighted mean frequencies of rainbow trout (RBT) chromosome 5 (Chr05) inversion complex genotypes across habitat types. Genotypes include homozygous ancestral (RBTAA), heterozygous (RBTAR), and homozygous rearranged (RBTRR). Frequencies represent Kootenai Basin collections binned by habitat type containing individuals with majority-RBT ancestry at the Chr05 complex, weighted by sample size (N).
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
Widespread admixture in the system was driven mainly by hybridization between coastal (CRT) and interior redband trout rather than rainbow × cutthroat trout. That matters because introduced CRT are polymorphic at major structural variants and can carry these into native redband populations.
Global ancestry estimates for Oncorhynchus collections across the Kootenai River Basin. Pie charts denote the mean proportion of coastal rainbow (CRT), interior redband (IRT), westslope cutthroat (WCT), and Yellowstone cutthroat (YCT) trout ancestry per site. Overlapping sites and temporal replicates are offset or collapsed for visibility. Sample locations within British Columbia, Canada are not pictured. The majority of hybridized populations have measurable CRT ancestry and most hybrids were between CRT and IRT.
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Craig D. Wells @craigdwells.bsky.social · 23/09/2026
Our new paper is out in @molecology.bsky.social! We asked why redband × westslope cutthroat hybridization can remain limited, while introduced coastal rainbow trout are associated with hybrid swarms. Our results point to inversions, dispersal, and genomic incompatibilities. doi.org/10.1111/mec....
doi.org
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Canadian Journal of Fisheries and Aquatic Sciences @cjfas.bsky.social · 08/08/2026
Long-term genetic outcomes of a mixed-source introduction of Westslope Cutthroat Trout ow.ly/plKC50Zn3qL 📊: Bell et al. | cjfas-2025-0417
Mean observed heterozygosity over time
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 02/08/2026
An inversion-rich genome shapes admixture outcomes, generating a mosaic of lineage-specific ancestries in the European sardine www.biorxiv.org/content/10.64898/20…
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Society for Conservation Biology @society4conbio.bsky.social · 24/07/2026
💥💥💥
npr.org
Video: Scientists watch orcas ram a sunfish so hard it explodes
Marine biologists off of Baja California recorded one orca teeing up another to smash a sunfish into pieces. Scientists say there could be a reason for this behavior — or it could be just for entertai...
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elizabethginexi.bsky.social @elizabethginexi.bsky.social · 29/05/2026
Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...
elizabethginexi.substack.com
Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule
Russell Vought is going destroy American Science
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Dr. Solomon David @solomonrdavid.bsky.social · 25/03/2026
NEW: Global Assessment of Migratory Freshwater Fishes @worldwildlife.org www.worldwildlife.org/publications... “Vital freshwater fish migrations are collapsing; hundreds of species need urgent, coordinated cross-border action” Please share!
Cover photo of the World Wildlife Fund’s Migratory Fishes report. Photo of a European Eel underwater.
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Clare Venney @clarevenney.bsky.social · 13/03/2026
My lab’s first publication is out now! MSc student Tia Attfield reviewed the current captive rearing literature in salmonids and provides perspectives on how epigenomics can help. Huge thanks to all our co-authors for their expert insights! onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Epigenetics in Captivity: Restoring Wild Phenotypes in Captive‐Reared Salmonids
Captive rearing is a common practice for the stocking, conservation, and supplementation of fish species worldwide, but captive-reared fish can exhibit altered phenotypes leading to reduced fitness i...
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Trevor Krabbenhoft @fishgenomes.bsky.social · 10/02/2026
Biological invasions present an interesting paradox: often little genetic variation is accompanied by dramatic ecological success. Led by PhD student Chris Osborne, we evaluated genetic diversity in a classic invader, brown treesnake on Guam. www.biorxiv.org/content/10.6... Photo: Pavel Kirilliov
Brown treesnake photo and karyogram of a haplotype phased genome assembly.
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Greg Halling @ghalling.bsky.social · 29/01/2026
The project is proposed at Pushpum, a sacred food- and medicine-gathering and ceremonial site within the more than 12 million acres Yakama Nation ceded to the federal government by treaty in 1855. If built, it would destroy the site. (Isabella Breda / Seattle Times)
buff.ly
Federal energy regulators OK pumped-storage project on Columbia River
A renewable energy project along the Columbia River, at a Yakama Nation sacred site, secured a key federal license.
