The history of the Y chromosome in man

Studies of the Y chromosome over the past few decades have opened a window into the history of our species, through the reconstruction and exploitation of a patrilineal (Y-genealogical) tree based on several hundred single-nucleotide variants (SNVs). A new study validates, refines and extends this tree by incorporating >65,000 Y-linked variants identified in 1,244 men representing worldwide diversity

The divergence of Neandertal and modern human Y chromosomes

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups

Cooperative effects on functionalised vesicles

were examined and successfully applied to enhance the aqueous hydrolysis of active esters and the upconversion of light. In addition, a fast screening technique for visible light photocatalysis reactions was developed. Chapter 1 briefly introduces into the topic of functionalised vesicles and explains the design of the projects in this thesis spanning from cooperative effects on functionalised vesicles to the development of a screening technique. Chapter 2 presents the concept of cooperative hydrolysis on the surface of membranes. Hydrolytic activity is provided by vesicles functionalised with an amphiphilic zinc complex, which acts as a Lewis acid and is able to hydrolyse aryl esters. We showed that co-embedding of different membrane additives into the surface of the vesicles increases the hydrolytic rate up to 16-fold. We examined different lipids and observed the highest cooperative enhancement of hydrolysis in fluid DOPC membranes. Mechanistic studies suggested that in such fluid membranes the reactions follow a Michaelis-Menten saturation kinetic, while in rigid DSPC vesicles second order kinetics are observed. Chapter 3 shows that, not only catalytic activity of functionalised vesicles can be enhanced using membrane additives, but also the selectivity. By co-embedding of an amphiphilic nonchiral hydrolysis catalyst with amphiphilic chiral additives into the membrane of a phospholipid vesicle we were able to introduce enantioselectivity to a non-chiral catalyst. This was shown for enantiomerically pure amino acid esters, which in the presence of an appropriate chiral additive show a twofold enhancement of the hydrolysis rate of one enantiomer. In Chapter 4 we tried to simplify the concept of functionalised vesicles for hydrolysis and instead of using custom made amphiphilic metal complexes we examined the direct adsorption of lanthanide ions onto the surface of the vesicles. We show that their interaction with vesicles prepared from zwitterionic phosphatidylcholine lipids provides soft particles with surface functionalised with lanthanide ions. This was confirmed via sensitisation of europium ions by pyrene that was co-embedded inside the phospholipid bilayer. Such assembly provides a high density of Lewis-acidic metal centres, which hydrolyse phosphodiesters 17 times faster compared to homogeneous aqueous lanthanide solutions. Chapter 5 is a study on triplet-triplet annihilation upconversion process in vesicles. We show that such light upconverting soft particles can be made on the basis of fluid DOPC vesicles in aqueous media. This process consists of the interaction between two sets of dyes (sensitizer and annihilator). We studied the effect of their position in the membrane on the upconversion efficiency: High local concentration of the dyes in the membrane increases the intensity of the detected delayed fluorescence. This was observed whether the dyes were on the surface of the bilayer or inside. Crucial for the upconversion to take place in vesicles is the fluidity of the membrane. In rigid membranes no upconversion is observed. In Chapter 6 we developed a high throughput screening technique for photocatalytic transformations using known indicators and microtiter plate instrumentation. Photocatalytic reactions often produce beside the desired products a stoichiometric by-product, such as reactive oxygen species or acids. These can be easily detected by an indicator allowing to perform 96 reactions at once and evaluate the reaction conversion by addition of the indicator measuring its absorbance. The concept is able to reproduce reported reaction results and correlates well with GC analysis. We used this system for identifying two new catalysts for the hydroxylation of boronic acids. We successfully employed the technique for photochemical reductions, monitoring the formation of aryl radicals from aryl halides. To confirm the robustness of the method for different substrates we screened various drugs bearing an aryl halide moiety and identified two new dehalogenation reactions

In-solution Y-chromosome capture-enrichment on ancient DNA libraries.

As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGC + YCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round

Confirmation of Genetic Associations at ELMO1 in the GoKinD Collection Supports Its Role as a Susceptibility Gene in Diabetic Nephropathy

Objective: To examine the association between single nucleotide polymorphisms (SNPs) in the engulfment and cell motility 1 (ELMO1) gene, a locus previously shown to be associated with diabetic nephropathy in two ethnically distinct type 2 diabetic populations, and the risk of nephropathy in type 1 diabetes. Research Design and Methods: Genotypic data from a genome-wide association scan (GWAS) of the Genetics of Kidneys in Diabetes (GoKinD) study collection were analyzed for associations across the ELMO1 locus. In total, genetic associations were assessed using 118 SNPs and 1,705 individuals of European ancestry with type 1 diabetes (885 normoalbuminuric control subjects and 820 advanced diabetic nephropathy case subjects). Results: The strongest associations in ELMO1 occurred at rs11769038 (odds ratio [OR] 1.24; P = 1.7 × 10−3) and rs1882080 (OR 1.23; P = 3.2 × 10−3) located in intron 16. Two additional SNPs, located in introns 18 and 20, respectively, were also associated with diabetic nephropathy. No evidence of association for variants previously reported in type 2 diabetes was observed in our collection. Conclusions: Using GWAS data from the GoKinD collection, we comprehensively examined evidence of association across the ELMO1 locus. Our investigation marks the third report of associations in ELMO1 with diabetic nephropathy, further establishing its role in the susceptibility of this disease. There is evidence of allelic heterogeneity, contributed by the diverse genetic backgrounds of the different ethnic groups examined. Further investigation of SNPs at this locus is necessary to fully understand the commonality of these associations and the mechanism(s) underlying their role in diabetic nephropathy

High-Density Single Nucleotide Polymorphism Genome-Wide Linkage Scan for Susceptibility Genes for Diabetic Nephropathy in Type 1 Diabetes: Discordant Sibpair Approach

OBJECTIVE— Epidemiological and family studies have demonstrated that susceptibility genes play an important role in the etiology of diabetic nephropathy, defined as persistent proteinuria or end-stage renal disease (ESRD) in type 1 diabetes

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations

The ancestry and affiliations of Kennewick Man

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia