Daniels, R. J. | Search bioRxiv

bioRxiv2023

Benchmarking sample pooling for epigenomics of natural populations

Interest in the role of DNA methylation (DNAm) has grown in ecological and evolutionary research of natural populations. While researchers are typically interested in comparing population-level variation, individual sequencing is the current standard. Natural populations have low effect sizes and thus need large sample sizes to detect differences. The cost of sequencing the necessary samples can be prohibitive in DNAm work. Pooling DNA before library preparation is a powerful tool to reduce costs but no recommendations exist for DNAm pooling in ecology-epigenetics research. We test if pooled and individual libraries provide similar global and region-specific DNA methylation signals in a natural system of response to pollution. We generated whole-epigenome data for two freshwater invasive molluscs (Corbicula flumina and Dreissena polymorpha) collected from a polluted and unpolluted locality, Lake Maggiore, Italy. Our results support that pooling effectively captures the same genome-wide and global treatment-level signals as individual libraries but we note that pooled libraries yielded orders of magnitude more input data and differentially-methylated regions (DMRs) detected compared with individual libraries. We estimated greatly lower power for regions from individual libraries compared with pooled libraries. The post-hoc process of computationally pooling data from individual libraries produced results comparable to pooled libraries in volumes but had discrepancies between DMRs. We discuss the possible causes for the discrepancies and put our results in the context of the benefits and drawbacks of sample pooling for epigenomics of natural populations.

genomics↗

bioRxiv2022

Genetic heritage of the BaPhuthi highlights an over ethnicised notion of 'Bushman' in the Maloti-Drakensberg, Southern Africa

Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In Southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear as ethnicity labels are continually changed through time and most communities were extirpated. The eastern KhoeSan may reflect an essentialistic biological distinction from neighbouring Bantu-speaking communities or it may not be tied to race and instead denote communities with a nomadic life-way distinct from agro-pastoralism. The BaPhuthi of the 1800s in the Maloti-Drakensberg, Southern Africa had a substantial San constituency and a life-way of nomadism, cattle raiding, and horticulture. The BaPhuthi heritage could provide insights into the history of the eastern KhoeSan. We examine for the first time genetic affinities of 23 BaPhuthi to distinguish if KhoeSan ancestry reflects biologically distinct heritage or a shared life-way. Data were merged with 52 global populations. The Principle Component Analysis, ADMIXTURE clustering and F3 tests show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu-speaking communities. The BaPhuthi have strong affinities with Nguni communities, as the non-Nguni show strong evidence of recent African admixture possibly related to late-iron age migrations. The BaPhuthi may have an interesting connection to the early iron-age Bantu-speaking communities as MALDER detected no signals for late-iron age admixture. We demonstrate how the essentialistic understanding of references in historic literature creates misconstrued notions of ethnic/biological distinctions when San and Bushman may have reflected ambiguous references to the non-sedentary polities and practices.

genomics↗