BACKGROUND
the markers of the male-specific region of the y-chromosome  exhibit the highest inter-population diversity in the human genome.
though some other genome regions contain more polymorphic sites, y-chromosomal markers exhibit higher variation of allele frequencies across different populations than markers on other chromosomes; this phenomenon is generally attributed to strong genetic drift in combination with the patrilocality common to most human populations; indeed, in matrilocal populations the pattern is different .
thus for most human populations, y-chromosomal markers form one of the most informative tools for tracing their demographic history .
through numerous academic publications, the study of y-chromosome variation has grown into an important field of population genetics.
the msy is also a valuable tool for tracing individual genealogies, and it is thus widely used in genetic genealogy, one of the most popular fields of citizen science.
individual and population origin are interrelated, resulting in mutual interactions: for example, academic papers in the field of population genetics are widely discussed on genealogical internet forums  <cit> , and, similarly, the y-chromosome tree of the international society of genetic genealogy  <cit>  has become a standard resource for population geneticists .
“citizen science” in the oxford english dictionary is defined as: “scientific work undertaken by members of the general public, often in collaboration with or under the direction of professional scientists and scientific institutions”  <cit> .
genetic genealogy is one of the manifestations of citizens’ activity in the field of scientific research  <cit> .
however, direct collaboration between population geneticists and genetic genealogists has been limited .
the information value of the msy often depends on discovering snps which subdivide haplogroups with broad geographic distribution into branches, revealing the fine population structure.
progress in such discoveries has recently moved from a slow linear phase to a rapid exponential phase due to the use of next-generation sequencing technologies, resulting in a number of high-quality papers applying this approach to overall patterns of paternal population history  and to the phylogeography of specific haplogroups .
to the best of our knowledge, only a few studies based on full y-chromosome sequencing include y-chromosomes belonging to haplogroup q  <cit> , and none of them focused specifically on it.
this haplogroup is well known because it makes up about 90% of indigenous native american y-chromosomes, but is also present in north eurasia  <cit> .
a rare clade called q <dig> has been detected in y-chromosomal resequencing studies  <cit>  and was found at low frequencies in iraqis  <cit> , iranians  <cit> , israelis  <cit> , indian brahmins  <cit>  and pashtuns  <cit> .
rare haplogroups can be very informative for tracing human migration routes , and here we concentrate on improving resolution in the q3-l <dig> portion of the first q1’ <dig> versus q <dig> bifurcation of haplogroup q-m <dig>  <cit> .
we combined the efforts of population geneticists and genetic genealogists to use the potential of full y-chromosome sequencing for reconstructing haplogroup q3-l <dig> phylogeography and suggest possible linkages to events in population history.
RESULTS
we constructed a detailed frequency distribution map of haplogroup q-m <dig>  which demonstrated, in agreement with the previous studies, the haplogroup’s presence throughout asia and the americas with frequency peaks in america and central siberia.
there are three major trunks: q <dig>  q <dig>  and q <dig> .
the first two trunks split into multiple branches, some of which are known to be purely asian, while others are both asian and  american .
little is known about the distribution of the third branch known formerly as q1b and now as q <dig>  <cit> , which is in focus of this study.fig.
<dig> overview of haplogroup q. a global frequency distribution map of haplogroup q-m <dig>  the map was constructed using q-m <dig> frequencies in  <dig> populations .
b phylogenetic structure of haplogroup q-m <dig>
distribution of q3-l275
to evaluate the q <dig> distribution, we analyzed both academic data from indigenous populations and data from genealogical projects.
the frequency distribution map based on academic data  reveals that haplogroup q3-l <dig> is confined to west asia and neighboring parts of central and south asia – mainly pakistan, west india, and up to 7% in iran .
the map based on genealogical project data  also reveals the presence of haplogroup q3-l <dig> in west asia and neighboring areas, with a maximum frequency in pakistan, but also throughout europe.
when data on ashkenazi jew genealogical projects are included , the q <dig> frequencies in europe become almost as high as in west asia .fig.
