Nonfluorescent Y chromosomes. Cytologic evidence of origin

Summary Twelve presumptive structurally altered Y chromosomes were studied with Q-, G-, G-11, C-, Cd, and lateral asymmetric banding techniques and were compared with normal X and Y chromosmes and with an abnormal [i(Yq)] Y chromosome that exhibited intact fluorescence. Significant to this work is the fact that the Y chromosome has a small block of Giemsa-11 heterochromatin adjacent to the centromere on the long arm, while the X chromosome does not, which allows a distinction between the X-and Y-derived chromosomes. Two of the twelve altered chromosomes of either X or Y origin are small nonfluorescent rings. Each ring has a G-11-positive band of heterochromatin at the centromere, confirming Y origin. Each of the normal-length nonfluorescent presumed Ys and a Y with a fluorescent band in the center have one G-11 band at the centromere and another at an equal distance from the end of the long arm, the bands also being Cd positive, indicating that these chromosomes are pseudodicentric. The likely mechanism of origin is a break at the distal bright heterochromatin/ euchromatin junction (or within the bright segment in the chromosome with the bright center band), fusion of the sister chromatids at the breakpoints, and loss of the distal segment.     

Melanesian origin of Polynesian Y chromosomes

BACKGROUND: Two competing hypotheses for the origins of Polynesians are the 'express-train' model, which supposes a recent and rapid expansion of Polynesian ancestors from Asia/Taiwan via coastal and island Melanesia, and the 'entangled-bank' model, which supposes a long history of cultural and genetic interactions among Southeast Asians, Melanesians and Polynesians. Most genetic data, especially analyses of mitochondrial DNA (mtDNA) variation, support the express-train model, as does linguistic and archaeological evidence. Here, we used Y-chromosome polymorphisms to investigate the origins of Polynesians. RESULTS: We analysed eight single nucleotide polymorphisms (SNPs) and seven short tandem repeat (STR) loci on the Y chromosome in 28 Cook Islanders from Polynesia and 583 males from 17 Melanesian, Asian and Australian populations. We found that all Polynesians belong to just three Y-chromosome haplotypes, as defined by unique event polymorphisms. The major Y haplotype in Polynesians (82% frequency) was restricted to Melanesia and eastern Indonesia and most probably arose in Melanesia. Coalescence analysis of associated Y-STR haplotypes showed evidence of a population expansion in Polynesians, beginning about 2,200 years ago. The other two Polynesian Y haplotypes were widespread in Asia but were also found in Melanesia. CONCLUSIONS: All Polynesian Y chromosomes can be traced back to Melanesia, although some of these Y-chromosome types originated in Asia. Together with other genetic and cultural evidence, we propose a new model of Polynesian origins that we call the 'slow-boat' model: Polynesian ancestors did originate from Asia/Taiwan but did not move rapidly through Melanesia; rather, they interacted with and mixed extensively with Melanesians, leaving behind their genes and incorporating many Melanesian genes before colonising the Pacific.     

The Dual Origin and Siberian Affinities of Native American Y Chromosomes

The Y chromosomes of 549 individuals from Siberia and the Americas were analyzed for 12 biallelic markers, which defined 15 haplogroups. The addition of four microsatellite markers increased the number of haplotypes to 111. The major Native American founding lineage, haplogroup M3, accounted for 66% of male Y chromosomes and was defined by the biallelic markers M89, M9, M45, and M3. The founder haplotype also harbored the microsatellite alleles DYS19 (10 repeats), DYS388 (11 repeats), DYS390 (11 repeats), and DYS391 (10 repeats). In Siberia, the M3 haplogroup was confined to the Chukotka peninsula, adjacent to Alaska. The second major group of Native American Y chromosomes, haplogroup M45, accounted for about one-quarter of male lineages. M45 was subdivided by the biallelic marker M173 and by the four microsatellite loci alleles into two major subdivisions: M45a, which is found throughout the Americas, and M45b, which incorporates the M173 variant and is concentrated in North and Central America. In Siberia, M45a haplotypes, including the direct ancestor of haplogroup M3, are concentrated in Middle Siberia, whereas M45b haplotypes are found in the Lower Amur River and Sea of Okhotsk regions of eastern Siberia. Among the remaining 5% of Native American Y chromosomes is haplogroup RPS4Y-T, found in North America. In Siberia, this haplogroup, along with haplogroup M45b, is concentrated in the Lower Amur River/Sea of Okhotsk region. These data suggest that Native American male lineages were derived from two major Siberian migrations. The first migration originated in southern Middle Siberia with the founding haplotype M45a (10-11-11-10). In Beringia, this gave rise to the predominant Native American lineage, M3 (10-11-11-10), which crossed into the New World. A later migration came from the Lower Amur/Sea of Okhkotsk region, bringing haplogroup RPS4Y-T and subhaplogroup M45b, with its associated M173 variant. This migration event contributed to the modern genetic pool of the Na-Dene and Amerinds of North and Central America.     

