Human chromosomal polymorphism. VII. The distribution of chromosomal Q-polymorphic bands in different human populations

The distribution of chromosomal Q-polymorphic bands was studied in different human populations. The populations studied showed no differences in the relative amount of Q bands in all the 12 polymorphic loci of seven autosomes, but interpopulation differences did exist in the absolute amount of Q bands in all the 12 potentially polymorphic loci of seven autosomes, these differences consisting of uniform increases or decreases in this absolute amount. Comparisons of the mean number of Q-heterochromatin bands with fluorescence levels 4 and 5 per individual showed a consistent prevalence of this quantitative parameter of chromosomal Q polymorphism in females as compared to males in all the national groups. It is suggested that there is some dosage compensation of chromosomal Q-heterochromatin material in females due to the absence of a chromosome in their genome, which is able to "compensate" for the large Q band in chromosome Y which is present only in the karyotype of males.     

Chromosomal Q-heterochromatin regions in native highlanders of Pamir and Tien-Shan and in newcomers

The variability of human chromosomal Q-heterochromatin regions (Q-HR) was studied in 385 newcomers well adapted to the extreme environmental conditions of Pamir and Tien-Shan, as well as in 284 representatives of the native population of these regions. Newcomers were found to represent a highly homogeneous group as regards all the quantitative characteristics of Q-HR variability, but at the same time they differed significantly from both native residents and individuals of similar nationality (Russians) living permanently at low altitude. Differences between these three groups in the amount of Q-HRs in their genome are discussed as evidence in favour of the hypothesis of the possible selective value of chromosomal Q-heterochromatin material in human adaptation to extreme environmental high-altitude conditions.     

Chromosomal Q-heterochromatin regions in the indigenous population of the northern part of West Siberia and in new migrants

The variability of Q-heterochromatin regions (Q-HR) was studied in native residents of the northern part of West Siberia, viz Yakuts (n = 127), Selkups (n = 90) and Khants (n = 54), as well as in newcomers including oil-borers (n = 43) and children (n = 113) living permanently in this part of the USSR. The major quantitative characteristics of chromosomal Q-HR variability were shown to be very similar in oil-borers and natives, and this is considered to be the result of specific selection of individuals according to the amount of Q-HRs in their genome. The hypothesis on the possible selective value of chromosomal Q-HRs in human adaptation to extreme environmental conditions of the extreme north is discussed.     

Human chromosomal polymorphism. V. Chromosomal Q polymorphism in African populations

Summary The distribution pattern of Q-heterochromatin variants in seven autosomes (3, 4, 13–15, 21, and 22) was studied in three aboriginal Negroid populations of Africa (Mozambique, Angola, and Ethiopia). It was shown that among African Negroids there are no individuals completely lacking Q-heterochromatin bands with fluorescence levels 4 and 5. The mean number of Q variants per individual was 3.47, 4.80, and 4.85 in the Ethiopian, Mozambique, and Angola populations, respectively. The observed homo- and heteromorphic frequencies always agreed with those predicted by the law of Hardy-Weinberg. The populations of tropical lowland Negroids (Mozambique and Angola) proved to be significantly homogeneous both in the frequency of Q variants and the mean number of these variants per individual, so they were examined as a single group. However, comparative analysis of highland (Ethiopians) and lowland Negroids revealed statistically significant differences. The following questions are discussed: (1) the possible selective value of chromosomal Q heterochromatin material in the adaptation of human populations to high-altitude climate; (2) the possible existence of intraracial heterogeneity in Negroids living in different ecological zones of Africa; (3) the possible taxonomic value of an inverted Q-heterochromatin band in chromosome 3 in ethnic anthropology.     

Refining the genetic portrait of Portuguese Roma through X-chromosomal markers

Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.     

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.     

Human chromosomal polymorphism

Summary Chromosomal Q polymorphism was studied in 157 adolescents of Yakut nationality (67 males and 90 females) living in Eastern Siberia, on the territory of the Yakut ASSR. Of the 157 subjects, 123 had chromosomal Q variants while 34 (21.7%) had no Q-heterochromatin bands with fluorescence levels 4 and 5. The mean number of Q variants per individual ranged from 0 to 5, with a mean of 1.64. No differences were observed in the frequency of Q variants between sexes. The observed homo- and heteromorph frequencies always agreed with those predicted by the law of Hardy-Weinberg. Of the 157 subjects, four (2.55%) had pericentric inversion of the Q-heterochromatin band in chromosome 3. The following topics are discussed: (1) possible selective value of chromosomal Q-heterochromatin material in the adaptation of human populations to extreme environmental factors, in particular to cold; (2) the taxonomic value of chromosomal Q polymorphism in ethnic anthropology.     

