Cities as evolutionary incubators for the global spread of the Spotted Lanternfly

This Zenodo repository contains all scripts, pipelines, and metadata associated with the study:

Cities as evolutionary incubators for the global spread of the Spotted Lanternfly.

*¹Fang Meng, ¹Anthony A Snead, ¹²³Aria Yang Zhang, ⁴Jason Munshi-South, *¹Kristin M Winchell

This research investigates the role of urbanization in shaping the genetic diversity, population structure, demographic history, and adaptive evolution of the invasive spotted lanternfly (Lycorma delicatula) across both its native (China) and invasive (USA) ranges. We integrate whole genome resequencing, mitochondrial phylogeography, and eco-evolutionary modeling to understand how urban environments can facilitate rapid evolution and biological invasions.

1. Momi2_models.ipynb, momi2_all_model.py 

Contains all demographic inference analyses performed with momi2, including: Construction of the Site Frequency Spectrum (SFS) Eight alternative demographic scenarios Visualization of demographic history and effective population sizes

2. SLF_GATK_HPC_Pipeline_Final.sh

High-performance computing (HPC) shell scripts for preprocessing and analysis of whole-genome data using tools available on NYU’s Greene HPC cluster. These include pipelines for: Quality control: FastQC Read alignment: BWA-MEM Mark duplicates: Picard Variant calling and filtering: GATK (HaplotypeCaller, GenotypeGVCFs, hard-filtering) Mitochondrial genome mapping: bwa mem, samtools, bcftools, and custom consensus scripts Post-processing: vcftools, bcftools, plink, and others Refer to SLF_GATK_HPC_Pipeline_Final/ and ANGSD_pipeline/ for complete example job scripts.

3. ANGSD_pipeline.sh

Contains scripts and parameter files used with ANGSD for: Estimating genome-wide diversity Population structure and genetic distance.

4. MT_DNA_Haplotype_Analysis.sh

Complete pipeline for mitogenomic haplotype analysis: Consensus mitogenome generation Multiple sequence alignment using MAFFT Maximum likelihood phylogenetic reconstruction with IQ-TREE Visualization using ggtree, pegas, and lineage assignments Includes scripts for integrating our samples with published mitogenomes (Du et al. 2021)

5. run_netural_simulation_C2.sh, run_baypass_C2.sh, reshaper_baypass.py

Filtered VCF files were converted into BayPass-compatible geno and allele count matrices using reshaper_baypass.py(https://gitlab.com/YDorant/Toolbox/-/blob/master/reshaper_baypass.py).

Neutral simulations:
run_neutral_simulation_C2.sh generates the neutral null distribution for the C2 statistic under the BayPass core model.

Empirical C2 analysis:
run_baypass_C2.sh runs the BayPass core model on the empirical data to identify SNPs showing population differentiation associated with the C2 contrast.

6. Metadata

Metadata for 118 SLF samples and Environmental Data: Contains metadata files for the 118 spotted lanternfly samples used in the study, along with all associated environmental data.

7. Mutiple R scripts

This script will contain all R scripts used for: Genetic diversity statistics (ROH,heterozygosity etc.) Population structure (PCA, Admixture, sNMF) Isolation by Distance / Environment (IBD, IBE) Genotype-environment association (RDA) Selection scan integration and GO term enrichment (pcadapt, C2 contrast etc.) 

Data Accessibility

Whole-genome sequencing data for 98 adult Lycorma delicatula collected in the United States were generated using the Illumina NovaSeq 6000 platform and are publicly available in the NCBI Sequence Read Archive under BioProject PRJNA1136004. Sequencing data for an additional 20 adults collected in Shanghai, China, using the NovaSeq X Plus platform are available under BioProject PRJNA1258978. Metadata for all 118 individuals, associated environmental variables, and all scripts required to reproduce the analyses are archived on Zenodo under DOI 10.5281/zenodo.16172524.