A 122.5-kilobase deletion of the P gene underlies the high prevalence of oculocutaneous albinism type 2 in the Navajo population

Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population

Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago Territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was -8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of -6 and -4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24-29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.

A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus

Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3-19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.

Autosomal recessive diseases among the Athabaskans of the southwestern United States: anthropological, medical, and scientific aspects

The peopling of the Americas by Native Americans occurred in 4 waves of which the last was Nadene language speakers of whom Athabaskans are the largest group. As the Europeans were entering the Southwestern states of the USA, Athabaskan hunting-gathering tribes were migrating South from Canada along the Rocky Mountains and undergoing potential bottlenecks reflected in autosomal recessive diseases shared by Apaches and Navajos. About 300 years ago, the Navajo developing a sedentary culture learned from Pueblo Indians while the Apache remained hunter-gathers. Although most of the tribe was rounded up and forced to relocate to Bosque Redondo, the adult breeding population was large enough to prevent a genetic bottleneck. However, some Navajo underwent further population bottlenecks while hiding from the brutal US Army action (under Kit Carson’s guidance). This led to an increased frequency of other autosomal recessive diseases. Recent advances in population genetics, pathophysiology of the diseases, and social/ethical issues concerning their study are reviewed.

Weaving the Strands of Life (Iiná Bitł'ool): History of Genetic Research Involving Navajo People

To date, some genetic studies offer medical benefits but lack a clear pathway to benefit for people from underrepresented backgrounds. Historically, Indigenous people, including the Diné (Navajo people), have raised concerns about the lack of benefits, misuse of DNA samples, lack of consultation, and ignoring of cultural and traditional ways of knowing. Shortly after the Navajo Nation Human Research Review Board was established in 1996, the Navajo Nation recognized growing concerns about genetic research, and in 2002 they established a moratorium on human genetic research studies. The moratorium effectively has protected their citizens from potential genetic research harms. Despite the placement of the moratorium, some genetic research studies have continued using blood and DNA samples from Navajo people. To understand the history of genetic research involving Navajo people, the authors conducted a literature review of genetic or genetics-related research publications that involved Navajo people, identifying 79 articles from the years 1926 to 2018. To their knowledge, no known literature review has comprehensively examined the history of genetic research in the Navajo community. This review divides the genetic research articles into the following general classifications: bacteria or virus genetics, blood and human leukocyte antigens, complex diseases, forensics, hereditary diseases, and population genetics and migration. The authors evaluated the methods reported in each article, described the number of Navajo individuals reported, recorded the academic and tribal approval statements, and noted whether the study considered Diné cultural values. Several studies focused on severe combined immunodeficiency disease, population history, neuropathy, albinism, and eye and skin disorders that affect Navajo people. The authors contextualize Diné ways of knowing related to genetics and health with Western scientific concepts to acknowledge the complex philosophy and belief system that guides Diné people and recognizes Indigenous science. They also encourage researchers to consider cultural perspectives and traditional knowledge that has the potential to create stronger conclusions and better-informed, ethical, and respectful science.

Adaptation and co-adaptation of skin pigmentation and vitamin D genes in native Americans

We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.

Shades of complexity: New perspectives on the evolution and genetic architecture of human skin

Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.

Integrated small copy number variations and epigenome maps of disorders of sex development

Small copy number variations (CNVs) have typically not been analyzed or reported in clinical settings and hence have remained underrepresented in databases and the literature. Here, we focused our investigations on these small CNVs using chromosome microarray analysis (CMA) data previously obtained from patients with atypical characteristics or disorders of sex development (DSD). Using our customized CMA track targeting 334 genes involved in the development of urogenital and reproductive structures and a less stringent analysis filter, we uncovered small genes with recurrent and overlapping CNVs as small as 1 kb, and small regions of homozygosity (ROHs), imprinting and position effects. Detailed analysis of these high-resolution data revealed CNVs and ROHs involving structural and functional domains, repeat elements, active transcription sites and regulatory regions. Integration of these genomic data with DNA methylation, histone modification and predicted RNA expression profiles in normal testes and ovaries suggested spatiotemporal and tissue-specific gene regulation. This study emphasized a DSD-specific and gene-targeted CMA approach that uncovered previously unanalyzed or unreported small genes and CNVs, contributing to the growing resources on small CNVs and facilitating the narrowing of the genomic gap for identifying candidate genes or regions. This high-resolution analysis tool could improve the diagnostic utility of CMA, not only in patients with DSD but also in other clinical populations. These integrated data provided a better genomic-epigenomic landscape of DSD and greater opportunities for downstream research.

Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions

Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5' and 3' LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = -0.18, P < 0.05) and stem length (r = -0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3' LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion.

Congenital and acquired disorders presenting as psychosis in children and young adults

A review of the published literature found 60 congenital and acquired disorders with symptoms that include psychosis in youth. The prevalence, workup, genetics, and associated neuropsychiatric features of each disorder are described. Eighteen disorders (30%) have distinct phenotypes (doorway diagnoses); 18 disorders (30%) are associated with intellectual disability; and 43 disorders (72%) have prominent neurologic signs. Thirty-one disorders (52%) can present without such distinct characteristics, and are thus more easily overlooked. A systematic and cost-effective differential diagnostic approach based on estimated prevalence and most prominent associated signs is recommended.

Evolution of albinism in cave planthoppers by a convergent defect in the first step of melanin biosynthesis

Albinism, the reduction or loss of melanin pigment, is found in many diverse cave-dwelling animals. The mechanisms responsible for loss of melanin pigment are poorly understood. In this study we use a melanogenic substrate assay to determine the position where melanin synthesis is blocked in independently evolved cave planthoppers from Hawaii and Croatia. In this assay, substrates of enzymes responsible for melanin biosynthesis are added to fixed specimens in vitro and their ability to rescue black melanin pigmentation is determined. L-tyrosine, the first substrate in the pathway, did not produce melanin pigment, whereas L-DOPA, the second substrate, restored black pigment. Substrates in combination with enzyme inhibitors were used to test the possibility of additional downstream defects in the pathway. The results showed that downstream reactions leading from L-DOPA and dopamine to DOPA-melanin and dopamine-melanin, the two types of insect melanin, are functional. It is concluded that albinism is caused by a defect in the first step of the melanin synthesis pathway in cave-adapted planthoppers from widely separated parts of the world. However, Western blots indicated that tyrosine hydroxylase (TH), the only enzyme shown to operate at the first step in insects, is present in Hawaiian cave planthoppers. Thus, an unknown factor(s) operating at this step may be important in the evolution of planthopper albinism. In the cavefish Astyanax mexicanus, a genetic defect has also been described at the first step of melanin synthesis suggesting convergent evolution of albinism in both cave-adapted insects and teleosts.

Autosomal recessive diseases among the Athabaskans of the southwestern United States: recent advances and implications for the future

Genetic and linguistic data suggest that the Na-Dene, of which the Athabaskans are the largest group, are part of a later immigration into the Americas than the first Amerind immigration. Whether a second and third immigration can be separated seems unlikely but continued cross-Bering Strait exchanges may have masked what was a greater separation in the past. The movement of tribes into Siberia appears to have involved a genetic bottleneck leading to at least one disease allele shared by Eskimo/Aleuts and Navajos and a second possibly shared by the Navajo and a Siberian population, but not the same Siberian population that share deep linguistic affinities with the Navajo. A second bottleneck appears to have occurred with the migration of Athabaskans from Northwest North America to the Southwestern United States along the Rocky Mountains. This bottleneck is reflected in several rare recessive diseases shared by the Navajo and Apache. Finally, the Navajo were captured and imprisoned under conditions which led to severe population loss. This, and the "hiding away" of a small number of Navajos in what is now the Western portion of the reservation, led to a Navajo-specific bottleneck(s) resulting in an increased frequency of several rare recessive diseases among the Navajo. Prejudice against human genetic research is high among the Southwestern Athabaskans but attempts to bridge the gap are now occurring. The involvement of Navajo scientists in this process is especially encouraging.