<dig> frequency distribution map of haplogroup q3-l <dig>  a data from indigenous populations from academic papers .
b data from genealogical projects .
the plotted frequencies were calculated as number of q3-l <dig> carriers in the corresponding genealogical project divided to the total number of persons in the project
n
n
the table contains populations where haplogroup q3-l <dig> was found
athese samples were assigned to haplogroup q3-l <dig> based on their str haplotypes
phylogenetics of q3-l275
we sequenced a large portion of the y-chromosome in  <dig> samples belonging to haplogroup q <dig> and in one outgroup q <dig> sample.
this dataset allowed us to reconstruct a detailed phylogenetic tree of haplogroup q <dig>  calibrated using a mutation rate of  <dig>  × 10− <dig> mutations per bp per year  <cit>  .
the first split in the tree occurred in the upper paleolithic, around  <dig>  years ago , giving rise to the q3e branch and its brother q3a’d branch .
the first split in the latter generated q3d and the remaining q3a’c around  <dig> ky bp; q3a’c subsequently split into q3a, q3b, and q3c.
thus, at the beginning of the neolithic period, the five main branches within q <dig> already existed.
q3c and q3d were represented in our dataset by single sample each; q3e split into sub-branches around 6- <dig> ky bp; q3b split around  <dig> ky bp; q3a did not exhibit splits till 3- <dig> ky bp when it demonstrated a remarkable set of phylogenetic splits .fig.
<dig> phylogenetic tree of haplogroup q3-l <dig> based on full sequences of the y-chromosome.
additional file 2: table s <dig> provides the detailed version of this tree.
notes contain ages  of the principal clades.
samples used for age calculations are shown in italic
a
a
a
a
a
a
a
athese ages were not calculated because corresponding samples were not sequenced with the bigy technology
these events started with the ternary split of q3a into q3a1’ <dig>  q3a <dig>  and q3a <dig> .
two of these branches themselves split immediately: the quarternary split of q3a1’ <dig>  occurred  <dig> +/- <dig>  ky bp and the ternary split of q3a <dig> occurred  <dig> +/- <dig>  ky bp.
thus, from  <dig>  to  <dig>  years ago there were no splits within the q3a lineages examined, but around  <dig> – <dig>  years ago this branch has split into seven sub-branches.
though phylogenetic analysis identified the sequence of these splits, the confidence intervals of their dates overlap considerably, showing that these events occurred within a narrow time interval.
the tree demonstrates a final set of events within the last two thousand years: q3a1’ <dig> split into q3a <dig> and q3a2; q3a <dig> split into two sub-branches  <dig> +/- <dig>  ky bp, and these sub-branches in turn split between the 2nd and 10th centuries ad .
phylogeography of q3-l275
we analyzed  <dig> haplogroup q <dig> samples from a diverse set of genealogical projects  and assigned each to one of the q <dig> branches.
figure  <dig> shows geographic places of origin for these individuals, thus indicating the geographic distribution of the branches.fig.
<dig> phylogeographic summary: geographic locations of individual branches.
colors of branches correspond to colors on the inset maps and fig.
3
figure  <dig> links the deepest upper paleolithic split  to west and south asia: most q3e samples  were found in pakistan and india, although some were also found in europe and north asia ; these latter samples fall into the narrower q3e-yp <dig> sub-branch and might represent a later spread of q3e, rather than its place of origin.
the following splits were once again geographically linked to south and west asia: most of q3b samples  came from west asia and neighboring parts of south and central asia, although one sample was found in portugal.
the areas of q3c and q3d could not be identified reliably as these branches were found in single samples.
these two samples came from poland and inner mongolia  <cit> , respectively, indicating the wide geographic distribution of q <dig> branches.
in contrast to these narrowly distributed clades, their brother clade q3a is represented by multiple samples found mainly in west asians and europeans .
the remarkable phylogenetic structure of the clade has a clear reflection in geography.
the ternary split of this branch resulted in a west asian branch q3a <dig> and two branches found in both asia and europe .
the latter branch in turn split into five sub-branches , some of which were west asian and others european .
one of these european branches, q3a <dig>  was found in germans and dutch , while another was found in ashkenazi jews  and accounts for 5% of their paternal pool .
this is the branch which split much later than the main set of phylogenetic events within q3a, and whose sub-branches expanded between the second and tenth centuries ad.
discussion
origin, dissemination, and expansion of the haplogroup q3-l275
haplogroup q3-l <dig> results from the first known split within haplogroup q, which occurred in the paleolithic epoch: according to previous studies  <cit> , haplogroup q split into the q3-l <dig> and q1’2-l <dig> branches around  <dig> ky ago.
thus the location of this split might help identify the homeland of haplogroup q, from where it spread throughout eurasia and the americas.
our findings better support a west asian or central asian homeland of q <dig> than any other area: a higher frequency was found in west asia and in neighboring pakistan; and early branches were identified in west asia, central asia and south asia.
