Néandertal et Afrique, le retour

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans

10.1101/227660 ◽

2017 ◽

Author(s):

Matthias Steinrücken ◽

Jeffrey P. Spence ◽

John A. Kamm ◽

Emilia Wieczorek ◽

Yun S. Song

Keyword(s):

Genetic Material ◽

Genetic Load ◽

Modern Human ◽

Human Populations ◽

Effective Population ◽

Weak Selection ◽

Modern Humans ◽

High Coverage ◽

Model Based ◽

And Migration

AbstractGenetic evidence has revealed that the ancestors of modern human populations outside of Africa and their hominin sister groups, notably the Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence-tracts along modern-day human genomes provides insight into the ancient structure and migration patterns of these archaic populations. Furthermore, it facilitates studying the selective processes that lead to the accumulation or depletion of introgressed genetic variation. Recent studies have developed methods to localize these introgressed regions, reporting long regions that are depleted of Neanderthal introgression and enriched in genes, suggesting negative selection against the Neanderthal variants. On the other hand, enriched Neanderthal ancestry in hair- and skin-related genes suggests that some introgressed variants facilitated adaptation to new environments. Here, we present a model-based method called diCal-admix and apply it to detect tracts of Neanderthal introgression in modern humans. We demonstrate its efficiency and accuracy through extensive simulations. We use our method to detect introgressed regions in modern human individuals from the 1000 Genomes Project, using a high coverage genome from a Neanderthal individual from the Altai mountains as reference. Our introgression detection results and findings concerning their functional implications are largely concordant with previous studies, and are consistent with weak selection against Neanderthal ancestry. We find some evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals, resulting from small effective population size, rather than Dobzhansky-Müller incompatibilities. Finally, we investigate the role of the X-chromosome in the divergence between Neanderthals and modern humans.

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Archaic mitochondrial DNA inserts in modern day nuclear genomes

10.21203/rs.2.14881/v3 ◽

2019 ◽

Author(s):

Robert Bücking ◽

Murray P Cox ◽

Georgi Hudjashov ◽

Lauri Saag ◽

Herawati Sudoyo ◽

...

Keyword(s):

Mitochondrial Dna ◽

Nuclear Dna ◽

Modern Human ◽

Next Generation Sequencing Data ◽

Human Populations ◽

Sequencing Data ◽

Modern Humans ◽

High Coverage ◽

Nuclear Genomes ◽

Generation Sequencing

Abstract Background: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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Archaic mitochondrial DNA inserts in modern day nuclear genomes

10.21203/rs.2.14881/v1 ◽

2019 ◽

Author(s):

Robert Bücking ◽

Murray P Cox ◽

Georgi Hudjashov ◽

Lauri Saag ◽

Herawati Sudoyo ◽

...

Keyword(s):

Mitochondrial Dna ◽

Nuclear Dna ◽

Modern Human ◽

Next Generation Sequencing Data ◽

Human Populations ◽

Sequencing Data ◽

Modern Humans ◽

High Coverage ◽

Nuclear Genomes ◽

Generation Sequencing

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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Archaic mitochondrial DNA inserts in modern day nuclear genomes

10.21203/rs.2.14881/v2 ◽

2019 ◽

Author(s):

Robert Bücking ◽

Murray P Cox ◽

Georgi Hudjashov ◽

Lauri Saag ◽

Herawati Sudoyo ◽

...

Keyword(s):

Mitochondrial Dna ◽

Nuclear Dna ◽

Modern Human ◽

Next Generation Sequencing Data ◽

Human Populations ◽

Sequencing Data ◽

Modern Humans ◽

High Coverage ◽

Nuclear Genomes ◽

Generation Sequencing

Abstract Background: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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Limits of long-term selection against Neandertal introgression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1814338116 ◽

2019 ◽

Vol 116 (5) ◽

pp. 1639-1644 ◽

Cited By ~ 48

Author(s):

Martin Petr ◽

Svante Pääbo ◽

Janet Kelso ◽

Benjamin Vernot

Keyword(s):

Negative Selection ◽

Modern Human ◽

Model Parameters ◽

Human Populations ◽

Modern Humans ◽

High Coverage ◽

Protein Coding ◽

The Past ◽

Wide Range

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.

