Y-Chromosomes and Evolution Research Paper

Until  recently,  little was known  about  the  extent and  distribution of diversity  in the  Y-chromosome. This problem stemmed from a basic difficulty in identifying   genetic  variation   on  this  chromosome. None of the traditional genetic markers  are found on the Y and attempts at identifying molecular variation progressed slowly until the late 1990s. A major breakthrough came about  in 1997 when a novel technique known as Denaturing High Pressure Liquid Chromatography (DHPLC) was  developed  and  allowed the rapid screening of a large number  of DNA fragments   from  the  Y-chromosome, leading  to  an increase in the speed of identification of new molecular variants.   Recent   developments   resulting   from   the Human  Genome  Project, such as the availability  of a draft sequence of the human genome and the activities of the so-called SNP (single nucleotide polymorphism) consortium are leading to an even faster identification of  molecular  variants   on  the  Y-chromosome.  The recent availability of a large number of genetic markers on the Y-chromosome has led to an increasing interest in the use of this chromosome in human  evolutionary studies, both to explore human origins and ancient diversification as well as to examine recent population history.

1.    Transmission Of The Y-Chromosome

Part  of  what  makes  the  Y-chromosome of  special interest  for  human  population genetic  studies  is its peculiar mode of transmission. The passage of the Y from   one   generation   to   the   next   is  immediately apparent: it determines the male sex. In other words, it is only transmitted from fathers to their male offspring. The  fact  that  the  Y-chromosome is transmitted  between generations  only by one sex means that  if one reconstructs a genealogy  of ancestors,  only  a single line of inheritance  needs to be followed. Another  type of DNA that shows a uniparental mode of inheritance is mitochondrial DNA (mtDNA), which is transmitted only  by  females. Thus, the Y-chromosome and mtDNA allow respectively the reconstruction of the male and female lines of inheritance   or   lineages   (Jobling   and   Tyler-Smith 1995).

2.    Variability Of The Y-Chromosome

Although the Y-chromosome determines the male sex, very few genes have been identified on the Y and none of the classical genetic markers  are encoded  by this chromosome. There is considerable cytogenetic variability of the Y but such variation is difficult to interpret for evolutionary studies.  Similarly, most of the variants identified by molecular methods  before DHPLC consisted  of complex molecular  rearrangements that were difficult to characterize  and interpret  in a population setting. The increasing number  of variants  that are now being identified can be categorized  into two basic types: biallelic and multiallelic. The biallelic markers  consist  of  nucleotide  substitution or  small insertion  deletions while the multiallelic markers generally  consist  of  regions  of  the  DNA   in  which  a variable number of Short Tandem Repeats (STR) of a DNA  motif occur (for example a variable number  of the tetranucleotide CATG).  One basic difference between  these two  types  of markers  is that  biallelic polymorphisms generally  represent  single evolutionary events while mutations at the STR loci occur at a relatively  higher  rate  and  the  mutational process  is frequently  reversible. This means that  identical  STR alleles might have a different evolutionary history,  as the  same  allele might  be generated  by  independent mutational events,  thus  potentially  erasing  an  evolutionary  signal when  probing  too  far  back  in time. However,   the  combination  of  these  two  types  of markers  actually increases the power of evolutionary analyses based on the Y-chromosome. Slowly evolving biallelic markers can be used to define the basic relationships between  Y-chromosomes in an  unambiguous form. The rapidly evolving STR markers can then be used to assess the relationships of Y-chromosomes within the basic lineages defined by the biallelic markers.  Both  kinds of markers  can also be used to estimate the age of Y-chromosome lineages based on different evolutionary models, with the consistency of the two estimates thus providing greater confidence in such estimates  (Pritchard et al. 1999, Thomson et al. 2000).

