Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates.
Abstract
The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two
active domains that act as signalling molecules during embryo development, namely
for the development of the nervous and skeletal systems and the formation of the testis
cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates
species have three (Sonic hedgehog--Shh; Indian hedgehog--Ihh; and Desert hedgehog--Dhh),
each with different expression patterns and functions, which likely helped promote
the increasing complexity of vertebrates and their successful diversification. In
this study, we used comparative genomic and adaptive evolutionary analyses to characterize
the evolution of the Hh genes in vertebrates following the two major whole genome
duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly
available databases, we used an extensive dataset of 45 avian and three non-avian
reptilian genomes to show that birds have all three Hh paralogs. We find suggestions
that following the WGD events, vertebrate Hh paralogous genes evolved independently
within similar linkage groups and under different evolutionary rates, especially within
the catalytic domain. The structural regions around the ion-binding site were identified
to be under positive selection in the signaling domain. These findings contrast with
those observed in invertebrates, where different lineages that experienced gene duplication
retained similar selective constraints in the Hh orthologs. Our results provide new
insights on the evolutionary history of the Hh gene family, the functional roles of
these paralogs in vertebrate species, and on the location of mutational hotspots.
Type
Journal articleSubject
AnimalsBinding Sites
Evolution, Molecular
Gene Duplication
Genomics
Hedgehog Proteins
Models, Molecular
Multigene Family
Phylogeny
Poultry
Protein Structure, Tertiary
Reptiles
Vertebrates
Permalink
https://hdl.handle.net/10161/11141Published Version (Please cite this version)
10.1371/journal.pone.0074132Publication Info
Pereira, Joana; Johnson, Warren E; O'Brien, Stephen J; Jarvis, Erich D; Zhang, Guojie;
Gilbert, M Thomas P; ... Antunes, Agostinho (2014). Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh
and Dhh) in vertebrates. PLoS One, 9(12). pp. e74132. 10.1371/journal.pone.0074132. Retrieved from https://hdl.handle.net/10161/11141.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
Collections
More Info
Show full item recordScholars@Duke
Erich David Jarvis
Adjunct Professor in the Dept. of Neurobiology
Dr. Jarvis' laboratory studies the neurobiology of vocal communication. Emphasis is
placed on the molecular pathways involved in the perception and production of learned
vocalizations. They use an integrative approach that combines behavioral, anatomical,
electrophysiological and molecular biological techniques. The main animal model used
is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations.
The generality of the discoveries is tested in other vocal

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy
Rights for Collection: Scholarly Articles
Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info