Inheritance of a novel mutated allele of the OCA2 gene associated with high incidence of oculocutaneous albinism in a Polynesian community

Oculocutaneous albinism type 2 (OCA2) is a human autosomal-recessive hypopigmentation disorder associated with pathological mutations of the OCA2 gene. In this study, we investigated a form of OCA in a Polynesian population with an observed phenotype characterized by fair skin, some brown nevi present in the sun-exposed areas and green or blue eyes. Hair presented with a unique red coloration since birth, with tones ranging across individuals from Yellow-Red to Brown-Red, or Auburn. We genetically screened for mutations in the OCA2 and MC1R genes as their products have previously been shown to be associated with red hair/fair skin and OCA2. The SLC45A2 gene was also screened to identify any possible relation to skin color variation. We have identified a novel missense substitution in the OCA2 gene (Gly775Asp) responsible for OCA2 in individuals of Polynesian heritage from Tuvalu. The estimated incidence of this form of OCA2 in the primary study community is believed to occur at one of the highest recorded rates of albinism at approximately 1 per 669 individuals. In addition, we have analyzed four unrelated individuals with albinism who have Polynesian heritage from three other separate communities and found they carry the same OCA2 mutation. We also analyzed an out-group comprising three unrelated individuals with albinism of Melanesian ancestries from two separate communities, one Australian Aboriginal and three Australian Caucasians, and did not detect this mutation. We hypothesize that this mutation may be Polynesian specific and that it originated from a common founder.

Navajo microvillous inclusion disease is due to a mutation in MYO5B

Microvillous Inclusion Disease (MID) is a rare, autosomal recessive gastrointestinal disease of increased frequency among the Navajos. Previous work has shown a deficiency of RAB8 in one Japanese patient, while homozygous mutations in MYO5B were found in 7 of 10 mostly Middle Eastern families. We have identified a shared homozygous mutation in MYO5B in seven affected Navajos with the expected heterozygosity in five parents. We have developed a simple restriction enzyme based assay that allows for rapid screening for this mutation.

Regressive evolution in Astyanax cavefish

A diverse group of animals, including members of most major phyla, have adapted to life in the perpetual darkness of caves. These animals are united by the convergence of two regressive phenotypes, loss of eyes and pigmentation. The mechanisms of regressive evolution are poorly understood. The teleost Astyanax mexicanus is of special significance in studies of regressive evolution in cave animals. This species includes an ancestral surface dwelling form and many con-specific cave-dwelling forms, some of which have evolved their recessive phenotypes independently. Recent advances in Astyanax development and genetics have provided new information about how eyes and pigment are lost during cavefish evolution; namely, they have revealed some of the molecular and cellular mechanisms involved in trait modification, the number and identity of the underlying genes and mutations, the molecular basis of parallel evolution, and the evolutionary forces driving adaptation to the cave environment.

Variants of the melanocortin 1 receptor gene (MC1R) and P gene as indicators of the population origin of an individual

The population origin of an individual is often requested to be determined from specimens left at a crime scene for identifying a suspect and individual identity. The melanocortin 1 receptor gene (MC1R) and P gene are associated with human pigmentation. Although several studies have reported that these genes are highly polymorphic in human populations, it is unclear if the allele variants can be used to determine the population origin of an individual. We aimed to determine the ethnic origin of an individual by using single nucleotide polymorphisms (SNPs). Eighteen SNPs in the MC1R gene and P genes were genotyped in 52 individuals by the direct sequencing method, and 4 SNPs (MC1R gene: R163Q and P gene: IVS5 + 1001, IVS13 + 113, and H615R) were selected on the basis of differences in frequencies. Subsequently, we genotyped these four SNPs in 422 volunteers from six ethnically defined populations using a polymerase chain reaction-based assay. The results revealed that the allele variants were present with high frequencies in Asian populations but were low in European and African populations. On the basis of these results, we defined a specific combination of a genotype (R163Q) and a diplotype group (IVS5 + 1001, IVS13 + 113, and H615R). This study indicates that the specific combination of a genotype and a diplotype group would be effective in estimating the population origin of an individual from a list of population groups.

