Early replacement of West Eurasian male Y chromosomes from the east, bioRxiv, 2019-12-06

AbstractThe genomes of humans outside Africa originated almost entirely from a single migration out ∼50,000-60,000 years ago1,2, followed closely by mixture with Neanderthals contributing ∼2% to all non-Africans3,4. However, the details of this initial migration remain poorly-understood because no ancient DNA analyses are available from this key time period, and present-day autosomal data are uninformative due to subsequent population movementsreshaping5. One locus, however, does retain extensive information from this early period the Y-chromosome, where a detailed calibrated phylogeny has been constructed6. Three present-day Y lineages were carried by the initial migration the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations6,7. We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to EastSouth-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model8,9, and thus informing and constraining models of the initial expansion.

biorxiv genetics 100-200-users 2019

Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing, bioRxiv, 2019-12-06

AbstractDespite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotic cells has been hindered by their low levels of mRNA, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline that overcomes these obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. We have demonstrated that PETRI-seq effectively captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and little bias. Although bacteria express only thousands of mRNAs per cell, captured mRNA levels were sufficient to distinguish between the transcriptional states of single cells within isogenic populations. In E. coli, we were able to identify single cells in either stationary or exponential phase and define consensus transcriptomes for these sub-populations. In wild type S. aureus, we detected a rare population of cells undergoing prophage induction. We anticipate that PETRI-seq will be widely useful for studying transcriptional heterogeneity in microbial communities.

biorxiv systems-biology 100-200-users 2019

 

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