3.    The Origin And Diversification Of Human Populations

3.1    Human Origins

As biallelic markers  on the Y-chromosome generally represent  events  that  occurred  only  once  in human evolution it is possible to examine the relatedness of Y-chromosomes worldwide and represent their ancestral relationships on a phylogenetic  tree. The analysis of 167 genetic markers  in 1,062 males from  21 populations around the world recently allowed the identification  of  116  Y-chromosome types  (Underhill   et  al. 2000). Based on the common ancestry of certain types, it is possible to group human Y-chromosomes into ten basic lineages (Fig. 1). Interestingly,  the most ancient splits on the tree separate  lineages I and II, which are almost  exclusively seen in African  populations, from all other lineages which have a wider geographic distribution. This observation is in agreement with an origin of human  populations in Africa followed by a migration out of that continent  of a sample of African men. Descendants of these initial migrants would have founded   small  populations  outside   of  Africa  that would have remained small in size until the end of the last glaciation  (around 16,000 years ago) when they would have expanded  in numbers,  spreading  geographically to all inhabitable areas. Such an expansion  is clearly evidenced in the Y-chromosome by the large proportion  of mutations that  are specific to a particular chromosome type. Estimates of the age of Y-chromosome lineages indicate that their initial differentiation is about   59,000 years  old  with  a  migration   out  of Africa around 44,000 years ago (Pritchard et al. 1999, Thomson et  al.  2000).  These  findings  are  more  in agreement  with a model of recent African  origins of modern  humans;  however  the  dates  obtained  with these data  are considerably  younger  than  those  estimated  from mtDNA and autosomal markers  (Horai et al. 1995, Goldstein  et al. 1995). This inconsistency might  be due to natural selection acting with variable intensity in different genetic systems or could relate to demographic differences between men and women. Overall, the Y-chromosome shows  a  reduced  level of variation  when  compared with other genetic systems and such variation is highly structured by geography  (Seielstad et al. 1998). This makes the Y particularly suitable for the study of the history of specific geographic  regions.

3.2    Human Population Diversification

The analysis of Y-chromosome diversity at 22 biallelic markers in 1,007 males from 25 populations of Europe and  the  Middle  East  identified  20 different  lineages (Semino et al. 2000). However, over 95 percent of the men examined have one of 10 lineages, several of which are closely related. Examining the distribution of these lineages in European populations it was observed that two closely related  lineages showed East–West  gradients  in  frequency,   with  one  of  them  being  particularly  frequent   in  the  Basque  and  the  other   in Eastern Europe (Poland, Hungary, and Ukraine). Phylogenetic and genetic dating analyses suggest that these two types of Y-chromosomes were brought to Europe  by people of the Aurignacian culture,  which spread  to Europe  about  35,000 to 40,000 years ago. The East-West  gradient  is possibly  explained  by the demographic contraction  caused  by  the  last  glacial maximum  (20,000 to  13,000 years  ago)  that  would have led human populations to seek temporary refuge in more hospitable  areas from which they would have subsequently  expanded.  A third  Y-chromosome  lineage  is about  20,000 years  old  and  is restricted  to Europe  (where it is seen at highest frequency amongst central   Eastern   Europeans)  although  it  is  closely related  to  Y-chromosomes  frequent   in  the  Middle East. The age and distribution of this lineage suggest that  it was introduced by people  of the  Gravettian culture that  appeared  in Europe  around 20,000 years ago.  These  people  found  refuge  in  central  Europe during the last glacial maximum, after which they expanded  into  Western  Europe.  Finally,  a group  of younger and closely related haplotypes show a gradient in frequency  from  the Middle  East  into  Europe and might have been spread by the people that introduced the  practice  of  agriculture   into  Europe about   10,000  years  ago.  Y-chromosome data  thus indicate that two Paleolithic and one Neolithic migrations are at the origin of most of the current European population as manifested  by three  main  population clusters seen when lineage frequencies are compared between populations (Fig. 2). The three clusters observed (Western Europe, Eastern Europe, and the Middle  East)  correspond to  the  two  major  glacial refuges and to the area of origin of agriculture.

