Y chromosome lineages in men of west African descent

The early African experience in the Americas is marked by the transatlantic slave trade from ～1619 to 1850 and the rise of the plantation system. The origins of enslaved Africans were largely dependent on European preferences as well as the availability of potential laborers within Africa. Rice production was a key industry of many colonial South Carolina low country plantations. Accordingly, rice plantations owners within South Carolina often requested enslaved Africans from the so-called "Grain Coast" of western Africa (Senegal to Sierra Leone). Studies on the African origins of the enslaved within other regions of the Americas have been limited. To address the issue of origins of people of African descent within the Americas and understand more about the genetic heterogeneity present within Africa and the African Diaspora, we typed Y chromosome specific markers in 1,319 men consisting of 508 west and central Africans (from 12 populations), 188 Caribbeans (from 2 islands), 532 African Americans (AAs from Washington, DC and Columbia, SC), and 91 European Americans. Principal component and admixture analyses provide support for significant Grain Coast ancestry among African American men in South Carolina. AA men from DC and the Caribbean showed a closer affinity to populations from the Bight of Biafra. Furthermore, 30-40% of the paternal lineages in African descent populations in the Americas are of European ancestry. Diverse west African ancestries and sex-biased gene flow from EAs has contributed greatly to the genetic heterogeneity of African populations throughout the Americas and has significant implications for gene mapping efforts in these populations.     

African Y chromosome and mtDNA divergence provides insight into the history of click languages

BACKGROUND: About 30 languages of southern Africa, spoken by Khwe and San, are characterized by a repertoire of click consonants and phonetic accompaniments. The Jumid R:'hoansi (!Kung) San carry multiple deeply coalescing gene lineages. The deep genetic diversity of the San parallels the diversity among the languages they speak. Intriguingly, the language of the Hadzabe of eastern Africa, although not closely related to any other language, shares click consonants and accompaniments with languages of Khwe and San. RESULTS: We present original Y chromosome and mtDNA variation of Hadzabe and other ethnic groups of Tanzania and Y chromosome variation of San and peoples of the central African forests: Biaka, Mbuti, and Lisongo. In the context of comparable published data for other African populations, analyses of each of these independently inherited DNA segments indicate that click-speaking Hadzabe and Jumid R:'hoansi are separated by genetic distance as great or greater than that between any other pair of African populations. Phylogenetic tree topology indicates a basal separation of the ancient ancestors of these click-speaking peoples. That genetic divergence does not appear to be the result of recent gene flow from neighboring groups. CONCLUSIONS: The deep genetic divergence among click-speaking peoples of Africa and mounting linguistic evidence suggest that click consonants date to early in the history of modern humans. At least two explanations remain viable. Clicks may have persisted for tens of thousands of years, independently in multiple populations, as a neutral trait. Alternatively, clicks may have been retained, because they confer an advantage during hunting in certain environments.     

Rare deep-rooting Y chromosome lineages in humans: lessons for phylogeography

There has been considerable debate on the geographic origin of the human Y chromosome Alu polymorphism (YAP). Here we report a new, very rare deep-rooting haplogroup within the YAP clade, together with data on other deep-rooting YAP clades. The new haplogroup, found so far in only five Nigerians, is the least-derived YAP haplogroup according to currently known binary markers. However, because the interior branching order of the Y chromosome genealogical tree remains unknown, it is impossible to impute the origin of the YAP clade with certainty. We discuss the problems presented by rare deep-rooting lineages for Y chromosome phylogeography.     

Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood

It has been known for over a decade that a majority of men who self report as members of the Jewish priesthood (Cohanim) carry a characteristic Y chromosome haplotype termed the Cohen Modal Haplotype (CMH). The CMH has since been used to trace putative Jewish ancestral origins of various populations. However, the limited number of binary and STR Y chromosome markers used previously did not provide the phylogenetic resolution needed to infer the number of independent paternal lineages that are encompassed within the Cohanim or their coalescence times. Accordingly, we have genotyped 75 binary markers and 12 Y-STRs in a sample of 215 Cohanim from diverse Jewish communities, 1,575 Jewish men from across the range of the Jewish Diaspora, and 2,099 non-Jewish men from the Near East, Europe, Central Asia, and India. While Cohanim from diverse backgrounds carry a total of 21 Y chromosome haplogroups, 5 haplogroups account for 79.5% of Cohanim Y chromosomes. The most frequent Cohanim lineage (46.1%) is marked by the recently reported P58 T->C mutation, which is prevalent in the Near East. Based on genotypes at 12 Y-STRs, we identify an extended CMH on the J-P58* background that predominates in both Ashkenazi and non-Ashkenazi Cohanim and is remarkably absent in non-Jews. The estimated divergence time of this lineage based on 17 STRs is 3,190 ± 1,090 years. Notably, the second most frequent Cohanim lineage (J-M410*, 14.4%) contains an extended modal haplotype that is also limited to Ashkenazi and non-Ashkenazi Cohanim and is estimated to be 4.2 ± 1.3 ky old. These results support the hypothesis of a common origin of the CMH in the Near East well before the dispersion of the Jewish people into separate communities, and indicate that the majority of contemporary Jewish priests descend from a limited number of paternal lineages.     

Cytological map of human Y chromosome

The cytological map of human Y chromosome is investigated at high resolution using Q-banding technique. There was no segmentation of the short arm which is in disagreement with current International Nomenclature. Also, the band q11.22 was not seen in the long arm using different individuals with variable size of Y chromosome. Furthermore, the length variation of nonfluorescent segment is also noted which was not suggested by the nomenclature.     

Homogeneity and distinctiveness of Polish paternal lineages revealed by Y chromosome microsatellite haplotype analysis

Different regional populations from Poland were studied in order to assess the genetic heterogeneity within Poland, investigate the genetic relationships with other European populations and provide a population-specific reference database for anthropological and forensic studies. Nine Y-chromosomal microsatellites were analysed in a total of 919 unrelated males from six regions of Poland and in 1,273 male individuals from nine other European populations. AMOVA revealed that all of the molecular variation in the Polish dataset is due to variation within populations, and no variation was detected among populations of different regions of Poland. However, in the non-Polish European dataset 9.3% ( P<0.0001) of the total variation was due to differences among populations. Consequently, differences in R(ST)-values between all possible pairs of Polish populations were not statistically significant, whereas significant differences were observed in nearly all comparisons of Polish and non-Polish European populations. Phylogenetic analyses demonstrated tight clustering of Polish populations separated from non-Polish groups. Population clustering based on Y-STR haplotypes generally correlates well with the geography and history of the region. Thus, our data are consistent with the assumption of homogeneity of present-day paternal lineages within Poland and their distinctiveness from other parts of Europe, at least in respect to their Y-STR haplotypes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00439-002-0728-0.     

A synopsis of the human Y chromosome

Summary Phenotypic features and functions known to depend on the presence of the Y chromosome or the H-Y antigen are discussed in relation to structural anomalies of the Y chromosome and other abnormalities of sexual and somatic development.Recent knowledge about molecular organization of constitutive heterochromatin in relation to the human Y is presented.An attempt is made at assigning different functions, genes and DNA sequence to different regions of the Y chromosome.     

