Using genetic approaches to uncover the invasion history of bullfrogs in the Southwest

Eberle et al., 2025 (in prep) Population genetics of introduced bullfrogs (Rana catesbeiana) in New Mexico, USA

In this study, we investigated the invasion history of bullfrogs across their introduced range in New Mexico by evaluating their genetic composition. We aimed to answer the following objectives: (1) assess the level of genetic diversity and identify haplotypes within bullfrog populations in New Mexico, (2) compare genetic diversity of native and invasive bullfrog populations, (3) infer the number of introductions into New Mexico, and (4) identify potential native source populations.

R SCRIPTS AND ANALYSES

Mann Whitney-U test for native vs. invasive populations

Mann_whitney_u_data.csv - Input file with diversity indices by population

Mann_whitney_U_bullfrogs.qmd - This script includes code for running a Shapiro normality test to ensure data is not normally distributed. It also includes code to run the Mann-Whitney U test and plots the results in a boxplot.

Haplotype and Nucleotide Diversity Indices calculation

NM_Bullfrog_Rscript - This script includes code for running haplotype and nucleotide diversity indices using sequence data as an input. Theta diversity indices calculation is also included in the code but not used in the study. Both input files are used in this code.

NorthernGila33 - contains sequence data for Gila samples

NMonly_Alignment_Trimmed - contains sequence data for all NM samples

IQ-Tree Run

IQ-Tree Run including one run to find best fit model and a second run to run the best fit model using 1000 bootstrap values. Files include output .log files including the commands and the input files in .fasta format.

sequence_Raca_cytb_haplotypes - input file containing sequences

sequence_Raca_cytb_haplotypes_bestmodel - log file for best-fit model finder

sequence_Raca_cytb_haplotypes_final_alignment alignment_shortened - log file running the best-fit model

AMOVA

These files in format (.arp) were used to run an AMOVA analysis in Arlequin 3.5. These files have been modified from existing files from Kamath et al. 2016 to include New Mexico sequences and other Rana catesbeiana cyt b sequences on Genbank. AMOVA compared each region of invasive and native populations to New Mexico populations.

(.arp) files are directly input to Arlequin software. Files contain haplotypes and sample sizes for each region in order.

(.hap) files are contained in same folder and include sequences and associated haplotype.

Settings in Arlequin:
AMOVA: Locus by Locus AMOVA, 10,000 permutations, compute distance matrix by pairwise differences

Population comparisons: Compute pairwise FST, 10,000 permutations, significance level 0.05, compute distance matrix by pairwise differences

Questions? Contact me at ceberle17@unm.edu