Apportionment of global human genetic diversity based on craniometrics and skin color

A number of analyses of classical genetic markers and DNA polymorphisms have shown that the majority of human genetic diversity exists within local populations (approximately 85%), with much less among local populations (approximately 5%) or between major geographic regions or "races" (approximately 10%). Previous analysis of craniometric variation (Relethford [1994] Am J Phys Anthropol 95:53-62) found that between 11-14% of global diversity exists among geographic regions, with the remaining diversity existing within regions. The methods used in this earlier paper are extended to a hierarchical partitioning of genetic diversity in quantitative traits, allowing for assessment of diversity among regions, among local populations within regions, and within local populations. These methods are applied to global data on craniometric variation (57 traits) and skin color. Multivariate analysis of craniometric variation shows results similar to those obtained from genetic markers and DNA polymorphisms: roughly 13% of the total diversity is among regions, 6% among local populations within regions, and 81% within local populations. This distribution is concordant with neutral genetic markers. Skin color shows the opposite pattern, with 88% of total variation among regions, 3% among local populations within regions, and 9% within local populations, a pattern shaped by natural selection. The apportionment of genetic diversity in skin color is atypical, and cannot be used for purposes of classification. If racial groups are based on skin color, it appears unlikely that other genetic and quantitative traits will show the same patterns of variation.     

Characterization of the bioactive motif of neuregulin-1, a fibroblast-derived paracrine factor that regulates the constitutive color and the function of melanocytes in human skin

Interactions between melanocytes and neighboring cells in the skin (keratinocytes and fibroblasts) play important roles in regulating human skin color. We recently reported that neuregulin-1 (NRG1) is highly expressed in fibroblasts from Fitzpatrick type VI skin (the darkest) and at least in part determines the constitutive color of human skin. We have now characterized the bioactive motif of NRG1 that is involved in modulating melanin production in human melanocytes. We found that 8-mer motifs (PSRYLCKC and LCKCPNEF) increased melanin production but did not increase the proliferation of melanocytes; the minimum fragment that could elicit that effect was the tetrapeptide LCKC. This smaller bioactive peptide might have an advantage in clinical applications in which it modulates only pigmentation and does not stimulate melanocyte proliferation.     

The evolution of human skin pigmentation: A changing medley of vitamins,genetic variability,and UV radiation during human expansion

This review examines putative, yet likely critical evolutionary pressures contributing to human skin pigmentation and subsequently, depigmentation phenotypes. To achieve this, it provides a synthesis of ideas that frame contemporary thinking, without limiting the narrative to pigmentation genes alone. It examines how geography and hence the quality and quantity of UV exposure, pigmentation genes, diet-related genes, vitamins, anti-oxidant nutrients, and cultural practices intersect and interact to facilitate the evolution of human skin color. The article has a strong focus on the vitamin D-folate evolutionary model, with updates on the latest biophysical research findings to support this paradigm. This model is examined within a broad canvas that takes human expansion out of Africa and genetic architecture into account. A thorough discourse on the biology of melanization is provided (includes relationship to BH₄ and DNA damage repair), with the relevance of this to the UV sensitivity of folate and UV photosynthesis of vitamin D explained in detail, including the relevance of these vitamins to reproductive success. It explores whether we might be able to predict vitamin-related gene polymorphisms that pivot metabolism to the prevailing UVR exposome within the vitamin D-folate evolutionary hypothesis context. This is discussed in terms of a primary adaptive phenotype (pigmentation/depigmentation), a secondary adaptive phenotype (flexible metabolic phenotype based on vitamin-related gene polymorphism profile), and a tertiary adaptive strategy (dietary anti-oxidants to support the secondary adaptive phenotype). Finally, alternative evolutionary models for pigmentation are discussed, as are challenges to future research in this area.     

