Aim Palaeoecological data are crucial for comprehending large-scale biodiversity patterns and the natural and anthropogenic drivers that influence them over time. Over the last decade, the availability of open-access research databases of palaeoecological proxies has substantially increased. These databases open the door to research questions needing advanced numerical analyses and modelling based on big-data compilations. However, compiling and analysing palaeoecological data pose unique challenges that require a guide for producing standardized and reproducible compilations. Innovation We present a step-by-step guide of how to process fossil pollen data into a standardized dataset compilation ready for macroecological and palaeoecological analyses. We describe successive criteria that will enhance the quality of the compilations. Though these criteria are project and research question-dependent, we discuss the most important assumptions that should be considered and adjusted accordingly. Our guide is accompanied by an R-workflow—called FOSSILPOL—and corresponding R-package—called R-Fossilpol—that provide a detailed protocol ready for interdisciplinary users. We illustrate the workflow by sourcing and processing Scandinavian fossil pollen datasets and show the reproducibility of continental-scale data processing. Main Conclusions The study of biodiversity and macroecological patterns through time and space requires large-scale syntheses of palaeoecological datasets. The data preparation for such syntheses must be transparent and reproducible. With our FOSSILPOL workflow and R-package, we provide a protocol for optimal handling of large compilations of fossil pollen datasets and workflow reproducibility. Our workflow is also relevant for the compilation and synthesis of other palaeoecological proxies and as such offers a guide for synthetic and cross-disciplinary analyses with macroecological, biogeographical and palaeoecological perspectives. However, we emphasize that expertise and informed decisions based on palaeoecological knowledge remain crucial for high-quality data syntheses and should be strongly embedded in studies that rely on the increasing amount of open-access palaeoecological data. 

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/geb.13693

A guide to the processing and standardization of global palaeoecological data for large‐scale syntheses using fossil pollen

Pollen taxonomic harmonisation involves the standardisation of the nomenclature of pollen and fern spores with similar morphotypes at the determination level that is common to all grains or spores with that morphotype within the pollen sequence(s) of interest. Such harmonisation is required prior to subsequent investigations such as numerical analysis, comparing, mapping, synthesis, and environmental reconstruction involving several pollen sequences. Here we present two approaches to harmonisation. These are a 'top-down' and a 'bottom-up' approach. The bottom-up approach is preferred. It is based on the concept of the regional pollen flora for the sequence(s) in the spatial area(s) of study. We present bottom-up harmonisation tables for the continental or sub-continental scales developed for the Humans on Planet Earth (HOPE) project. The tables are for North America, Latin America, Europe, Asia (three parts), and Indo-Pacific. These harmonisations are project-specific and sequence-specific, relating to the geographical area and to the sequences in the area under consideration, both of which are linked to the research questions being addressed. A new bottom-up harmonisation with a consistent taxonomic level and nomenclature is needed when additional sequences or areas are added. However, the HOPE tables can serve as a starting point for further research involving multi-sequence analyses or syntheses. 

Approaches to pollen taxonomic harmonisation in Quaternary palynology


 The fossil record is spatiotemporally heterogeneous: taxon occurrence data have patchy spatial distributions, and this patchiness varies through time. Large-scale quantitative paleobiology studies that fail to account for heterogeneous sampling coverage will generate uninformative inferences at best and confidently draw wrong conclusions at worst. Explicitly spatial methods of standardization are necessary for analyses of large-scale fossil datasets, because nonspatial sample standardization, such as diversity rarefaction, is insufficient to reduce the signal of varying spatial coverage through time or between environments and clades. Spatial standardization should control both geographic area and dispersion (spread) of fossil localities. In addition to standardizing the spatial distribution of data, other factors may be standardized, including environmental heterogeneity or the number of publications or field collecting units that report taxon occurrences. Using a case study of published global Paleobiology Database occurrences, we demonstrate strong signals of sampling; without spatial standardization, these sampling signatures could be misattributed to biological processes. We discuss practical issues of implementing spatial standardization via subsampling and present the new R package divvy to improve the accessibility of spatial analysis. The software provides three spatial subsampling approaches, as well as related tools to quantify spatial coverage. After reviewing the theory, practice, and history of equalizing spatial coverage between data comparison groups, we outline priority areas to improve related data collection, analysis, and reporting practices in paleobiology.

Spatial standardization of taxon occurrence data—a call to action

Click to increase image sizeClick to decrease image size AcknowledgmentsWe are grateful to the Indonesia Endowment Fund for Education (LPDP RI) for funding and supporting our master’s studies at IPB University.Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThe work was supported by the Lembaga Pengelola Dana Pendidikan. 

Paleoneurology of amniotes: new directions in the study of fossil endocasts

The postdoctoral blueprint part two: the faculty application


 Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite—or even spurred by—this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/06257CFF62B32846B5C90F939BCC744E/S0094837323000039a.pdf/div-class-title-challenges-and-directions-in-analytical-paleobiology-div.pdf

Challenges and directions in analytical paleobiology

You’ve finally completed your dissertation research and have your PhD in hand—yay! Maybe you’re also in the middle of a postdoctoral position. If you’re reading this article, chances are you are actively searching for and applying for faculty positions. (Check out reference [1] if you’re early in the application process and [2] for additional advice!) Unfortunately, many graduate students and postdocs are not taught the skills necessary for acquiring a faculty position after passing the “looks good on paper” part of the application and securing an on-campus interview. One of the last crucial steps in earning a faculty position is your academic job talk. No matter how great of a scientist you are, if you cannot give a compelling job talk, chances are low that you will be hired. Yet many candidates receive little guidance on how to ace this unique and vital test.

To help address this gap, we have put together these ten simple rules that will help you give an effective job talk. To be clear, these are rules developed for the academic job talk in a research-heavy department, which is typically in a seminar format. These rules are not targeted toward other formats such as chalk talks or teaching demonstrations, although some pointers may still apply. We are a group primarily composed of University of California, Los Angeles (UCLA) faculty, postdocs, and graduate students who participated in two recent job searches in the Ecology and Evolutionary Biology Department. We evaluated ten job talks over the span of 2 months and discussed their strengths and weaknesses in a weekly seminar course. These ten rules are based on our discussions of what worked (and what didn’t) across the variety of job talks we observed, as well as our various experiences on the job market and search committees over the years.

/pdf/ten-simple-rules-for-giving-an-effective-academic-job-talk-pkhxdlua6g.pdf

Ten simple rules for giving an effective academic job talk

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Challenges and directions in analytical paleobiology

Ten simple rules for giving an effective academic job talk