Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sampling and Sequencing
2.2. Transcriptome Assembly and Annotation
2.3. Analyses of Positive Selection
3. Results
3.1. Transcriptome Assemblies Recover Most Conserved Genes
3.2. Ortholog Search Strategy Identifies Phototransduction Genes
3.3. Analysis for Positive Selection Identifies Genes under Positive Selection
3.3.1. PAML
3.3.2. BAli-Phy
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | arr1 | arr2 | Cam | Gq | Gprk1 | inaC | inaC Copy | inaD | inaE | ninaC | norpA | trp | trpl |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Aspisoma sp. | |||||||||||||
Bicellonycha wickershamorum | |||||||||||||
Ellychnia sp. | |||||||||||||
Lucidota atra | |||||||||||||
Micronaspis floridana | |||||||||||||
Microphotus sp. | |||||||||||||
Phausis reticulata | |||||||||||||
Photinus australis | |||||||||||||
Photinus carolinus | * | ||||||||||||
Photinus macdermotti | |||||||||||||
Photinus marginellus | |||||||||||||
Photinus pyralis | |||||||||||||
Photinus scintillans | |||||||||||||
Photuris “A” | |||||||||||||
Photuris frontalis | |||||||||||||
Photuris sp. | |||||||||||||
Photuris sp. 1 | |||||||||||||
Photuris sp. 2 larva | |||||||||||||
Pyractomena borealis | |||||||||||||
Pyractomena dispersa |
Summary of Positive Selection Analyses | PAML | BAli-Phy | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
MAFFT Alignment | Bali-Phy Alignment | |||||||||||||||
Model | lnl | lrt | np | df | p-Value | Omega | Model | lnl | lrt | np | df | p-Value | Omega | Bayes Factor | Level of Support | |
arr2 | null | −3504.00804 | 43.58565 | 19 | 1 | <0.00001 | 0.0545 | null | −3447.79062 | 56.286878 | 19 | 1 | <0.00001 | 0.0459 | 9.502073 | Positive |
alt | −3482.21521 | 20 | alt | −3419.64718 | 20 | |||||||||||
Gq | null | −6134.51482 | 0.050698 | 35 | 1 | 0.82202 | 0.1139 | null | −5227.9707 | 5.017252 | 34 | 1 | 0.0251 | 0.0305 | 82.27678 | Strong |
alt | −6134.48947 | 36 | alt | −5225.46207 | 35 | |||||||||||
Gprk1 | null | −9493.07143 | 1.05478 | 45 | 1 | 0.30443 | 0.0087 | null | −9526.73339 | 0.411348 | 41 | 1 | 0.52131 | 0.0081 | 0.623359 | None |
alt | −9492.54404 | 46 | alt | −9526.52772 | 42 | |||||||||||
inaC | null | −17053.9096 | 64.3459 | 61 | 1 | <0.00001 | 0.0186 | null | −16617.8413 | 0.06558 | 58 | 1 | 0.79788 | 0.013 | 0.778239 | None |
alt | −17021.7366 | 62 | alt | −16617.8085 | 59 | |||||||||||
inaD | null | −19140.0313 | 28.04327 | 45 | 1 | <0.00001 | 0.1139 | null | −18588.4152 | 22.296904 | 43 | 1 | <0.00001 | 0.0921 | 5.128159 | Positive |
alt | −19126.0097 | 46 | alt | −18577.2668 | 44 | |||||||||||
inaE | null | −21162.9887 | 0.938762 | 45 | 1 | 0.33261 | 0.0576 | null | −20557.5219 | 0.925638 | 42 | 1 | 0.33601 | 0.0429 | 0.673093 | None |
alt | −21162.5193 | 46 | alt | −20557.0591 | 43 | |||||||||||
ninaC | null | −17058.6637 | 43.75643 | 15 | 1 | <0.00001 | 0.1104 | null | −16930.1126 | 45.098156 | 15 | 1 | <0.00001 | 0.1092 | 0.990066 | None |
alt | −17036.7855 | 16 | alt | −16907.5635 | 16 | |||||||||||
norpA | null | −19292.2825 | 0.01304 | 43 | 1 | 0.90909 | 0.0226 | null | −18587.9541 | 3.361894 | 42 | 1 | 0.06673 | 0.0145 | 1.041881 | None |
alt | −19292.276 | 44 | alt | −18586.2732 | 43 | |||||||||||
trpl | null | −23948.4017 | 16.06823 | 33 | 1 | 0.000061 | 0.2298 | null | −27362.9713 | 114.4442 | 33 | 1 | <0.00001 | 0.0821 | 8.59116 | Positive |
alt | −23940.3676 | 34 | alt | −27305.7492 | 34 |
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Martin, G.J.; Lower, S.E.; Suvorov, A.; Bybee, S.M. Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae). Insects 2021, 12, 561. https://doi.org/10.3390/insects12060561
Martin GJ, Lower SE, Suvorov A, Bybee SM. Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae). Insects. 2021; 12(6):561. https://doi.org/10.3390/insects12060561
Chicago/Turabian StyleMartin, Gavin J., Sarah E. Lower, Anton Suvorov, and Seth M. Bybee. 2021. "Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae)" Insects 12, no. 6: 561. https://doi.org/10.3390/insects12060561
APA StyleMartin, G. J., Lower, S. E., Suvorov, A., & Bybee, S. M. (2021). Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae). Insects, 12(6), 561. https://doi.org/10.3390/insects12060561