Data from: Habitat selection in transformed landscapes and the role of forest remnants and shade coffee in the conservation of resident birds

1. Biodiversity conservation in transformed landscapes is becoming increasingly important. However, most assessments of the value of modified habitats rely heavily on species presence and/or abundance, masking ecological processes such as habitat selection and phenomena like ecological traps, which may render species persistence uncertain. High species richness has been documented in tropical agroforestry systems but comparisons with native habitat remnants generally lack detailed information on species demography and habitat use. 2. We generated a multi-species, multi-measure framework to evaluate the role of habitat selection in the adaptation of species to transformed landscapes, and demonstrate that its use could affect how we value the contribution different land uses make to biodiversity conservation. 3. We analyzed seven years of capture-mark-recapture and observation data for twelve species of resident birds present in native forest remnants and shade coffee plantations in a mega-diverse region. We assessed whether species behaved adaptively by evaluating the correlation between measures of habitat preference (occurrence, abundance, fidelity, inter-seasonal variance and age) and performance (body condition, muscle, primary molt, breeding and juveniles) in forest and coffee, and generated hypotheses about their role in species persistence. 4. We documented adaptive habitat selection for seven species, non-ideal selection for four, and maladaptive selection for one. While many species showed equal-preference and/or equal performance in many traits, in general we found more evidence for birds preferring and/or performing better in forest than coffee, although relationships between our indicators and population adaptation need to be studied further before our proposed framework can be applied to more species and landscapes. 5. While shade coffee can act as a biodiversity-friendly matrix providing complementary or supplementary habitat to a wide range of resident bird species, protecting remnants of native vegetation is still of paramount importance for biodiversity conservation in agricultural landscapes. 28-Aug-20191. 人为改造景观中的生物多样性保护正变得愈发重要。然而，当前多数针对生境改造区域价值的评估高度依赖物种存在与否及其种群丰度，这掩盖了诸如生境选择一类的生态过程，以及生态陷阱（ecological traps）一类的现象，而这些过程与现象可能会使物种种群存续的前景变得不确定。现有研究已证实热带农林业系统拥有较高的物种丰富度，但相较于原生植被残留斑块的相关研究，这类系统通常缺乏关于物种种群统计特征与生境利用情况的详细数据。2. 本研究构建了一个多物种、多指标的分析框架，用于评估生境选择在物种适应人为改造景观过程中所发挥的作用，并证明运用该框架可改变我们对不同土地利用方式在生物多样性保护中贡献的评估逻辑。3. 本研究分析了某生物多样性极高区域内，原生森林残留斑块与遮阴咖啡种植园中12种留鸟的7年标记重捕与观测数据。通过评估森林与咖啡种植园中生境偏好指标（包括出现情况、种群丰度、栖息保真度、季间变异度与年龄结构）与种群表现指标（包括身体状况、肌肉状态、初级飞羽换羽、繁殖情况及幼鸟种群规模）之间的相关性，本研究判断物种是否展现出适应性行为，并据此提出了关于生境选择在物种种群存续中所起作用的相关假说。4. 本研究记录到7个物种展现出适应性生境选择、4个物种展现出非理想生境选择，另有1个物种展现出适应不良的生境选择。尽管多数物种在多项性状上表现出无差异的生境偏好与/或无差异的种群表现，但整体而言，我们发现更多证据表明，相较于遮阴咖啡种植园，留鸟更倾向于选择原生森林，且在原生森林中的种群表现更佳。不过，在将本研究提出的框架推广至更多物种与景观前，仍需进一步探究本研究使用的各类指标与种群适应性之间的关联。5. 尽管遮阴咖啡种植园可作为利于生物多样性的景观基质，为多种留鸟提供补充性生境，但在农业景观中开展生物多样性保护时，保护原生植被残留斑块仍具有至高无上的重要性。2019年8月28日