Phred M. Benham

Conflicts of Interest The authors declare no conflicts of interest. Supporting Information Filename Description mec70093-sup-0001-AppendixS1.xlsxExcel 2007 spreadsheet , 21.6 KB Appendix S1: Quail samples sequenced as part of this study. mec70093-sup-0002-DataS1.pdfPDF document, 1.5 MB Data S1: mec70093-sup-0002-DataS1.pdf. References , , , and . 2024. “Divergent Reference Genomes Compromise the Reconstruction of Demographic Histories, Selection Scans, and Population Genetic Summary Statistics.

1 INTRODUCTION Habitat loss is a primary driver of biodiversity loss (Brooks et al., 2002). At the genetic level, habitat-induced diversity loss can exacerbate extinction risk through increased mutational load and a reduced capacity to adapt to future environmental change (Forester et al., 2022; Frankham, 2005). Consequently, the preservation of genetic diversity is now recognized as a major priority for the conservation of global diversity (Díaz et al., 2020).

Abstract Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing technologies to span highly repetitive regions of the genome should provide novel insights into patterns of TE diversity.