Data from: Genomics meets applied ecology: characterizing habitat quality for sloths in a tropical agroecosystem

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field-based estimates of fitness components and Approximate Bayesian Computation (ABC) procedures to estimate habitat-specific dispersal rates and characterize habitat quality in two-toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field-based observations indicated that birth and survival rates were similar in a sparsely-shaded cacao farm and adjacent cattle pasture-forest mosaic. Sloth density was threefold higher in pasture compared to cacao, whereas home range size and overlap were greater in cacao compared to pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 SNP and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstory can, in some cases, constitute lower quality habitat than pasture-forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field-based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.

理解异质景观中的栖息地质量如何调控个体的分布与适合度，是生态学的核心研究议题之一。尽管个体平均适合度通常被视为评估栖息地质量的关键指标，但要全面理解异质景观中的栖息地质量，仍需估算不同生境类型间的扩散速率。基因组学技术的可及性不断提升，结合野外种群统计方法，为将扩散速率估算纳入栖息地质量评估提供了全新契机。本研究将基因组亲缘关系分析方法、野外种群适合度组分估算方法与近似贝叶斯计算（Approximate Bayesian Computation, ABC）流程相结合，旨在估算不同生境的专属扩散速率，并解析栖息于哥斯达黎加某农业生态系统中的二趾树懒（*Choloepus hoffmanni*）的栖息地质量。野外观测显示，在一片稀疏遮荫的可可种植园及其邻近的牛牧地-森林镶嵌景观中，树懒的出生率与存活率相近。相较于可可种植园，牧地中的树懒种群密度为其3倍；但可可种植园中的树懒家域面积与家域重叠度更高。通过对利用3431个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点与11个微卫星位点的基因型鉴定出的亲缘个体对的空间分布进行ABC流程分析，估算得到两种生境中的扩散速率并无显著差异。本研究结果表明，在部分情境下，稀疏冠层下种植的作物生境，其质量可能低于牛牧地-森林镶嵌景观，这或许与食物资源或捕食者群落的差异有关。综上，本研究证实，将野外种群统计方法与基因组学技术相结合，可为解析异质景观中动物种群的栖息地质量提供高效可靠的研究手段。