Y-chromosome-specific microsatellite variation in Australian aboriginals.

Y-chromosome-specific microsatellite variation in Australian aboriginals.

Vandenberg N, van Oorschot RA, Tyler-Smith C, Mitchell RJ.

Department of Genetics and Human Variation, La Trobe University, Bundoora, Victoria, Australia.

The frequency distributions of 4 highly polymorphic Y-chromosome-specific microsatellites (DYS19, DYS390, DYS391, and DYS392) were determined in 79 unrelated Australian Aboriginal males from the Northern Territory. These results are compared with those observed in worldwide populations at both the locus and the haplotype level. Common alleles in Aboriginals are DYS19*15 (49%), DYS19*14 (28%), DYS390*19 (39%), DYS390*24 (20%), DYS391*10 (72%), DYS392*11 (63%), and DYS392*13 (28%). No evidence of reduced gene diversity was observed for these Y-chromosome alleles. DYS390 exhibits the most complex arrangement, displaying a bimodal distribution composed of common alleles (*22-*26), and rare short alleles (*18-*20), with an intermediate allele (*21) being absent. DYS390*20, previously reported only in Papuans and Samoans, is observed for the first time in Aboriginals. Compared with a recent study of Aboriginals, our sample exhibits considerable diversity in the haplotypes associated with the rare DYS390*19 allele, indicating that this allele is of considerable antiquity, if it arose as a single deletion event. Combining all 4 Y-chromosome-linked microsatellites produced 41 unique haplotypes, which were linked using a median-joining network. This network shows that most (78%) of our Aboriginal haplotypes fall into 2 distinct clusters, which likely represent 2 separate lineages. Seven haplotypes are shared with haplotypes found in a recent study of Aboriginals, and 7 are shared with a Spanish population. The cluster of Aboriginal haplotypes associated with the short DYS390 alleles does not share any haplotypes with the Spanish, indicating that this cluster of haplotypes is unique to Australian Aboriginals. Limited data from 4 worldwide populations used to construct haplotypes based on 3 loci (DYS19, DYS390, DYS392) show that only 4 of these haplotypes are seen in Australian Aboriginals. Shared haplotypes may be the result of admixture and/or recurrent mutation at these loci. Expanding the haplotype analysis to include biallelic markers on the Y chromosome will resolve this issue.

 

 

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis
Georgi Hudjashova, Toomas Kivisilda,b,c, Peter A. Underhilld, Phillip Endicotte, Juan J. Sanchezf, Alice A. Lind, Peidong Sheng, Peter Oefnerh, Colin Renfrewc,i, Richard Villemsa, and Peter Forsterj, 2007.

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n = 172) and Y variation (n = 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa ≈50–70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event ≈50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged ≈8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Conclusions
The mitochondrial and Y chromosomal results presented here point toward one early founder group settling both Australia and NG soon after the exodus from Africa ≈50–70,000 years ago, at a time when the lowered sea levels joined the two islands into one land mass, necessitating sea travel only across narrow straits such as Wallace’s Line. The deep and specific phylogenetic lineages today within this former landmass indicate a small founding population size and subsequent isolation of Australia and, to a lesser extent, of NG, from the rest of the world. These founder events and the lack of contact could underlie the divergent morphological development seen in the Australian human fossil record and could also help explain the remarkably restricted range of Pleistocene Australian lithic industries and bone artifacts compared with contemporaneous cultures elsewhere in the world (55).

Estimated dates for mtDNA:

Region	Hg	N	ρ	SE	Age, yr
Aus/Mel	M	50	7,9	1,1	53,400 ± 7,500
Aus/Mel	Q’M29	27	6,6	1,4	44,300 ± 9,800
Aus/Mel	Q	22	4,7	1,0	32,000 ± 6,500
Mel	Q1	11	3,2	0,9	21,500 ± 6,100
Aus/Mel	Q2	4	4,5	1,4	30,400 ± 9,300
Mel	Q3	7	3,1	0,8	21,300 ± 5,500
Mel	M29	5	2,8	1,2	18,900 ± 8,300
Mel	M27	7	5,9	1,4	39,600 ± 9,800
Mel	M28	8	3,0	1,0	20,300 ± 6,500
Mel	M28a	6	1,7	0,7	11,300 ± 4,500
Aus	M42	6	6,0	1,3	40,600 ± 9,000
Aus/Mel	N	51	7,9	1,1	53,200 ± 7,300
Aus	N12	4	2,5	1,1	16,900 ± 7,200
Aus	S	12	3,8	0,8	25,400 ± 5,200
Aus	S1	4	3,3	1,1	22,000 ± 7,700
Aus	S2	4	2,3	0,8	15,200 ± 5,100
Aus/Mel	R	33	8,6	1,2	58,400 ± 8,400
Aus/Mel	P	31	7,6	0,9	51,700 ± 5,800
Mel	P1	6	4,5	1,0	30,400 ± 6,500
Mel	P2	7	1,9	0,6	12,600 ± 4,000
Aus/Mel	P3	5	5,8	1,2	39,200 ± 8,200
Aus/Mel	P4	8	9,8	1,9	65,900 ± 13,200
Aus	P4b	3	7,0	1,7	47,300 ± 11,700
Mel	P4a	5	3,8	1,1	25,700 ± 7,500

