More Like this

1. MetaIPM: Placing integral projection models into a metapopulation framework

   https://doi.org/10.1111/2041-210X.14156  

   Erickson, Richard A. ; Peirce, James P. ; Sandland, Greg J. ; Thompson, Hannah M. ; Coulter, Alison A. ; Glover, David C. ( June 2023 , Methods in Ecology and Evolution)

   Metapopulation models include spatial population dynamics such as dispersion and migration between subpopulations. Integral projection models (IPMs) can include demographic rates as a function of size. Traditionally, metapopulation models do not included detailed populaiton models such as IPMs. In some situations, both local population dynamics (e.g. size‐based survival) and spatial dynamics are important.

   We present a Python package,MetaIPM, which places IPMs into a metapopulation framework, and allow users to readily construct and apply these models that combine local population dynamics within a metapopulation framework.

   MetaIPMincludes an IPM for each subpopulation that is connected to other subpopulations via a metapopulation movement model. These movements can include dispersion, migration or other patterns. The IPM can include for size‐specific demographic rates (e.g. survival, recruitment) as well as management actions, such as length‐based harvest (e.g. gear specific capture sizes, varying slot limits across political boundaries). The model also allows for changes in metapopulation connectivity between locations, such as a fish passage ladders to enhance movement or deterrents to reduce movement. Thus, resource managers can useMetaIPMto compare different management actions such as the harvest gear type (which can be length‐specific) and harvest locations.

   We demonstrate howMetaIPMmay be applied to inform managers seeking to limit the spread of an invasive species in a system with important metapopulation dynamics. Specifically, we compared removal lengths (all length fish versus longer fish only) for an invasive fish population in a fragmented, inland river system.MetaIPMallowed users to compare the importance of harvesting source populations away from the invasion front, as well as species at the invasion front. The model would also allow for future comparisons of different deterrent placement locations in the system.

   Moving beyond our example system, we describe howMetaIPMcan be applied to other species, systems and management approaches. TheMetaIPMpackages includes Jupyter Notebooks documenting the package as well as a second set of JupyterNotebooks showing the application of the package to our example system.

    

   more » « less
2. Quantifying Structural Uncertainty in Paleoclimate Data Assimilation With an Application to the Last Millennium

   https://doi.org/10.1029/2020GL090485  

   Amrhein, Daniel E. ; Hakim, Gregory J. ; Parsons, Luke A. ( November 2020 , Geophysical Research Letters)

   Paleoclimate reconstruction relies on estimates of spatiotemporal relationships among climate quantities to interpolate between proxy data. This work quantifies how structural uncertainties in those relationships translate to uncertainties in reconstructions of past climate. We develop and apply a data assimilation uncertainty quantification approach to paleoclimate networks and observational uncertainties representative of data for the last millennium. We find that structural uncertainties arising from uncertain spatial covariance relationships typically contribute 10% of the total uncertainty in reconstructed temperature variability at small (∼200 km), continental, and hemispheric length scales, with larger errors (50% or larger) in regions where long‐range climate covariances are least certain. These structural uncertainties contribute far more to errors in uncertainty quantification, sometimes by a factor of 5 or higher. Accounting for and reducing uncertainties in climate model dynamics and resulting covariance relationships will improve paleoclimate reconstruction accuracy.

    

   more » « less
3. An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life

   https://doi.org/10.1111/2041-210X.13182  

   Chang, Jonathan ; Rabosky, Daniel L. ; Smith, Stephen A. ; Alfaro, Michael E. ; Silvestro, ed., Daniele ( April 2019 , Methods in Ecology and Evolution)

   Comprehensive, time‐scaled phylogenies provide a critical resource for many questions in ecology, evolution and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging.

   We introduce the Fish Tree of Life website and associatedrpackagefishtreeto provide convenient access to sequences, phylogenies, fossil calibrations and diversification rate estimates for the most diverse group of vertebrate organisms, the ray‐finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by therpackage, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyse the data.

   We demonstrate functionality with an overview of the website, and show three examples of advanced usage through therpackage. First, we test for the presence of long branch attraction artefacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package.

   This resource makes a large comparative vertebrate dataset easily accessible via the website, while therpackage enables the rapid reuse and reproducibility of research results via its ability to easily integrate with otherrpackages and software for molecular biology and comparative methods.

    

   more » « less
4. Database interoperability, uncertainty quantification and reproducible workflows in the paleogeosciences

   https://doi.org/10.5281/zenodo.6780665  

   McKay, N ; Emile-Geay, J. ; Khider, D ( June 2022 , Earthcube Annual Meeting 2022)

   McHenry, K ; Schreiber, L (Ed.)

   The paleogeosciences are becoming more and more interdisciplinary, and studies increasingly rely on large collections of data derived from multiple data repositories. Integrating diverse datasets from multiple sources into complex workflows increases the challenge of creating reproducible and open science, as data formats and tools are often noninteroperable, requiring manual manipulation of data into standardized formats, resulting in a disconnect in data provenance and confounding reproducibility. Here we present a notebook that demonstrates how the Linked PaleoData (LiPD) framework is used as an interchange format to allow data from multiple data sources to be integrated in a complex workflow using emerging packages in R for geochronological uncertainty quantification and abrupt change detection. Specifically, in this notebook, we use the neotoma2 and lipdR packages to access paleoecological data from the Neotoma Database, and paleoclimate data from compilations hosted on Lipdverse. Age uncertainties for datasets from both sources are then quantified using the geoChronR package, and those data, and their associated age uncertainties, are then investigated for abrupt changes using the actR package, with accompanying visualizations. The result is an integrated, reproducible workflow in R that demonstrates how this complex series of multisource data integration, analysis and visualization can be integrated into an efficient, open scientific narrative. 

   more » « less
5. Eocene Araucaria Sect. Eutacta from Patagonia and floristic turnover during the initial isolation of South America

   https://doi.org/10.1002/ajb2.1467  

   Rossetto‐Harris, Gabriella ; Wilf, Peter ; Escapa, Ignacio H. ; Andruchow‐Colombo, Ana ( May 2020 , American Journal of Botany)

   Eocene floras of Patagonia document biotic response to the final separation of Gondwana. The conifer genusAraucaria, distributed worldwide during the Mesozoic, has a disjunct extant distribution between South America and Australasia. Fossils assigned to AustralasianAraucariaSect.Eutactausually are represented by isolated organs, making diagnosis difficult.Araucaria pichileufensisE.W. Berry, from the middle Eocene Río Pichileufú (RP) site in Argentine Patagonia, was originally placed in Sect.Eutactaand later reported from the early Eocene Laguna del Hunco (LH) locality. However, the relationship ofA. pichileufensisto Sect.Eutactaand the conspecificity of theAraucariamaterial among these Patagonian floras have not been tested using modern methods.

   We review the type material ofA. pichileufensisalongside large (n= 192) new fossil collections ofAraucariafromLHandRP, including multi‐organ preservation of leafy branches, ovuliferous complexes, and pollen cones. We use a total evidence phylogenetic analysis to analyze relationships of the fossils to Sect.Eutacta.

   We describeAraucaria huncoensissp. nov. fromLHand improve the whole‐plant concept forAraucaria pichileufensisfromRP. The two species respectively resolve in the crown and stem of Sect.Eutacta.

   Our results confirm the presence and indicate the survival of Sect.Eutactain South America during early Antarctic separation. The exceptionally complete fossils significantly predate several molecular age estimates for crownEutacta. The differentiation of twoAraucariaspecies demonstrates conifer turnover during climate change and initial South American isolation from the early to middle Eocene.

    

   more » « less