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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. Sulfur speciation matters

   https://doi.org/10.1038/s41561-024-01621-z  

   Sverjensky, Dimitri A (January 2025, Nature Geoscience)
3. Parameter Identifiability of a Multitype Pure-Birth Model of Speciation

   https://doi.org/10.1089/cmb.2022.0330  

   Dragomir, Dakota; Allman, Elizabeth S.; Rhodes, John A. (March 2023, Journal of Computational Biology)
4. Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers

   https://doi.org/10.1126/science.adf1323  

   Liang, Mei; Chen, Wenjie; LaFountain, Amy M.; Liu, Yuanlong; Peng, Foen; Xia, Rui; Bradshaw, H. D.; Yuan, Yao-Wu (February 2023, Science)

   A genetic locus–involved Mimulus speciation encodes a set of small regulatory RNAs. 

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5. Gene regulation and speciation in a migratory divide between songbirds

   https://doi.org/10.1038/s41467-023-44352-2  

   Louder, Matthew I. M.; Justen, Hannah; Kimmitt, Abigail A.; Lawley, Koedi S.; Turner, Leslie M.; Dickman, J. David; Delmore, Kira E. (January 2024, Nature Communications)

   Abstract Behavioral variation abounds in nature. This variation is important for adaptation and speciation, but its molecular basis remains elusive. Here, we use a hybrid zone between two subspecies of songbirds that differ in migration – an ecologically important and taxonomically widespread behavior---to gain insight into this topic. We measure gene expression in five brain regions. Differential expression between migratory states was dominated by circadian genes in all brain regions. The remaining patterns were largely brain-region specific. For example, expression differences between the subspecies that interact with migratory state likely help maintain reproductive isolation in this system and were documented in only three brain regions. Contrary to existing work on regulatory mechanisms underlying species-specific traits, two lines of evidence suggest that trans- (vs. cis) regulatory changes underlie these patterns – no evidence for allele-specific expression in hybrids and minimal associations between genomic differentiation and expression differences. Additional work with hybrids shows expression levels were often distinct (transgressive) from parental forms. Behavioral contrasts and functional enrichment analyses allowed us to connect these patterns to mitonuclear incompatibilities and compensatory responses to stress that could exacerbate selection on hybrids and contribute to speciation. 

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