Convergent regulatory evolution and loss of flight in paleognathous birds

@article{Sackton2019ConvergentRE,
  title={Convergent regulatory evolution and loss of flight in paleognathous birds},
  author={Timothy B Sackton and Phil Grayson and Alison Cloutier and Zhirui Hu and Jun S. Liu and Nicole E. Wheeler and Paul P. Gardner and Julia A. Clarke and Allan j. Baker and Michele E. Clamp and Scott V. Edwards},
  journal={Science},
  year={2019},
  volume={364},
  pages={74 - 78}
}
All roads lead to regulation Species from widely divergent taxa can experience similar changes in traits. What underlying genetic drivers cause these parallel changes remains an open question. Sackton et al. looked across groups of birds that have repeatedly lost flight, the ratites and tinamous, and found that there is convergence in the regulatory regions associated with genes related to flight, but not within the protein coding regions. Changes within these regulatory regions influenced limb… Expand
Noncoding regions underpin avian bill shape diversification at macroevolutionary scales.
TLDR
It is shown that homologs of the identified protein-coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals and suggests that identifying genotype-phenotype association on a genome-wide scale over macroevolutionary time is feasible. Expand
Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
TLDR
Using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait, it is shown that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. Expand
Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds
TLDR
The evolutionary history of the Palaeognathae populations, genes, and TEs is reconstructed and the findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes. Expand
A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales
TLDR
A generalizable test is developed that offers a resounding “yes” to both extensively debated questions about molecular convergence and how much genomic molecular convergence contributes to convergent phenotypic evolution, such as echolocation in bats and whales. Expand
Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents
TLDR
Convergent changes in gene regulation play a primary role in the complex trait of desert adaptation in rodents, indicating that different instances of adaptation to deserts include a combination of unique and shared changes. Expand
Parallel Genomic Changes Drive Repeated Evolution of Placentas in Live-Bearing Fish
TLDR
Comparison of whole genomes of 26 poeciliid species representing six out of nine independent origins of placentation revealed that the evolution of the placenta coincides with convergent shifts in the evolutionary rate of 78 protein-coding genes, mainly observed in transporter- and vesicle-located genes. Expand
Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders
TLDR
This study demonstrates, in the case of independent evolution of web loss, that similar selective pressures act on many of the same genes to produce the same phenotypes and behaviors. Expand
Gradual evolution towards flightlessness in steamer ducks *
Flightlessness in birds is the product of changes in suites of characters—including increased body size and reduced anterior limbs—that have evolved repeatedly and independently under similarExpand
Evolutionary dynamics of sex chromosomes of paleognathous birds
TLDR
The analysis of Z chromosome evolution and gene expression across 12 paleognaths shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive. Expand
Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds
TLDR
The analysis of Z chromosome evolution and gene expression across 12 paleognaths shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 135 REFERENCES
Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.
TLDR
Evidence of widespread convergence at the gene level is presented by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment by identifying Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. Expand
A genetic signature of the evolution of loss of flight in the Galapagos cormorant
TLDR
A comparative and predictive genomics approach is developed that uses the genome sequences of P. harrisi and its flighted relatives to find candidate genetic variants that likely contributed to the evolution of loss of flight. Expand
Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
TLDR
It is demonstrated how the ASHCE driven avian-specific expression of gene Sim1 driven byASHCE may be associated with the evolution and development of flight feathers, and the importance of cis-regulatory rewiring during macroevolutionary changes is highlighted. Expand
Phylogenomic evidence for multiple losses of flight in ratite birds
TLDR
A phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Expand
Genome-Wide Convergence during Evolution of Mangroves from Woody Plants
TLDR
A new method for detecting convergence at conservative Sites (CCS) is developed and applied to the genomic sequences of mangroves and ∼400 genes that have experienced convergence over the background level of convergence in the nonmangrove relatives are estimated. Expand
Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages
TLDR
It appears that similar evolutionary processes created independent accelerated regions in the genomes of different apes, and that these lineage-specific changes to conserved noncoding sequences may have differentially altered expression of a core set of developmental genes across ape evolution. Expand
Comparative genomics reveals insights into avian genome evolution and adaptation
TLDR
This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. Expand
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
TLDR
This work recovers a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II), and confirms the existence of an empirical anomaly zone in palaeognaths. Expand
The genetic causes of convergent evolution
  • D. Stern
  • Biology, Medicine
  • Nature Reviews Genetics
  • 2013
TLDR
Evidence for parallel and collateral evolution has been found in many taxa, and an emerging hypothesis is that they result from the fact that mutations in some genetic targets minimize pleiotropic effects while simultaneously maximizing adaptation. Expand
Whole-genome analyses resolve early branches in the tree of life of modern birds
TLDR
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea. Expand
...
1
2
3
4
5
...