increasing the dataset of ancient dna might in future identify additional early branches, helping to locate a possible homeland more precisely.
the very few samples from present-day  or ancient  <cit>  china do not contradict this hypothesis, as they came from the western provinces located in central asia or historically linked to this area.
the single portuguese sample likely reflects the origin of the carrier, rather than more general population history.
thus, q <dig> was one of the paleolithic west eurasian haplogroups.
its west/central asian homeland proposed here is hypothetical, because present-day genetic patterns do not necessarily reflect ancient ones as these can be modified by the more recent demographic events.
though tmrca times of haplogroup emergence often do not correspond to demographic events, we note that the initial haplogroup q <dig> breakup  is consistent with demographic changes in the post-last glacial maximum period.
the following phases of q <dig> history – between  <dig> and  <dig> ky bp – occurred again in west and central asia.
these older branches did not reach europe with the neolithic wave  but one of the later branches – q3a – is now found in both asia and europe.
the fractionation of this branch around  <dig> ky bp allows us to speculate that it probably entered europe from the near east via historical contacts between states in iran and the eastern mediterranean, or from central asia via the north pontic steppe along the chain of nomadic populations  <cit> .
in europe there are at least two branches: one in dutch and germans, and another in ashkenazi jews.
these branches split from a common root 3000+/-700 years ago : before the jewish migration into europe in roman times  <cit> .
further screening in both europe and the levant is needed to determine whether the ancestors of the ashkenazi acquired this lineage from the levantine homeland or from the european host populations.
the aforementioned set of events belongs to the history of the q <dig> lineage rather than the history of any specific population.
we caution against interpreting branching patterns as simple signals of a bottleneck followed by a demographic expansion, because modern phylogenies represent the occurrence of the last bottleneck, not necessarily the only bottleneck the lineages have ever experienced.
the ages of the entire ashkenazi cluster q3a <dig>  and its sub-clusters  fall into the early middle ages.
most scholars believe that at that time ashkenazi ancestors lived in europe, though they did not appear in written records with this name.
the clear phylogenetic expansion within q3a <dig> , the expansion date, and nearby absence of q3a <dig> in non-ashkenazi europeans indicate that this pre-ashkenazi population – at least those who carried q <dig> – grew rapidly and was already isolated in the early middle ages.
lessons from collaboration of academic and citizen researchers
our study was initiated by a citizen researcher  <cit>  carrying out his research in association and with the support of the genome geography lab , so the first lesson is that such collaborations can shed light on the phylogeography of rare haplogroups which might otherwise remain undescribed.
indeed, there were previously four sequenced q <dig> y-chromosome in the academic literature  <cit> , while our study presents  <dig> more.
this now makes q <dig> one of the most extensively studied haplogroups in terms of the number of full y-sequences relative to haplogroup carriers.
at least three branches of academic science – population genetics, forensic genetics and evolutionary genetics – provide extensive studies of y-chromosomal variation in human populations.
in the sphere of citizen science, y-chromosomal variation is covered by the field called genetic genealogy, though it attracts attention of other citizen researchers as well.
genetic genealogical communities include many enthusiasts concentrating on one haplogroup each, while population geneticists  are normally involved in multiple projects and simultaneously analyze many haplogroups.
so, genetic genealogists may offer specialization , while population geneticists might contribute generalization .
another difference stimulating mutual interest is the size of y-chromosome sequence databases and strategies used to populate them.
the genealogical databases contain thousands of sequenced y-chromosomes  <cit> , which is larger by an order of magnitude than academic datasets .
however, genealogical databases contain many samples of unknown or doubtful population origin and these databases are drastically biased towards european-ancestry individuals.
in contrast, y chromosomes sequenced in academic research were often preselected to achieve uniform geographic or phylogenetic coverage and their population of origin is well-defined.
thus, one may consider whether the samples in academic databases are by an order of magnitude more valuable for phylogeographic analysis.
apart from the full y-chromosome sequences , there are large databases of y-chromosome genotypes with low to medium resolution.
both academic and citizen databases contain haplogroup frequencies and str haplotypes in population samples, and in both cases the sample sizes vary from dozens to hundreds of individuals per population.
there are two types of academic databases: the samples in population-genetic databases were collected from indigenous individuals, while the samples in forensic databases were collected from all individuals residing in the given area, without subdividing between individuals from indigenous groups and descendants of recent immigrants  <cit> .
