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1. Gene Expression Divergence Between Locally Adapted Inland Annual and Coastal Perennial Ecotypes of Mimulus guttatus Across Developmental Stages

   https://doi.org/10.1111/mec.70080  

   Olsen, Jason D; Gould, Billie A; Chen, Yani; Lowry, David B (November 2025, Molecular Ecology)

   ABSTRACT The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ significantly in morphology, physiology, and development, yet our understanding of their underlying genetic basis remains limited. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. Here, we compared gene expression at different developmental time points between ecologically reproductively isolated coastal perennial and inland annual ecotypes of the yellow monkeyflower,Mimulus guttatus. We took two major approaches to understand differences in gene regulation between the ecotypes at the level of gene networks. First, we evaluated expression variation between the ecotypes in candidate molecular pathways. Next, we conducted gene co‐expression network analyses to identify new candidate mechanisms driving ecotypic divergence. Overall, we found significant differences in global expression between the ecotypes and across developmental stages. Among the candidate pathways we evaluated, genes in the jasmonic acid pathway were the most significantly enriched for divergent gene expression. This includes the most differentially expressed gene in our analyses, which is a key gene (cytochrome P450 CYP94B1) involved in the degradation of bioactive jasmonic acid. Our gene co‐expression network analysis revealed different but complementary insights into the differential regulation of genes between the ecotypes, especially at a more microscopic level of these organisms. Overall, our research further supports the hypothesis that plant hormone pathways play a crucial role in the evolution of plant ecotypes and, consequently, the emergence of new species. 

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2. Disentangling the developmental origins of a novel phenotype: enhancement versus reversal of environmentally induced gene expression

   https://doi.org/10.1098/rspb.2022.1764  

   Levis, Nicholas A.; McKay, Daniel J.; Pfennig, David W. (October 2022, Proceedings of the Royal Society B: Biological Sciences)

   Increasing evidence suggests that many novel traits might have originated via plasticity-led evolution (PLE). Yet, little is known of the developmental processes that underpin PLE, especially in its early stages. One such process is ‘phenotypic accommodation’, which occurs when, in response to a change in the environment, an organism experiences adjustments across variable parts of its phenotype that improve its fitness. Here, we asked if environmentally induced changes in gene expression are enhanced or reversed during phenotypic accommodation of a novel, complex phenotype in spadefoot toad tadpoles ( Spea multiplicata ). More genes than expected were affected by both the environment and phenotypic accommodation in the liver and brain. However, although phenotypic accommodation primarily reversed environmentally induced changes in gene expression in liver tissue, it enhanced these changes in brain tissue. Thus, depending on the tissue, phenotypic accommodation may either minimize functional disruption via reversal of gene expression patterns or promote novelty via enhancement of existing expression patterns. Our study thereby provides insights into the developmental origins of a novel phenotype and the incipient stages of PLE. 

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3. Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates

   https://doi.org/10.1093/molbev/msaf100  

   Szasz-Green, Taylor; Shores, Katherynne; Vanga, Vineel; Zacharias, Luke; Lawton, Andrew K; Dapper, Amy L (May 2025, Molecular Biology and Evolution)

   Josephs, Emily (Ed.)

   Abstract Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence. 

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4. Craniofacial-specific transcriptomics uncovers novel genes underlying jaw divergence in dietary specialist pupfishes

   https://doi.org/10.1093/genetics/iyaf207  

   Palominos, M Fernanda; Muhl, Vanessa; Martin, Christopher H (September 2025, GENETICS)

   Peichel, C (Ed.)

   Abstract Changes in gene expression underlie most phenotypic differences among closely related species. While previous studies in model systems have identified conserved genes and pathways involved in craniofacial evolution, less is known about gene expression differences associated with craniofacial divergence in rapidly evolving species. Here, we investigate craniofacial-specific gene expression in a nascent adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas, which includes 3 trophic specialists with highly divergent craniofacial morphologies (two scale-eaters and a molluscivore) derived from an ancestral Caribbean-wide generalist. We compared gene expression in the most morphologically divergent craniofacial region with the relatively conserved caudal region across 5 Cyprinodon species and 9 populations. We focused on the hatchling stage, the earliest developmental stage at which craniofacial differences among species are evident. Our approach revealed a large proportion of differentially expressed genes (DEGs) found exclusively in the craniofacial region of the specialists only. By intersecting these specialist-specific craniofacial-exclusive genes with genomic regions harboring fixed single-nucleotide variants under selection in the specialists, we identified 14 candidate genes. We confirmed novel craniofacial expression for 2 of these candidates, pycr3 and atp8a1, genes not previously associated with craniofacial development or function, in hatchlings using in situ mRNA hybridization and observed species-specific differences in the pharyngeal arches and craniofacial muscles, respectively. Our findings demonstrate how an “evolutionary mutant” model can reveal novel gene expression patterns, highlighting the power of integrating tissue-species transcriptomics with speciation genomics to identify novel regulators of craniofacial evolution. 

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5. Similar Genetic Routes Are Independently Targeted for Mimetic Color Convergence in Bumble Bees

   https://doi.org/10.1093/molbev/msaf187  

   Hines, Heather M; Dabak, Tunc; Rahman, Sarthok Rasique; Terranova, Tatiana; Tian, Li; Smith, Cecil; Koch, Jonathan_Berenguer Uhuad; Lozier, Jeffrey D (September 2025, Molecular Biology and Evolution)

   Takahashi, Aya (Ed.)

   Abstract Bumble bees (Bombus) exhibit exceptional diversity in setal body color patterns, largely as a result of convergence onto multiple Mullerian mimicry patterns globally. When multiple species cross the same sets of mimicry complexes, they can acquire the same color polymorphisms, providing replicates of phenotypic evolution. This study examines the genetic basis of parallel color pattern acquisition in three bumble bee taxon pairs in western North America that shift between orange-red and black mid-abdominal segmental coloration in Rocky Mountain and Pacific Coastal mimicry regions: polymorphic Bombus vancouverensis and B. melanopygus, and sister species B. huntii and B. vosnesenskii. Initial gene targets are identified using a genome-wide association study, while cross-developmental transcriptomics reveals genetic pathways leading to final pigmentation genes. The data show all three lineages independently target the regulatory region of a segmental-fate determining Hox gene, Abdominal B (Abd-B), for this color transition. For B. vancouverensis and B. melanopygus, this involves different deletions in the same location, and all mimicry pairs differentially express Abd-B and ncRNAs in this locus. Transcriptomics reveals a shared core gene network across species, where Abd-B interacts with nubbin and pigment enzyme ebony to decrease black melanin production in favor of paler, redder morphs. Expression of multiple genes in the melanin biosynthesis pathway is modified to promote this phenotype, with differing roles by taxon. Replicated morphologies unveil key genes and a Hox gene hotspot, while enabling evolutionary tracking of genetic changes to phenotypic changes and informing how gene regulatory networks evolve. 

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