Awesome Genetics List

Contents

• Whales
• Gain of Function
  • Polar Ice Fish Adaptations
  • The Human ARHGAP11B Gene

Whales

• Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest extant relatives of whales - 1999. Nikaido, Rooney, Okada. This paper provides a comprehensive analysis of the phylogenetic relationships among cetartiodactyls, a group of mammals that includes whales and hippos. The authors used a combination of molecular and morphological data to construct a phylogeny of cetartiodactyls, and found that hippos are the closest extant relatives of whales. This study provides important insights into the evolutionary history of cetartiodactyls and the origins of whales.

• A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals - 2015. The authors conducted a comprehensive phylogenomic analysis to investigate the timing and role of molecular adaptations during the transition of cetartiodactyl mammals from terrestrial to aquatic environments.

• A genomics approach reveals insights into the importance of gene losses for mammalian adaptations - 2018. The authors used a comparative genomics approach to investigate the role of gene losses in mammalian adaptations, highlighting the evolutionary significance of gene loss events.

Gain of Function

• Genomic Analysis of a Key Innovation in an Experimental E. coli Population - Blount, et al. 2012. The authors conducted a genomic analysis of an experimental E. coli population to investigate the genetic basis of a key innovation, providing insights into the mechanisms of evolutionary adaptation.

• X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase - MOLECULAR BASIS FOR THE BIRTH OF A NYLON OLIGOMER-DEGRADING ENZYME - Negoro, et al. 2005.The authors conducted an X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase, providing insights into the structural basis of its enzymatic function.

  • Nylon-oligomer Degrading Enzyme/Substrate Complex: Catalytic Mechanism of 6-Aminohexanoate-dimer Hydrolase - Negoro, et al. 2007. The authors investigated the catalytic mechanism of 6-aminohexanoate-dimer hydrolase through structural analysis of the enzyme/substrate complex, providing insights into its enzymatic function.

  • Three-dimensional Structure of Nylon Hydrolase and Mechanism of Nylon-6 Hydrolysis* - Negoro, et al. 2011. The authors investigated the three-dimensional structure of nylon hydrolase and elucidated the mechanism of Nylon-6 hydrolysis, providing insights into the enzymatic function and evolution of nylon-degrading enzymes.

• Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system - 2015. The authors investigated the evolutionary resurrection of flagellar motility in bacteria through the rewiring of the nitrogen regulation system, providing insights into the mechanisms underlying the evolution of complex traits.

• Transcription factor expression levels and environmental signals constrain transcription factor innovation - 2023. The authors investigated the relationship between transcription factor expression levels, environmental signals, and the innovation of transcription factors, providing insights into the constraints on transcription factor evolution.

• Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes - 2013. The authors investigated the evolutionary history of the TRIMCyp gene fusion in primate genomes, providing insights into the processes of gene birth, decay, and reconstruction.

• Evolution of the rodent Trim5 cluster is marked by divergent paralogous expansions and independent acquisitions of TrimCyp fusions - 2019. The authors investigated the evolution of the rodent Trim5 cluster, highlighting the divergent paralogous expansions and independent acquisitions of TrimCyp fusions, providing insights into the evolutionary dynamics of gene clusters.

• Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci - 2022. The authors investigated the horizontal gene transfer events in the whitefly Bemisia tabaci, providing insights into the acquisition of plant genes and their potential functional roles in the insect’s biology.

Polar Ice Fish Adaptations

Occurring in both the Arctic and Antarctic, polar ice fish have evolved a number of adaptations to survive in extreme cold environments. These adaptations include the evolution of antifreeze proteins, which prevent ice crystal formation in their blood, and the loss of hemoglobin and myoglobin, which reduces the viscosity of their blood and allows for more efficient oxygen transport.

This is one of the most stunning instances of convergent molecular evolution ever discovered.

While the Antarctic icefish built its antifreeze gene by copying and retrofitting an existing digestive gene (trypsinogen), the Arctic cod created its antifreeze gene de novo - literally “from scratch” - out of non-coding “junk” DNA.

• Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish - 1997. The authors investigated the evolution of antifreeze glycoprotein genes in Antarctic notothenioid fish, providing insights into the molecular mechanisms underlying the adaptation to extreme cold environments.

• Origin of antifreeze protein genes: A cool tale in molecular evolution - 1998. The authors investigated the origin of antifreeze protein genes, providing insights into the molecular evolution of these genes and their role in the adaptation of organisms to cold environments.

• Diverse Origins of Near-Identical Antifreeze Proteins in Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms of New Gene Birth and Protein Sequence Convergence - 2024. The authors investigated the origins of near-identical antifreeze proteins in unrelated fish lineages, providing insights into the evolutionary mechanisms of new gene birth and protein sequence convergence.

The Human ARHGAP11B Gene

• The Original Discovery: Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion - 2015. The authors investigated the role of the human-specific gene ARHGAP11B in promoting basal progenitor amplification and neocortex expansion, providing insights into the molecular mechanisms underlying human brain evolution.

• The Ferret Expansion Study: Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex - 2018. The authors investigated the effects of the human-specific gene ARHGAP11B on neocortical expansion in developing ferret neocortex, providing insights into the functional role of this gene in brain development.