# Reading List

[EcoEvoDevo Lab](https://hackmd.io/@aphanotus/AngeliniLab)


This reading list is meant as a resource for new lab members -- or anyone!

## Soapberry bugs

- [Bug Story](https://bugsinourbackyard.org/bug-story/) - *Bugs in our Backyard*'s general audience background on soapberry bug natural history
- [Fawcett et al. 2018 *Nature Communications*](https://www.nature.com/articles/s41467-018-04102-1) - This paper from our lab describes soapberry bugs as an experimental system for the investigation of polyphenism. It establishes nutrition of the determinging factor in wing polyphenism, links it to insulin signaling, and describes differences among *J. haematoloma* populations. Also uses GMM to characterized wing shape.
- [Angelini et al. 2022 *Int Comp Biol*](https://doi.org/10.1093/icb/icac092) - Transcriptome comparisons in the bugs by sex, morph and nutrition
- [*Jadera haematoloma* genome](https://hackmd.io/@aphanotus/rk_j9N-CH) - Quick summary of the soapberry bug genome project
- [Carrol & Boyd 1992 *Evolution*](https://www.jstor.org/stable/2409756?origin=crossref&seq=1#metadata_info_tab_contents) - Scott Carroll's textbook example host shift in *Jadera*
- [Xu et al. 2015 *Nature*](https://www.nature.com/articles/nature14286) - Two insulin receptors determine alternative wing morphs in planthoppers
- [Tsai 2013 ZooKeys](https://zookeys.pensoft.net/articles.php?id=3089) - Exhaustive review of info on *J. haematoloma* at the time of its publication
- [Cenzer 2017 *American Naturalist*](https://www.journals.uchicago.edu/doi/full/10.1086/693456) - Maladaptive plasticity masks the effects of natural selection in the red-shouldered soapberry bug

## Milkweed bugs

- [Angelini & Kaufman 2004 *Developmental Biology*](https://www.sciencedirect.com/science/article/pii/S0012160604002623?via%3Dihub) - *Oncopeltus* mouthpart patterning
- [Aspiras et al. 2011 *Developmental Biology*](https://www.sciencedirect.com/science/article/pii/S001216061101270X?via%3Dihub) - Sex-specific gene interactions in the patterning of insect genitalia (mostly *Oncopletus*; some *Tribolium*)
- [Bonhag & Wick 1953 *J Morphology*](https://onlinelibrary.wiley.com/doi/10.1002/jmor.1050930202) - Anatomy of the male and female reproductive systems of the milkweed bug

## Sex determination

- [Laslo, Just & Angelini 2021 *JEZB*](https://doi.org/10.1002/jez.b.23125) - A review of sex determination mechanisms across insects and ideas about the evolution of that process
- [Just et al. 2023 *ProcB*](https://royalsocietypublishing.org/doi/10.1098/rspb.2022.2083) - Functional genetic characterization of somatic sex determination in the milkweed bug *Oncopeltus fasciatus*

## Scaling and weapons

- [O'Brien et al. 2018 *Animal Behavior*](https://www.sciencedirect.com/science/article/pii/S0003347218302483?via%3Dihub) - Devin published this paper before joining our lab group. It provides a good description of scaling as it applies to weapons. The paper also introduces Devin's idea of comparing a focal trait to a reference trait.
- [Moczek & Nijhout 2002 *Evolution & Development*](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1525-142X.2002.02014.x) - Developmental mechanisms of threshold evolution in a polyphenic beetle

## Beetle moutparts

- [Angelini et al. 2012 *Genetics*](https://www.genetics.org/content/190/2/639) - Patterning of the Adult Mandibulate Mouthparts in the Red Flour Beetle, *Tribolium castaneum*
- [Gotoh et al. 2014 *PLoS Genetics*](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004098) - Developmental Link between Sex and Nutrition; *doublesex* Regulates Sex-Specific Mandible Growth via Juvenile Hormone Signaling in Stag Beetles

## CRISPR

- [Reding & Pick 2020 *Genetics*](https://www.genetics.org/content/215/4/1027) - The paper to report use of CRISPR in *Oncopeltus*
- Check out the lab protocols for [RNA synthesis](https://hackmd.io/@aphanotus/rnasynth) and [microinjection](https://hackmd.io/@aphanotus/microinjection)

## Bumble Bees

- [Bumble Bees In Our Backyard](https://bugsinourbackyard.org/bumblebees/) - *Bugs in our Backyard*'s general audience background on bumble bees
- [Goulson et al. 2015 *Science*](https://science.sciencemag.org/content/347/6229/1255957) - Bee declines driven by combined stress from parasites, pesticides, and lack of flowers
- [Simmons & Angelini 2017 *Scientific Reports*](https://www.nature.com/articles/srep44773) - Imidacloprid increases the expression of antimicrobial peptides in *Bombus impatiens*, in a captive semifield experiment
- [Young et al. 2023 bioRxiv](https://www.biorxiv.org/content/10.1101/2023.11.30.569473v1) - Preprint from our lab reporting the analysis of microbiome composition in bumblebees as it correlates with infection by the parasite *Crithidia bombi*.
- [Cameron et al. 2007 *Biological Journal of the Linnean Society*](https://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2007.00784.x) - A comprehensive phylogeny of the bumble bees (*Bombus*)
- [Insect Macro Photography](https://hackmd.io/s/r1FcQYF-m) - Our lab guide to photography

## Bee microbiota

- [Kwong & Moran 2016 *Nature Review Microbiology*](https://www.nature.com/articles/nrmicro.2016.43) - Gut microbial communities of social bees
- [Qiime2](https://docs.qiime2.org/) - Documentation for the Qiime2 suite of microbiome anaylsys tools

## *Vanessa*

- CRISPR
- [Zhang et al. 2021 *Genome Biology and Evolution*](https://doi.org/10.1093/gbe/evab145) - Report of the genome and transcriptome of the painted lady. (Visit NCBI database for the raw sequences: [genome](https://www.ncbi.nlm.nih.gov/assembly/GCA_905220365.1), [transcripts](https://www.ncbi.nlm.nih.gov/genome/98756?genome_assembly_id=1806767))

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