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Humans: Evolution and Environment: C06 - History of Human populations, palaeoecology and ancient DNA, C08 - Bioarchaeology from the Midst of Shells, C14 - Modern Humans origins in Eurasia, C62 - Coastal geoarchaeology: the research of shellmounds, WS32 -

10.30861/9781407306032 ◽

2009 ◽

Keyword(s):

Ancient Dna ◽

Human Populations ◽

Modern Humans ◽

History Of

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Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations

10.1101/2020.01.13.905174 ◽

2020 ◽

Author(s):

Xinjun Zhang ◽

Bernard Kim ◽

Kirk E. Lohmueller ◽

Emilia Huerta-Sánchez

Keyword(s):

False Positive ◽

False Positive Rate ◽

Genomic Variation ◽

Human Populations ◽

Deleterious Mutations ◽

Modern Humans ◽

Recombination Rates ◽

Limited Impact ◽

Adaptive Mutations ◽

Adaptive Introgression

AbstractAdmixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been previously identified as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetics processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble adaptive introgression. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants. We further examined candidates of AI in modern humans identified from previous studies and show that, although deleterious variants may hinder the performance of AI detection in modern humans, most signals remained robust when deleterious variants are included in the null model. While deleterious variants may have a limited impact on detecting signals of adaptive introgression in humans, we found that at least two AI candidate genes, HYAL2 and HLA, are particularly susceptible to high false positive rates due to the recessive deleterious mutations. By quantifying parameters that affect heterosis, we show that the high false positives are largely attributed to the high exon densities together with low recombination rates in the genomic regions, which can further be exaggerated by the population growth in recent human evolution. Although the combination of such parameters is rare in the human genome, caution is still warranted in other species with different genomic composition and demographic histories.

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ntEdit: scalable genome sequence polishing

Bioinformatics ◽

10.1093/bioinformatics/btz400 ◽

2019 ◽

Vol 35 (21) ◽

pp. 4430-4432 ◽

Cited By ~ 8

Author(s):

René L Warren ◽

Lauren Coombe ◽

Hamid Mohamadi ◽

Jessica Zhang ◽

Barry Jaquish ◽

...

Keyword(s):

Human Genome ◽

Genome Sequence ◽

Sequence Data ◽

Bloom Filter ◽

Supplementary Information ◽

Routine Practice ◽

High Coverage ◽

Illumina Sequence ◽

Genome Assemblies ◽

Indel Rate

Abstract Motivation In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes. Results We first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled Escherichia coli and Caenorhabditis elegans sequence data. Generally, ntEdit performs well at low sequence depths (<20×), fixing the majority (>97%) of base substitutions and indels, and its performance is largely constant with increased coverage. In all experiments conducted using a single CPU, the ntEdit pipeline executed in <14 s and <3 m, on average, on E.coli and C.elegans, respectively. We performed similar benchmarks on a sub-20× coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30–40 m on those sequences. We show how ntEdit ran in <2 h 20 m to improve upon long and linked read human genome assemblies of NA12878, using high-coverage (54×) Illumina sequence data from the same individual, fixing frame shifts in coding sequences. We also generated 17-fold coverage spruce sequence data from haploid sequence sources (seed megagametophyte), and used it to edit our pseudo haploid assemblies of the 20 Gb interior and white spruce genomes in <4 and <5 h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024. Availability and implementation https://github.com/bcgsc/ntedit Supplementary information Supplementary data are available at Bioinformatics online.

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The early Aurignacian dispersal of modern humans into westernmost Eurasia

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2016062117 ◽

2020 ◽

Vol 117 (41) ◽

pp. 25414-25422

Author(s):

Jonathan A. Haws ◽

Michael M. Benedetti ◽

Sahra Talamo ◽

Nuno Bicho ◽

João Cascalheira ◽

...

Keyword(s):

Iberian Peninsula ◽

Modern Human ◽

Human Populations ◽

Southern Europe ◽

Modern Humans ◽

Present Evidence ◽

Western Margin ◽

Human Presence ◽

Human Dispersal ◽

Central Portugal

Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.

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