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Description
Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to

Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to have evolved from a Y-specific inversion that suppressed recombination across the boundary. In addition to the two PARs, there is also a human-specific X-transposed region (XTR) that was duplicated from the X to the Y chromosome. Genetic diversity is expected to be higher in recombining than nonrecombining regions, particularly because recombination reduces the effects of linked selection, allowing neutral variation to accumulate. We previously showed that diversity decreases linearly across the previously defined pseudoautosomal boundary (rather than drop suddenly at the boundary), suggesting that the pseudoautosomal boundary may not be as strict as previously thought. In this study, we analyzed data from 1271 genetic females to explore the extent to which the pseudoautosomal boundary varies among human populations (broadly, African, European, South Asian, East Asian, and the Americas). We found that, in all populations, genetic diversity was significantly higher in the PAR1 and XTR than in the non-PAR regions, and that diversity decreased linearly from the PAR1 to finally reach a non-PAR value well past the pseudoautosomal boundary in all populations. However, we also found that the location at which diversity changes from reflecting the higher PAR1 diversity to the lower nonPAR diversity varied by as much as 500 kb among populations. The lack of genetic evidence for a strict pseudoautosomal boundary and the variability in patterns of diversity across the pseudoautosomal boundary are consistent with two potential explanations: (1) the boundary itself may vary across populations, or (2) that population-specific demographic histories have shaped diversity across the pseudoautosomal boundary.
ContributorsCotter, Daniel Juetten (Author) / Wilson Sayres, Melissa (Thesis director) / Stone, Anne (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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Description

In 1942, the United States Supreme Court Case of Skinner v. Oklahoma ruled that states could not legally sterilize those inmates of prisons deemed habitual criminals. Skinner v. Oklahoma was about the case of Jack Skinner, an inmate of the Oklahoma State Penitentiary in McAlester, Oklahoma, who was subject to

In 1942, the United States Supreme Court Case of Skinner v. Oklahoma ruled that states could not legally sterilize those inmates of prisons deemed habitual criminals. Skinner v. Oklahoma was about the case of Jack Skinner, an inmate of the Oklahoma State Penitentiary in McAlester, Oklahoma, who was subject to sterilization under the Oklahoma Habitual Criminal Sterilization Act of 1935. The case, decided on 1 June 1942, determined that state laws were unconstitutional if those laws enabled states to forcibly sterilize inmates deemed to be habitual criminals. Such laws violated the Equal Protection Clause of the Fourteenth Amendment to the US Constitution. The Skinner v. Oklahoma decision also reflected tensions in US eugenic policies when juxtaposed against similar policies of the Nazi regime in Europe, especially with regard to sterilization measures.

Created2016-08-27
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Description

Franz Josef Kallmann studied the biological and genetic factors of psychological disorders in Germany and the United States in the twentieth century. His studies at the New York State Psychiatric Institute in New York City, New York, focused on the genetic factors that cause psychiatric disorders. Kallmann was one of

Franz Josef Kallmann studied the biological and genetic factors of psychological disorders in Germany and the United States in the twentieth century. His studies at the New York State Psychiatric Institute in New York City, New York, focused on the genetic factors that cause psychiatric disorders. Kallmann was one of the first to use twins to study how a mental disorder is passed on by comparing the occurrence of epilepsy and schizophrenia in both fraternal and identical twins. Kallmann helped to develop and popularize the methodology of twin studies to examine the genetic component of psychiatric disorders and he showed a factor for the psychiatric disease schizophrenia.

Created2017-04-06
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Curt Jacob Stern studied radiation and chromosomes in humans and fruit flies in the United States during the twentieth century. He researched the mechanisms of inheritance and of mitosis, or the process in which the chromosomes in the nucleus of a single cell, called the parent cell, split into identical

Curt Jacob Stern studied radiation and chromosomes in humans and fruit flies in the United States during the twentieth century. He researched the mechanisms of inheritance and of mitosis, or the process in which the chromosomes in the nucleus of a single cell, called the parent cell, split into identical sets and yield two cells, called daughter cells. Stern worked on the Drosophila melanogaster fruit fly, and he provided early evidence that chromosomes exchange genetic material during cellular reproduction. During World War II, he provided evidence for the harmful effects of radiation on developing organisms. That research showed that mutations can cause problems in developing fetuses and can lead to cancer. He helped explain how genetic material transmits from parent to progeny, and how it functions in developing organisms.