Y chromosome polymorphisms in Native American and Siberian populations: identification of Native American Y chromosome haplotypes

We have initiated a study of ancient male migrations from Siberia to the Americas using Y chromosome polymorphisms. The first polymorphism examined, a C→T transition at nucleotide position 181 of the DYS199 locus, was previously reported only in Native American populations. To investigate the origin of this DYS199 polymorphism, we screened Y chromosomes from a number of Siberian, Asian, and Native American populations for this and other markers. This survey detected the T allele in all five Native American populations studied at an average frequency of 61%, and in two of nine native Siberian populations, the Siberian Eskimo (21%) and the Chukchi (17%). This finding suggested that the DYS199 T allele may have originated in Beringia and was then spread throughout the New World by the founding populations of the major subgroups of modern Native Americans. We further characterized Native American Y chromosome variation by analyzing two additional Y chromosome polymorphisms, the DYS287 Y Alu polymorphic (YAP) element insertion and a YAP-associated A→G transition at DYS271, both commonly found in Africans. We found neither African allele associated with the DYS199 T allele in any of the Native American or native Siberian populations. However, we did find DYS287 YAP+ individuals who harbored the DYS199 C allele in one Native American population, the Mixe, and in one Asian group, the Tibetans. A correlation of these Y chromosome alleles in Native Americans with those of the DYS1 locus, as detected by the p49a/p49f (p49a,f) probes on TaqI-digested genomic DNA, revealed a complete association of DYS1 alleles (p49a,f haplotypes) 13, 18, 66, 67 and 69 with the DYS199 T allele, while DYS1 alleles 8 and 63 were associated with both the DYS199 C and T allele. Received: 18 November 1996 / Accepted: 19 May 1997     

The degeneration of Y chromosomes

Y chromosomes are genetically degenerate, having lost most of the active genes that were present in their ancestors. The causes of this degeneration have attracted much attention from evolutionary theorists. Four major theories are reviewed here: Muller's ratchet, background selection, the Hill Robertson effect with weak selection, and the 'hitchhiking' of deleterious alleles by favourable mutations. All of these involve a reduction in effective population size as a result of selective events occurring in a non-recombining genome, and the consequent weakening of the efficacy of selection. We review the consequences of these processes for patterns of molecular evolution and variation at loci on Y chromosomes, and discuss the results of empirical studies of these patterns for some evolving Y-chromosome and neo-Y-chromosome systems. These results suggest that the effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes leading to degeneration are operative. It is, however, currently unclear which of the various processes is most important; some directions for future work to help to resolve this question are discussed.     

Satellited Y chromosomes: Structure,origin, and clinical significance

Summary Three cases of inherited satellited Y chromosomes (Yqs) were analysed using several cytogenetic techniques. The cytogenetic data of the 14 cases of Yqs chromosomes described to date were reviewed. All Yqs chromosomes carry an active nucleolus organizer region (NOR) in their long arm and must have developed from translocations involving the short arms of the acrocentric autosomes. The structure of the heterochromatic satellite region in the Yqs chromosomes shows conspicuous inter-familial differences; this permits the reconstruction of the translocations from which the various Yqs were derived. Some causal factors leading to the development of Yqs chromosomes are considered: the specific localization of the four satellite DNAs and highly methylated DNA sequences in the karyotype, and some new experimental data on the spatial arrangement of heterochromatic regions in interphase nuclei. These provide distinct evidence for a preferential involvement of the autosomes 15 and 22 in the translocations with the Y heterochromatin. All clinical reports documenting Yqs males born with malformations were reviewed. It appears that the presence of an extra NOR and NOR-associated heterochromatin in the Yqs chromosomes does not cause any phenotypic abnormalities (as long as the Y euchromatin is intact). The possibility that a Yqs chromosome predisposes to non-disjunction and/or to translocations of other chromosomes is discussed.     

The origin and behavior of two isodicentric bisatellited chromosomes.

Karyotyping revealed three cell lines in a boy with mental retardation and few other abnormalities. Thirty cells exhibited a normal karyotype, and 54 had an extra acrocentric chromosome of E group size with satellites on the long and short arms. The remaining 20 cells each had, in addition to the first marker (M1), a second tiny bisatellited chromosome (M2). C-banding demonstrated that both markers were dicentric. G-, C-, and Q-banding and satellite association data were consistent with the markers having originated from chromosome 15 material. We propose that M1 was formed from a meiotic breakage and a chromatid fusion in the proximal long arms of an acrocentric pair. This would have produced a symmetrical isodicentric chromosomes, plus one or two acentric fragments. M2 then could have resulted from a dicentric bridge-break-synthesis-reunion phenomenon. This model of abnormal meiotic exchange can be generalized to encompass the formation of other dicentric isochromosome cases of isochromosome X.     

Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history

In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.     

The evolutionary history of grey wolf Y chromosomes

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male‐specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y‐linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.     

Polymorphism and differentiation of rainbow trout Y chromosomes.

Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.     

Supernumerary chromosomes in the karyotype of the Siberian spruce, P. obovata

Results of karyological study of ornamental forms of Picea obovata Ledeb. are presented. Typical chromosome number (2n) is 24, but some trees have one or two additional chromosomes (2n = 24 + 1B; 2n = 24 + 2B). Heritability of additional chromosomes, pollen fertility, morphological features of cones, and seed quality in trees with and without additional chromosomes were studied. System of B-chromosomes is of importance for population and species adaptation and possibly plays a role in adaptation of P. obovata under introduction.     

Native American Y chromosomes in Polynesia: the genetic impact of the Polynesian slave trade

Since Thor Heyerdahl asserted that Polynesia was first colonized from the Americas (Heyerdahl 1950), geneticists have sought--but have not found--any evidence to support his theories. Here, Native American Y chromosomes are detected on the Polynesian island of Rapa. However, this, together with other odd features of the island's Y-chromosomal gene pool, is best explained as the genetic impact of a 19th century Peruvian slave trade in Polynesia. These findings underscore the need to account for history before turning to prehistory and the value of archival research to understanding modern genetic diversity. Although the impact of the Atlantic slave trade on the distribution of modern genetic diversity has been well appreciated, this represents the first study investigating the impact of this underappreciated episode on genetic diversity in the Pacific.     

Mitochondrial DNA evidence for admixed origins of central Siberian populations

The Yakuts of northeastern Siberia are a Turkic-speaking population of horse- and cattle-breeders surrounded by Tungusic-speaking reindeer-herders and hunter-gatherers. Archaeological and ethnohistorical data suggest that Yakuts stem from a common ancestral population with the Buryats living near Lake Baikal. To address this hypothesis, we obtained sequences of the first hypervariable segment (HV1) of the mitochondrial DNA control region from Yakuts and Buryats and compared these with sequences from other Eurasian populations. The mtDNA results show that the Buryats have close affinities with both Central Asian Turkic groups and Mongols, while the Yakuts have close affinities with northeastern Siberian, Tungusic-speaking Evenks and south Siberian, Turkic-speaking Tuvans. This different ancestry of the Yakuts and the Tuvans (compared with other Turkic-speaking groups) most likely reflects extensive admixture that occurred between Turkic-speaking steppe groups and Evenks as the former migrated into Siberia. Moreover, the Yakuts are unique among Siberian populations in having a high number of haplotypes shared exclusively with Europeans, suggesting, contrary to the historical record, that occasionally Yakut men took Russian women as wives.     

The origin of the genetical diversity of Microtus mandarinus chromosomes

Here we describe our comparative studies on two types of X chromosomes, namely X(M) and X(SM,) of the mandarin vole (Microtus mandarinus). By chromosome G- and C-banding analysis, we have found that two different types of X chromosomes exist in mandarin voles. The two types of X chromosomes present two different G- and C-banding patterns: the X(M) chromosome is a longer metacentric X chromosome which is C-band negative; and the X(SM) is a shorter submetacentric X chromosome which has one C-band at the centromere and another one at the middle part of the short arm. The X(SM) has 6 G-bands including one on the kinetochore, one in the middle of the short arm, and four on the long arm. The X(M) has 7 G-bands including one on the kinetochore, two on the short arm, and four on the long arm. We have further found that female voles can be grouped into three types based on the composition of the X chromosome but the male voles have only one type. The three female groups are: (1) female voles (X(M)X(SM)), in which the two X chromosomes are different, the longer one is metacentric and the shorter is submetacentric; (2) female vole (X(SM)X(SM)), in which the two X chromosomes are both submetacentric; (3) female vole (X(M)O), in which there is only one X chromosome that is metacentric. Surprisingly, we have never found female voles with X(M)X(M), females with X(SM)O or males with X(M)Y. We hypothesize that the X(SM) chromosome is derived from the X(M) through its breakage and re-joining. The paper also discusses the formation of X(M)O females.     

Spatial distribution of chromosomes 1 and Y in human spermatozoa.

The positions of chromosomes 1 and Y inside human spermatozoa were determined by differential staining techniques. In 85/100 cells the two chromosomes were in close contact and in association with a vacuole. This observation is in contrast to previous findings for chromosome No. 9 and the Y-chromosome whose positions do not appear to be correlated.