R code for implementing models from Consequences of resource supplementation for disease risk in a partially migratory population

Anthropogenic landscape features such as urban parks and gardens, landfills and farmlands can provide novel, seasonally reliable food sources that impact wildlife ecology and distributions. In historically migratory species, food subsidies can cause individuals to forgo migration and form partially migratory or entirely sedentary populations, eroding a crucial benefit of migration: pathogen avoidance through seasonal abandonment of transmission sites and mortality of infected individuals during migration. Since many migratory taxa are declining, and wildlife populations in urban areas can harbour zoonotic pathogens, understanding the mechanisms by which anthropogenic resource subsidies influence infection dynamics and the persistence of migration is important for wildlife conservation and public health. We developed a mathematical model for a partially migratory population and a vector-borne pathogen transmitted at a shared breeding ground, where food subsidies increase the nonbreeding survival of residents. We found that higher resident nonbreeding survival increased infection prevalence in residents and migrants, and lowered the fraction of the population that migrated. The persistence of migration may be especially threatened if residency permits emergence of more virulent pathogens, if resource subsidies reduce costs of infection for residents, and if infection reduces individual migratory propensity.This article is part of the theme issue ‘Anthropogenic resource subsidies and host–parasite dynamics in wildlife’.

诸如城市公园与绿地、垃圾填埋场与农田等人为景观特征（anthropogenic landscape features），可提供新颖且季节性稳定的食物来源，进而影响野生动物的生态与分布格局。对于历史上具有迁徙习性的物种而言，食物补给（food subsidies）可促使个体放弃迁徙，进而形成部分迁徙或完全定居的种群，削弱了迁徙的核心益处——通过季节性脱离病原体传播位点以及迁徙途中感染个体的死亡来实现的病原体规避效果。鉴于诸多迁徙类群正面临种群衰退，且城市区域的野生动物种群可携带人畜共患病原体（zoonotic pathogens），因此厘清人为资源补给如何影响感染动态与迁徙存续性的机制，对野生动物保护与公共卫生均具有重要意义。我们构建了一个针对部分迁徙种群以及在共享繁殖地传播的媒介传播病原体（vector-borne pathogen）的数学模型，其中食物补给可提升定居个体的非繁殖季存活率。研究结果表明，定居个体的非繁殖季存活率越高，定居个体与迁徙个体的感染率便越高，同时种群中的迁徙个体占比则越低。若定居习性促使强毒力病原体出现、若资源补给降低了定居个体的感染代价、若感染削弱了个体的迁徙倾向，则迁徙的存续性可能会受到尤为严重的威胁。本文隶属于"Anthropogenic resource subsidies and host–parasite dynamics in wildlife"专题专辑。