Created2017-06-23
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In 2002, after applying for government assistance in the state of Washington, Lydia Fairchild was told that her two children were not a genetic match with her and that therefore, biologically, she could not be their mother. Researchers later determined that the genetic mismatch was due to chimerism, a condition

In 2002, after applying for government assistance in the state of Washington, Lydia Fairchild was told that her two children were not a genetic match with her and that therefore, biologically, she could not be their mother. Researchers later determined that the genetic mismatch was due to chimerism, a condition in which two genetically distinct cell lines are present in one body. The state accused Fairchild of fraud and filed a lawsuit against her. Following evidence from another case of chimerism documented in The New England Journal of Medicine in a woman named Karen Keegan, Fairchild was able to secure legal counsel and establish evidence of her biological maternity. A cervical swab eventually revealed Fairchild’s second distinct cell line, showing that she had not genetically matched her children because she was a chimera. Fairchild’s case was one of the first public accounts of chimerism and has been used as an example in subsequent discussions about the validity and reliability of DNA evidence in legal proceedings within the United States.

Created2021-06-01
Description
Studying human genetic variation opens the possibility of understanding the details of population migrations, how humans develop and function, and why they get sick. To fully understand these things, genetic variation must be comprehensively characterized across globally diverse human populations and evolutionary knowledge can be used to inform studies of

Studying human genetic variation opens the possibility of understanding the details of population migrations, how humans develop and function, and why they get sick. To fully understand these things, genetic variation must be comprehensively characterized across globally diverse human populations and evolutionary knowledge can be used to inform studies of disease. In my dissertation I use computational methods to study human genetic variation. Each of my dissertation chapters focuses on a unique topic in the field of human evolutionary genetics. In the first chapter, I present PopInf, a computational pipeline to visualize principal components analysis output and assign ancestry to samples with unknown genetic ancestry, given a reference population panel of known origins. This pipeline facilitates visualization and identification of genetic ancestry across samples, so that this ancestry can be accounted for in studies of health and disease risk. In the next chapter, I investigate factors that shape patterns of genetic variation within and among four small-scale pastoral populations in northern Kenya. I find that geography predominantly shapes patterns of genetic variation in northern Kenyan human populations. In the next chapter, I investigate the extent to which Neanderthal introgression impacts liver cancer etiology. I find a pattern of overall enrichment of somatic mutations on Neanderthal introgressed haplotypes. Finally, through simulations, I investigate the effects of standard autosomal versus sex chromosome complement-informed alignment, variant calling and variant filtering strategies on variants called on the human sex chromosomes. I show that aligning to a reference genome informed on the sex chromosome complement of samples improves variant calling on the sex chromosome compared to aligning to a default reference, and variant calling is improved in males when calling the sex chromosomes haploid rather than diploid and when using haploid-based thresholds for filtering variants on the sex chromosomes. I provide recommendations for alignment, variant calling and filtering on the sex chromosomes based on these findings.
ContributorsOill, Angela Maria (Author) / Wilson, Melissa A (Thesis advisor) / Stone, Anne C (Thesis advisor) / Buetow, Kenneth H (Committee member) / Mathew, Sarah (Committee member) / Pfeifer, Susanne P (Committee member) / Arizona State University (Publisher)
Created2022
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Description

Theophilus Shickel Painter studied the structure and
function of chromosomes in the US during in the early to mid-twentieth century. Painter worked at
the University of Texas at Austin in Austin, Texas. In the 1920s
and 1930s, Painter studied the chromosomes of the salivary gland
giant

Theophilus Shickel Painter studied the structure and
function of chromosomes in the US during in the early to mid-twentieth century. Painter worked at
the University of Texas at Austin in Austin, Texas. In the 1920s
and 1930s, Painter studied the chromosomes of the salivary gland
giant chromosomes of the fruit fly (Drosophila
melanogaster), with Hermann J. Muller. Muller and Painter
studied the ability of X-rays to cause changes in the chromosomes
of fruit flies. Painter also studied chromosomes in mammals.
He investigated the development of the male gamete, a process
called spermatogenesis, in several invertebrates and vertebrates,
including mammals. In addition, Painter studied the role the
Y-chromosome plays in the determination and development of the male
embryo. Painter's research concluded that egg cells fertilized by
sperm cell bearing an X-chromosome resulted in a female embryo,
whereas egg cells fertilized by a sperm cell carrying a
Y-chromosome resulted in a male embryo. Painter's work with
chromosomes helped other researchers determine that X- and
Y-chromosomes are responsible for sex determination.

Created2014-11-22