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Python is used in a wide range of geoscientific applications, such as in processing images for remote sensing, in generating and processing digital elevation models, and in analyzing time series. This book introduces methods of data analysis in the geosciences using Python that include basic statistics for univariate, bivariate, and multivariate data sets, time series analysis, and signal processing; the analysis of spatial and directional data; and image analysis. The text includes numerous examples that demonstrate how Python can be used on data sets from the earth sciences. The supplementary electronic material (available online through Springer Link) contains the example data as well as recipes that include all the Python commands featured in the book.
During the last 5 Ma the Earth's ocean-atmosphere system passed through several major transitions, many of which are discussed as possible triggers for human evolution. A classic in this context is the possible influence of the closure of the Panama Strait, the intensification of Northern Hemisphere Glaciation, a stepwise increase in aridity in Africa, and the first appearance of the genus Homo about 2.5 - 2.7 Ma ago. Apart from the fact that the correlation between these events does not necessarily imply causality, many attempts to establish a relationship between climate and evolution fail due to the challenge of precisely localizing an a priori unknown number of changes potentially underlying complex climate records. The kernel-based Bayesian inference approach applied here allows inferring the location, generic shape, and temporal scale of multiple transitions in established records of Plio-Pleistocene African climate. By defining a transparent probabilistic analysis strategy, we are able to identify conjoint changes occurring across the investigated terrigenous dust records from Ocean Drilling Programme (ODP) sites in the Atlantic Ocean (ODP 659), Arabian (ODP 721/722) and Mediterranean Sea (ODP 967). The study indicates a two-step transition in the African climate proxy records at (2.35-2.10) Ma and (1.70 - 1.50) Ma, that may be associated with the reorganization of the Hadley-Walker Circulation. .
Despite more than half a century of hominin fossil discoveries in eastern Africa, the regional environmental context of hominin evolution and dispersal is not well established due to the lack of continuous palaeoenvironmental records from one of the proven habitats of early human populations, particularly for the Pleistocene epoch. Here we present a 620,000-year environmental record from Chew Bahir, southern Ethiopia, which is proximal to key fossil sites. Our record documents the potential influence of different episodes of climatic variability on hominin biological and cultural transformation. The appearance of high anatomical diversity in hominin groups coincides with long-lasting and relatively stable humid conditions from similar to 620,000 to 275,000 years bp (episodes 1-6), interrupted by several abrupt and extreme hydroclimate perturbations. A pattern of pronounced climatic cyclicity transformed habitats during episodes 7-9 (similar to 275,000-60,000 years bp), a crucial phase encompassing the gradual transition from Acheulean to Middle Stone Age technologies, the emergence of Homo sapiens in eastern Africa and key human social and cultural innovations. Those accumulative innovations plus the alignment of humid pulses between northeastern Africa and the eastern Mediterranean during high-frequency climate oscillations of episodes 10-12 (similar to 60,000-10,000 years bp) could have facilitated the global dispersal of H. sapiens.
Spectral analysis is a technique of time-series analysis that decomposes signals into linear combinations of harmonic components. Rooted in the 19th century, spectral analysis gained popularity in palaeoclimatology since the early 1980s. This was partly due to the availability of long time series of past climates, but also the development of new, partly adapted methods and the increasing spread of affordable personal computers. This paper reviews the most important methods of spectral analysis for palaeoclimate time series and discusses the prerequisites for their application as well as advantages and disadvantages. The paper also offers an overview of suitable software, as well as computer code for using the methods on synthetic examples.
Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.
Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.
The Chew Bahir Drilling Project (CBDP) aims to test possible linkages between climate and evolution in Africa through the analysis of sediment cores that have recorded environmental changes in the Chew Bahir basin. In this statistical project we consider the Chew Bahir palaeolake to be a dynamical system consisting of interactions between its different components, such as the waterbody, the sediment beneath lake, and the organisms living within and around the lake. Recurrence is a common feature of such dynamical systems, with recurring patterns in the state of the system reflecting typical influences. Identifying and defining these influences contributes significantly to our understanding of the dynamics of the system. Different recurring changes in precipitation, evaporation, and wind speed in the Chew Bahir basin could result in similar (but not identical) conditions in the lake (e.g., depth and area of the lake, alkalinity and salinity of the lake water, species assemblages in the water body, and diagenesis in the sediments). Recurrence plots (RPs) are graphic displays of such recurring states within a system. Measures of complexity were subsequently introduced to complement the visual inspection of recurrence plots, and provide quantitative descriptions for use in recurrence quantification analysis (RQA). We present and discuss herein results from an RQA on the environmental record from six short (< 17 m) sediment cores collected during the CBDP, spanning the last 45 kyrs. The different types of variability and transitions in these records were classified to improve our understanding of the response of the biosphere to climate change, and especially the response of humans in the area.
Abrupt or gradual?
(2018)
We used a change point analysis on a late Pleistocene-Holocene lake-sediment record from the Chew Bahir basin in the southern Ethiopian Rift to determine the amplitude and duration of past climate transitions. The most dramatic changes occurred over 240 yr (from similar to 15,700 to 15,460 yr) during the onset of the African Humid Period (AHP), and over 990 yr (from similar to 4875 to 3885 yr) during its protracted termination. The AHP was interrupted by a distinct dry period coinciding with the high-latitude Younger Dryas stadial, which had an abrupt onset (less than similar to 100 yr) at similar to 13,260 yr and lasted until similar to 11,730 yr. Wet-dry-wet transitions prior to the AHP may reflect the high-latitude Dansgaard-Oeschger cycles, as indicated by cross-correlation of the potassium record with the NorthGRIP ice core record between similar to 45-20 ka. These findings may contribute to the debates regarding the amplitude, and duration and mechanisms of past climate transitions, and their possible influence on the development of early modern human cultures.