Y chromosomes in PNG and Aborigines.

Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional differentiation.

Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional  differentiation.

Huoponen K, Schurr TG, Chen Y, Wallace DC.
Laboratory of Genetics, Department of Biology, University of Turku, Turku, Finland.

The mitochondrial DNA (mt-DNA) variation of in the Walbiri tribe of the Northern Territories, Australia, was characterized by high resolution restriction fragment length polymorphism (HR-RFLP) analysis and control region sequencing. Surveying each mt-DNA for RFLPs with 14 different restriction enzymes detected 24 distinct haplotypes, whereas direct sequencing of the control region hypervariable segment I (HVS-I) of these mt-DNAs revealed 34 distinct sequences. Phylogenetic analysis of the RFLP haplotype and HVS-I sequence data depicted that the Walbiri have ten distinct haplotype groups (haplogroups), or mt-DNA lineages. The majority of the Walbiri RFLP haplotypes lacked polymorphisms common to Asian populations. In fact, most of the Walbiri haplogroups were unique to this population, although a few appeared to be sub-branches of larger clusters of mt-DNAs that included other Aboriginal Australian and/or Papua New Guinea haplotypes. The similarity of these haplotypes suggested that Aboriginal Australian and Papua New Guinea populations may have once shared an ancient ancestral population(s), and then rapidly diverged from each other once geographically separated. Overall, the mt-DNA data corroborate the genetic uniqueness of Aboriginal Australian populations.

More on Aborigines, showing a population movement from PNG into Australia.

Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations

Peopling of Sahul : mtDNA variation in aboriginal Australian and Papua New Guinean populations.
A J Redd and M Stoneking

We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul.

One of the other studies in this blog puts one of the M clades from SE Asia at about 87k old. The origin of Aborigines has been under debate for quite a while, with Southern India having some support as onepoint of immigration into Australia.along with PNG. This is going to be subject for a few posts. This stuff directly impacts on the OOA date, as genetic dating of Aborigines can set a lower limit to the migration date. 55k minimum for an entry into Northern Oz as a minimum now, so add about 15k for transit time and you are looking at about 70k absolute minimum (it’s probably a hell of a lot bit older). The changes in paleo-vegetation in Australia date it earlier, about 65k, so another 10k could be easily added to this.

Iberian Y chromsomes

A borrowed image for reference.

Neanderthals could have died out because their bodies overheated

Neanderthals may have died out because their bodies overheated as the Earth grew warmer. 
By Richard Gray, Science Correspondent 

 Neanderthal DNA reveals key differences from modern humans. Analysis of DNA obtained from Neanderthal remains has revealed key differences from modern humans that suggest their bodies produced excess heat.

While in the cold climate of an ice age this would have provided the species with an advantage, as the earth warmed they would have been less able to cope. Ultimately this would have caused their extinction around 24,000 years ago.

Scientists at Newcastle University have put forward the theory after examining a particular form of genetic material which was obtained from the fossilised bones of Neanderthals.

By comparing it with that found in modern humans, they discovered that Neanderthals had key differences in the sections responsible for producing energy in all living cells.

Professor Patrick Chinnery, a neurogeneticist at Newcastle University, believes the differences in this mitochondrial DNA could have caused Neanderthals to be inefficient at producing energy, meaning their cells leaked heat.

He said: “The question is why did Neanderthals disappear? There are lots of explanations to do with changes in climate and the food supply.

“Differences in these mitochondrial DNA sequences might explain why modern humans were able to survive while Neanderthals were not.

