We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the USA. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the USA, but identified a deep east-west split (~0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern USA, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the USA displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

中文翻译：

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美国灰狐（Urocyon cinereoargenteus）分布的线粒体基因组揭示了大平原缝合带的重大系统地理学断裂

我们检查了整个美国的灰狐（Urocyon cinereoargenteus）的系统地理结构，以确定东部和西部血统之间的次要接触区的位置，并研究了其他种内隐性发散的可能性。我们生成并分析了来自75个样本的完整线粒体基因组序列数据以及来自378个样本的部分控制区域线粒体DNA序列，以通过基于群体和个体的分析（包括差异（FST和SAMOVA），中值连接）进行调查，研究了遗传多样性和结构水平网络和系统发育。我们使用完整的线粒体基因组来推断美国Urocyon主要谱系的系统发生关系和日期分歧时间。尽管进行了大规模采样，我们没有在美国境内找到其他更多的Urocyon主要血统，但是发现了大平原缝合带发生次深层的东西裂（约80万年）并进行了二次接触，并确认海峡岛狐狸（Urocyon littoralis）嵌套在U内.cinereoargenteus。美国东部北部纬度地区的遗传多样性下降，与冰川后重新定殖和范围扩大相一致。除了东西向的差异外，基于形态学的亚种虽然没有独特的单倍型，但在地理上往往是有限的，因此没有形成单系群。美国的灰狐显示出深层的，隐秘的分歧，表明需要对生物分类进行修订。在常见的地理学断裂过程中的二次接触，即大平原缝合带，那里的环境变量显示出明显的上升趋势，表明正在进行的进化过程可能会加剧这种分歧。用核标记物进行的后续研究应调查在缝合区是否发生杂交，并刻画当代人口结构的特征，以帮助确定保护单位。在该地区其他广泛的食肉动物的比较工作应测试是否正在发生类似的进化模式和过程。