Socio-economic responses to Late Holocene climate variability and environmental change in the Peruvian Andes

This thesis provides new palaeoenvironmental data from the Peruvian Andes and develops our understanding of socio-economic responses to environmental and climatic changes within the Late Holocene. The three study areas of the Callejón de Huaylas (Ancash Region); Chillón Valley (Lima Region); Chicha-Soras Valley (Apurímac Region), provide a transect across the Andes to better understand regional differences in social responses to, and variations in, environmental change. The analysis of wetland records located within the key agricultural belt of the Peruvian Andes (3000-4000m a.s.l.), provide valuable records of past human land-use. By analysing palaeoecological (pollen, non-pollen palynomorphs, phytoliths and micro-charcoal) and geochemical (micro-XRF core scanning) signatures within these records, we can ascertain how past societies responded to known periods of major climate change, such as the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA). The results of this research have demonstrated that pre-Hispanic societies were able to cope with changes in climate by adapting agricultural practices, including the construction of reservoirs, agricultural terraces, and the use of wet pasture meadows (bofedales), and in doing so were able to deal with variability within natural resources, such as water availability. They also ensured the stability of their agricultural systems with continuity within the land-use records occurring over hundreds of years. It has also demonstrated considerable potential for high-resolution analysis of environmental change and the detection of both longer-scale regional climate change (MCA and LIA) and short-term climatic fluctuations (El Niño). Understanding how pre-Hispanic societies mitigated the risk posed by climate variability is important for future land-use, water, and soil conservation practices. The future preservation of the wetlands within the study is highly important for both climate change regulation and for conserving a valuable archive of human-environment interactions

Pre-Hispanic terrace agricultural practices and long-distance transfer of plant taxa in the southern-central Peruvian Andes revealed by phytolith and pollen analysis

The archaeological excavation of two abandoned prehispanic agricultural terraces (Infiernillo and Tocotoccasa) in the Chicha-Soras Valley (Apurimac) in southern-central Peru revealed the presence of palaeosols. The palaeosols represent soil that developed following construction of agricultural terraces during the Middle Horizon. The soil profiles at the current surface developed following reconstruction of the terraces during the Late Intermediate Period. Phytolith analysis revealed an unexpected presence of Arecaceae (palm family) and Marantaceae (arrowroot family) in both terraces, which has been attributed to local cultivation and/or transportation and use of soil, dung, plant material or implements (made of Arecaceae) on the terrace surfaces. Pollen analysis of a nearby wetland (Ayapampa) did not provide evidence for Arecaceae or Marantaceae. Both phytolith and pollen analysis of the terraces and wetland (respectively) indicated that Zea mays was cultivated locally during the Middle Horizon and Late Intermediate Period, although phytoliths of maize are absent from the wetland record during the Middle Horizon. The presence of Solanaceae and Chenopodiaceae/Amaranthaceae pollen in the wetland may be indicative of cultivation of further important taxa during the Middle Horizon and Late Intermediate Period, which continued into the Late Horizon together with Zea mays

Adaptive capacity of farming communities to climate change in the Peruvian Andes: past, present and future (preliminary findings of the ACCESS project)

Climate variability has had a marked influence on water availability, traditional farming (agro-pastoral) practices, and therefore the livelihood of human communities in the Peruvian Andes since at least the Middle Horizon cultural period (AD 600-1000). Current global climate warming poses a more significant threat, however, enhancing vulnerability and creating a greater risk to all assets. To better understand the challenges faced by rural communities living with climate variability, as well as the opportunities afforded through appropriate adaptive strategies, a research pilot project (ACCESS) was conducted in the Cordillera Blanca and Cordillera Negra, Ancash region. The preliminary findings reveal that variability in precipitation over the past 1500 years was coincident with major cultural changes and advancement in water management practices, although the precise temporal relationships remain uncertain. Nevertheless, the construction of canals and reservoirs, as well as agricultural terraces, clearly indicates that past cultures in the Ancash region recognised the need to enhance resilience and for the sustainable management of natural resources. At the present day, our data indicate that local communities in both Cordilleras are experiencing the effects of climate change, especially water shortages, increasing temperatures and glacier retreat, soil degradation, and greater problems with crop pests. These concerns are worsened by a shortage of agricultural land, conflict between communities and a lack of state intervention. Adaptive strategies proposed by communities include improved water management, economic diversification, greater community collaboration and state investment. The concerns over water availability are in agreement with the preliminary hydrological and crop-water modelling findings of the project, which indicate that with rising temperatures and variable precipitation patterns, improved water management in both cordilleras will be required to maintain effective levels of irrigation for sustainable farming and economic development. Finally, we highlight the importance of restoration of ancient water management and agricultural infrastructure, as well as the significance of indigenous knowledge amongst local communities, as a means of enhancing adaptive capacity in the face of climate change

