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

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.

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