“We compared mitochondrial DNA sequences from Neanderthals that have been obtained by other researchers with a huge database of human sequences from around the world to see how different it was from modern humans.

“We found a number of differences within a certain part of the mitochondrial DNA that were quite unlike anything we see in modern humans.

“It is difficult to get a definitive answer, as it is rather like looking through a misty window. We can only get clues to what went on.”

Mitochondria are tiny structures found inside all living cells and are the biological power stations that produce the energy cells need to survive by converting sugar from food into energy.

The research by Professor Chinnery, which was recently presented at a conference held by the American Society on Human Genetics, is the latest attempt to find out why our ancient cousins died out.

Scientists have also been attempting to read the entire Neanderthal genome in the hope that it will shed more light on the differences between them and modern humans.

Recent work by scientists at the Max Planck Institute in Germany revealed that Neanderthals shared a language gene that is only found in modern humans. The controversial findings raised the debate about whether Neanderthals were capable of speech.

Neanderthals are thought to have evolved from a common ancestor shared with modern humans around 400,000 years ago. It is thought they died out around 10,000 years after modern humans began spreading in to Europe.

There is a great deal of debate about what actually sealed Neanderthals fate, with the changing climate, dwindling food supplies and modern humans themselves all being blamed for killing the species off.

Technically, this would really only account for their mt DNA becoming extinct. Which would explain why it is a no-show in the modern genome even though lots of other archaic genes seem to have made an appearance. A New Scientist article on the same subject here.

Blogging will be pretty thin on the ground here until after Christmas, as I shall be busy with my kids and festive stuff. So have a Merry Christmas, and sorry of your comments don’t register for a while, as I shan’t be around for most of the rest of the week.

Traces of early Eurasians in the Mansi of northwest Siberia revealed by mitochondrial DNA analysis

Traces of early Eurasians in the Mansi of northwest Siberia revealed by mitochondrial DNA analysis.

Derbeneva OA, Starikovskaya EB, Wallace DC, Sukernik RI.
Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, 10 Lavrent’ev Avenue, Novosibirsk 630090, Russia.

The mitochondrial DNA (mtDNA) of 98 Mansi, an ancient group (formerly known as “Vogul”) of Uralic-speaking fishers and hunters on the eastern slope of the northern Ural Mountains, were analyzed for sequence variants by restriction fragment–length polymorphism analysis, control-region sequencing, and sequencing of additional informative sites in the coding region. Although 63.3% of the mtDNA detected in the Mansi falls into western Eurasian lineages (e.g., haplogroups UK, TJ, and HV), the remaining 36.7% encompass a subset of eastern Eurasian lineages (e.g., haplogroups A, C, D, F, G, and M). Among the western Eurasian lineages, subhaplogroup U4 was found at a remarkable frequency of 16.3%, along with lineages U5, U7, and J2. This suggests that the aboriginal populations residing immediately to the east of the Ural Mountains may encompass remnants of the early Upper Paleolithic expansion from the Middle East/southeastern Europe. The added presence of eastern Eurasian mtDNA lineages in the Mansi introduces the possibilities that proto-Eurasians encompassed a range of macrohaplogroup M and N lineages that subsequently became geographically distributed and that the Paleolithic expansion may have reached this part of Siberia before it split into western and eastern human groups.

I’ll read this in more depth when I’m feeling less muzzy. If, in my sleep deprived state I’ve read it correctly, they represent a very early expansion into the central Asian area. According to a news item I’ve read there are only about 200 Mansi left. The area they come from is in Siberia, just North of Kazakhstan.

Croatian mt DNA and Y chromosomes

Review of Croatian genetic heritage as revealed by mitochondrial DNA and Y chromosomal lineages.

Pericic M, Barac Lauc L, Martinovic Klaric I, Janicijevic B, Rudan P.
Institute for Anthropological Research, Amruseva 8, 10000 Zagreb, Croatia.