Human chromosomal polymorphism. III. Chromosomal Q polymorphism in Mongoloids of northern Asia

Summary Q-heterochromatin variants in seven autosomes (3, 4, 13–15, 21, 22) were studied in two Mongoloid populations of northern Asia (Chukchi and Khakass). Q-staining was obtained using propylquinacrine mustard. Of 132 Chukchi individuals aged 13 to 20 years, 124 had Q-polymorphic chromosomes, while eight (6.0%) had no bands with fluorescence levels 4 and 5. The mean number of Q variants was 2.2 per individual.Of the 120 Khakass individuals aged 14 to 17 years, 112 had Q-polymorphic chromosomes, while eight (6.7%) had no Q variants with fluorescence levels 4 and 5. The mean number of Q variants was 2.5 per individual. No differences were found in the frequency of Q variants between sexes in the two populations. There was complete agreement between the observed homo-and heteromorphic frequencies and those predicted by the law of Hardy-Weinberg. As the Mongoloid populations of northern Asia showed statistically significant homogeneity both in the frequency of Q variants and the distribution of homo-and heteromorphic variants, they were examined as a single group—that of northern Mongoloids. The following questions are discussed: (1) the possible selective value of chromosomal Q-heterochromatin material in the adaptation of human populations to certain extreme environmental factors, in particular to cold and hypoxia; (2) the intraracial heterogeneity of Asian Mongoloids; (3) the taxonomic value of chromosomal Q polymorphism in ethnic anthropology.     

Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura

Robertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution by creating new sex chromosomes from autosomes. These translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given the dramatic differences between autosomes and sex chromosomes. To study the genomic events following a Y chromosome reversal, we investigated an autosome‐Y translocation in Drosophila pseudoobscura. The ancestral Y chromosome fused to a small autosome (the dot chromosome) approximately 10–15 Mya. We used single molecule real‐time sequencing reads to assemble the D. pseudoobscura dot chromosome, including this Y‐to‐dot translocation. We find that the intervening sequence between the ancestral Y and the rest of the dot chromosome is only ～78 Kb and is not repeat‐dense, suggesting that the centromere now falls outside, rather than between, the fused chromosomes. The Y‐to‐dot region is 100 times smaller than the D. melanogaster Y chromosome, owing to changes in repeat landscape. However, we do not find a consistent reduction in intron sizes across the Y‐to‐dot region. Instead, deletions in intergenic regions and possibly a small ancestral Y chromosome size may explain the compact size of the Y‐to‐dot translocation.     

Sex-biased evolutionary forces shape genomic patterns of human diversity

Comparisons of levels of variability on the autosomes and X chromosome can be used to test hypotheses about factors influencing patterns of genomic variation. While a tremendous amount of nucleotide sequence data from across the genome is now available for multiple human populations, there has been no systematic effort to examine relative levels of neutral polymorphism on the X chromosome versus autosomes. We analyzed ~210 kb of DNA sequencing data representing 40 independent noncoding regions on the autosomes and X chromosome from each of 90 humans from six geographically diverse populations. We correct for differences in mutation rates between males and females by considering the ratio of within-human diversity to human-orangutan divergence. We find that relative levels of genetic variation are higher than expected on the X chromosome in all six human populations. We test a number of alternative hypotheses to explain the excess polymorphism on the X chromosome, including models of background selection, changes in population size, and sex-specific migration in a structured population. While each of these processes may have a small effect on the relative ratio of X-linked to autosomal diversity, our results point to a systematic difference between the sexes in the variance in reproductive success; namely, the widespread effects of polygyny in human populations. We conclude that factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability.     

MALE HYBRID STERILITY IN DROSOPHILA: INTERACTIONS BETWEEN AUTOSOMES AND SEX CHROMOSOMES IN CROSSES OF D. MOJAVENSIS AND D. ARIZONENSIS

By backcrossing hybrids from the cross Drosophila mojavensis female × Drosophila arizonensis male to both parental species we show that several interspecific combinations of autosomes with one or the other sex chromosome (X or Y) result in sperm abnormalities. Two of these incompatibilities will cause the same type of nonreciprocal F₁ male sterility that is observed in this pair of species, but the possibility of an additional incompatibility that would have the same result, e.g., an incompatibility between the mojavensis Y and the arizonensis X chromosomes, cannot be excluded. The incompatibility between the arizonensis Y chromosome and the mojavensis fourth chromosome found to occur for all tested populations of mojavensis race B (Vigneault and Zouros, 1986) is shown also to occur for race A of this species. We further show that a dominance relationship exists between heterospecific homologous autosomes in their interactions with the sex chromosomes and that the direction of the dominance depends on whether the sex chromosome is the X or the Y. The present role of these incompatibilities in preventing gene flow between the two species may be minor, but their genetic basis and mode of action may provide useful insights about the genetic events that have played a significant role in earlier stages of speciation.     

