Data from: Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches due to avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analyzed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenic analyses indicates that pathogen genotypes are less spatially structured – exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured due to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

城市化进程可将原本连续的自然景观破碎化为斑块状栖息地，后者散布于不断扩张的城市基质之中。栖息于破碎化景观中的动物，往往会因回避穿插其间的人类开发区域，而减少在不同栖息地斑块间的移动，这可能同时降低斑块间的基因流（gene flow）与病原体传播效率。具有较大家域的肉食性哺乳动物，例如短尾猫（Lynx rufus），对栖息地破碎化可能尤为敏感。我们针对短尾猫及其直接传播的病毒性病原体——猫科免疫缺陷病毒（Feline Immunodeficiency Virus, FIV）开展遗传分析，以探究城市化对短尾猫移动行为的影响。我们推测，包括大型高速公路在内的城市开发活动会限制短尾猫的移动，并导致宿主与病原体种群出现遗传结构分化。我们对南加州城市区域内的106只短尾猫以及19份来自血清阳性个体的FIV分离株进行了分子标记分析。研究结果显示，两处主要栖息地斑块间的基因流受限，导致被包括一条大型高速公路在内的城市开发区域分隔的短尾猫种群出现了遗传分化，形成两个不同的亚种群。然而，通过系统发育分析确定的FIV分离株间遗传多样性分布模式显示，病原体基因型的空间结构较弱——在栖息地斑块间呈现更为均匀的分布。我们由此得出结论：足以实现疾病传播的移动与接触行为发生频率足够高，使得病毒种群未出现遗传结构分化；但短尾猫种群因有效迁移水平低下导致基因流受限，因此形成了遗传结构。本研究证实，在评估种群连通性时，采用可差异化检测亚种群间移动与基因流的多分子标记手段具备重要应用价值。