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Intro
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Using phylogenies to connect genotype to phenotype
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Matching human regulatory regions to independently lost mammalian traits
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Taste receptors in mammals
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Birds inherited only the umami (meat) receptor from their dinosaur ancestors
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Hummingbirds can taste sugar due to changes in the gene other binds use to taste meat (or insects)
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Non-coding 'Dark matter of the genome: a regulatory network?
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CNEEs: evolutionarily conserved non-coding enhancer regions
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Noncoding enhancers: long-range control of gene expression
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Phylogenetic hidden Markov model detects CNEEs using Phastcons
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A role for gene regulation in the origin of feathers
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Conserved non-exonic elements (CNEES) act as enhancers for feather genes
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High origination rates of feather CNEEs, but not feather genes, when feathers evolved
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Bird-specific regulatory evolution: what makes a bird a bird?
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Bird-specific CNEEs associated with genes for limb and body size evolution
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CNEEs and the convergent evolution of flightlessness in Palaeognathae
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Skeletal modifications for flightlessness
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11 new palaeognath genomes
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42-species whole genome alignment for birds using ProgressiveCactus
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Relationships of rheas unclear
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Coalescent analyses resolve the position of rheas and reveal an ancient rapid radiation
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Gene tree distribution suggests a near polytomy at base of ratites
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Anomaly zone: most common gene tree does not match the species tree
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Evolutionary change: genes or gene regulation? Evolution at Two Levels in Humans and Chimpanzees
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A convergently accelerated CNEE detected with a novel Bayesian method
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Additional examples of convergently accelerated CNEES
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Rapid regulatory evolution near 1000 developmental genes
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Genes showing convergent regulatory evolution in 3 lineages of ratites
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Assay for Transposase-Accessible Chromatin
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Differences in ATAC-se peaks between thea and chicken suggest changes in limb gene regulation
31
Combined information from multiple sources suggests candidate enhancers for flightlessness phenotypes
32
Volant version of CNEE drives gene expression in the developing forelimb of chicken but flightless version does not
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Measuring gene expression and open chromatin across fore- and hindlimbs of paleognath embryos
Description:
Explore the PhyloG2P approach to understanding bird biology in this comprehensive seminar. Delve into the use of phylogenies to connect genotype to phenotype, focusing on the evolution of taste receptors, feathers, and flight in birds. Examine the role of non-coding DNA, particularly conserved non-exonic elements (CNEEs), in gene regulation and their impact on bird-specific traits. Investigate the convergent evolution of flightlessness in Palaeognathae through genomic analyses and coalescent studies. Learn about novel Bayesian methods for detecting convergently accelerated CNEEs and their application in identifying regulatory changes associated with flightlessness. Discover how combining multiple sources of information, including ATAC-seq and gene expression studies, provides insights into the genetic basis of limb development and flightlessness in birds. Gain a deeper understanding of the interplay between genes and gene regulation in driving evolutionary changes in avian biology.

Wings, Feathers, Flight - The PhyloG2P Approach to Understanding Bird Biology

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