A PCR product derived from female DNA with regional localization on the Y chromosome.

A 154-bp PCR product amplified from human female DNA mapped onto the Y chromosome under high-stringency in situ hybridization conditions. The female DNA sequence revealed an 89% homology with the HSDYZ1 sequence. When the same primers were used to amplify male DNA, a 154-bp DNA fragment was also obtained, showing a 98% homology with HSDYZ1. However, although the HSDYZ1 sequence is widely distributed along the long arm of the Y chromosome, both of these particular PCR products are di-regionally localized within this distal block of constitutive heterochromatin. In situ hybridization under lower stringency showed that these 154-bp sequences map both onto the autosomes and the Y chromosome. Overall, this paper shows (i) a new class of DNA sequences shared by the autosomes and the Y chromosome; and (ii) a substructured organization of some DNA repeats within the DYZ1 family that forms a large part of the constitutive heterochromatin of the Y chromosome.     

Comparison of the nuclear organiser region activity in four taxa of the family Canidae

Four species of the family Canidae were cytogenetically studied. The activity of NORs was detected with the use of silver staining. The number of NORs was characteristic for a given karyotype. For the dog found on autosomes 7, 17, 20 and on sex chromosome (Y), for the racoon dog on autosomes 1, 4, 13 and on sex chromosome (Y), for the silver fox only on autosomes 8, 9, 13 and for the blue fox on autosomes 13, 15, 17, 18, 20 and 22. The results demonstrate that NOR activity is similar in all the analysed species of the Canidae. Simultaneously, NOR activity for a medium-sized chromosome pair is distinctly higher than for two other autosome pairs (the longest and the smallest pair). Considerable variability was observed within individuals.     

Scale-specific sex-biased dispersal in the Valais shrew unveiled by genetic variation on the Y chromosome, autosomes, and mitochondrial DNA

We investigated sex specificities in the evolutionary processes shaping Y chromosome, autosomes, and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of population structure that were not consistent across maternal, paternal, and biparentally inherited markers. Differentiation on a Y microsatellite was lower than expected from the comparison with autosomal microsatellites and mtDNA, and it was mostly due to genetic variance among populations within valleys, whereas the opposite was observed on other markers. In addition, there was no pattern of isolation by distance for the Y, whereas there was strong isolation by distance on mtDNA and autosomes. We use a hierarchical island model of coancestry dynamics to discuss the relative roles of the microevolutionary forces that may induce such patterns. We conclude that sex-biased dispersal is the most important driver of the observed genetic structure, but with an intriguing twist: it seems that dispersal is strongly male biased at large spatial scale, whereas it is mildly biased in favor of females at local scale. These results add to recent reports of scale-specific sex-biased dispersal patterns, and emphasize the usefulness of the Y chromosome in conjunction with mtDNA and autosomes to infer sex specificities.     

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X‐linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo‐Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.     

Chromosome assignment of two cloned DNA probes hybridizing predominantly to human sex chromosomes

Summary In situ hybridization experiments were carried out with two clones, YACG 35 and 2.8, which had been selected from two genomic libraries strongly enriched for the human Y chromosome. Besides the human Y chromosome, both sequences strongly hybridized to the human X chromosome, with few minor binding sites on autosomes. In particular, on the X chromosome DNA from clone YACG 35 hybridized to the centromeric region and the distal part of the short arm (Xp2.2). On the Y chromosome, the sequence was assigned to one site situated in the border region between Yq1.1 and Yq1.2. DNA from clone 2.8 also hybridized to the centromeric region of the X and the distal part of the short arm (Xq2.2). On the Y, however, two binding sites were observed (Yp1.1 and Yq1.2). The findings indicate that sex chromosomal sequences may be localized in homologous regions (as suggested from meiotic pairing) but also at ectopic sites.     