the samples in citizen science  databases come from the customers themselves, and therefore are more similar to forensic databases, as they reflect the population of a customer’s country, including recent immigrants and temporary visitors.
this is a problem for applying genealogical databases to historical and prehistorical reconstructions.
some genealogical projects  try to solve this problem by organizing the customer samples according to their deepest known paternal origin rather than by country of present-day residence.
there are genealogical projects for many countries and ethnic groups.
the same country or populations were often studied in academic research, allowing direct comparison of the results .
the higher q <dig> frequencies from both datasets are in general agreement.
for example, the frequency of q <dig> in ashkenazi ranges from 1% to 5% according to academic, and from 2% to 6% according to genealogical, datasets; in pakistan and india it ranges from 0% to 5% according to academic data and from 1% to 9% according to genealogical datasets .
in populations where q <dig> is rare, both similarities and differences of two datasets could be stochastic.
thus, to compare the datasets we looked at their overall patterns revealed by the gene geographic maps .
q <dig> is present on both maps in west and south asia and absent or very rare in other parts of asia.
but the maps differ in their european sections: academic data indicate very few spots and very low frequencies , while genealogical projects show from 0% to 5% frequency of q <dig> .
this difference could be caused by two factors.
first, there are some rare q <dig> branches which are present in both indigenous and general populations, but occasionally were missed in academic samples .
second, individuals of paternal jewish ancestry might appear in non-jewish genealogical projects, but were not included in academic samples due to strict sampling criteria and genealogical information collected during sampling.
both academic and citizen scientists of our team believe that, despite genealogical projects often providing important data, overestimating their information value should be avoided.
for example, the differences in haplogroup frequencies from academic data on the same population could be caused by peculiarities of genealogical sampling.
the social activity and ethnic origin of a project’s administrators and participants can make a genealogical sample non-random, as it tends to include clusters of relatives , or is biased to a particular geographic locality.
genealogical projects differ in the criteria they apply for including customer samples.
thus projects which provide results similar to academic data on the same population reliably describe the gene pool of stable regional/ethnic populations.
data from these projects can then be used along with academic datasets, increasing the total sample size and revealing additional genetic lineages.
it should be noted, however, that as mentioned geographic coverage in genealogical projects is strongly biased to europe, and there are many non-sampled regions in asia , in contrast to the larger number of populations and global coverage achieved in academic datasets .
this difference should also be considered when pooling both kinds of data.
finally, geneticists and genealogists often differ in their approach to interpreting the data.
geneticists typically consider the entire gene pool, consisting of many haplogroups, and draw conclusions based on their relative frequencies in different populations.
even in studies dedicated to a single haplogroup, conclusions about population history take into account the data from other components of the gene pool.
genealogists, on the contrary, focus on the history of a single lineage.
this is fully justified for understanding the genealogy of an individual, as he has a single paternal lineage.
but there is no ‘genealogy of populations’: a population does not have a single root , marked by a specific haplogroup.
instead, a population typically consists of individuals with different origins and different haplogroups.
as a result, the “one haplogroup history – one population/ethnic history” hypothesis would be a dangerous oversimplification, and in addition inappropriately expands the history of an ethnic group to a time depth far exceeding the formation the group itself .
we believe that haplogroups indeed mark features of population history, but caution should be observed when combining these features into an entire picture.
different approaches should be used for reconstructing individual  and population  paternal histories, and collaborative studies of geneticists and genealogists can help to avoid one-sided interpretations.
CONCLUSIONS
haplogroup q3-l <dig> represents the oldest known split within eurasian/american haplogroup q, and most likely occurred in west or central asia in the upper paleolithic period.
it could be hypothesized that during the mesolithic and neolithic epochs, q <dig> remained a minor component of the west asian y-chromosome pool.
it gave rise to five branches  which spread across west, central and parts of south asia.
around 3– <dig> millennia ago , the q3a branch, like several other y lineages  <cit> , underwent a rapid expansion, splitting into seven branches, some of which entered europe.
one of these branches, q3a <dig>  was acquired by a population ancestral to ashkenazi jews and grew within this population during the 1st millennium ad, reaching up to 6% in present-day ashkenazi.
this study dataset was generated by a y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists.
this positive experience of collaboration between academic and citizen science provides a model for further joint projects.
merging data and skills of academic and citizen scientists promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations.

