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Rare functional variant - Wikipedia

A rare functional variant is a genetic variant which alters gene function, and which occurs at low frequency in a population

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disease-rare variant hypothesis;

Evidence from studies of nuclear and mitochondrial DNA extracted from Neanderthal fossils and humans points to fascinating hypotheses concerning the types of interbreeding that occurred between these two species. Humans and Neanderthals share a small percentage of nuclear DNA. However, humans and Neanderthals do not possess the same mitochondrial DNA. In mammals, mitochondrial DNA is exclusively maternally inherited. Taking into account an understanding of interspecific hybridity, the available data leads to the hypothesis that only male Neanderthals were able to mate with female humans. If Haldane’s Law applied to the progeny of Neanderthals and humans, then female hybrids would survive, but male hybrids would be absent, rare, or sterile. Interbreeding between male Neanderthals and female humans, as the only possible scenario, accounts for the presence of Neanderthal nuclear DNA, the scarcity of Neanderthal Y-linked genes, and the lack of mitochondrial DNA in modern human populations.

RVFam: an R package for rare variant association analysis with family data

According to Haldane’s law, the heterogametic offspring of interspecific hybrids are likely to be absent, rare or sterile (27). In mammals, the heterogametic sex is the male sex with two different sex chromosomes, X and Y. In 1922, J.B.S. Haldane wrote a key paper on “Sex ratio and unisexual sterility in hybrid animals”, where he showed that fertile XY progeny are unlikely (28). The high mutation rate of male sex-determining genes on the Y chromosome may account for why nature rarely permits heterogametic offspring from interspecific hybrids (27).

Therefore one of the key challenges in rare variant association ..

Rare disease rare variant hypothesis; Urban design dissertation proposal;

Haldane’s law has been shown in a number of different hybrid crosses from the Camelidae, Equidae, and Anatidae. If Haldane’s Law applies to the offspring of Neanderthals and humans, we would expect to find female hybrids quite commonly, but male hybrids much more rarely. Any male hybrids who survived, would have carried a Y chromosome very similar to that of the original hybridizing male.

Figure 1: Possible outcomes of Neanderthal-Human Interbreeding. Mammals contain two different types of DNA: (i) nuclear DNA, which is from both parents and contributes directly to the phenotype, and (ii) mitochondrial DNA, which is involved in energy regulation and is exclusively maternally inherited. Nuclear DNA from Neanderthals has been found in the human genome. Mitochondrial DNA from Neanderthals has not been found in humans. While not conclusive, these findings could indicate that male Neanderthals were able to reproduce with female humans, but that the reciprocal cross was absent, rare or sterile. If Haldane’s Law applies to Neanderthals and humans, female offspring were more common.

Common disease-common variant - Wikipedia

The common disease-common variant ..

If Haldane’s Law applies to the progeny of Neanderthals and humans then female hybrids would have been much commoner than male hybrids. Interbreeding between male Neanderthals and female humans accounts for the presence of Neanderthal nuclear DNA, the scarcity of Neanderthal Y-linked genes, and the lack of Neanderthal mtDNA in modern human populations. Thus, gene flow from Neanderthals to humans was the product of male Neanderthals mating with female humans to produce fertile female hybrids.

The lack of Neanderthal mtDNA in humans suggests that initial hybridization involved a Neanderthal male. With a Neanderthal father, there would be no Neanderthal mtDNA in resultant hybrids. If Haldane’s law applies, few Neanderthal Y chromosomes would have survived. Nonetheless, the Neanderthal autosomes would have happily mingled and interchanged with human autosomes, eventually losing their identity in the process. In a scenario previously not considered by other researchers (29), if male Neanderthals mated with female humans, Haldane’s law would account for the apparent absence of Neanderthal Y-linked genes in the human population.

The hypothesis has held true in the case of putative causal variants in apolipoprotein E, ..
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  • Common vs. Rare Allele Hypotheses for Complex Diseases

    Rare functional variant;

  • RareMETALS2 - Genome Analysis Wiki

    Where Brown's weak version of the linguistic relativity hypothesis proposes that language influences ..

  • alternative alternative hypothesis to be specified ..

    to linguistically rare ..

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The blue social bookmark and publication sharing system.

We studied 912 human and 542 E. coli genes with assigned secondary structures. Orthologs from 14 mammalian and 19 E. coli strains were extracted and site-specific evolutionary rates inferred using models implemented in CodonPhyML [3], an extension of PhyML.

Hypothesis Journal » Neanderthal-human Hybrids

Taken together our analysis of mtDNA, variants that overlap genotyping arrays (PCA, admixture,
f3, and D-statistic analyses) and rare variants provide evidence of ancestry from 3 nonoverlapping
subsets of the sequence read data. Each is consistent with Native American ancestry.
In sum, our analyses here, based on the human sequence reads associated with the Kennewick
Man provided in the Short Read Archive, all point to the Native American ancestry of the
sample. Our results mitigate any concern over errors by Rasmussen et al. because, while we used
some of the same software used by Rasmussen to process and analyze the data, the pipelines
used here were independently established. We also added a new method based on rare variants
and again found evidence for Native American ancestry.

Hypothesis Neanderthal-human Hybrids

It has been asserted that “…cranial morphology provides as much insight into population structure and affinity as genetic data”2. However, although recent and previous craniometric analyses have consistently concluded that Kennewick Man is unlike modern Native Americans, they disagree regarding his closest population affinities, the cause of the apparent differences between Kennewick Man and modern Native Americans, and whether the differences are historically important (for example, represent an earlier, separate migration to the Americas), or simply represent intra-population variation2, 3, 7, 10, 26, 27, 28. These inconsistencies are probably owing to the difficulties in assigning a single individual when comparing to population-mean data, without explicitly taking into account within-population variation. Reanalysis of W. W. Howells’ worldwide modern human craniometric data set29 (Supplementary Information 9) shows that biological population affinities of individual specimens cannot be resolved with any statistical certainty. While our individual-based craniometric analyses confirm that Kennewick Man tends to be more similar to Polynesian and Ainu peoples than to Native Americans, Kennewick Man’s pattern of craniometric affinity falls well within the range of affinity patterns evaluated for individual Native Americans (Supplementary Information 9). For example, the Arikara from North Dakota (the Native American tribe representing the geographically closest population in Howells’ data set to Kennewick), exhibit with high frequency closest affinities with Polynesians (Supplementary Information 9). Yet, the Arikara have typical Native-American mitochondrial DNA haplogroups30, as does Kennewick Man. We conclude that the currently available number of independent phenetic markers is too small, and within-population craniometric variation too large, to permit reliable reconstruction of the biological population affinities of Kennewick Man.

Principles of complex trait genetics - UpToDate

The co-translational hypothesis predicts selection for rare codons in loops connecting protein subunits, such as secondary structures [1]. Rare codons are translated at a slower rate, causing translational pauses that may aid in protein folding. Furthermore, synonymous rates vary substantially from site-to-site in many genes and synonymous mutations have been implicated in genetic fitness and several diseases [2]. Despite this, synonymous substitution rates are often assumed neutral. Here we investigate how the synonymous rate is related to secondary structure and codon usage.

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