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1. TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research

   https://doi.org/10.1177/0748730420934672  

   Ness-Cohn, Elan ; Iwanaszko, Marta ; Kath, William L. ; Allada, Ravi ; Braun, Rosemary ( October 2020 , Journal of Biological Rhythms)

   null (Ed.)

   The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues, coordinating physiological processes. The effect of this rhythm on health has generated increasing interest in discovering genes under circadian control by searching for periodic patterns in transcriptomic time-series experiments. While algorithms for detecting cycling transcripts have advanced, there remains little guidance quantifying the effect of experimental design and analysis choices on cycling detection accuracy. We present TimeTrial, a user-friendly benchmarking framework using both real and synthetic data to investigate cycle detection algorithms’ performance and improve circadian experimental design. Results show that the optimal choice of analysis method depends on the sampling scheme, noise level, and shape of the waveform of interest and provides guidance on the impact of sampling frequency and duration on cycling detection accuracy. The TimeTrial software is freely available for download and may also be accessed through a web interface. By supplying a tool to vary and optimize experimental design considerations, TimeTrial will enhance circadian transcriptomics studies. 

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2. Partial reuse of circadian clock genes along parallel clines of diapause in two moth species

   https://doi.org/10.1111/mec.16940  

   Yu, Yue ; Huang, Li‐Li ; Xue, Fang‐Sen ; Dopman, Erik B. ( April 2023 , Molecular Ecology)

   Understanding the molecular basis of repeated evolution improves our ability to predict evolution across the tree of life. Only since the last decade has high‐throughput sequencing enabled comparative genome scans to thoroughly examine the repeatability of genetic changes driving repeated phenotypic evolution. The Asian corn borer (ACB),Ostrinia furnacalis(Guenée), and the European corn borer (ECB),Ostrinia nubilalis(Hübner), are two closely related moths displaying repeatable phenological adaptation to a wide range of climates on two separate continents, largely manifesting as changes in the timing of diapause induction and termination across latitude. Candidate genes underlying diapause variation in North American ECB have been previously identified. Here, we sampled seven ACB populations across 23 degrees of latitude in China to elucidate the genetic basis of diapause variation and evolutionary mechanisms driving parallel clinal responses in the two species. Using pooled whole‐genome sequencing (Pool‐seq) data, population genomic analyses revealed hundreds of single nucleotide polymorphisms (SNP) whose allele frequencies covaried with mean diapause phenotypes along the cline. Genes involved in circadian rhythm were over‐represented among candidate genes with strong signatures of spatially varying selection. Only one of two circadian clock genes associated with diapause evolution in ECB showed evidence of reuse in ACB (period [per]), butperalleles were not shared between species nor with their outgroup, implicating independent mutational paths. Nonetheless, evidence of adaptive introgression was discovered at putative diapause loci located elsewhere in the genome, suggesting that de novo mutations and introgression might both underlie the repeated phenological evolution.

    

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3. Cross‐species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots

   https://doi.org/10.1002/pld3.18  

   Huang, He ; Gehan, Malia A. ; Huss, Sarah E. ; Alvarez, Sophie ; Lizarraga, Cesar ; Gruebbling, Ellen L. ; Gierer, John ; Naldrett, Michael J. ; Bindbeutel, Rebecca K. ; Evans, Bradley S. ; et al ( October 2017 , Plant Direct)

   Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plantArabidopsis thaliana(Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside ofArabidopsis,however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function ofBrachypodium distachyon(Brachypodium) andSetaria viridis(Setaria) orthologs ofEARLY FLOWERING3,a key clock gene inArabidopsis. To identify both cycling genes and putativeELF3functional orthologs inSetaria, a circadianRNA‐seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles ofSetariagenes under circadian conditions. The function ofELF3orthologs fromArabidopsis, Brachypodium,andSetariawas tested for complementation of anelf3mutation inArabidopsis. We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF3 and SvELF3 could be integrated into similar complexesin vivoas AtELF3. Thus, we find that, despite 180 million years of separation,BdELF3andSvELF3can functionally complement loss ofELF3at the molecular and physiological level.

    

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4. Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor

   https://doi.org/10.1186/s12864-021-08282-x  

   Das, Biplabendu ; de Bekker, Charissa ( January 2022 , BMC Genomics)

   Circadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. Brood-tending nurse ants are usually younger individuals and show “around-the-clock” activity. With age or in the absence of brood, nurses transition into foraging ants that show daily rhythms in activity. Ants can adaptively shift between these behavioral castes and caste-associated chronotypes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity inCamponotus floridanuscarpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains.

   We found that nurse brains have three times fewer 24 h oscillating genes than foragers. However, several hundred genes that oscillated every 24 h in forager brains showed robust 8 h oscillations in nurses, including the core clock genesPeriodandShaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment and output pathway, including genes said to be involved in regulating insect locomotory behavior. We also found thatVitellogenin, known to regulate division of labor in social insects, showed robust 24 h oscillations in nurse brains but not in foragers. Finally, we found significant overlap between genes differentially expressed between the two ant castes and genes that show ultradian rhythms in daily expression.

   This study provides a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify a putative molecular mechanism underlying plastic timekeeping: several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found inC. floridanus, thus, likely represent a more general phenomenon that warrants further investigation.

    

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5. Rapid genetic adaptation to a novel ecosystem despite a large founder event

   https://doi.org/10.1111/mec.17121  

   Sparks, Morgan M. ; Schraidt, Claire E. ; Yin, Xiaoshen ; Seeb, Lisa W. ; Christie, Mark R. ( September 2023 , Molecular Ecology)

   Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole‐genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72—a 2040‐fold decrease. As expected with a severe founder event, we show reductions in genome‐wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species‐specific agent‐based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.

    

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