Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data.

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal-extinction-sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography

Amazonia is the primary source of Neotropical biodiversity.

The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (∼1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas

CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases

© 2019 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society. Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

Taxonomic sufficiency represents the level of taxonomic detail needed to detect ecological patterns to a level that match the requirement of a study. Most bioassessments apply the taxonomic sufficiency concept and assign specimens to the family or genus level given time constraints and the difficulty to correctly identify species. This holds particularly true for stream invertebrates because small and morphologically similar larvae are hard to distinguish. Low taxonomic resolution may hinder detecting true community dynamics, which thus leads to incorrect inferences about community assembly processes. DNA metabarcoding is a new, affordable and cost-effective tool for the identification of multiple species from bulk samples of organisms. As it provides high taxonomic resolution, it can be used to compare results obtained from different identification levels. Measuring the effect of taxonomic resolution on the detection of community dynamics is especially interesting in extreme ecosystems like intermittent streams to test if species at intermittent sites are subsets of those from perennial sources or if independently recruiting taxa exist. Here we aimed to compare the performance of morphological identification and metabarcoding to detect macroinvertebrate community dynamics in the Trebbia River (Italy). Macroinvertebrates were collected from four perennial and two intermittent sites two months after flow resumption and before the next dry phase. The identification level ranged from family to haplotype. Metabarcoding and morphological identifications found similar alpha diversity patterns when looking at family and mixed taxonomic levels. Increasing taxonomic resolution with metabarcoding revealed a strong partitioning of beta diversity in nestedness and turnover components. At flow resumption, beta diversity at intermittent sites was dominated by nestedness when family-level information was employed, while turnover was evidenced as the most important component when using Operational Taxonomic Units (OTUs) or haplotypes. The increased taxonomic resolution with metabarcoding allowed us to detect species adapted to deal with intermittency, like the chironomid Cricotopus bicinctus and the ephemeropteran Cloeon dipterum. Our study thus shows that family and mixed taxonomic level are not sufficient to detect all aspects of macroinvertebrate community dynamics. High taxonomic resolution is especially important for intermittent streams where accurate information about species-specific habitat preference is needed to interpret diversity patterns induced by drying and the nestedness/ turnover components of beta diversity are of interest to understand community assembly processes

Chilean Bromeliaceae: diversity, distribution and evaluation of conservation status

Abstract Chile is home to 23 species of Bromeliaceae, including 2 subspecies and 4 varieties. Twenty species are endemic to the country. We examined 883 herbarium specimens from 27 herbaria for our treatment of the Bromeliaceae for the ''Flora de Chile''. These data and field observations resulted in a comprehensive database that we used to generate distribution maps for each species. We applied ecological niche modelling to reveal distribution areas and centers of Bromeliaceae diversity. We further analysed the collecting dates of the herbarium specimens to assess possible changes in species abundance. In this study we assess the conservation status of the bromeliad species in Chile. IUCN categories were assigned to the 27 bromeliad taxa as follows: Critically endangered: 4, Endangered: 6, Vulnerable: 11, Near threatened: 2, Least concern: 4. No species has become ''Extinct'' up to now. We also put forth a hypothesis about their biogeographic history

Transitions between biomes are common and directional in Bombacoideae (Malvaceae)

This is the final version. Available from Wiley via the DOI in this record.Aim: To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location: The tropics. Time period: The Cenozoic. Major taxa studied: The plant subfamily Bombacoideae (Malvaceae). Methods: We inferred ancestral biomes based on a fossil-dated molecular phylogeny of 103 species (59% of the clade) and recorded the number of transitions among biomes using biogeographical stochastic mapping based on the dispersal-extinction-cladogenesis model. We then estimated diversification rates using state-specific speciation and extinction rate (SSE) methods. Furthermore, we tested the sensitivity of the results to model choice, phylogenetic uncertainty, measurement error and biome definition. Results: We found numerous transitions from evergreen rain forest to seasonally dry biomes, and fewer in the opposite direction. These results were robust to methodological choices. Biome type did not influence diversification rates, although this result was subject to uncertainty, especially related to model choice and biome definition. Main conclusions: Our results contradict the idea of evolutionary biome conservatism in Bombacoideae, and support previous findings that evergreen rain forests serve as a source for the flora of seasonally dry biomes. The impact of biome classification and biome definition on the results suggest caution when using a biome concept for biogeographical reconstruction and diversification rate analysis.German Research FoundationKnut and Alice Wallenberg FoundationSwedish Foundation for Strategic ResearchRoyal Botanic GardensKew. CDBSwedish Research Counci

Pre‐adaptation and adaptation shape trait‐environment matching in the Neotropics

This is the final version. Available from Wiley via the DOI in this record. Phylogenetic data (BEAST configuration file, MCC tree and posterior set of trees), trait, environment, and occurrence data, and R script to extract trait data from monographs can be found in the supplementary files in Dryad repository: https://doi.org/10.5061/dryad.vhhmgqnzq.Aim: Functional traits shape the distribution of taxa across environments. However, it remains unclear whether trait and environmental niche evolution are correlated, and what happened first: trait change facilitating environment shifts (pre-adaptation) or environmental change leading to trait change (adaptation). We focus on a species-rich Neotropical legume radiation to shed light on this enigma. Location: Neotropics. Time Period: Cenozoic. Major Taxa Studied: Fabaceae: Papilionoidae: Swartzia. Methods: We assembled leaflet, fruit and petal size data from monographs and herbarium collections for 86 to 96% of the c. 180 Swartzia species, inferred a dated Swartzia phylogenetic tree from existing DNA sequences covering 38% of the species and integrated these with distribution, soil and climate data. We used phylogenetic linear regression to quantify trait–environment relationships and applied comparative methods to evaluate modes of correlated evolution between traits and environments. Results: Leaflet and petal size were strongly linked to climate, while fruit size was not associated with climate or soil characteristics. Evolutionary transitions to relatively low rainfall and low temperature environments were conditional on the evolution of small leaflets, whereas transitions to wet and warm environments were preceded by the evolution of larger leaflets. In contrast, transitions to the warmest or coldest environments were followed, rather than preceded, by petal loss. Main Conclusion: Our results show that the macroevolution of functional traits has influenced the broad-scale distribution of Swartzia across Neotropical rainforest, seasonally dry, montane and inundated habitats. We suggest that trait evolution is conditional on environmental change but both pre-adaptive and adaptive processes may occur. These processes are important to understand the distribution of diversity at both regional (e.g. Amazonia) and global biogeographical scales.German Research Foundation (DFG