Incorporating Topological and Age Uncertainty into Event-Based Biogeography of Sand Spiders Supports Paleo-Islands in Galapagos and Ancient Connections among Neotropical Dry Forests

Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are rarely accounted for, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. Using a custom R script, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now submerged; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean + Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter (“+J”) are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation.

Community-Based Importance and Quantification of Ecosystem Services, Disservices, Drivers, and Neotropical Dry Forests in a Rural Colombian Municipality

Few studies analyze people’s preferences for ecosystem services (ES), disservices (ED) and drivers of change in less populated, tropical municipalities. Understanding such preferences and needs by the community and stakeholder groups before actually assessing, modelling, and measuring the supply of ES is key for decision-making and planning in municipalities, as well as for the conservation of nearby neotropical dry forests. We studied these dynamics in a small rural municipality in Colombia with limited data availability using semi-structured interviews and surveys, as well as ES-proxies and geospatial analyses. We then analyzed the supply and importance of two community identified ES and one ED from adjacent neotropical dry forests during 2005–2017. We found that respondents recognized air purification and food production as the most important ES. Increased temperatures and fires were the most important ED, while fires were also identified as an important driver of change. Air purification, via pollutant deposition to forest cover, remained approximately constant (116 ton/year), while food production (49 ton/ha) and fire occurrence, an ED, increased. Findings show how transdisciplinary research and participatory knowledge co-production among local communities, researchers and land management institutions can improve governance, decision making, policy uptake and planning efforts.

Incorporating topological and age uncertainty into event-based biogeography supports paleo-islands in Galapagos and ancient connections among Neotropical dry forests

Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are seldom taken into account, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. By using a custom R script made available here, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now drowned; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean+Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter (+J) are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation.

Diversity of phenological patterns of Handroanthus ochraceus (Bignoniaceae) in Costa Rica

The study of phenological patterns in plant communities is of vital importance for understanding the temporal cycles of ecosystems, but there is little information on the diversity of phenological patterns that can occur at the intraspecific level, as well as the genetic or environmental factors causing this variation. In Handroanthus ochraceus, a deciduous tree species of neotropical dry forests, ecophysiological studies have proposed the release of water stress as the mechanism that triggers flowering and the sprouting of new leaves. During four years, I observed the cycles of leaf fall, flowering, fruiting, and new leaf production in seven Costa Rican sites that differed in their proximity to water courses and in soil moisture. Six were located in dry forest areas, and one in premontane forest. There were two general phenological patterns: the explosive, where trees depend on the first rains for floral anthesis and the expansion of leaf meristems, and the staggered pattern, with unsynchronized flowering at the beginning and middle of the dry season, independently of rainfall. Although this phenological variation has been previously recognized, the occurrence of these two patterns is not determined by the proximity of water courses, contradicting phenological models proposed for this tree species.

Seasonality in abundance and detection bias of birds in a tropical dry forest in north-eastern South America

Seasonal fluctuations in bird abundance are expected in semi-arid environments, but estimates may be biased if detectability is not considered. In a tropical dry forest in north-eastern Brazil, we evaluated whether bird abundance is highly seasonal, and associated with time-specific variability in detectability. We mark-recaptured birds with mist nets over three field visits (3487 records from 75 species), and used closed-capture models to estimate detectability and abundance in birds divided into three groups (all, residents, insectivores). In the two dry periods, the best models resulted in capture estimates at least three times larger than recapture, and both estimates were twice that of when rains occurred on the day preceding sampling. Abundance varied between dry and wet periods from 4.0 (from 115 ± 34 to 479 ± 144) to 13 times (183 ± 8 to 2463 ± 351). Estimates were 1.5–3.2 times greater in the dry period when behavioural responses of birds were excluded from capture-recapture models. Meanwhile, in the wet period the relative abundance was between 33–76% smaller than best-fit models estimated. This study found variation in avian abundance greater than that observed in other Neotropical dry forests, and indicates that biases may be common when not including detectability.

Assessing ecosystem services in Neotropical dry forests: a systematic review

SUMMARYThere is an increasing consensus on the importance of understanding ecosystem service (ES) provision in order to facilitate decision making and the sustainable management of Neotropical dry forests (NTDFs), yet research on the ESs provided by NTDFs is limited. We identified the main existing gaps and trends in the quantification of provisioning, regulating and supporting ESs in NTDFs. Systematic web-based searches showed that research has been increasing in recent decades in NTDFs, supporting greater ES knowledge and assessment. Carbon storage and biodiversity are the main subjects under study, while ESs relating to water and soil lack investigation. The most common approaches for assessing ES were fauna and plant inventories, carbon dynamics and ecological processes.