Trans-specific polymorphisms between cryptic Daphnia species

Shared polymorphisms, loci with identical alleles across species, are of unique interest in evolutionary biology as they may represent cases of selection maintaining ancient genetic variation post-speciation, or contemporary selection promoting convergent evolution. In this study, we investigate the abundance of shared polymorphism between two members of the Daphnia pulex species complex. We test whether the presence of shared mutations is consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from six taxa in the D. pulex species group and examined the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that North American and European D. pulex diverged over ten million years ago, yet retained tens of thousands of shared polymorphisms. We suggest that the number of shared polymorphisms bet..., , , # *Trans-specific polymorphisms between cryptic Daphnia species*

* This repository hosts the data utilized for analyzing the shared polymorphism dataset of *Daphnia* species.
Github link: [https://github.com/connor122721/SharedPolymorphismsDaphnia](https://github.com/connor122721/SharedPolymorphismsDaphnia)
* Please let me know if you need any assistance navigating any specific analyses: [[e-mail]](mailto:[e-mail]) 

## *Daphnia* Trans-Species Polymorphism Dataset Repository:

* **Sample Data:**
* Samples metadata used in initial analyses of multi-species dataset: *samples.fin.3.9.22.csv*
* Samples subset by one individual from each Multi-locus Genotype (MLG), which was used in most analyses as indicated in manuscript/github: *samples.fin.9.8.22.csv*
* Any instances of \"NA\" or null values in the metadata are the result of missing data between SRA uploaders. 
* These two sample sheets have identical column names (see below), but the samples ...,