 the markers of the male-specific region of the y-chromosome exhibit the highest inter-population diversity in the human genome. though some other genome regions contain more polymorphic sites, y-chromosomal markers exhibit higher variation of allele frequencies across different populations than markers on other chromosomes; this phenomenon is generally attributed to strong genetic drift in combination with the patrilocality common to most human populations; indeed, in matrilocal populations the pattern is different. thus for most human populations, y-chromosomal markers form one of the most informative tools for tracing their demographic history. through numerous academic publications, the study of y-chromosome variation has grown into an important field of population genetics. the msy is also a valuable tool for tracing individual genealogies, and it is thus widely used in genetic genealogy, one of the most popular fields of citizen science. individual and population origin are interrelated, resulting in mutual interactions: for example, academic papers in the field of population genetics are widely discussed on genealogical internet forums, and, similarly, the y-chromosome tree of the international society of genetic genealogy has become a standard resource for population geneticists. “citizen science” in the oxford english dictionary is defined as: “scientific work undertaken by members of the general public, often in collaboration with or under the direction of professional scientists and scientific institutions”. genetic genealogy is one of the manifestations of citizens’ activity in the field of scientific research. however, direct collaboration between population geneticists and genetic genealogists has been limited. the information value of the msy often depends on discovering snps which subdivide haplogroups with broad geographic distribution into branches, revealing the fine population structure. progress in such discoveries has recently moved from a slow linear phase to a rapid exponential phase due to the use of next-generation sequencing technologies, resulting in a number of high-quality papers applying this approach to overall patterns of paternal population history and to the phylogeography of specific haplogroups. to the best of our knowledge, only a few studies based on full y-chromosome sequencing include y-chromosomes belonging to haplogroup q, and none of them focused specifically on it. this haplogroup is well known because it makes up about 90% of indigenous native american y-chromosomes, but is also present in north eurasia. a rare clade called q has been detected in y-chromosomal resequencing studies and was found at low frequencies in iraqis, iranians, israelis, indian brahmins and pashtuns. rare haplogroups can be very informative for tracing human migration routes, and here we concentrate on improving resolution in the q3-l portion of the first q1’ versus q bifurcation of haplogroup q-m. we combined the efforts of population geneticists and genetic genealogists to use the potential of full y-chromosome sequencing for reconstructing haplogroup q3-l phylogeography and suggest possible linkages to events in population history.  we constructed a detailed frequency distribution map of haplogroup q-m which demonstrated, in agreement with the previous studies, the haplogroup’s presence throughout asia and the americas with frequency peaks in america and central siberia. there are three major trunks: q q and q. the first two trunks split into multiple branches, some of which are known to be purely asian, while others are both asian and american. little is known about the distribution of the third branch known formerly as q1b and now as q, which is in focus of this study.fig. overview of haplogroup q. a global frequency distribution map of haplogroup q-m the map was constructed using q-m frequencies in populations. b phylogenetic structure of haplogroup q-m distribution of q3-l275 to evaluate the q distribution, we analyzed both academic data from indigenous populations and data from genealogical projects. the frequency distribution map based on academic data reveals that haplogroup q3-l is confined to west asia and neighboring parts of central and south asia – mainly pakistan, west india, and up to 7% in iran. the map based on genealogical project data also reveals the presence of haplogroup q3-l in west asia and neighboring areas, with a maximum frequency in pakistan, but also throughout europe. when data on ashkenazi jew genealogical projects are included, the q frequencies in europe become almost as high as in west asia.fig. frequency distribution map of haplogroup q3-l a data from indigenous populations from academic papers. b data from genealogical projects. the plotted frequencies were calculated as number of q3-l carriers in the corresponding genealogical project divided to the total number of persons in the project n n the table contains populations where haplogroup q3-l was found athese samples were assigned to haplogroup q3-l based on their str haplotypes phylogenetics of q3-l275 we sequenced a large portion of the y-chromosome in samples belonging to haplogroup q and in one outgroup q sample. this dataset allowed us to reconstruct a detailed phylogenetic tree of haplogroup q calibrated using a mutation rate of  × 10− mutations per bp per year. the first split in the tree occurred in the upper paleolithic, around  years ago, giving rise to the q3e branch and its brother q3a’d branch. the first split in the latter generated q3d and the remaining q3a’c around ky bp; q3a’c subsequently split into q3a, q3b, and q3c. thus, at the beginning of the neolithic period, the five main branches within q already existed. q3c and q3d were represented in our dataset by single sample each; q3e split into sub-branches around 6- ky bp; q3b split around ky bp; q3a did not exhibit splits till 3- ky bp when it demonstrated a remarkable set of phylogenetic splits.fig. phylogenetic tree of haplogroup q3-l based on full sequences of the