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Alex Fraik @akfraik.bsky.social · 09/01/2026
Work by Bell, Kovach, Whiteley and colleagues demonstrates that even inbred trout source populations can be used for genetic rescue. Great news for folks considering translocation efforts, but are faced with the challenge of identifying suitable (genetically diverse) donor populations #ConsGen
sciencedirect.com
Inbred source populations result in genetic rescue of imperiled trout populations
Genetic rescue—assisted translocation to reduce inbreeding and increase population viability—is a promising conservation strategy for mitigating the e…
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Craig D. Wells @craigdwells.bsky.social · 05/12/2025
A number of known Pacific Salmon sex chromosomes are synthesized in the context of their synteny to Northern Pike in Christensen et al. 2025 (doi.org/10.1093/g3jo...) I've also been keeping an expanded list of putative sex chromosomes in chromosome-level Salmonid assemblies based on sdY placement.
doi.org
Validate User
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Reposted by Craig D. Wells
Marty Kardos @martykardos.bsky.social · 04/12/2025
Our Editorial for our upcoming special issue in Molecular Ecology: Conservation Genomics—Making a Difference onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Conservation Genomics—Making a Difference
Conservation genomics has increasingly transitioned from a promising concept to a science that integrates a range of advanced analytical approaches, providing new insights into inbreeding, genetic lo....
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Laura Bertola @lauradbertola.bsky.social · 28/11/2025
The value of structural variants to conservation genomics in the pangenome era academic.oup.com/jhered/advan...
academic.oup.com
The value of structural variants to conservation genomics in the pangenome era
Abstract. Structural variants (SVs) comprise an axis of genetic diversity with strong consequences for phenotype and fitness, making them a potentially imp
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Reposted by Craig D. Wells
Alex Fraik @akfraik.bsky.social · 18/11/2025
Ancestors of Fishers translocated decades ago into the Rockies in northern ID and MT persist! #consgen #fishers academic.oup.com/jmammal/adva...
academic.oup.com
The genetic implications of translocations on Fisher (Pekania pennanti) populations in Montana and Idaho
Genetic structure of fishers in the US Northern Rocky Mountains is influenced by translocation history. Fishers in Northern Idaho and Montana are derived f
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 14/10/2025
De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference www.biorxiv.org/content/10.1101/202…
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Alex Fraik @akfraik.bsky.social · 16/10/2025
Neat job alert 🧬🐺🦌 Montana Fish Wildlife & Parks is hiring a wildlife conservation geneticist based in Missoula, MT. The position is joint with @umontana.bsky.social, working with Dr. Ryan Kovach on lots of neat wildlife #consgen projects. Reach out to Ryan with questions.
mtstatejobs.taleo.net
Wildlife Conservation Geneticist
Click the link provided to see the complete job description.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 11/10/2025
Effects of deleterious mutations on the fixation of chromosomal inversions on autosomes and sex chromosomes www.biorxiv.org/content/10.1101/202…
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Jonathan Romiguier @selfishmeme.bsky.social · 15/09/2025
If you’ve heard about our study on ants producing two different species but are still confused about how it works (and don’t have time to read the paper), this 10-minute video made by @bengthomas.bsky.social is very informative: www.youtube.com/watch?v=Z-O4... Paper: www.nature.com/articles/s41...
youtube.com
The Ants That Broke Biology
YouTube video by 7 Days of Science
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The Seattle Times @seattletimes-rss.bsky.social · 12/09/2025
Legal battle reignites over Lower Snake River Dams, salmon
seattletimes.com
Legal battle reignites over Lower Snake River Dams, salmon
The Trump administration pulled back a landmark agreement over the operations of dams in the Columbia Basin. Now the legal fight has reignited.
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Maren Wellenreuther @marenwellenreuther.bsky.social · 05/09/2025
Size matters—but maybe not how we thought. Most chromosomal inversions are just a few hundred bp. Ignoring these “small players” could mean we’ve misunderstood how genomes evolve -out in TREE authors.elsevier.com/a/1ljL1cZ3X3...