The aim of this review is to summarize the existing data collected in high-resolution phylogenetic studies of mitochondrial DNA and Y chromosome variation in mainland and insular Croatian populations. Mitochondrial DNA polymorphisms were explored in 721 individuals by sequencing mtDNA HVS-1 region and screening a selection of 24 restriction fragment length polymorphisms (RFLPs), diagnostic for main Eurasian mtDNA haplogroups. Whereas Y chromosome variation was analyzed in 451 men by using 19 single nucleotide polymorphism (SNP)/indel and 8 short tandem repeat (STR) loci. The phylogeography of mtDNA and Y chromosome variants of Croatians can be adequately explained within typical European maternal and paternal genetic landscape, with the exception of mtDNA haplogroup F and Y-chromosomal haplogroup P* which indicate a connection to Asian populations. Similar to other European and Near Eastern populations, the most frequent mtDNA haplogroups in Croatians were H (41.1%), U5 (10.3%), and J (9.7%). The most frequent Y chromosomal haplogroups in Croatians, I-P37 (41.7%) and R1a-SRY1532 (25%), as well as the observed structuring of Y chromosomal variance reveal a clearly evident Slavic component in the paternal gene pool of contemporary Croatian men. Even though each population and groups of populations are well characterized by maternal and paternal haplogroup distribution, it is important to keep in mind that linking phylogeography of various haplogroups with known historic and prehistoric scenarios should be cautiously performed.

No real surprises in this paper.

 

Y chromosome haplogroups: a correlation with testicular dysgenesis syndrome?

Y chromosome haplogroups: a correlation with testicular dysgenesis syndrome?

McElreavey K, Quintana-Murci L.
Reproduction, Fertility and Populations, Institut Pasteur, Paris, France. kenmce@pasteur.fr

Testicular dysgenesis syndrome encompasses low sperm quality, hypospadias, cryptorchidism and testicular cancer. Epidemiological studies and genetic data from familial cases suggest that testicular dysgenesis syndrome has a common etiology. The Y chromosome is known to encode genes that are involved in germ cell development or maintenance. We have therefore investigated if different classes of Y chromosomes in the general population (Y chromosome haplogroups) are associated with aspects of the testicular dysgenesis syndrome. We defined the Y chromosome haplogroups in individuals from different European counties who presented with either (i) oligo- or azoospermia associated with a Y chromosome microdeletion, (ii) unexplained reduced sperm counts (<20 x 10(6)/ml) or (iii) testicular cancer. We failed to find Y chromosome haplotype associations with either microdeletion formation or testicular cancer. However, in a study of the Danish population, we found that a specific Y chromosome haplogroup (hg26) is significantly overrepresented in men with unexplained reduced sperm counts compared with a Danish control population. The factors encoded by genes on this class of Y chromosome may be particularly susceptible to environmental influences that cause testicular dysgenesis syndrome. Our current data highlight the need for further analyses of clinically well-defined patient groups from a wide range of ethnic and geographic origins.

Another study that suggests a Y chromosome prone to infertility.

Evidence for the association of Y-chromosome haplogroups with susceptibility to spermatogenic failure in a Chinese Han population

Evidence for the association of Y-chromosome haplogroups with susceptibility to spermatogenic failure in a Chinese Han population

Yang Y, Ma M, Li L, Zhang W, Xiao C, Li S, Ma Y, Tao D, Liu Y, Lin L, Zhang S.
Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, P R China.

INTRODUCTION: Y chromosomes are genetically highly variable due to frequent structural rearrangements. The variations may create a genetic background for the susceptibility to Y-related spermatogenic impairment, although few data have been accumulated about the possible correlation between the Y-chromosome haplotype and the predisposition of men to spermatogenic failure.

 OBJECTIVE: To investigate the possible association of Y-chromosome background with spermatogenic failure.

METHODS: The distribution of 18 Y-chromosome haplogroups was compared between 414 infertile men with azoospermia or oligozoospermia and 262 normozoospermic men with or without AZFc deletions in a Han population of Southwest China.

RESULTS: A significant population difference in Y-haplogroup distribution was found between the groups of normozoospermia and azoospemia or oligozoospermia, and between the patient groups with oligozoospermia and azoospermia without AZFc deletions. Interpopulation comparison of Y haplogroup frequencies showed that the distribution of the haplogroups C, K* and O3* were significantly different between the groups.

CONCLUSION: This study provides evidence for the association of Y-chromosome background with impaired spermatogenesis, suggesting that Y variations play a role in the occurrence and even the severity of spermatogenic failure. Furthermore, both AZFc deletions and other Y-chromosome structural variations may be important for determining the susceptibility to spermatogenic failure. Our findings emphasise the necessity of more extensive study on Y-chromosome variations for better understanding of spermatogenesis and its pathology.

I’m very pro the idea of the Y chromsome being subject to natural selection. Some types being better sperm producers than others would explain that.