Me trying to get a handle on the Quercus phylogeny

Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens!

Read it in Science
dx.doi.org/10.1126/scie...

@ucberkeleyofficial.bsky.social
@hhmi-science.bsky.social

'They saw them on their dishes when eating': The mushroom making people hallucinate dozens of tiny humans Only recently described by science, the mysterious mushrooms are found in different parts of the world, but they give people the same exact visions.

With most psychedelic drugs, you never know what you're going to get. But this mysterious mushroom from China - without fail - causes users to hallucinate tiny people: crawling up walls, popping out from under furniture and marching under doors. www.bbc.com/future/artic...

I literally could not stop myself from inappropriately laughing out loud for real

Does anyone know of a method for testing GO enrichment in the context of the genome structure? For example, I have a highly significant GO category because my significant windows hit a cluster of 8 copies of a gene family. I could do a permutation, but seems like there must be a better way.

Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...

Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry.

But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out!

doi.org/10.1126/scie...

🧵1/6

This was the product of a decade of work, led by Jochen Wolf @jochenwolflab.bsky.social) and kick-started by @frodefossoy.bsky.social & Bård Stokke, made possible by field teams from dozens of countries! @rytikerttunen.bsky.social @biosulc.bsky.social @btobirds.bsky.social @gregowens.bsky.social

It really highlights to me how car-centric design makes everything so much worse for general living.

zoom in on neighbourhood.

These homes were built in 1999, originally surrounded by forest. The globe and mail wrote a story about them 8 years later, once the rest of the neighbourhood filled in. vibrantvictoria.ca/forum/index....

Google maps of neighbourhood in langford

I want to highlight the weirdest neighbourhood in Greater Victoria. In Langford, if you take exit #15 you enter a 6-lane road surrounded by a classic mix of strip malls and big box stores. Nestled of all of this, accessible only through a parking lot, is a small street of 16 single family homes.

distracted boyfriend meme. I'd rather check my snakemake script progress for the 100th time than start reviewing a paper

Get your CVs updated. Zoology Department, University of Otago is hiring a Lecturer in Evolutionary Ecology!

@zoologyotago.bsky.social

otago.taleo.net/careersectio...

Demographic history, genetic load, and the efficacy of selection in the globally invasive mosquito Aedes aegypti Abstract. Aedes aegypti is the main vector species of yellow fever, dengue, Zika and chikungunya. The species is originally from Africa but has experienced

Excited to see the final version of this paper with @samurscicop.bsky.social and Daniel Matute out in @genomebiolevol.bsky.social!

We took a dive into the complicated demographic history of Aedes aegypti mosquitoes and its impact on the distribution of genetic diversity
doi.org/10.1093/gbe/...

Four figure panels from the paper. At upper left, a map of Asia showing the breeding ranges of six subspecies of greenish warblers, five of which are in the main ring: viridanus in blue in west Siberia, ludlowi in green in the western Himalayas, trochiloides in yellow in the central and eastern Himalayas, obscuratus in orange in central China, plumbeitarsus in red in eastern Siberia. The western form nitidus in grey, is also shown. In the lower left panel is a plot of genomic PC1 vs. PC2, with each little diamond symbol representing a single bird. This shows viridanus and plumbeitarsus as very distinct, while being connected by gradual or stepwise change through the populations around the southern ring. This is also shown in the lower central panel, which plots location around the ring vs. PC1. In the right panel, genotypes at 12 different Large Haploblock Regions are shown for 257 individuals arranged in order around the ring. Distinct differences between viridanus (in blue) and plumbeitarsus (in red) are seen, with more gradual variation through the ring connecting them. A single backcross of an F1 and a plumbeitarsus is seen in the lower row of this panel.

OK who's ready for some science?

Do you like speciation? Genomics? Hybridization? Bioinformatics? Then this is for you:

Published today: "The Distribution & Dispersal of Large Haploblocks in a Superspecies"

Bonus interest if you like ring species and cute greenish birds:

doi.org/10.1111/mec....