y-chromosome. additional file 2: table s provides the detailed version of this tree. notes contain ages of the principal clades. samples used for age calculations are shown in italic a a a a a a a athese ages were not calculated because corresponding samples were not sequenced with the bigy technology these events started with the ternary split of q3a into q3a1’ q3a and q3a. two of these branches themselves split immediately: the quarternary split of q3a1’ occurred +/- ky bp and the ternary split of q3a occurred +/- ky bp. thus, from to  years ago there were no splits within the q3a lineages examined, but around –  years ago this branch has split into seven sub-branches. though phylogenetic analysis identified the sequence of these splits, the confidence intervals of their dates overlap considerably, showing that these events occurred within a narrow time interval. the tree demonstrates a final set of events within the last two thousand years: q3a1’ split into q3a and q3a2; q3a split into two sub-branches +/- ky bp, and these sub-branches in turn split between the 2nd and 10th centuries ad. phylogeography of q3-l275 we analyzed haplogroup q samples from a diverse set of genealogical projects and assigned each to one of the q branches. figure  shows geographic places of origin for these individuals, thus indicating the geographic distribution of the branches.fig. phylogeographic summary: geographic locations of individual branches. colors of branches correspond to colors on the inset maps and fig. 3 figure  links the deepest upper paleolithic split to west and south asia: most q3e samples were found in pakistan and india, although some were also found in europe and north asia; these latter samples fall into the narrower q3e-yp sub-branch and might represent a later spread of q3e, rather than its place of origin. the following splits were once again geographically linked to south and west asia: most of q3b samples came from west asia and neighboring parts of south and central asia, although one sample was found in portugal. the areas of q3c and q3d could not be identified reliably as these branches were found in single samples. these two samples came from poland and inner mongolia, respectively, indicating the wide geographic distribution of q branches. in contrast to these narrowly distributed clades, their brother clade q3a is represented by multiple samples found mainly in west asians and europeans. the remarkable phylogenetic structure of the clade has a clear reflection in geography. the ternary split of this branch resulted in a west asian branch q3a and two branches found in both asia and europe. the latter branch in turn split into five sub-branches, some of which were west asian and others european. one of these european branches, q3a was found in germans and dutch, while another was found in ashkenazi jews and accounts for 5% of their paternal pool. this is the branch which split much later than the main set of phylogenetic events within q3a, and whose sub-branches expanded between the second and tenth centuries ad. discussion origin, dissemination, and expansion of the haplogroup q3-l275 haplogroup q3-l results from the first known split within haplogroup q, which occurred in the paleolithic epoch: according to previous studies, haplogroup q split into the q3-l and q1’2-l branches around ky ago. thus the location of this split might help identify the homeland of haplogroup q, from where it spread throughout eurasia and the americas. our findings better support a west asian or central asian homeland of q than any other area: a higher frequency was found in west asia and in neighboring pakistan; and early branches were identified in west asia, central asia and south asia. increasing the dataset of ancient dna might in future identify additional early branches, helping to locate a possible homeland more precisely. the very few samples from present-day or ancient china do not contradict this hypothesis, as they came from the western provinces located in central asia or historically linked to this area. the single portuguese sample likely reflects the origin of the carrier, rather than more general population history. thus, q was one of the paleolithic west eurasian haplogroups. its west/central asian homeland proposed here is hypothetical, because present-day genetic patterns do not necessarily reflect ancient ones as these can be modified by the more recent demographic events. though tmrca times of haplogroup emergence often do not correspond to demographic events, we note that the initial haplogroup q breakup is consistent with demographic changes in the post-last glacial maximum period. the following phases of q history – between and ky bp – occurred again in west and central asia. these older branches did not reach europe with the neolithic wave but one of the later branches – q3a – is now found in both asia and europe. the fractionation of this branch around ky bp allows us to speculate that it probably entered europe from the near east via historical contacts between states in iran and the eastern mediterranean, or from central asia via the north pontic steppe along the chain of nomadic populations. in europe there are at least two branches: one in dutch and germans, and another in ashkenazi jews. these branches split from a common root 3000+/-700 years ago: before the jewish migration into europe in roman times. further screening in both europe and the levant is needed to determine whether the ancestors of the ashkenazi acquired this lineage from the levantine homeland or from the european host populations. the aforementioned set of events belongs to the history of the q lineage rather than the history of any specific population. we caution against interpreting branching patterns as simple signals of a bottleneck followed by a demographic expansion, because modern phylogenies represent the occurrence of the last bottleneck, not necessarily the only bottleneck the lineages have ever experienced. the ages of the entire ashkenazi cluster q3a and its