DOI: 10.5061/dryad.8cz8w9gwx
title: A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years

description: The successes of introduced populations in novel habitats often provide
 powerful examples of evolution and adaptation. In the 1950’s, opossum
 shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota,
 USA were transported and introduced to Twin Lakes in Colorado, USA by
 fisheries managers to supplement food sources for trout. Shrimp were
 subsequently introduced from Twin Lakes into numerous lakes throughout
 Colorado. Because managers kept detailed records of the timing of the
 introductions, we had the opportunity to test for evolutionary divergence
 within a known time interval. Here, we used reduced representation genomic
 data to investigate patterns of genetic diversity and test for genetic
 divergence between populations and for evidence of adaptive evolution
 within the introduced populations in Colorado. We found overall very low
 levels of genetic diversity across all populations, with evidence for some
 genetic divergence between the Minnesota source population and the
 introduced populations in Colorado. There was also little differentiation
 among the Colorado populations, consistent with the known provenance of a
 single founding population, with the exception of the population from
 Gross Reservoir, Colorado. Demographic modeling suggests that the
 population in Gross Reservoir is of hybrid origin, with an earlier
 founding population from an unknown source being later supplemented from
 another population. Despite the overall low genetic diversity we observed,
 FST outlier and environmental association analyses identified multiple
 loci exhibiting signatures of selection and adaptive variation related to
 elevation and lake depth. The success of introduced species is thought to
 be limited by genetic variation, but our results imply that populations
 with limited genetic variation can become established in a wide range of
 novel environments.
description: # A lack of genetic diversity and minimal adaptive evolutionary divergence
 in introduced Mysis shrimp after 50 years
 ## Description of the data
 and file structure **blast_fasta_RDA.fasta** 350 bp consensus sequences
 around each candidate SNP flagged by redundancy analysis.
 **blast_fasta_pcadapt.fasta** 350 bp consensus sequences around each
 candidate SNP flagged by PCADAPT. Note some of the reads were flagged as
 truncated by samtools **mysis_clean_10_for_neutral_popstats.vcf** 3,803
 SNPs generated following the recommendations of Schmidt et al. 2021 for
 popualtion genetic statistics. None of these SNPs were found in the
 adaptive SNP list from PCAdapt, or RDA, so they are likely unbiased by
 strong FST outliers or selection. **mysis_clean_imputed_names_fix.vcf**
 18,441 SNPs imputed in Linkimpute that were used for redundancy analysis,
 PCAdapt, and SNMF. **mysis_clean_imputed_neutral_names_fix.vcf** 18,220
 putative neutral SNPs with SNPs flagged as FST outliers from PCAdapt
 filtered out. Dataset was imputed with linkimpute before undergoing
 further filtering. **mysis_clean_non_imputed.vcf** 18,441 SNPs prior to
 imputation in Linkimpute so users can impose stricter filtering regimes
 based on missingness or replicate ADMIXTURE analyses.
 **mysis_env_final.csv** Environmental data for all sampled Lakes. Empty
 values are missing (blank) or NA. Variables measured by DS and BJ for all
 lakes apart form Clearwater Lake include: state: The state the United
 States of America where the sampled lake is located. Either CO (Colorado)
 or MI (Minnesota) county: State county where the sampled lake is
 water_name: Name of the sampled lake or reservoir code: Short code for
 sampled lakes. CAR = Carter Lake, CLER= Clearwater Lake, DIL=Dillon
 Reservoir, GDL= Grand Lake, GRO = Gross Reservoir, JEF= Jefferson
 Reservoir, TWL= Twin Lakes, RUE= Ruedi Reservoir. date_sampled: date in
 m/d/y when the genotyped shrimp were sampled. area-hectares: surface area
 of sampled lake in hectares depth-meters: Max water depth in meters of the
 sampled lake elevation-meters_above_sea_level: elevation of sampled lake
 in meters above sea level cond-microSiemens: Conductivity of sampled lake
 in microSeimens secchi-meters: secchi depth of sampled lake in meters
 turbidity-Nephelometric_Turbidity_Units: turbidity of sampled lake in
 nephelometric turbidity units min_Dissolved_Oxygen_on_bottom-mg_per_L:
 Minimum dissolved oxygen on the bottom of the sampled lake in mg per L
 mean_august_surface_temp_C: mean August surface temperature of the sampled
 lake in C num_yrs_Aug_temp: Number of years of collected data to measure
 mean August surface temperature mysis_detected: yes (Y), no (N) if Mysis
 have been found in the sampled lake. Only used for invaded (Colorado)
 lakes number_stocking_events: Number of times Mysis are known to have been
 stocked in a sampled lake based on historical records. stocked: yes(Y), no
 (N) if Mysis are known to have been stocked in a sampled lake
 connected_to_stocked_lake: yes(Y), no (N) if sampled lake is known to be
 connected to a lake known to have been stocked with Mysis
 **mysis_popmap_final.txt** Popmap used for populations in Stacks.
 Individuals are separated by lake. **mysis_adaptive_snps.vcf** 221
 putative adaptive SNPs identified by PCADAPT and redundancy analysis
 **mysis_clean_imputed.vcf** 18,441 SNPs imputed in Linkimpute
 **mysis_neutral_snps.vcf** 18,220 neutral SNPs (candidate SNPs removed)
 for PCA and DAPC analysis ## Code/Software Scripts All in R markdown files
 with annotations and some personal commentary to help interperpret the
 data **001- Bioinformatics Pipeline Final.Rmd** This includes workflow
 used to de-multiplex, and filter the raw ddRAD data from Admera Health.
 **stacks_tests.xlsx** Shows the result of multiple runs of Stacks
 denovo_map.pl to optimize the parameter used for final genotype calling.
 **002- Population_Genetics_final.Rmd** Workflow to analyse neutral
 population structure.
 **003-Identification_of_Population_Structure_Associated_with_Habitat_final.Rmd** Workflow to generate FST outlier SNP list that were filtered out of the dataset for "neutral" popualtion genetics, code for redundancy analysis and adaptive PCA.