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This paper discusses opportunities for developments in spatial clustering methods to help leverage broad scale community science data for building species distribution models (SDMs). SDMs are tools that inform the science and policy needed to mitigate the impacts of climate change on biodiversity. Community science data span spatial and temporal scales unachievable by expert surveys alone, but they lack the structure imposed in smaller scale studies to allow adjustments for observational biases. Spatial clustering approaches can construct the necessary structure after surveys have occurred, but more work is needed to ensure that they are effective for this purpose. In this proposal, we describe the role of spatial clustering for realizing the potential of large biodiversity datasets, how existing methods approach this problem, and ideas for future work. 

The growth of biodiversity data sets generated by citizen scientists continues to accelerate. The availability of such data has greatly expanded the scale of questions researchers can address. Yet, error, bias, and noise continue to be serious concerns for analysts, particularly when data being contributed to these giant online data sets are difficult to verify. Counts of birds contributed to eBird, the world’s largest biodiversity online database, present a potentially useful resource for tracking trends over time and space in species’ abundances. We quantified counting accuracy in a sample of 1,406 eBird checklists by comparing numbers contributed by birders (N = 246) who visited a popular birding location in Oregon, USA, with numbers generated by a professional ornithologist engaged in a long-term study creating benchmark (reference) measurements of daily bird counts. We focused on waterbirds, which are easily visible at this site. We evaluated potential predictors of count differences, including characteristics of contributed checklists, of each species, and of time of day and year. Count differences were biased toward undercounts, with more than 75% of counts being below the daily benchmark value. Median count discrepancies were −29.1% (range: 0 to −42.8%; N = 20 species). Model sets revealed an important influence of each species’ reference count, which varied seasonally as waterbird numbers fluctuated, and of percent of species known to be present each day that were included on each checklist. That is, checklists indicating a more thorough survey of the species richness at the site also had, on average, smaller count differences. However, even on checklists with the most thorough species lists, counts were biased low and exceptionally variable in their accuracy. To improve utility of such bird count data, we suggest three strategies to pursue in the future. (1) Assess additional options for analytically determining how to select checklists that include less biased count data, as well as exploring options for correcting bias during the analysis stage. (2) Add options for users to provide additional information that helps analysts choose checklists, such as an option for users to tag checklists where they focused on obtaining accurate counts. (3) Explore opportunities to effectively calibrate citizen-science bird count data by establishing a formalized network of marquis sites where dedicated observers regularly contribute carefully collected benchmark data. 

Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old‐growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird‐pollinated understorey herb,Heliconia tortuosa, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation and pollinator assemblages on genetic diversity and levels of inbreeding inH. tortuosa. We found that inbreeding was up to three times higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long‐distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants—an inference we tested using empirically parameterized simulations. Higher levels of inbreeding inH. tortuosaare therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understorey plant.

 

The spatial habitat heterogeneity hypothesis posits that habitat complexity increases the abundance and diversity of species. In tropical forests, lianas add substantial habitat heterogeneity and complexity throughout the vertical forest profile, which may maintain animal abundance and diversity. The effects of lianas on tropical animal communities, however, remain poorly understood. We propose that lianas have a positive effect on animals by enhancing habitat complexity. Lianas may have a particularly strong influence on the forest bird community, providing nesting substrate, protection from predators, and nutrition (food). Understory insectivorous birds, which forage for insects that specialize on lianas, may particularly benefit. Alternatively, it is possible that lianas have a negative effect on forest birds by increasing predator abundances and providing arboreal predators with travel routes with easy access to bird nests. We tested the spatial habitat heterogeneity hypothesis on bird abundance and diversity by removing lianas, thus reducing forest complexity, using a large‐scale experimental approach in a lowland tropical forest in the Republic of Panama. We found that removing lianas decreased total bird abundance by 78.4% and diversity by 77.4% after 8 months, and by 40.0% and 51.7%, respectively, after 20 months. Insectivorous bird abundance and diversity 8 months after liana removal were 91.8% and 89.5% lower, respectively, indicating that lianas positively influence insectivorous birds. The effects of liana removal persisted longer for insectivorous birds than other birds, with 77.3% lower abundance and 76.2% lower diversity after 20 months. Liana removal also altered bird community composition, creating two distinct communities in the control and removal plots, with disproportionate effects on insectivores. Our findings demonstrate that lianas have a strong positive influence on the bird community, particularly for insectivorous birds in the forest understory. Lianas may maintain bird abundance and diversity by increasing habitat complexity, habitat heterogeneity, and resource availability.

 

Hummingbirds are important pollinators of many native Neotropical plants but their abundance and diversity in landscapes dominated by intensive human uses such as agriculture have rarely been examined, despite such land‐uses prevailing in the tropics. We examined how tropical deforestation affects hummingbird community structure in premontane forest patches embedded in a tropical countryside of Coto Brus Canton, Costa Rica. We captured hummingbirds in fourteen landscapes representing a gradient in patch size and forest amount, and tested for the effects of these variables on (1) hummingbird captures at flowers (pollinator availability); (2) species richness; and (3) filtering of functional traits. After accounting for sampling effects, both hummingbird availability and species richness declined by 40% and 50%, respectively, across the gradient in deforestation that we observed (9–66% forest within 1000 m). Focal patch size was the strongest predictor, even after statistically accounting for the amount of forest and matrix composition of landscapes. These reductions in availability and richness were well predicted by functional traits; morphologically specialized species with the capacity to transport long‐distance outcrossed pollen and low functional redundancy within the pollinator network showed the greatest sensitivity to landscape change. We hypothesize that declines in hummingbird availability, diversity, and functional traits are important mechanisms driving the observed pollen limitation of ornithophilous flowers in fragmented tropical landscapes. Efforts to conserve large forest patches and enhance matrix permeability are critical for maintaining forest hummingbird communities and pollination services under current and predicted deforestation regimes.