sub-clusters fall into the early middle ages. most scholars believe that at that time ashkenazi ancestors lived in europe, though they did not appear in written records with this name. the clear phylogenetic expansion within q3a, the expansion date, and nearby absence of q3a in non-ashkenazi europeans indicate that this pre-ashkenazi population – at least those who carried q – grew rapidly and was already isolated in the early middle ages. lessons from collaboration of academic and citizen researchers our study was initiated by a citizen researcher carrying out his research in association and with the support of the genome geography lab, so the first lesson is that such collaborations can shed light on the phylogeography of rare haplogroups which might otherwise remain undescribed. indeed, there were previously four sequenced q y-chromosome in the academic literature, while our study presents more. this now makes q one of the most extensively studied haplogroups in terms of the number of full y-sequences relative to haplogroup carriers. at least three branches of academic science – population genetics, forensic genetics and evolutionary genetics – provide extensive studies of y-chromosomal variation in human populations. in the sphere of citizen science, y-chromosomal variation is covered by the field called genetic genealogy, though it attracts attention of other citizen researchers as well. genetic genealogical communities include many enthusiasts concentrating on one haplogroup each, while population geneticists are normally involved in multiple projects and simultaneously analyze many haplogroups. so, genetic genealogists may offer specialization, while population geneticists might contribute generalization. another difference stimulating mutual interest is the size of y-chromosome sequence databases and strategies used to populate them. the genealogical databases contain thousands of sequenced y-chromosomes, which is larger by an order of magnitude than academic datasets. however, genealogical databases contain many samples of unknown or doubtful population origin and these databases are drastically biased towards european-ancestry individuals. in contrast, y chromosomes sequenced in academic research were often preselected to achieve uniform geographic or phylogenetic coverage and their population of origin is well-defined. thus, one may consider whether the samples in academic databases are by an order of magnitude more valuable for phylogeographic analysis. apart from the full y-chromosome sequences, there are large databases of y-chromosome genotypes with low to medium resolution. both academic and citizen databases contain haplogroup frequencies and str haplotypes in population samples, and in both cases the sample sizes vary from dozens to hundreds of individuals per population. there are two types of academic databases: the samples in population-genetic databases were collected from indigenous individuals, while the samples in forensic databases were collected from all individuals residing in the given area, without subdividing between individuals from indigenous groups and descendants of recent immigrants. the samples in citizen science databases come from the customers themselves, and therefore are more similar to forensic databases, as they reflect the population of a customer’s country, including recent immigrants and temporary visitors. this is a problem for applying genealogical databases to historical and prehistorical reconstructions. some genealogical projects try to solve this problem by organizing the customer samples according to their deepest known paternal origin rather than by country of present-day residence. there are genealogical projects for many countries and ethnic groups. the same country or populations were often studied in academic research, allowing direct comparison of the results. the higher q frequencies from both datasets are in general agreement. for example, the frequency of q in ashkenazi ranges from 1% to 5% according to academic, and from 2% to 6% according to genealogical, datasets; in pakistan and india it ranges from 0% to 5% according to academic data and from 1% to 9% according to genealogical datasets. in populations where q is rare, both similarities and differences of two datasets could be stochastic. thus, to compare the datasets we looked at their overall patterns revealed by the gene geographic maps. q is present on both maps in west and south asia and absent or very rare in other parts of asia. but the maps differ in their european sections: academic data indicate very few spots and very low frequencies, while genealogical projects show from 0% to 5% frequency of q. this difference could be caused by two factors. first, there are some rare q branches which are present in both indigenous and general populations, but occasionally were missed in academic samples. second, individuals of paternal jewish ancestry might appear in non-jewish genealogical projects, but were not included in academic samples due to strict sampling criteria and genealogical information collected during sampling. both academic and citizen scientists of our team believe that, despite genealogical projects often providing important data, overestimating their information value should be avoided. for example, the differences in haplogroup frequencies from academic data on the same population could be caused by peculiarities of genealogical sampling. the social activity and ethnic origin of a project’s administrators and participants can make a genealogical sample non-random, as it tends to include clusters of relatives, or is biased to a particular geographic locality. genealogical projects differ in the criteria they apply for including customer samples. thus projects which provide results similar to academic data on the same population reliably describe the gene pool of stable regional/ethnic populations. data from these projects can then be used along with academic datasets, increasing the total sample size and revealing additional