Two Tests of Y Chromosomal Variation in Male Fertility of Drosophila Melanogaster

Deficiency mapping with Y autosome translocations has shown that the Y chromosome of Drosophila melanogaster carries genes that are essential to male fertility. While the qualitative behavior of these lesions provides important insight into the physiological importance of the Y chromosome, quantitative variation in effects on male fertility among extant Y chromosomes in natural populations may have a significant effect on the evolution of the Y chromosome. Here a series of 36 Y chromosome replacement lines were tested in two ways designed to detect subtle variation in effects on male fertility and total male fitness. The first test involved crossing males from the 36 lines to an excess of females in an attempt to measure differences in male mating success (virility) and male fecundity. The second test challenged males bearing each of the 36 Y chromosomes to competition in populations with males bearing a standard, phenotypically marked (BsY) chromosome. These tests indicated that the Y chromosome lines did not differ significantly in either male fertility or total fitness, but that interactions with autosomes approached significance. A deterministic population genetic model was developed allowing Y autosome interaction in fertility, and it is shown that, consistent with the experimental observations, this model cannot protect Y-linked polymorphism.     

Human chromosomal polymorphism. I. Chromosomal Q polymorphism in Mongoloid populations of central Asia

Summary A comparative study of frequencies and types of Q-polymorphic variants in seven autosome pairs (3, 4, 13–15, 21, and 22) was performed in three steppe Mongoloid populations of Central Asia (Kazakhs, Dunghans, Mongolians) and three highland Kirghiz populations of Pamir and Tien-Shan. The three steppe Mongoloid populations showed statistically significant homogeneity both in the frequency of Q-polymorphic variants and the distribution of homo- and heteromorphs, with complete agreement of observed frequencies with those theoretically predicted by the law of Hardy-Weinberg. Similar homogeneity was revealed in the three highland Kirghiz populations of Pamir and Tien-Shan. However, comparative analysis of highland and steppe Mongoloids revealed significant differences in the following variables: (1) mean number of Q variants per individual, 2.50 and 3.49 in the highland and steppe populations, respectively; (2) frequency of Q variants in 7 of the 12 autosomes studied; and (3) distribution of homo- and heteromorphs in four autosomal pairs (13–15, 21) with a preponderance of individuals with increased homomorph (-/-) frequency in highlanders.The following questions are discussed: (1) the possible selective value of chromosomal Q-heterochromatin material in the adaptation of human populations to extreme environmental factors, in particular to the high-altitude environment of Pamir and Tien-Shan; (2) the existence of intraracial heterogeneity in Mongoloids living in different ecological zones; and (3) the possible taxonomic value of Q-variant inversion in chromosome 3.     

The Y chromosomes of Drosophila simulans are highly polymorphic for their ability to suppress sex-ratio drive

The sex-ratio trait, known in several species of Drosophila including D. simulans, results from meiotic drive of the X chromosome against the Y. Males that carry a sex-ratio X chromosome produce strongly female-biased progeny. In D. simulans, drive suppressors have evolved on the Y chromosome and on the autosomes. Both the frequency of sex-ratio X and the strength of the total drive suppression (Y-linked and autosomal) vary widely among geographic populations of this worldwide species. We have investigated the pattern of Y-linked drive suppression in six natural populations representative of this variability. Y-linked suppressors were found to be a regular component of the suppression, with large differences between populations in the mean level of suppression. These variations did not correspond to differences in frequency of discrete types of Y chromosomes, but to a more or less wide continuum of phenotypes, from nonsuppressor to partial or total suppressor. We concluded that a large diversity of Y-linked suppressor alleles exists in D. simulans and that some populations are highly polymorphic. Our results support the hypothesis that a Y-chromosome polymorphism can be easily maintained by a balance between meiotic drive and the cost of drive suppression.     

Fluorescent (F) bodies in the spermatozoa of man and the great apes

Mature spermatozoa of the chimpanzee (Pan troglodytes), the gorilla (Gorilla gorilla), and the orangutan (Pongo pygmaeus) were stained with quinacrine dihydrochloride. Fluorescent (F) bodies were visualized in the spermatozoa of the chimpanzee and gorilla but were absent in the orangutan, in which there is no brilliant fluorescence in any chromosome. The F bodies appeared to be randomly located in the sperm heads of these two species, as they usually are in human spermatozoa. However, the proportion of sperm showing one or more F bodies in the chimpanzee and gorilla was not comparable to what is usually found in man. The F bodies in the chimpanzee presumably represent brilliant regions in the autosomes, since the Y chromosome has no brilliant fluorescence in this species. This is contrary to man, in which the F body is an useful indicator of the Y chromosome. In the gorilla, the F bodies probably correspond to both the Y chromosome and to some brilliant regions in the autosomes.