Post by djoser-xyyman on Mar 16, 2018 12:42:32 GMT -5
North Africans traveling north
Karl Skoreckia,b,1 and Doron M. Behara
aMolecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel; and
bRuth and Bruce Rappaport Faculty of Medicine
Humans have always loved to move and to
mate. In doing so, we generate complex patterns
of diversity in language, custom, and
culture across and within geographic regions.
However, the richest and most durable signals
of migration and admixture are evident
in patterns of DNA sequence variation (1, 2).
The study by Botigué et al. (3) reported in
PNAS analyzes DNA sequence variation in
Africa, the Near East, and Europe to advance
our understanding of the peopling of Europe
with a focus on the relatively recent contribution
of North African ancestry to the contemporary
population genetic structure of
southern Europe.
The population history of Europe during
the last ∼50,000 y corresponds to two major
geologic time periods: the Pleistocene before
∼11,500 y ago, transitioning into the Holocene
(Fig. 1). The major events of the
Pleistocene include the initial pioneering colonization
by humans during the Upper Paleolithic,
as part of the overall dispersal of
modern humans out of Africa (Fig. 1A). Subsequently,
during the most recent major Ice
Age (Last Glacial Maximum) extending from
25,000 to 19,500 y ago, people found refuge
in a number of well-defined geographic
areas, including southwest Europe (Franco-
Cantabrian/ Iberian), along the Mediterranean
coast including the Italian peninsula,
the Balkans, the Levant, and on the east European
steppes (Fig. 1B) (4, 5). The subsequent
transition from Pleistocene to Holocene (disrupted
briefly by a less severe cooling lasting
about a millennium; Fig. 1C) also ushered in
the dispersal to Europe of Near East migrants,
bringing with them Neolithic skill sets
and practices, including different forms of
agriculture and animal domestication (Fig.
1D) (6). Both the recolonization from Ice Age
population refugia and the Neolithic migration
generated a backdrop for a reducing
south to north European cline of DNA sequence
diversity. Ever since, numerous
migrations have followed along multiple intercontinental
routes from the Copper Age
to this day, including trans-Mediterranean
movements (Fig. 1D), which are directly relevant
to understanding population genetic
structure in southern Europe (7).
Much of the genetic trace of the more
remote and recent migratory events has been
fruitfully elucidated by examining the
distribution of ever more finely resolved phylogenies
or haplogroups at the nonrecombining
uniparental regions of the genome:
namely, the Y chromosome and mitochondrial
DNA, as has been recently summarized
for Europe (5). However, population genetics
studies corresponding to the Holocene, which
initiated 10 millennia of relative climatic stability
to this day, has particularly benefited
from combining such uniparental lineage
analysis with genomewide approaches (2).
The rapid transition during the last decade to
analysis of genomewide variation has enabled
levels of resolution of population genetic
structure, which eluded single locus analysis
(8–11). This is because each independent locus
has its own coalescent history and continues
to add information until the point
where the spacing of loci falls below the scale
of linkage disequilibrium (the nonrandom association
of neighboring markers) in the populations
of interest. For more than a decade,
it has been possible, and now straightforward
and affordable using DNA BeadChip technology,
to determine for any individual genome,
the biparental allelic states (genotype)
for a subset of almost all known single nucleotide
variants (SNVs), or better still, the
phased combination of genotypes for a group
of SNVs at any and all given genomic regions
of interest (haplotype). The technical ability
to interrogate genomewide variation was accompanied
by the development of analytic
approaches based on either allele frequency
or haplotype comparisons. The various categories
of such analytic approaches, their
strengths, and limitations have been summarized
recently (2).
Using these approaches, multiple studies
examining autosomal biparental variation
among Europeans have yielded a set of
consistent conclusions, which generate a
multilayered pattern, to which Botigué et al.