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Andy Lee, PhD @andylee.bsky.social · 11/07/2025
New paper with @birdpicsandscience.bsky.social out TODAY!! We found that choosing "highly informative loci" (aka high fst loci) may bias results in common population genetic analyses onlinelibrary.wiley.com/doi/10.1111/... Explainer thread to come! #PopGen #PopulationGenomics #Evolution
onlinelibrary.wiley.com
‘Highly‐Informative’ Genetic Markers Can Bias Conclusions: Examples and General Solutions
High-grading bias is the overestimation power in a subset of loci caused by model overfitting. Using both empirical and simulated datasets, we show that high-grading bias can cause severe overestimat...
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Craig D. Wells @craigdwells.bsky.social · 29/05/2025
Here are some beautiful examples of non-hybridized Redband Trout (O. mykiss gairdneri) from Montana. These fish are increasingly rare in Montana and are the state's only native Rainbow Trout (state rank: S1). FWP has recently spawned wild fish aiming to create a conservation hatchery broodstock.
A post-spawn Redband Trout from Bear Creek (Libby Creek drainage), Montana. This fish was used in 2025 spawning efforts aimed at starting a conservation hatchery broodstock.A post-spawn Redband Trout from Wolf Creek (Fisher River drainage), Montana. This fish was used in 2025 spawning efforts aimed at starting a conservation hatchery broodstock.
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Craig D. Wells @craigdwells.bsky.social · 25/05/2025
Grateful to be included as a minor co-author on this paper! The assemblies in this paper have been a great resource for other work in the pipeline
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Genetics Society of America @genetics-gsa.bsky.social · 25/04/2025
📢 NEW GENOME ALERT  In #G3journal, Lecomte et al. produced a chromosome-level genome assembly of brook trout and performed a comparative analysis to identify homology with sister species lake trout and Atlantic salmon. Read more: buff.ly/if3vgmp
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Nature @nature.com · 24/04/2025
Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics go.nature.com/4jGqiUc
go.nature.com
Eugenics is on the rise again: human geneticists must take a stand
Scientists must push back against the threat of rising white nationalism and the dangerous and pseudoscientific ideas of eugenics.
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 23/02/2025
The Greenland shark genome: insights into deep-sea ecology and lifespan extremes www.biorxiv.org/content/10.1101/202…
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Dr. Or M. Bialik |📚|🔬|🌊|⚒️ @obialik.bsky.social · 05/02/2025
It started in Egypt, with the construction of the Aswan dams, and continued across the basin through verid actions. Now the Mediterranean is receiving less fresh water, and less nutrients - lowering primary productivity and disrupting coastal and marine ecosystems. 🧪🌊 www.nature.com/articles/s41...
Biogeochemical impacts. Mean differences in (a) Chlorophyll concentration, (b) Primary Production Rate, and (c) Carbon export between the reference (REF) and the extreme water reduction (EXT) scenario. No significant differences (C.V. in reference simulation > % difference) are blanked out. Carbon export has been estimated from the Primary Production Rate (assuming a C:N ratio of 106:16), applying the empirical relationships suggested by Eppley and Peterson (1979). Figure created by the authors using Matlab.
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Aja Tengstedt @atengstedt.bsky.social · 31/01/2025
Hello world! Excited to kick things off on 🦋 with great news: The third chapter of my PhD, with @michaelmhansen.bsky.social and a bunch of other great people, has just been published 🚀. We explore genomic 👣 of hybridization between European and American eel. Check it out! doi.org/10.1111/mec....
doi.org
Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)
Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and Am...
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Alex Fraik @akfraik.bsky.social · 31/01/2025
GREAT work by @craigdwells.bsky.social, Paul Spruell, et al. using genetics to evaluate the origins of migratory West Slope Cutthroat Trout sampled in the lower Pend Oreille basin. They found most fish assigned to populations above an impassable dam, which may be disrupting connectivity #ConsGen 🐟 🧬
afspubs.onlinelibrary.wiley.com
AFS Publications
Impact statement Most Westslope Cutthroat Trout captured below Albeni Falls Dam were genetically assigned to regions upstream of the dam, indicating that this barrier disrupts their natural metapop...
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