Emerging model systems in evo-devo: cavefish and microevolution of development

Cavefish and their conspecific surface-dwelling ancestors (Astyanax mexicanus) are emerging as a model system to study the microevolution of development. Here we describe attributes that make this system highly promising for such studies. We review how the Astyanax system is being used to understand evolutionary forces underlying loss of eyes and pigmentation in cavefish. Pigment regression is probably explained by neutral mutations, whereas natural selection is a likely mechanism for loss of eyes. Finally, we discuss several research frontiers in which Astyanax is poised to make significant contributions in the future: evolution of constructive traits, the craniofacial skeleton, the central nervous system, and behavior.

Oculocutaneous albinism type 2 (OCA2) with homozygous 2.7-kb deletion of the P gene and sickle cell disease in a Cameroonian family. Identification of a common TAG haplotype in the mutated P gene

In this study, we report on a Cameroonian family from the Ewondo ethnic group, presenting with three oculocutaneous albinism type 2 (OCA2) patients homozygous for the 2.7-kb deletion of the P gene. In one of these patients OCA2 was associated with sickle cell anaemia and in two with the sickle cell trait. We took this opportunity to determine single nucleotide polymorphism (SNP) haplotypes within the P gene in this family in comparison with a group of 53 OCA2 patients homozygous for the same mutation and with a matched unrelated full-coloured control group of 49 subjects, originating from seven different ethnic groups of Southern Cameroon including Ewondo. A combination of five exonic and intronic SNPs in the OCA2 gene was genotyped by sequencing PCR products. We found 3 different haplotypes (TAGCT, TAGTT and TAGCC with frequencies of 0.66, 0.28 and 0.06, respectively) associated with the mutation in the 53 OCA2 patients, while 11 different haplotypes were observed in the control group. These observations suggest that the mutation appeared on the relatively frequent haplotype TAGCT, and that the two other haplotypes are derived from two independent recombination events. These haplotypic data, associated with a value of 1/15,000 for the prevalence of the 2.7-kb mutation, a present effective population size of 10,000,000 for Cameroon and a recombination rate of 0.0031, allowed us to estimate that this mutation originated 4,100-5,645 years ago.

Periodontal disease in Kuna albinism: a comparative study

BACKGROUND

In classic albinism, all parts of the body are normal except for the absence of melanin. It is believed that lack of this pigment in periodontal tissues might influence periodontal disease progression. This study was designed to determine the relationship between periodontal diseases and albinism by comparing the clinical periodontal status of a group of native Panamanian Kuna albinos (from San Blas, Panama) to Kuna non-albinos of the same communities.

METHODS

An experimental group of 30 subjects (Kuna albinos aged > or =12 years) was selected and divided into three subgroups according to age. Likewise, a control group of 30 subjects (Kuna non-albinos) was selected and divided in subgroups.

RESULTS

Assessment of oral hygiene and gingival inflammation in albinos by the Silness and Löe plaque index and Löe and Silness gingival index, respectively, was unremarkable compared to control groups. No statistically significant differences were found for number of teeth present, gingival index, plaque index, clinical attachment loss (CAL), probing depth, or gingival recession. As expected, age was a factor in the severity of the periodontal disease; 58% of individuals aged > or =36 years had at least one site with CAL > or =7 mm.

CONCLUSION

Based on the overwhelming similarity of results found between experimental and control groups, albinism does not represent a clinical risk factor in the pathogenesis or exacerbation of periodontal diseases for these individuals.

Non-reporting and inconsistent reporting of race and ethnicity in articles that claim associations among genotype, outcome, and race or ethnicity

BACKGROUND

The use of race as a category in medical research is the focus of an intense debate, complicated by the inconsistency of presumed independent variables, race and ethnicity, on which analysis depends. Interpretation is made difficult by inconsistent methods for determining the race or ethnicity of a participant. The failure to specify how race or ethnicity was determined is common in the published literature.

HYPOTHESIS

Criteria by which they assign a research participant to racial or ethnic categories are not reported by published articles.

METHODS

Methods were reviewed for assigning race and ethnicity of research participants in 268 published reports reporting associations among race (or ethnicity), health outcome and genotype.

