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Reposted by Xavier Dallaire

John P. Sullivan @halooie1.bsky.social · 30/07/2025

Can speciation leave essentially no phylogenetic signal? A fascinating study of the Caribbean hamlet (Hypoplectrus: Serranidae) radiation by Helmkampf et al. in Science. www.science.org/doi/full/10....

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Reposted by Xavier Dallaire

Nicolas Bierne @couplingdmi.bsky.social · 01/07/2025

#PopGen New preprint of the team on the discovery of a very high rate of polymorphic duplication in a marine bivalve. Imagine looking at the distribution of the allelic coverage fraction at heterozygous calls in an indivdual and getting this distribution 👇 😱😱😱

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Reposted by Xavier Dallaire

Darren Irwin (he / him) @darrenirwin.bsky.social · 17/03/2025

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....

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.

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Reposted by Xavier Dallaire

PLOS Biology @plosbiology.org · 07/01/2025

PRDM9 helps determine the location of recombination hotspots in many mammals. Study of salmonid fish reveals that #PRDM9 function is conserved across vertebrates, and this peculiar evolutionary runaway caused by PRDM9 has been active for 100s of millions of years🧪 @plosbiology.org plos.io/3DIvFCG

Top: pictures of Salmo salar and Oncorhynchus mykiss (credit: US Fish and Wildlife Service, public domain). Bottom: Structure of the identified PRDM9 alleles in S. salar PRDM9 α1.a.2 and O. mykiss PRDM9 α1.a.1. Colored boxes represent unique ZFs, characterized by the 3 amino acids in contact with DNA (3-letter code).

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Xavier Dallaire @xdallaire.bsky.social · 16/12/2024

New #phylogeography preprint is out, just in time for the holidays! Here we explore glacial lineages, mito-nuclear discordance and local ancestry tract detection using low-coverage WGS (2X), all in Arctic Char of course! 🐟🏔️ @jeansebmoore.bsky.social @michaelmhansen.bsky.social #PopGen

Local ancestry inferred through local PCA. Fig. 5 on the manuscript : Representative case of a low-recombining diverged putative haploblock corresponding to a local PCA outlier region (win8) on LG9 (NC_036849.1). a) Position of the MDS outlier region (red) on the linkage group (above) and standardized PC1 coordinates in PCAs for successive non-overlapping 100-SNP windows inside and around the outlier region (below). Each sample is represented by a line colored according to their haplogroup inferred from panel b). b). PCA for SNPs in the outlier region where the three major clusters found on PC1 are attributed to the 2 homozygotes (AA, blue, left; BB, yellow, right) and their heterozygote (AB, green, middle). Intermediate genotypes (A0, light blue; 0B, light green) were assigned to individuals outside of the cluster distributions. The histogram (above) represents the density of individuals along the first axis of the PCA. c) Proportion of inferred haplogroups for the win8 haploblock across sampling sites.

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Reposted by Xavier Dallaire

Becky Taylor @beckystaylor.bsky.social · 18/11/2024

Wanting to share our new preprint relevant to the #consgen community! Want to measure runs of homozygosity but don’t have enough depth for Plink or BCFtools? We show that it can be done as low as ~3-5X in ROHan but careful parameterization and interpretation is key: www.authorea.com/users/857111...

authorea.com

Accurate runs of homozygosity estimation from low coverage genome sequences in non-model species

Runs of homozygosity (ROH) are increasingly being analyzed using whole genome sequences in non-model species as a measure of inbreeding and to assess demographic history, thus providing useful informa...

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Reposted by Xavier Dallaire

Philippe Hénault @philhenault.bsky.social · 18/11/2024

Great paper led by my colleagues Anne Beemelmanns, Raphaël Bouchard & Sozos Michaelides. In this study, SNP panels were designed for Lake Whitefish, Brook trout & Arctic Charr for usage in indigenous-led & commercial fisheries management initiatives, including mine 😎. doi.org/10.1111/1755...

doi.org

Development of SNP Panels from Low‐Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada

Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational...

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