Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Pedersen, Mikkel Winther; Sanctis, Bianca De; Saremi, Nedda F.; Sikora, Martin; Puckett, Emily E.; Gu, Zhenquan; Moon, Katherine L.; Kapp, Joshua D.; Vinner, Lasse; Vardanyan, Zaruhi; Ardelean, Ciprian F.; Arroyo-Cabrales, Joaquı́n; Cahill, James A.; Heintzman, Peter D.; Zazula, Grant D.; MacPhee, R. D. E.; Shapiro, Beth; Durbin, Richard; Willerslev, Eske

doi:10.1016/j.cub.2021.04.027

Cited by 48 publications

(57 citation statements)

References 72 publications

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“…Our workflow can be applied to any nonrecombining data set, including, but not limited to, the Y-chromosome and the mitochondrial genome, and can also be used for phylogenetic placement of environmental DNA samples into preestimated trees. PathPhynder has already been used to place ancient environmental bear DNA into a mitochondrial phylogeny ( Pedersen et al 2021 ). It is also possible to construct mitochondrial and possibly Y-chromosome trees using exclusively ancient samples, and then use pathPhynder to place additional, lower coverage aDNA data, as recently done for environmental mammoth mtDNA ( Wang, Pedersen, et al 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Placing Ancient DNA Sequences into Reference Phylogenies

Martiniano

Sanctis

Durbin

2022

Molecular Biology and Evolution

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Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in over-conservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published ancient DNA sequences, using a newly compiled Y variation dataset (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male ancient DNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.

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Section: Discussionmentioning

confidence: 99%

Placing Ancient DNA Sequences into Reference Phylogenies

Martiniano

Sanctis

Durbin

2022

Molecular Biology and Evolution

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“…These methods include shotgun metagenomics, whereby any molecules in the sedaDNA mixture are randomly sequenced (e.g. [15,36,[43][44][45][46]), and target enrichment, in which sedaDNA molecules of interest are selectively enriched prior to sequencing (e.g. barcode or mitochondrial loci [16,[47][48][49]).…”

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

“…With the application of shotgun metagenomics and target enrichment approaches, it is now possible to recover haplotypic and genomic information directly from sedaDNA [43][44][45][47][48][49], which enables the exploration of populationlevel changes and has the potential to detect the arrival or disappearance of alleles and lineages in a region, as recently showcased for Neanderthals from a cave in Spain [48]. This expansion of sedaDNA into environmental palaeogenomics, together with the integration of sedaDNA and traditional palaeogenomic data derived from body fossils [55], will open up new approaches to understanding past biodiversity changes that are inaccessible with other palaeoecological proxies.…”

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

“…Although palaeogenetic data from multiple taxa have been used to contrast demographic histories (e.g. [61,62]), recent genomic studies have inferred the genetic ancestries and histories of multiple mammalian taxa from a single Pleistocene cave sedaDNA sample [44,45]. Another study inferred a clear parallel between dog and human lineage diversification by overlaying their population histories [25].…”

Section: Integrating Data From Humans Animals and Sedimentsmentioning

confidence: 99%

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Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

et al. 2021

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Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

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“…Sediments are also an important source of ancient DNA (aDNA) ( 2 , 3 ), allowing the molecular detection of ancient flora and fauna. Automated sample preparation ( 4 ) and the application of methods for targeted DNA retrieval ( 4 , 5 ) have enabled studies of Pleistocene sediment DNA to move beyond the recovery of DNA from species that were well represented in the fossil record of the sites studied, such as mammoth, horse, and bear ( 6 – 8 ), to taxa that were present in much smaller numbers, including hominins ( 4 , 5 , 9 , 10 ). This offers exciting new opportunities to investigate the geographical and temporal distribution of Pleistocene hominin groups where few or no skeletal elements are available.…”

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confidence: 99%

Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

Massilani

Morley

Mentzer

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.

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Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Cited by 48 publications

References 72 publications

Placing Ancient DNA Sequences into Reference Phylogenies

Placing Ancient DNA Sequences into Reference Phylogenies

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

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