Biology subjects

Prohaska, A.

Publications and source records attributed to Prohaska, A..

6 recordsLinked to original sources

bioRxiv2025

Environmental DNA Reveals Reykjavik's Human and Ecological History

Iceland was among the last large islands settled by humans, with colonization (Landnam) in the late 9th century CE (Common Era) and is often portrayed as an ecological disaster driven by the Norse settlers. Here, we revisit this narrative through environmental DNA (eDNA) and multiproxy analyses of sediment cores from Lake Tjornin in central Reykjavik, one of Icelands earliest and longest-occupied settlements. Originally a marine embayment, Tjornin became a freshwater lake around 660 CE. Our record reveals a human presence decades before the long-accepted arrival date of 877 CE, marked by the Landnam volcanic tephra. Early settlement brought livestock, barley cultivation, and other introduced taxa that enhanced nutrient cycling and unexpectedly increased local biodiversity. Contrary to the conventional view of rapid deforestation, eDNA shows that birch and willow expanded during the settlement period, likely supported by deliberate management. Pronounced ecological and land use shifts occurred after 1200 CE, but these were coeval with the Little Ice Age cooling, compounded by volcanic eruptions, storm surges, and plague, rather than anthropogenic degradation. Crop cultivation ceased, arboreal taxa retracted, and grazing pressure maintained open landscapes. Even more profound ecological changes came after c. 1750 CE with urbanization and industrialization, as wastewater discharge, heavy-metal pollution, and fossil fuel use reshaped Tjornins ecosystem. These findings challenge the prevailing model of Norse-induced environmental collapse, revealing instead a dynamic human-environment relationship shaped by both cultural practices and external stressors. By applying eDNA to a long-occupied urban catchment, we demonstrate the power of genomic methods to refine settlement chronologies, reassess ecological baselines and changes, and integrate natural and cultural histories. This approach offers a model for revisiting human-environment interactions in urban centers worldwide.

genomics↗

bioRxiv2024

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria x ananassa). Taking into account the requirements of both growers and consumers when selecting high quality cultivars is a real challenge. Here, we used an original diversity panel enriched with unique European accessions and the 50K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by GWAS, and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition and appearance occurred simultaneously in European and American populations. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosome regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new QTL, demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf-life. Moreover, major QTL for firmness, glossiness, skin resistance and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness and skin resistance. Overall, our study provides a potential avenue for extending shelf-life without compromising flavor and color as well as the genetic markers needed to achieve this goal.

genetics↗

bioRxiv2023

Strawberry phenotypic plasticity in flowering time is driven by interaction between genetic loci and temperature

The flowering time, which determines when the fruits or seeds can be harvested, is known to be sensitive to plasticity, i.e. the ability of a genotype to display different phenotypes in response to environmental variations. In the context of climate change, strawberry breeding can take advantage of phenotypic plasticity to create high-performing varieties adapted either to local conditions or to a wide range of climates. To decipher how the environment affects the genetic architecture of flowering time in cultivated strawberry (Fragaria xananassa) and modify its QTL effects, we used a bi-parental segregating population grown for two years at widely divergent latitudes (5 European countries) and combined climatic variables with genomic data (Affymetrix(R) SNP array). We detected 10 unique flowering time QTL and demonstrated that temperature modulates the effect of plasticity-related QTL. We propose candidate genes for the three main plasticity QTL, including FaTFL1 which is the most relevant candidate in the interval of the major temperature-sensitive QTL (6D_M). We further designed and validated a genetic marker for the 6D_M QTL which offers great potential for breeding programs, for example for selecting of early-flowering strawberry varieties well adapted to different environmental conditions. HighlightsA GXE study of a segregating strawberry population in Europe showed that temperature is the main driver of flowering time plasticity. A genetic marker was designed for the main QTL.

genetics↗

bioRxiv2023

Importance of eDNA taphonomy and provenance for robust ecological inference: insights from interfacial geochemistry

Context for and purposeRetrieval of modern and ancient environmental DNA (eDNA) from sediments has revolutionized our ability to reconstruct present and past ecosystems. Little emphasis has been placed, however, on the fundamentals of the DNA-sediment associations and, consequently, our understanding of taphonomy and provenance of eDNA in sediments remains extremely limited. If we are to be able to accurately infer community dynamics across time and space from eDNA data, we need to understand how depositional processes and sedimentary associations of DNA molecules in different settings influence our interpretation. Approach and methodsHere, we introduce interfacial geochemical principles to the field of eDNA and discuss current interpretational biases. We outline a way to increase the scope and resolution of ecological interpretations from eDNA by combining mineralogic composition with experimental adsorption data. We apply distribution coefficients to assess the relationship between the DNA fraction in water columns and DNA fraction sequestered by suspended sediment particles. We further evaluate the challenges with drawing ecological inference using eDNA from sedimentary systems that receive input from different ecosystem types as a consequence of sedimentary processes. Main results: We show thatO_LIThe retention of DNA in aqueous environments depends on the mineralogy of sediment particles and on the number of particles loaded in the water column. C_LIO_LIDNA attached to sediment particles from distal systems can be deposited in proximal systems and skew the interpretation of the proximal sediment samples. C_LIO_LIHigh particle loading in the water column can deplete suspended DNA and cause inaccurate interpretation of aqueous DNA samples. C_LIO_LIHigh particle loading in surface sediment pore waters enhances sequestration of DNA from benthic communities relative to that of water column communities, resulting in skewed estimates of species richness and abundance from sedimentary DNA. C_LI We discuss how to integrate taphonomy and provenance knowledge into the reconstruction of modern and past ecosystems, and ecosystem monitoring from eDNA data. Conclusions and the wider implicationsOur findings demonstrate that integrating information about eDNA taphonomy and provenance into modern and past ecosystem reconstruction from eDNA data can enhance the scope, resolution and accuracy of our interpretations.

biochemistry↗

bioRxiv2022

Long-term ecological responses of a Dipterocarp forest to climate changes and nutrient availability

O_LIUnderstanding the long-term impact of projected climate change on tropical rainforests is critical given their central role in the Earths system. Palaeoecological records can provide a valuable perspective on this problem. Here we examine for the first time the effects of past climatic changes on the dominant forest type of Southeast Asia - Dipterocarp forest. C_LIO_LIWe use a range of proxies extracted from a 1,400-year-old lacustrine sedimentary sequence from north-eastern Philippines to model long-term vegetation responses of Dipterocarp forest, including its dominant tree group Dipterocarps, to changes in precipitation, fire and nutrient availability over time. C_LIO_LIOur results show a positive relationship between Dipterocarps pollen accumulation rates (PARs) and leaf wax hydrogen isotope values, which suggests a negative effect of drier conditions on Dipterocarp tree abundance. Furthermore, we find a positive relationship between Dipterocarp PARs and the proxy for phosphorus availability, which suggests phosphorus controls the productivity of these keystone trees on longer time scales. Other plant taxa show widely varying relationships with the abiotic factors, demonstrating a high diversity of functional responses. C_LIO_LIOur findings provide novel insights into Dipterocarp forest responses to changing climatic conditions in the past, and highlight potential impacts of future climate change on this globally important ecosystem. C_LI

ecology↗

bioRxiv2018

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

evolutionary biology↗