Thanks! That’s something we’re aware of but didn’t deal with in this study - it’s actually the first thing we mention in our limitations section. It’s definitely an important consideration that warrants investigation in future work.

Huge thanks to my incredible co-authors Anna Tigano (@annatigano.bsky.social), Arne Jacobs (@fishyomics.bsky.social), Aryn Wilder, and Nina Therkildsen for their brilliant contributions to this work. This truly represents years of collaborative effort across multiple institutions! 🧬🐟 7/7

This study offers valuable empirical insights distinguishing the roles of inversions (conditionally low-recombining) vs. centromeres (consistently low-recombining), illuminating the critical connection between genome structure and local adaptation with gene flow. 6/7

Meanwhile, putative centromeric regions showed high differentiation but LOW sequence divergence—suggesting they're unlikely to contribute to adaptive divergence with gene flow, despite their recombination-suppressing properties. 5/7

The most fascinating discovery? Different genomic features play distinct roles: Chromosomal inversions showed both high differentiation AND high sequence divergence—evidence they maintain locally adapted alleles despite gene flow. 4/7

With increasing gene flow, we observed more clustering of differentiated regions in the genome! This supports theoretical predictions that high gene flow favors concentrated genomic architectures of adaptation. 3/7

We found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. 2/7

7/7 🦊 Huge thanks to my amazing co-authors Matthew Genchev @jazlynmooney.bsky.social @elliecat.bsky.social and shoutout to Urocyon cinereoargenteus, our beautiful study species! 🐾📸 #Teamwork #Genomics

6/7 🌍 Why It Matters: With most species lacking conspecific references, genomic studies often rely on divergent genomes, risking biased population genomic inferences. Reference genome choice matters—use species-matched references or reference-free methods when possible to ensure accurate insights.

5/7 🎯 Selection Scans: Arctic fox and dog references identified more than twice the number of unique FST outlier windows compared to the gray fox reference. Each reference identified distinct gene ontology terms underlying outliers, reflecting different biological processes.

4/7 ⏳ Demography & Recombination: The gray fox genome produced higher and more stable estimates of historical population sizes. Additionally, recombination rates inferred from heterospecific genomes were inflated, particularly at chromosome ends, compared to the gray fox genome.

3/7 📊 Population Genomics: The conspecific gray fox genome detected more SNPs, especially rare variants, and yielded higher estimates of nucleotide diversity (π) and differentiation (FST) compared to dog and Arctic fox genomes.

2/7 🔍 What We Did: Using two lineages of gray foxes as a case study, we compared three reference genomes: domestic dog, Arctic fox, and a conspecific gray fox genome.