RESULTS

Of the 268 published reports reviewed, it was found that 192 (72%) did not explain their methods for assigning race or ethnicity as an independent variable. This was despite the fact that 180 (67%) of those reports reached conclusions about associations among genetics, health outcome and race or ethnicity.

CONCLUSIONS

More attention needs to be given to the definition of race and ethnicity in genetic studies, especially in those diseases where health disparities are known to exist.

Albinism (OCA2) in Amerindians

Homozygosity for a mutation in the P locus mapped to the human chromosome 15q11.2-12 results in tyrosinase-positive albinism (OCA2). This type of albinism has a worldwide distribution, with a prevalence of about 1 in 36,000 among European-Americans in the United States. It has a moderate to relatively high prevalence values (1 in 28 to 1 in 6,500) in various Amerindian populations in the southwestern United States, southern Mexico, eastern Panama, and southern Brazil. The wide distribution of the gene for OCA2 in Amerindian populations, and its relatively high frequency in several of these populations, are enigmatic because of the detrimental nature of OCA2 in the presence of certain environmental conditions. The relative Darwinian fitness of individuals with this inborn error of metabolism would have been reduced in early nomadic hunting-gathering populations because of their poor visual acuity and sensitivity to the sun. Nevertheless, specific situations allowed OCA2 to increase in frequency in certain Amerindian populations at various different times in history. The present objectives are to review the literature on albinism (OCA2) in Amerindians, and propose hypotheses for the variable frequencies of the OCA2 gene in Amerindian populations, which include chance processes (founder effect, bottleneck effect, and genetic drift) in small populations, natural selection, cultural selection, and the interaction of situations that led to the increase of the frequency of the albino gene in some generations. Special emphasis is placed on those Amerindian populations with a relatively high frequency of the OCA2 gene that have been best-studied, namely, the Cuna population of eastern Panama and the Hopi population in the southwestern US. Hypothetical scripts are presented for the present relatively high frequencies of the OCA2 gene in these populations. A hypothetical script is also presented, showing how a mutant gene could have reached a relatively high frequency in a small endogamous early Mayan population and then been spread by migrating groups to other geographical regions, following the rapid increase in size of that population. Comprehensive molecular studies of OCA2 genes in Amerindian populations could yield information on the possible origin of the albino gene present in many of these populations, in addition to the gene flow that occurred among some of them in past generations. The results of these studies could lead to more informed hypotheses concerning the wide distribution of OCA2 in Amerindian populations.

Regressive Evolution of Pigmentation in the Cavefish Astyanax

Many cave animals are colorless due to loss of pigment cells. Here, we review recent progress on how and why pigmentation has disappeared inAstyanax mexicanus, a single teleost species with conspecific surface-dwelling (surface fish) and many different cave-dwelling (cavefish) forms. During surface fish development, migratory neural crest cells form three types of pigment cells: silver iridophores, orange xanthophores, and black melanophores. Cavefish have eliminated or substantially reduced their complement of melanophores and exhibit albinism, loss of the capacity to synthesize melanin. Cell tracing, immunolocalization, and neural tube explant cultures show that cavefish have retained a colorless pre-melanophore (melanoblast) lineage derived from the neural crest. Thus, the cavefish neural crest produces melanoblasts that migrate normally but are blocked in differentiation and show defective melanogenesis. Cavefish melanoblasts can convert exogenous L-DOPA into melanin and therefore have active tyrosinase, the key enzyme in melanogenesis. In contrast, cavefish melanoblasts are unable to convert L-tyrosine to L-DOPA (and melanin), although this reaction is also catalyzed by tyrosinase. Thus, cavefish are tyrosinase-positive albinos that have a deficiency in L-tyrosine transport or utilization within the melanosome, the organelle in which melanin is synthesized. At least five different types ofAstyanaxcavefish show the same defect in melanogenesis. Genetic analysis shows that cavefish albinism is caused by loss of function mutations in a single gene,p/oca2, which encodes a large protein that probably spans the melanosome membrane. Different deletions in thep/oca2 protein-coding region are responsible for loss of function in at least two different cavefish populations, suggesting that albinism evolved by convergence. Based on current understanding of the genetic basis of albinism, we discuss potential mechanisms for regressive evolution of cavefish pigmentation.

Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism

The genetic basis of vertebrate morphological evolution has traditionally been very difficult to examine in naturally occurring populations. Here we describe the generation of a genome-wide linkage map to allow quantitative trait analysis of evolutionarily derived morphologies in the Mexican cave tetra, a species that has, in a series of independent caves, repeatedly evolved specialized characteristics adapted to a unique and well-studied ecological environment. We focused on the trait of albinism and discovered that it is linked to Oca2, a known pigmentation gene, in two cave populations. We found different deletions in Oca2 in each population and, using a cell-based assay, showed that both cause loss of function of the corresponding protein, OCA2. Thus, the two cave populations evolved albinism independently, through similar mutational events.

Single nucleotide polymorphisms in theMATP gene are associated with normal human pigmentation variation

Human physical pigmentation is determined by the type and amount of melanin and the process of pigmentation production probably involves more than 100 genes. A failure to synthesize melanin results in oculocutaneous albinism (OCA). A recently identified form of OCA results from mutations in the Membrane Associated Transporter Protein (MATP) gene. The role of MATP in human pigmentation is not clear. We investigated the role of two nonpathogenic nonsynonymous single nucleotide polymorphisms (SNPs) in the MATP gene to determine if they are associated with normal human skin, hair, and eye color variation. A total of 608 individuals from four different population groups (456 Caucasians, 31 Asians, 70 African-Americans, and 51 Australian Aborigines) were genotyped for c.814G>A (p.Glu272Lys) and c.1122C>G (p.Phe374Leu). Results indicate that the allele frequencies of both polymorphisms are significantly different between population groups. The two alleles, 374Leu and 272Lys, are significantly associated with dark hair, skin, and eye color in Caucasians. The odds ratios (ORs) of the LeuLeu genotype for black hair and olive skin are 25.63 and 28.65, respectively, and for the LysLys genotype are 43.23 and 8.27, respectively. The OR for eye color is lower at 3.48 for the LeuLeu and 6.57 for LysLys genotypes. This is the first report of this highly significant association of MATP polymorphisms with normal human pigmentation variation.

POPULATION GENETICS, HISTORY, AND HEALTH PATTERNS IN NATIVE AMERICANS

Over the past two decades, detailed studies of mitochondrial DNA and the Y chromosome have increased our understanding of the history and population genetics of Native American populations. Variation in autosomal DNA has also been investigated, but to a more limited extent. A low level of genetic diversity in Native American populations is a robust finding from all lines of evidence. In contrast to the previous multiple migration scenarios for the Pleistocene peopling of the Americas, it now seems that a single migration satisfactorily explains the genetic data. Native Americans show greater genetic similarity to populations in east central Asia than they do to the current easternmost Siberian populations. Recent studies on the Y chromosome indicate a date of entry (about 17,000 years ago) into the Americas roughly consistent with the archaeological record. Native Americans experienced two episodes of reduced population size: one with the peopling of the Americas and the other with European contact. The former is the more important determinant for the number of gene lineages and founding haplotypes seen in populations. It may also be an important determinant of the genetic variation underlying common complex diseases, and especially diabetes. The tribal structure of contemporary Native American populations is relevant to the distribution of rare Mendelian disorders because most tribes constitute relatively small, semi-independent gene pools. This leads us to expect that the allelic spectrum for Mendelian diseases will be simple within individual tribes but complex for Native Americans as a whole.

Human and mouse disorders of pigmentation

Disorders of pigmentation were among the first genetic diseases ever recognized because of their visually striking clinical phenotypes, resulting from defects of pigmentary melanocytes. Recent years have seen remarkable progress in understanding these diseases, largely as a result of the systematic parallel study of human patients and inbred mice with similar phenotypes. Our understanding of disorders of pigmentation indicates that these diseases may be most usefully considered as abnormalities of melanocyte development, function, or survival.