genetic lineages. it should be noted, however, that as mentioned geographic coverage in genealogical projects is strongly biased to europe, and there are many non-sampled regions in asia, in contrast to the larger number of populations and global coverage achieved in academic datasets. this difference should also be considered when pooling both kinds of data. finally, geneticists and genealogists often differ in their approach to interpreting the data. geneticists typically consider the entire gene pool, consisting of many haplogroups, and draw conclusions based on their relative frequencies in different populations. even in studies dedicated to a single haplogroup, conclusions about population history take into account the data from other components of the gene pool. genealogists, on the contrary, focus on the history of a single lineage. this is fully justified for understanding the genealogy of an individual, as he has a single paternal lineage. but there is no ‘genealogy of populations’: a population does not have a single root, marked by a specific haplogroup. instead, a population typically consists of individuals with different origins and different haplogroups. as a result, the “one haplogroup history – one population/ethnic history” hypothesis would be a dangerous oversimplification, and in addition inappropriately expands the history of an ethnic group to a time depth far exceeding the formation the group itself. we believe that haplogroups indeed mark features of population history, but caution should be observed when combining these features into an entire picture. different approaches should be used for reconstructing individual and population paternal histories, and collaborative studies of geneticists and genealogists can help to avoid one-sided interpretations.  haplogroup q3-l represents the oldest known split within eurasian/american haplogroup q, and most likely occurred in west or central asia in the upper paleolithic period. it could be hypothesized that during the mesolithic and neolithic epochs, q remained a minor component of the west asian y-chromosome pool. it gave rise to five branches which spread across west, central and parts of south asia. around 3– millennia ago, the q3a branch, like several other y lineages, underwent a rapid expansion, splitting into seven branches, some of which entered europe. one of these branches, q3a was acquired by a population ancestral to ashkenazi jews and grew within this population during the 1st millennium ad, reaching up to 6% in present-day ashkenazi. this study dataset was generated by a y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. this positive experience of collaboration between academic and citizen science provides a model for further joint projects. merging data and skills of academic and citizen scientists promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. 
during the mesolithic and neolithic epochs, q remained a minor component of the west asian y-chromosome pool and gave rise to five branches, which spread across west, central and parts of south asia. this positive experience of collaboration between academic and citizen science provides a model for further joint projects. the y-chromosome haplogroup q has three major branches: q q and q q is found in both asia and the americas where it accounts for about 90% of indigenous native american y-chromosomes; q is found in north and central asia; but little is known about the third branch, q also named q1b-l here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full y-chromosome sequencing for reconstructing haplogroup q phylogeography and suggest possible linkages to events in population history. this study dataset was generated by a massive y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. haplogroup q3-l derived from the oldest known split within eurasian/american haplogroup q, most likely occurred in west or central asia in the upper paleolithic period. one of these branches, q3a was acquired by a population ancestral to ashkenazi jews and grew within this population during the 1st millennium ad, reaching up to 5% in present day ashkenazi. around 3– millennia ago, the q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered europe.
 the y-chromosome haplogroup q has three major branches: q q and q q is found in both asia and the americas where it accounts for about 90% of indigenous native american y-chromosomes; q is found in north and central asia; but little is known about the third branch, q also named q1b-l here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full y-chromosome sequencing for reconstructing haplogroup q phylogeography and suggest possible linkages to events in population history.  we analyzed fully sequenced y-chromosomes and reconstructed the haplogroup q phylogenetic tree in detail. haplogroup q3-l derived from the oldest known split within eurasian/american haplogroup q, most likely occurred in west or central asia in the upper paleolithic period. during the mesolithic and neolithic epochs, q remained a minor component of the west asian y-chromosome pool and gave rise to five branches, which spread across west, central and parts of south asia. around 3– millennia ago, the q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered europe. one of these branches, q3a was acquired by a population ancestral to ashkenazi jews and grew within this population during the 1st millennium ad, reaching up to 5% in present day ashkenazi.  this study dataset was generated by a massive y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. this positive experience of collaboration between academic and citizen science provides a model for further joint projects. merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords y-chromosomehaplogroup qpopulation geneticsgenetic genealogyashkenaziphylogeographygene geographythe international conference on bioinformatics of genome regulation and structure\systems biology novosibirsk, russia august- september issue-copyright-statement© the author 2017 