Lungfish xkcd.com/3064

With @katiejenike.bsky.social and a bunch more of our fellow k-mer enthusiasts, we put together a manuscript on k-mers in biodiversity genomics. A guide if you will, that covers k-mers from basics to some really funky stuff...

genome.cshlp.org/content/35/2...

Does anyone have an insight into why overhead rates are so different between US and Canada? Canadian rates are generally around 25%. Is it that Canada just provides more government base funding so they can accept lower overhead rates?

Excited to see our work on the cover of Current Biology this month!

Read about it in the thread below. 🧪🦑🌊

My population isn’t working for QTL mapping. RIL issue.

Also thank you to the Kelp Rescue Initiative who were critical for sample collection and collaboration. They are doing amazing work applying some the genetic knowledge to real kelp restoration.

Also thank you to the many First Nations who contributed including Gitga'at, Gitxaała, Haida, Haisla, Heiltsuk, Kitasoo-Xai'xais, Kitselas, Kitsumkalum, K'ómoks, Mamalilikulla, Metlakatla, Tlowitsis, and Wei Wai Kum.

Many thanks to the team including @cneufeld.bsky.social, @brookeweigel.bsky.social, @samstarko.bsky.social and many others who aren't on bluesky or who I don't know their handle. This work was spearheaded through many challenges (including awful kelp DNA) by Jordan Bemmels.

Predicted changes in realized genetic load under different cross types for bull kelp (A–C) and giant kelp (D–F) suggest a penalty for selfing (A, B, D, and E) and reduced load in between-population crosses (C and F). Realized genetic load is measured as the proportion of sites homozygous for the derived allele at moderate- and high-impact sites in the SnpEff analysis.

One interesting pattern did emerge that the amount of inbreeding load (i.e. selfed vs outbred) varies between populations and this is related to Ne. Small populations have already achieved near their max load so selfing doesn’t increase it.

Lack of evidence for purging by natural selection in GERP (A and B) and SnpEff (C and D) analyses.

Does the small populations and selfing help purge deleterious alleles? We looked for sites conserved across brown algae, that did vary in our populations to measure genetic load and found that total load did not vary between small and big populations.

Genetic structure of bull kelp (A, C, and E) and giant kelp (B, D, and F) in British Columbia and Washington.

Genetic health indicators for bull kelp (A, C, E, and G) and giant kelp (B, D, F, and H).

We found geographic population structure with fairly strong IBD. Interestingly, selfing was common and about 10% of the adult kelp were selfed in both species. Some populations, particularly those in Puget Sound, had really small Ne and diversity.

Visual abstract for Kelp paper

Excited to announce our work on kelp genomics is now out at Current Biology. Lead by Postdoc extraordinaire Jordan Bemmels, we sequence WGS for 600+ bull and giant kelp across BC and Washington. authors.elsevier.com/a/1kSP93QW8S...

Science magazine front cover. Picture of a walnut in its opened shell. The text reads "All about timing. Mating type evolution in walnuts and pecans"

graphical abstract: "In Juglans (top left) and Carya, two morphs show complementary temporal separation between male and female flowering (heterodichogamy). Mating types are controlled by two nonhomologous single-locus mechanisms that arose in the common ancestor of each genus, respectively. (Bottom left) Simplified schematic of a putative functional regulatory element at the Juglans locus. (Bottom right) Strong genotypic correlations across the Carya locus indicate a lack of recombination between two colinear haplotypes with similar gene content."

Congrats to @jeffgroh.bsky.social et al on publication of "Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories"

www.science.org/doi/10.1126/...

Evolution of fast-growing piscivorous herring in the young Baltic Sea - Nature Communications The Atlantic herring is one of the world’s most abundant vertebrates and a typical plankton feeder of major ecological importance. This study shows that a piscivorous (fish-eating) ecotype of herring ...

An intriguing new evolutionary story has just dropped, from my friend and colleague Leif Andersson: a discrete population of large predatory herring in the Baltic Sea, apparently in the process of evolving into a new species. 🧪
www.nature.com/articles/s41...