(3) validate an important North African
layer (Fig. 1E). Within a global context, it is
apparent that European populations share
a distinctive background genetic layer that
is readily separable from components dominating
other continents, enabling quite reliable
individual assignment of European
ancestry, most evident in the Basque and Sardinian
populations (1, 8–12). A next layer is
evident as the consistent and reproducible
distinction between “northern” and “southern”
European population groups, with a
clinal distribution of genetic variation consistent
with a south to north expansion and/or a
larger effective population size in southern
than in northern Europe (10, 12, 13). Despite
comparatively low average levels of genetic
differentiation among Europeans, the decay
of genetic similarity as a function of geographic
distance within Europe gives rise to a
rather amazing ability to overlay a geographical
map of Europe with allele frequencybased
measures of genomewide variation
(9, 12). In certain cases, it is even possible to
assign the ethnic affiliation of an individual
with a high degree of fidelity for population
isolates such as Basque, Sardinian, Finns, and
Ashkenazi Jews (12, 14, 15), a genetic structure
within a given geographic region (16), or
even a village of origin (17).
In the European context, the question of
the trans-Mediterranean gene flow has also
been investigated. The maternal component
of African lineages to the contemporary gene
pool of Europeans could be readily estimated
due to the clear partitioning of Sub-Saharan
and European mtDNA lineages. Frequencies
of such African lineages vary widely within
Europe, ranging from 3% in southern Europe
to 0.7% in central Europe and 0.5% in
northern Europe (18, 19), with evidence that
as much as 35% of African lineages form
European-specific subclades, pointing to gene
flow from Sub-Saharan Africa to Europe as
early as 11,000 y ago (20). Similarly, the sharp
discontinuities between northwestern Africa
and the Iberian Peninsula at the level of the
Y chromosome were followed by evidence of
North African to south European migration,
particularly to the Iberian Peninsula (21, 22).
At the genomewide level, Auton et al. (23)
reported the highest genomewide haplotype
diversity of European samples in the Iberian
Peninsula, together with the highest sharing
of haplotypes with the Yoruba population of
any European population examined. A more
recent study reported that southern Europeans
have inherited 1–3% African ancestry,
with an average admixture timing of some
55 generations ago, coinciding with the end
of the Roman Empire and subsequent Arab
migrations (24).
This latter set of findings begs the question
of whether this level of Sub-Saharan admixture
is simply the carryover of Sub-Saharan
African admixture embedded within a much
Karl Skoreckia,b,1 and Doron M. Behara
aMolecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel; and
bRuth and Bruce Rappaport Faculty of Medicine
Humans have always loved to move and to
mate. In doing so, we generate complex patterns
of diversity in language, custom, and
culture across and within geographic regions.
However, the richest and most durable signals
of migration and admixture are evident
in patterns of DNA sequence variation (1, 2).
The study by Botigué et al. (3) reported in
PNAS analyzes DNA sequence variation in
Africa, the Near East, and Europe to advance
our understanding of the peopling of Europe
with a focus on the relatively recent contribution
of North African ancestry to the contemporary
population genetic structure of
southern Europe.
The population history of Europe during
the last ∼50,000 y corresponds to two major
geologic time periods: the Pleistocene before
∼11,500 y ago, transitioning into the Holocene
(Fig. 1). The major events of the
Pleistocene include the initial pioneering colonization
by humans during the Upper Paleolithic,
as part of the overall dispersal of
modern humans out of Africa (Fig. 1A). Subsequently,
during the most recent major Ice
Age (Last Glacial Maximum) extending from
25,000 to 19,500 y ago, people found refuge
in a number of well-defined geographic
areas, including southwest Europe (Franco-
Cantabrian/ Iberian), along the Mediterranean
coast including the Italian peninsula,
the Balkans, the Levant, and on the east European
steppes (Fig. 1B) (4, 5). The subsequent
transition from Pleistocene to Holocene (disrupted
briefly by a less severe cooling lasting
about a millennium; Fig. 1C) also ushered in
the dispersal to Europe of Near East migrants,
bringing with them Neolithic skill sets
and practices, including different forms of
agriculture and animal domestication (Fig.
1D) (6). Both the recolonization from Ice Age
population refugia and the Neolithic migration
generated a backdrop for a reducing
south to north European cline of DNA sequence
diversity. Ever since, numerous
migrations have followed along multiple intercontinental
routes from the Copper Age
to this day, including trans-Mediterranean
movements (Fig. 1D), which are directly relevant
to understanding population genetic
structure in southern Europe (7).
