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1. Speciation Genes

   https://doi.org/10.1016/B978-0-443-15750-9.00080-X  

   Blackman, Benjamin K (December 2024, Elsevier)

   Speciation genes, or loci harboring allelic variants that have contributed to the evolution of reproductive isolation between lineages, have been identified by recent efforts in many systems. The normal functions of these genes and their patterns of evolutionary change confirm several classic theoretical predictions and spur new questions about the process of speciation. 

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2. Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes

   https://doi.org/10.1093/jxb/ery244  

   Zahraeifard, Sara; Foroozani, Maryam; Sepehri, Aliasghar; Oh, Dong-Ha; Wang, Guannan; Mangu, Venkata; Chen, Bin; Baisakh, Niranjan; Dassanayake, Maheshi; Smith, Aaron P (June 2018, Journal of Experimental Botany)
3. Eco-evolutionary effects of keystone genes

   https://doi.org/10.1126/science.abo3575  

   Nosil, Patrik; Gompert, Zach (April 2022, Science)

   There is increasing evidence that genetic evolution can occur rapidly enough to affect the ecological dynamics of populations and communities ( 1 – 3 ). To better predict the future of ecosystems, it is necessary to understand how evolutionary changes within species influence and interact with ecological changes through processes known as “eco-evolutionary dynamics” ( 4 ). On page 70 of this issue, Barbour et al. ( 5 ) demonstrate that a gene affecting a plant’s resistance to herbivory also influences the persistence of the food web through the gene’s effect on plant growth (see the figure). Subsequent studies of natural selection in the wild can help explain how variations of such “keystone genes” can be maintained ( 6 , 7 ). The maintenance of genetic variation in keystone genes is required for eco-evolutionary dynamics to be perpetual rather than transient. 

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4. Accelerating Biological Insight for Understudied Genes

   https://doi.org/10.1093/icb/icab029  

   Reynolds, Kimberly A; Rosa-Molinar, Eduardo; Ward, Robert E; Zhang, Hongbin; Urbanowicz, Breeanna R; Settles, A Mark (May 2021, Integrative and Comparative Biology)

   Synopsis The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research. 

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5. Evolution of Phototransduction Genes in Lepidoptera

   https://doi.org/10.1093/gbe/evz150  

   Macias-Muñoz, Aide; Rangel Olguin, Aline G; Briscoe, Adriana D (August 2019, Genome Biology and Evolution)

   Abstract Vision is underpinned by phototransduction, a signaling cascade that converts light energy into an electrical signal. Among insects, phototransduction is best understood in Drosophila melanogaster. Comparison of D. melanogaster against three insect species found several phototransduction gene gains and losses, however, lepidopterans were not examined. Diurnal butterflies and nocturnal moths occupy different light environments and have distinct eye morphologies, which might impact the expression of their phototransduction genes. Here we investigated: 1) how phototransduction genes vary in gene gain or loss between D. melanogaster and Lepidoptera, and 2) variations in phototransduction genes between moths and butterflies. To test our prediction of phototransduction differences due to distinct visual ecologies, we used insect reference genomes, phylogenetics, and moth and butterfly head RNA-Seq and transcriptome data. As expected, most phototransduction genes were conserved between D. melanogaster and Lepidoptera, with some exceptions. Notably, we found two lepidopteran opsins lacking a D. melanogaster ortholog. Using antibodies we found that one of these opsins, a candidate retinochrome, which we refer to as unclassified opsin (UnRh), is expressed in the crystalline cone cells and the pigment cells of the butterfly, Heliconius melpomene. Our results also show that butterflies express similar amounts of trp and trpl channel mRNAs, whereas moths express ∼50× less trp, a potential adaptation to darkness. Our findings suggest that while many single-copy D. melanogaster phototransduction genes are conserved in lepidopterans, phototransduction gene expression differences exist between moths and butterflies that may be linked to their visual light environment. 

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