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Journal Article
Correction to: Red Deer Resequencing Reveals the Importance of Sex Chromosomes for Reconstructing Late Quaternary Events
Molecular Biology and Evolution, Volume 42, Issue 4, April 2025, msaf087, https://doi.org/10.1093/molbev/msaf087
Published: 28 April 2025
Journal Article
ACCEPTED MANUSCRIPT
Evolutionary and functional analysis of caspase-8 and ASC interactions to drive lytic cell death, PANoptosis
Molecular Biology and Evolution, msaf096, https://doi.org/10.1093/molbev/msaf096
Published: 25 April 2025
Journal Article
ACCEPTED MANUSCRIPT
Transposable elements drive regulatory and functional innovation of F-box genes
Molecular Biology and Evolution, msaf097, https://doi.org/10.1093/molbev/msaf097
Published: 25 April 2025
Journal Article
ACCEPTED MANUSCRIPT
Redistribution of ancestral functions underlies the evolution of venom production in marine predatory snails
Molecular Biology and Evolution, msaf095, https://doi.org/10.1093/molbev/msaf095
Published: 25 April 2025
Journal Article
ACCEPTED MANUSCRIPT
The demographic history of populations and genomic imprinting have shaped the transposon patterns in Arabidopsis lyrata
Molecular Biology and Evolution, msaf093, https://doi.org/10.1093/molbev/msaf093
Published: 24 April 2025
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Performance measures for the first simulation study vs the probability thre...
Published: 21 April 2025
Fig. 2.
Performance measures for the first simulation study vs the probability threshold used to identify transmission links. Top: Sensitivity, middle: specificity, bottom: precision. On the left, we show nondirectional transmission links, and on the right, we show directional transmission links. The red cu
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Performance measures for the second simulation study vs the probability thr...
Published: 21 April 2025
Fig. 4.
Performance measures for the second simulation study vs the probability threshold used to identify transmission links. Top: Sensitivity, middle: specificity, bottom: precision. On the left, we show nondirectional transmission links, and on the right we show directional transmission links. The red cu
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Benchmarking results for the parameters R of deme 1 a), R...
Published: 21 April 2025
Fig. 5.
Benchmarking results for the parameters R of deme 1 a), R of deme 2 b), π of deme 1 c), π of deme 2 d), ρ of deme 1 e), ρ of deme 2 f), κ g), and λ h). Each x axis represents the true value used in the simulation, and each y axis represents inferred values. Posterior mean values
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Combined transmission and phylogenetic tree for the first simulation study....
Published: 21 April 2025
Fig. 1.
Combined transmission and phylogenetic tree for the first simulation study. The tips of the tree are samples taken from infected hosts. The tree topology provides the dated phylogenetic tree, including the date of the most recent common ancestor for any set of samples. The transmission tree is added
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Combined transmission and phylogenetic tree for the second simulation study...
Published: 21 April 2025
Fig. 3.
Combined transmission and phylogenetic tree for the second simulation study. The tips of the tree are samples taken from infected hosts. The tree topology provides the dated phylogenetic tree, i.e. providing the date of the most recent common ancestor for any set of samples. The transmission tree is
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Parameter estimates in the tuberculosis analysis: the reproduction number ...
Published: 21 April 2025
Fig. 6.
Parameter estimates in the tuberculosis analysis: the reproduction number R a), sampling fraction π b), and probability to remain in a deme ρ c) are shown for both the HIV negative (left) and HIV positive (right) demes.
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Parameter estimates in the H7N7 analysis: the reproduction number R...
Published: 21 April 2025
Fig. 8.
Parameter estimates in the H7N7 analysis: the reproduction number R a), sampling proportion π b), and probability to remain in a deme ρ c) are shown for each of the four locations.
Journal Article
Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks
Molecular Biology and Evolution, Volume 42, Issue 4, April 2025, msaf083, https://doi.org/10.1093/molbev/msaf083
Published: 21 April 2025
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Posterior transmission probabilities in the tuberculosis analysis. The ...
Published: 21 April 2025
Fig. 7.
Posterior transmission probabilities in the tuberculosis analysis. The x axis indicates the infector, and the y axis indicates the infected. The shading in each cell indicates the posterior probability that the infector transmitted directly to the infected. We have left gaps to separate individu
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Posterior transmission probabilities in the H7N7 analysis. The x a...
Published: 21 April 2025
Fig. 9.
Posterior transmission probabilities in the H7N7 analysis. The x axis indicates the infector and the y axis indicates the infected. The shading in each cell indicates the posterior probability that the infector transmitted directly to the infected. We have left gaps to separate hosts at the four
Journal Article
ACCEPTED MANUSCRIPT
ERCnet: phylogenomic prediction of interaction networks in the presence of gene duplication
Molecular Biology and Evolution, msaf089, https://doi.org/10.1093/molbev/msaf089
Published: 18 April 2025
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Comparison of differentiation and divergence (FST and ...
Published: 18 April 2025
Fig. 4.
Comparison of differentiation and divergence ( F ST and d XY ) across genomic regions between neighboring populations. Violin plots display average values in 50 kb windows for centromeres (blue), inversions (yellow), telomeres (red), and the rest of the genome (dark gray) for a) F ST and b)
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Comparison of diversity across genomic regions within the four populations....
Published: 18 April 2025
Fig. 5.
Comparison of diversity across genomic regions within the four populations. a) Violin plots display average π values in 50 kb windows for centromeres (blue), inversions (yellow), telomeres (red), and the rest of the genome (dark gray). b) Average π in each of the four major inversions. c) Heatma
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Genome-wide distribution of FST, averaged in 50 kb wind...
Published: 18 April 2025
Fig. 2.
Genome-wide distribution of F ST , averaged in 50 kb windows, across the 24 chromosomes of the Atlantic silverside genome, for pairwise comparisons of neighboring populations as indicated in fig. 1b . Comparison between a) Nova Scotia (NS) and Quebec (QU), where gene flow is limited, b) between N
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Inversions and putative centromeres coincide with patterns of genomic diffe...
Published: 18 April 2025
Fig. 3.
Inversions and putative centromeres coincide with patterns of genomic differentiation and recombination suppression between populations. Black points show F ST in 50 kb windows between the GA and NY populations (left y -axis), and gray points show the recombination rate in their interpopulation
