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Developing a well-informed hypothesis of the selective pressures underlying divergence in a natural population requires a thorough understanding of both species structure and demographic history. In this study, we assess whole-genome sequences of round-tailed horned lizards (Phrynosoma modestum) from throughout the species range and combine phylogenetic analyses with genomic landscape scans to understand how current genetic diversity has been influenced by demographic histories and evolutionary pressures. Maximum likelihood (ML) phylogenetic analysis supports two lineages within the species, corresponding to a North\/South population divide that developed around 7\u2005million years ago (Ma) and displays little migration. However, intermediate genealogical divergence index values between the two lineages ultimately leave us unable to recommend a full taxonomic distinction. Genome-wide scans of population genetic statistics identified islands of divergence exhibiting differentiation patterns linked to models of reproductive isolation and within-population selection. Significantly negative values of Tajima's D and positive selection statistics in these islands offer support for selection acting on P. modestum, but patterns may also stem from recent population expansions. We posit that selection within populations has played a large role in shaping genomic divergence across the species' range. Taken together, our results provide perspective into how variable selective pressures shape the genomics of two divergent populations currently maintaining species integrity, despite significant signatures of geographic structure and divergence.<\/jats:p>","DOI":"10.1093\/gbe\/evag217","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T12:43:41Z","timestamp":1787921021000},"source":"Crossref","is-referenced-by-count":0,"title":["Understanding Genomic Landscapes of Differentiation in Round-Tailed Horned Lizards (\n                    <i>Phrynosoma modestum<\/i>\n                    )"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-1441-2890","authenticated-orcid":false,"given":"Julia","family":"Amoroso","sequence":"first","affiliation":[{"name":"Biology PhD Program, CUNY Graduate Center , New York, NY 10016 ,","place":["USA"]},{"name":"American Museum of Natural History Department of Invertebrate Zoology, , New York, NY ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9195-121X","authenticated-orcid":false,"given":"Keaka","family":"Farleigh","sequence":"additional","affiliation":[{"name":"University of Virginia Department of Biology, , Charlottesville, VA 22904 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9844-304X","authenticated-orcid":false,"given":"Erika","family":"Crispo","sequence":"additional","affiliation":[{"name":"Department of Biology, Pace University , New York, NY 10038 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4782-6788","authenticated-orcid":false,"given":"Christopher","family":"Blair","sequence":"additional","affiliation":[{"name":"Biology PhD Program, CUNY Graduate Center , New York, NY 10016 ,","place":["USA"]},{"name":"Department of Biological Sciences, New York City 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