Molecular biology of the human Y chromosome

We dedicate this review to Susumu Ohno, whose ideas motivated our interest in this exciting field of research     

DA/DAPI-Fluorescent heteromorphism of human Y chromosome

Summary Variation of DA/DAPI intensity in the Yq12 band was observed in five amniotic cell specimens and one blood specimen from the father of one fetus. Three distinct classes of Yq heterochromatin were identified by distamycin A (DA) treatment of the cell cultures and various staining techniques. The heterochromatin in the Yq11.23 sub-band does not under-condense when exposed to DA, and shows pale fluorescence with quinacrine staining, positive C-banding, and bright fluorescence with DA/DAPI technique. This class of heterochromatin was consistently observed in all specimens studied. The other two classes of heterochromatin are in the Yq12 band. Both show undercondensation when exposed to DA, quinacrine-bright fluorescence, and positive C-banding; howover, one class of heterochromatin shows DA/DAPI-bright fluorescence and the other shows pale fluorescence. The size and banding intensity of the two classes of heterochromatin in Yq12 are variable. These results provide cytological evidence of heterogeneity within the Y heterochromatin region containing AT-rich DNA.     

Selection at the Y chromosome of the African buffalo driven by rainfall

Selection coefficients at the mammalian Y chromosome typically do not deviate strongly from neutrality. Here we show that strong balancing selection, maintaining intermediate frequencies of DNA sequence variants, acts on the Y chromosome in two populations of African buffalo (Syncerus caffer). Significant correlations exist between sequence variant frequencies and annual rainfall in the years before conception, with five- to eightfold frequency changes over short time periods. Annual rainfall variation drives the balancing of sequence variant frequencies, probably by affecting parental condition. We conclude that sequence variants confer improved male reproductive success after either dry or wet years, making the population composition and dynamics very sensitive to climate change. The mammalian Y chromosome, interacting with ecological processes, may affect male reproductive success much more strongly than previously thought.     

Binding of quinacrine to the human Y chromosome

Human chromosome spreads were stained with 3H-quinacrine and their fluorescence observed. The exact location of specific spreads on each slide was noted and photographs taken. Autoradiographs were then prepared so that the quinacrine fluorescence of any specific chromosome could be compared directly with the distribution of grains over the same chromosome on the autoradiograph. The Y chromosome fluoresced much more intensely than any of the other chromosomes, but there were no more grains over the Y chromosome than over the other chromosomes. Therefore the enhanced fluorescence of the human Y chromosome is not due to an increased binding of quinacrine.     

A database for human Y chromosome protein data

The human Y chromosome is the sex determining chromosome. The number of proteins associated with this chromosome is 196 and 107 of the 196 proteins have yet not been characterised. Here, we describe the analysis of these 107 proteins by computing various physicochemical properties using sequence and predicted structural data to elucidate molecular function. We present the derived data in the form a form a database made freely available for download, review, refinement and update.

Availability

http://puratham.googlepages.com/ or http://puratham.googlepages.com/ftpconnection     

Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

Background

A central question in evolutionary biology is how cryptic species maintain species cohesiveness in an area of sympatry. The coexistence of sympatrically living cryptic species requires the evolution of species-specific signalling and recognition systems. In nocturnal, dispersed living species, specific vocalisations have been suggested to act as an ideal premating isolation mechanism. We studied the structure and perception of male advertisement calls of three nocturnal, dispersed living mouse lemur species, the grey mouse lemur (Microcebus murinus), the golden brown mouse lemur (M. ravelobensis) and the Goodman's mouse lemur (M. lehilahytsara). The first two species occur sympatrically, the latter lives allopatrically to them.

Results

A multi-parameter sound analysis revealed prominent differences in the frequency contour and in the duration of advertisement calls. To test whether mouse lemurs respond specifically to calls of the different species, we conducted a playback experiment with M. murinus from the field using advertisement calls and alarm whistle calls of all three species. Individuals responded significantly stronger to conspecific than to heterospecific advertisement calls but there were no differences in response behaviour towards statistically similar whistle calls of the three species. Furthermore, sympatric calls evoked weaker interest than allopatric advertisement calls.

Conclusion

Our results provide the first evidence for a specific relevance of social calls for speciation in cryptic primates. They furthermore support that specific differences in signalling and recognition systems represent an efficient premating isolation mechanism contributing to species cohesiveness in sympatrically living species.