Out of Africa by spontaneous migration waves

Bons, Paul D.; Bauer, Catherine; Bocherens, Hervé; Riese, Tamara de; Drucker, Dorothée G.; Francken, Michael; Menéndez, Lumila Paula; Uhl, Alexandra; Wißing, Christoph

doi:10.1371/journal.pone.0201998

Cited by 19 publications

(8 citation statements)

References 108 publications

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“…Six migration edges are tested for significance using 500 SNPs per block (-k 500). As “Out of Africa” is the most accepted theory [ 73 ] we used Yoruba population (YRI) of the African superpopulation an outgroup for building the migration trees.…”

Section: Methodsmentioning

confidence: 99%

Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations

et al. 2021

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Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be specific to human populations. The current immunogenetics resources gather the germline alleles, however, lack the population specificity of the alleles which poses limitations for disease-association studies related to immune responses in different human populations. Therefore, we systematically identified germline alleles from 26 different human populations around the world, profiled by “1000 Genomes” data. We identified 409 IGHV, 179 IGKV, and 199 IGLV germline alleles supported by at least seven haplotypes. The diversity of germline alleles is the highest in Africans. Remarkably, the variants in the identified novel alleles show strikingly conserved patterns, the same as found in other IG databases, suggesting over-time evolutionary selection processes. We could relate the genetic variants to population-specific immune responses, e.g. IGHV1-69 for flu in Africans. The population matched IG (pmIG) resource will enhance our understanding of the SHM-related B-cell receptor selection processes in (infectious) diseases and vaccination within and between different human populations.

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Section: Methodsmentioning

confidence: 99%

Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations

et al. 2021

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“…Six migration edges are tested for significance using 500 SNPs per block (-k 500). As “Out of Africa” is the most accepted theory (49) we used Yoruba population (YRI) of the African superpopulation an outgroup for building the migration trees.…”

Section: Methodsmentioning

confidence: 99%

Population matched (PM) germline allelic variants of immunoglobulin (IG) loci: New pmIG database to better understandIGrepertoire and selection processes in disease and vaccination

Khatri

Berkowska

Akker

et al. 2020

Preprint

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At the population level, immunoglobulin (IG) loci harbor inter-individual allelic variants in the many different germline IG variable (V), Diversity (D) and Joining (J) genes of the IG heavy (IGH), IG kappa (IGK) and IG lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These inter-individual allelic variants can be shared between or be specific to human populations. The current IG databases IMGT, VBASE2 and IgPdb hold information about germline alleles, most of which are partial sequences, obtained from a mixture of human (B-cell) samples, many with sequence errors and/or acquired (non-germline) IG variations, induced by somatic hypermutation (SHM) during antigen-specific B-cell responses. We systematically identified true germline alleles (without SHM) from 26 different human populations around the world, profiled by the “1000 Genomes data”. Our resource is uniquely enriched with complete IG allele sequences and their frequencies across human populations. We identified 409 IGHV, 179 IGKV, and 199 IGLV germline alleles supported by at least seven haplotypes (= minimum of four individuals), after removal of potential false-positives, based on using other genomic databases, i.e. ENSEMBL, TopMed, ExAC, ProjectMine. Remarkably, the positions of the identified variant nucleotides of the different alleles are not at random (as observed in case of SHM), but show striking patterns, restricted to limited nucleotide positions, the same as found in other IG data bases, suggesting over-time evolutionary selection processes. The identification of these specific patterns provides extra evidence that the identified variant nucleotides are not sequencing errors, but genuine allelic variants. The diversity of germline allelic variants in IGH and IGL loci is the highest in Africans, while the IGK locus is most diverse in Europeans. We also report on the presence of recombination signal sequences (RSS) in V pseudogenes, explaining their usage in V(D)J rearrangements. We propose that this new set of genuine germline IG sequences can serve as a new population-matched IG (pmIG) database for better understanding B-cell repertoire and B-cell receptor selection processes in disease and vaccination within and between different human populations. The database in format of fasta is available via GitHub (https://github.com/InduKhatri/pmIG). Contribution to the Field Statement We present a catalogue of immunoglobulin (IG) germline-alleles of unprecedented completeness and accuracy from 26 different human populations belonging to five different large ethnicities (Source: 1000 Genomes). We identified the population distribution of several known germline alleles and identified multiple new alleles, especially in African populations, indicative of high allelic diversity of IG genes in Africa. Strikingly, the identified variant nucleotides of the different alleles are not at random, but show striking patterns, restricted to limited nucleotide positions, the same as found in ot...

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“…Hominin expansions are considered as processes that occurred across time periods of millions of years and across continents. Therefore, these are often modeled as large-scale diffusion models [ 17 – 20 , 22 , 23 ]. However, processes such as the crossing of sea straits occur on much smaller spatio-temporal scales.…”

Section: Discussionmentioning

confidence: 99%

“…Hominin expansion is generally represented as a large-scale spatio-temporal process being driven by demographic and/or environmental factors and in general, as following a diffusionlike mechanism [15][16][17][18][19][20][21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Discovering the opposite shore: How did hominins cross sea straits?

Hölzchen

Hertler²,

Cachorro³

et al. 2021

PLoS ONE

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Understanding hominin expansions requires the comprehension of movement processes at different scales. In many models of hominin expansion these processes are viewed as being determined by large-scale effects, such as changes in climate and vegetation spanning continents and thousands or even millions of years. However, these large-scale patterns of expansions also need to be considered as possibly resulting from the accumulation of small-scale decisions of individual hominins. Moving on a continental scale may for instance involve crossing a water barrier. We present a generalized agent-based model for simulating the crossing of a water barrier where the agents represent the hominin individuals. The model can be configured to represent a variety of movement modes across water. Here, we compare four different behavioral scenarios in conjunction with a set of water barrier configurations, in which agents move in water by either paddling, drifting, swimming or rafting. We introduce the crossing-success-rate (CSR) to quantify the performance in water crossing. Our study suggests that more focus should be directed towards the exploration of behavioral models for hominins, as directionality may be a more powerful factor for crossing a barrier than environmental opportunities alone. A prerequisite for this is to perceive the opposite shore. Furthermore, to provide a comprehensive understanding of hominin expansions, the CSR allows for the integration of results obtained from small-scale simulations into large-scale models for hominin expansion.

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Out of Africa by spontaneous migration waves

Cited by 19 publications

References 108 publications

Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations

Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations

Population matched (PM) germline allelic variants of immunoglobulin (IG) loci: New pmIG database to better understandIGrepertoire and selection processes in disease and vaccination

Discovering the opposite shore: How did hominins cross sea straits?

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