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