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Data supporting the PhD Thesis 'Socio-economic responses to Late Holocene climate variability and environmental change in the Peruvian Andes'

Primary data included within the Handley 2022 PhD Thesis 'Socio-economic responses to Late Holocene climate variability and environmental change in the Peruvian Andes'. Data consists of pollen, phytolith, micro-XRF, and organic matter content records for three infilled basins in the Peruvian Andes (Huarca, Callejón de Huaylas, Ancash Region; Antaycocha, Chillón Valley, Lima Region; Ayapampa, Chicha-Soras Valley, Apurímac Region). The three sites provide a transect across the Andes to better understand regional differences in social responses to, and variations in, environmental change over the past 2500 years. The three basins span from full-Holocene (Huarca ~11,500 yrs) sequences to Late Holocene timescales (Antaycocha ~3000 yrs; Ayapampa ~4000 yrs). However the focus for most of the analysis for this thesis has focused on the last 2500 years as this is the period of greatest cultural and agricultural development in the Peruvian Andes. Pollen data was obtained by standard procedures following Faegri and Irersen (1989) and Moore, Web and Collinson (1991) and involving the sieving, heavy liquid density separation and acetolysis of pollen samples. Phytolith analysis was carried out using the dry-ashing method outlined in Parr et al., 2001, with the addition of a sonication step (Lombardo et al., 2016). Both phytolith and pollen analysis was carried out using a high-powered stereo microscope and the raw counts obtained from these analyses is included within this dataset. Micro-XRF data was obtained using a ITRAX core scanner housed at the British Ocean Sediment Core Research Facility, National Oceanography Centre, Southampton (BOSCORF). XRF exposure time was 15 seconds per sampling point, using a Mo tube and run at a voltage of 30KV and a current of 30mA. Data presented in this dataset are in counts per second as obtained via the ITRAX scanner. Organic Matter Content (OMC) was obtained via Loss on Ignition, with material being heated to 550oC (following Bengtsson and Enell, 1986)

Mitogen-Activated Protein Kinase-Dependent Interleukin-1α Intracrine Signaling Is Modulated by YopP during Yersinia enterocolitica Infection

Yersinia enterocolitica is a food-borne pathogen that preferentially infects the Peyer's patches and mesenteric lymph nodes, causing an acute inflammatory reaction. Even though Y. enterocolitica induces a robust inflammatory response during infection, the bacterium has evolved a number of virulence factors to limit the extent of this response. We previously demonstrated that interleukin-1α (IL-1α) was critical for the induction of gut inflammation characteristic of Y. enterocolitica infection. More recently, the known actions of IL-1α are becoming more complex because IL-1α can function both as a proinflammatory cytokine and as a nuclear factor. In this study, we tested the ability of Y. enterocolitica to modulate intracellular IL-1α-dependent IL-8 production in epithelial cells. Nuclear translocation of pre-IL-1α protein and IL-1α-dependent secretion of IL-8 into the culture supernatant were increased during infection with a strain lacking the 70-kDa virulence plasmid compared to the case during infection with the wild type, suggesting that Yersinia outer proteins (Yops) might be involved in modulating intracellular IL-1α signaling. Infection of HeLa cells with a strain lacking the yopP gene resulted in increased nuclear translocation of pre-IL-1α and IL-1α-dependent secretion of IL-8 similar to what is observed with bacteria lacking the virulence plasmid. YopP is a protein acetylase that inhibits mitogen-activated protein kinase (MAP kinase)- and NF-κB-dependent signal transduction pathways. Nuclear translocation of pre-IL-1α and IL-1α-dependent secretion of IL-8 in response to Yersinia enterocolitica infection were dependent on extracellular signal-regulated kinase (ERK) and p38 MAP kinase signaling but independent of NF-κB. These data suggest that Y. enterocolitica inhibits intracellular pre-IL-1α signaling and subsequent proinflammatory responses through inhibition of MAP kinase pathways