4.    Male And Female Migration In Human Evolution

A very interesting use of genetic data is in teasing apart male and female demographic history throughout human  evolution,  by comparing  population diversity of Y-chromosome, autosomal, and mtDNA markers in native  populations from  around the world.  In an initial  evaluation   it  was  observed  that  the  level of genetic  variability   across  populations based  on  Y-chromosome markers   was  much  greater  than  that observed with mtDNA markers (Seielstad et al. 1998). This  means  that  the  distribution of Y-chromosome variants  is geographically  more  localized  than  that of mtDNA variants.  A possible explanation for this global  pattern could  be  that   about   70  percent  of human populations practice patrilocality, that is women tend  to  move into  the areas  inhabited  by the  males they marry and consequently  move more, on an evolutionary  scale, than men. A subsequent  refined analysis restricted to South American populations failed to confirm  the generality  of a higher  migration  rate  of women  in native  populations (Mesa  et al. 2000). A detailed evaluation  of the proposal  that  females have generally  had  a  higher  migration   rate  than   males awaits the analysis of more genetic markers and populations. However,  it is possible  that  important regional  differences  in  male / female  migration   rates might be detected and that  these differences relate to the frequency with which patrilocality is practiced  in different parts of the world.

5.    Maternal And Paternal Origins Of Recently Founded Human Populations

The comparison of mtDNA and Y-chromosome markers  is also informative  when applied  to populations established  more recently and such data  can be used to refine information obtained from traditional historical sources. Particularly, analyzing different genetic systems can help establish the relative proportion of males and females from particular geographic  areas that  founded  a new population. In the province  of Antioquia in Colombia  it was seen that about  90 percent  of Y-chromosomes were European while 90 percent of the mtDNA lineages were Native American  (Carvajal-Carmona et al. 2000). This indicates that the population was founded mostly by European males and  Native  females. This finding  is consistent  with  the  geographic  isolation  of the  province and with historical records indicating that in early colonial times, on average only about 20 percent of the Spanish migrants to the New World were women. However,  this  result  is inconsistent  with  autosomal markers,  which indicate  that  this population is predominantly of European ancestry. This inconsistency between  bi and  uniparental markers  might  relate  to the collapse of the Native American population during the first century of Spanish colonization and to the fact that  Spanish  immigration  was a  long-term  process. These demographic factors  might  have resulted  in a progressive dilution of the founding Native American component as estimated  with autosomal markers.

Curiously,  the  analysis  of  rapidly  evolving  STRs indicates  that  the population of Antioquia seems to have  a  relatively  important Jewish  ancestry  as  evidenced by the finding in this population of Y-chromosome STR lineages seen at high frequency only in Jewish populations. However, no record is available of  a  Jewish  migration   to  Antioquia. Furthermore, almost simultaneously with the Spanish expansion  to America, Jews were expelled from Spain or forced to convert  to Christianity. The Y-chromosome findings suggest that  amongst  the Spanish founders  of Antioquia a relative large proportion of converts was represented.  No record  of such contribution is available probably  because the migration to the colonies of converts was considered  illegal under colonial rule.

6.    Conclusion

Developments resulting from the Human Genome Project have recently catapulted the use of Y-chromosome markers into the forefront of the study of human population origins and diversification.  The large number of markers currently available together with novel highly efficient technologies enable analyses of an unprecedented resolution  and scale. Evolutionary analyses are facilitated by the fact that slowly evolving markers  allow  the  unambiguous assessment  of  the evolutionary relationship between  Y-chromosomes. Rapidly  evolving markers  can refine analyses  within specific lineages or populations. These studies illuminate  not  only questions  related  to the origin  of our species and its early diversification  but also allow the probing  of more recent demographic events. The synthesis  of genetic data  with information obtained from  sources  including  geology, paleoanthropology, archaeology, and historical demography is allowing a refined reconstruction of human  evolution  stretching from our origins as a species all the way to the exploration of quite recent historical  events.

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