Syllabus
The course will be divided into sessions in the class, mostly covering theoretical background, which will lay the ground for exercise at home. All topics, data, tasks for their analyses and results will be managed and collected within Moodle. https://dl2.cuni.cz/course/view.php?id=2321
Block 1
Introduction to data formats
Data formats in paleoecology and biostratigraphy, data collection, file formats. Entering data into spreadsheet, calculations of percentages, import, export, data presentation (optional use of Tilia and/or C2 programs/or Rioja package in R).
Databases
Data bases and their use in biostratigraphy and palaeoecology. Data structure, relational tables. PostgreSQL. Import, export for numerical analyses. Examples of global data bases. Use of data from the databases.
Block 2
General information on dating and age-depth modelling
Calibration of single radiocarbon date. Various calibration curves. Classical and Bayesian age-depth modelling (CLAM, BACON, OXCAL). Adding different age controls to a sequence.
Quantification of numerical differences between fossil/modern assemblages
Introduction to dissimilarity indices. Calculation of dissimilarity indices for stratigraphic, determining the rate-of-change. Use of dissimilarity indices in further analyses.
Rate of change.
Classification and stratigraphically constrained classification, zonation, cluster analysis
How many zones are there in my stratigraphy? Divisive and agglomerative techniques (CONISS, CONSLINK, splitting, broken stick model), determining the change using a threshold.
Block 3
The dissimilarity between multivariate time-series
Comparison of two sequences assuming stratigraphic order of their samples
Introduction to multivariate data analysis
Data reduction by reducing number of dimensions. Use of dissimilarity indices. Introduction to ordination for use in palaeoecology. Indirect (PCA, CA, DCA) and direct (RDA, CCA) techniques. DCCA in paleoecology. NMDS.
Block 4
Reconstruction in paleoecology – modern analog technique and transfer functions
Modern training datasets. Classical and inverse methods. Weighted averaging, partial least squares regressions, modern analog technique, and analog matching.
Diversity in fossil assemblages
Why be concerned with diversity in the past? Two aspects of diversity: species richness and evenness. Introduction to diversity indices. Rarefaction, evenness.
Block 5
Introduction to quantitative palynology
POLLSCAPE, simulation of vegetation and pollen spectra. Pollen productivity estimates.
Block 6
Landscape Reconstruction Algorithm
Theory of pollen analysis with the use of landscape reconstruction algorithm. Past vegetation reconstruction.
Software for biostratigraphy: Tilia database and graphical program, C2 program
Collection of primary stratigraphical data, taxonomy, collection of various metadata
Neotoma Palaeoecology Database – use of Tilia with the database
Annotation
The participant will be introduced to the main format of palaeoecological data, will be able to recognize them, process them into the form of graphical output, and interpret it. The participant will list the main numerical analyses applicable to palaeoecological data, will be able to choose the best technique for statistical analysis and apply it to the data.
The student will also examine particular scientific questions by proper numerical analysis. Finally, the student will be able to interpret the results, compare and evaluate different outcomes.
The participant will learn to work with main open-access databases and design analyses for broader data syntheses.