Much of the genetic trace of the more
remote and recent migratory events has been
fruitfully elucidated by examining the
distribution of ever more finely resolved phylogenies
or haplogroups at the nonrecombining
uniparental regions of the genome:
namely, the Y chromosome and mitochondrial
DNA, as has been recently summarized
for Europe (5). However, population genetics
studies corresponding to the Holocene, which
initiated 10 millennia of relative climatic stability
to this day, has particularly benefited
from combining such uniparental lineage
analysis with genomewide approaches (2).
The rapid transition during the last decade to
analysis of genomewide variation has enabled
levels of resolution of population genetic
structure, which eluded single locus analysis
(8–11). This is because each independent locus
has its own coalescent history and continues
to add information until the point
where the spacing of loci falls below the scale
of linkage disequilibrium (the nonrandom association
of neighboring markers) in the populations
of interest. For more than a decade,
it has been possible, and now straightforward
and affordable using DNA BeadChip technology,
to determine for any individual genome,
the biparental allelic states (genotype)
for a subset of almost all known single nucleotide
variants (SNVs), or better still, the
phased combination of genotypes for a group
of SNVs at any and all given genomic regions
of interest (haplotype). The technical ability
to interrogate genomewide variation was accompanied
by the development of analytic
approaches based on either allele frequency
or haplotype comparisons. The various categories
of such analytic approaches, their
strengths, and limitations have been summarized
recently (2).
Using these approaches, multiple studies
examining autosomal biparental variation
among Europeans have yielded a set of
consistent conclusions, which generate a
multilayered pattern, to which Botigué et al.
(3) validate an important North African
layer (Fig. 1E). Within a global context, it is
apparent that European populations share
a distinctive background genetic layer that
is readily separable from components dominating
other continents, enabling quite reliable
individual assignment of European
ancestry, most evident in the Basque and Sardinian
populations (1, 8–12). A next layer is
evident as the consistent and reproducible
distinction between “northern” and “southern”
European population groups, with a
clinal distribution of genetic variation consistent
with a south to north expansion and/or a
larger effective population size in southern
than in northern Europe (10, 12, 13). Despite
comparatively low average levels of genetic
differentiation among Europeans, the decay
of genetic similarity as a function of geographic
distance within Europe gives rise to a
rather amazing ability to overlay a geographical
map of Europe with allele frequencybased
measures of genomewide variation
(9, 12). In certain cases, it is even possible to
assign the ethnic affiliation of an individual
with a high degree of fidelity for population
isolates such as Basque, Sardinian, Finns, and
Ashkenazi Jews (12, 14, 15), a genetic structure
within a given geographic region (16), or
even a village of origin (17).
In the European context, the question of
the trans-Mediterranean gene flow has also
been investigated. The maternal component
of African lineages to the contemporary gene
pool of Europeans could be readily estimated
due to the clear partitioning of Sub-Saharan
and European mtDNA lineages. Frequencies
of such African lineages vary widely within
Europe, ranging from 3% in southern Europe
to 0.7% in central Europe and 0.5% in
northern Europe (18, 19), with evidence that
as much as 35% of African lineages form
European-specific subclades, pointing to gene
flow from Sub-Saharan Africa to Europe as
early as 11,000 y ago (20). Similarly, the sharp
discontinuities between northwestern Africa
and the Iberian Peninsula at the level of the
Y chromosome were followed by evidence of
North African to south European migration,
particularly to the Iberian Peninsula (21, 22).
At the genomewide level, Auton et al. (23)
reported the highest genomewide haplotype
diversity of European samples in the Iberian
Peninsula, together with the highest sharing
of haplotypes with the Yoruba population of
any European population examined. A more
recent study reported that southern Europeans
have inherited 1–3% African ancestry,
with an average admixture timing of some
55 generations ago, coinciding with the end
of the Roman Empire and subsequent Arab
migrations (24).
This latter set of findings begs the question
of whether this level of Sub-Saharan admixture
is simply the carryover of Sub-Saharan
African admixture embedded within a much
