Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core

Abstract

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.

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity

“…Our dense within-year sampling over eight months exhibited pronounced seasonal variation of the zooplankton community, as earlier described for rotifers, based on just two sampling campaigns (Spring and Autumn; Onandia et al, 2021). According to our analyses, the community composition is further strongly affected by the environmental factors of the local habitat, such as water temperature, pH (as in Onandia et al, 2021;Tavernini, 2008), location, kettle hole size, and hydroperiod (permanent vs. ephemeral) (as in Kulkarni et al, 2019). Differences in water persistence, as among the ephemeral and permanent ponds, can influence species exchange (Ripley & Simovich, 2009;Florencio et al, 2015;Dulić et al, 2014).…”

“…A possibly unique set of environmental parameters in each kettle holes could also explain the very different seasonal dynamics of community composition and species richness in our individual kettle holes. This environmental impact is further supported by the correlation of Gower's distance (as proxy for heterogeneity of kettle holes) and community composition differences, such that the more similar local environments are, the more similar is their species composition (see also Kulkarni et al, 2019).…”

“…We however did not address coexistence theory. Future studies should put more emphasis on the internal structure of metacommunities, applying the recently proposed new conceptual framework of Leibold et al (2021). This would advance our comprehension of how specific species and sites contribute to the global system of metacommunities, thus expanding our knowledge of the complex and interactive relationships between processes and patterns in metacommunities.…”

“…When comparing open water and soil (2019 only), we found 58 species in the water samples (n=75), while only 9 of them were detected in our 15 sediment samples (figure 2 ). Among the zooplankton-specific hits of all open water samples, the speciesspecific percentage of hits (as a proxy of relative abundances; Krueger et al, 2021) revealed copepods and cladocerans (Cyclops insignis : 25.8 %, Cyclops strenuus : 16.7 %,Thermocyclops crassus 16.1 %, Daphnia magna : 4.8 %) and some rotifers (Polyarthra dolichoptera : 7.1 % andSynchaeta pectinata : 5.2 %) to be the most frequent hits, the soil was dominated by Brachionus calyciflorus : 34.7 % andDaphnia magna : 20.0 %.…”

“…Furthermore, studies on metacommunity dynamics usually rely solely on the analysis of spatial patterns, and often neglect temporal aspects of community dynamics (Jabot et al, 2020). Only a few studies are available that also consider the temporal scale, by analysing consecutive years (Cottenie & De Meester, 2005;Horvath et al, 2016) or an environmental gradient (hydroperiod) over consecutive years (Kulkarni et al, 2019). Such a detailed connection of field observations to metacommunity theory is important because it would allow a conceptual reduction of observed complexity to simpler models with higher explanatory power for the observed dynamics (Konopka, 2009;van Vliet et al, 2015).…”