Placing ancient DNA sequences into reference phylogenies

@article{Martiniano2020PlacingAD,
  title={Placing ancient DNA sequences into reference phylogenies},
  author={Rui Martiniano and Bianca De Sanctis and Pille Hallast and Richard Durbin},
  journal={bioRxiv},
  year={2020}
}
During the last decade, large volumes of ancient DNA (aDNA) data have been generated as part of whole-genome shotgun and target capture sequencing studies. This includes sequences from non-recombining loci such as the mitochondrial or Y chromosomes. However, given the highly degraded nature of aDNA data, post-mortem deamination and often low genomic coverage, combining ancient and modern samples for phylogenetic analyses remains difficult. Without care, these factors can lead to incorrect… 
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References

SHOWING 1-10 OF 61 REFERENCES
The study of human Y chromosome variation through ancient DNA
TLDR
This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation and focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.
Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females
TLDR
The findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages.
Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
TLDR
The first modern human population divergence time is estimated to be between 350,000 and 260,000 years ago, which increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans intomodern humans, as represented in the local fossil record.
A Southeast Asian origin for present-day non-African human Y chromosomes
TLDR
It is shown 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 East/Southeast Asia as the origin 50,000–55,000 years ago of all known surviving non-African male lineages (apart from recent migrants).
An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree.
Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
TLDR
The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.
Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent
TLDR
Genome-wide analysis of 67 ancient Near Eastern cattle remains reveals regional variation that has since been obscured by admixture in modern populations, and mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival.
Toward a new history and geography of human genes informed by ancient DNA.
A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
TLDR
A study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples, infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky, and hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Computational challenges in the analysis of ancient DNA
TLDR
These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments and show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
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