Technical note: A volumetric method for measuring the longitudinal arch of human tracks and feet

Fossil footprints (i.e., tracks) were believed to document arch anatomical evolution, although our recent work has shown that track arches record foot kinematics instead. Analyses of track arches can thereby inform the evolution of human locomotion, although quantifying this 3-D aspect of track morphology is difficult. Here, we present a volumetric method for measuring the arches of 3-D models of human tracks and feet, using both Autodesk Maya and Blender software. The method involves generation of a 3-D object that represents the space beneath the longitudinal arch, and measurement of that arch object's geometry and spatial orientation. We provide relevant tools and guidance for users to apply this technique to their own data. We present three case studies to demonstrate potential applications. These include, (1) measuring the arches of static and dynamic human feet, (2) comparing the arches of human tracks with the arches of the feet that made them, and (3) direct comparisons of human track and foot arch morphology throughout simulated track formation. The volumetric measurement tool proved robust for measuring 3-D models of human tracks and feet, in static and dynamic contexts. This tool enables researchers to quantitatively compare arches of fossil hominin tracks, in order to derive biomechanical interpretations from them, and/or offers a different approach for quantifying foot morphology in living humans.     

widgetcon: A website and program for quick conversion among common population genetic data formats

One of the most tedious steps in genetic data analyses is the reformatting data generated with one program for use with other applications. This conversion is necessary because comprehensive evaluation of the data may be based on different algorithms included in diverse software, each requiring a distinct input format. A platform‐independent and freely available program or a web‐based tool dedicated to such reformatting can save time and efforts in data processing. Here, we report widgetcon , a website and a program which has been developed to quickly and easily convert among various molecular data formats commonly used in phylogenetic analysis, population genetics, and other fields. The web‐based service is available at https://www.widgetcon.net . The program and the website convert the major data formats in four basic steps in less than a minute. The resource will be a useful tool for the research community and can be updated to include more formats and features in the future.     

Technical Note: Guidelines for the digital computation of 2D and 3D enamel thickness in hominoid teeth

The study of enamel thickness has received considerable attention in regard to the taxonomic, phylogenetic and dietary assessment of human and non‐human primates. Recent developments based on two‐dimensional (2D) and three‐dimensional (3D) digital techniques have facilitated accurate analyses, preserving the original object from invasive procedures. Various digital protocols have been proposed. These include several procedures based on manual handling of the virtual models and technical shortcomings, which prevent other scholars from confidently reproducing the entire digital protocol. There is a compelling need for standard, reproducible, and well‐tailored protocols for the digital analysis of 2D and 3D dental enamel thickness. In this contribution we provide essential guidelines for the digital computation of 2D and 3D enamel thickness in hominoid molars, premolars, canines and incisors. We modify previous techniques suggested for 2D analysis and we develop a new approach for 3D analysis that can also be applied to premolars and anterior teeth. For each tooth class, the cervical line should be considered as the fundamental morphological feature both to isolate the crown from the root (for 3D analysis) and to define the direction of the cross‐sections (for 2D analysis). Am J Phys Anthropol 153:305–313, 2014. © 2013 Wiley Periodicals, Inc.     

In vitro and in vivo confocal Raman study of human skin hydration: assessment of a new moisturizing agent, pMPC

The hydration capacities of a biomimetic polymer, 2-methacryloyloxethylphosphorylcholine polymer (pMPC), alone and microencapsulated, in association with another well known hydrating polymer, Hyaluronic acid, were investigated in vitro on skin models and in vivo on volunteers by using confocal Raman microspectroscopy. The hydration impact and the relative water content in the Stratum corneum were calculated from the Raman spectra using the OH (water)/CH3 (protein) ratio. Moreover, the follow-up of the presence of pMPC through the Stratum corneum was possible with confocal Raman microspectroscopy, using a characteristic vibration of pMPC, different from that of the encapsulating material. From our in vitro measurements, the improved hydration of the Stratum corneum was confirmed by the use of the encapsulated form of pMPC, which was higher when combined with Hyaluronic acid. On the basis of these in vitro findings, we validated this trend in in vivo measurements on 26 volunteers, and found a good correlation with the in vitro results. Mechanical and ultrastructural studies have been carried out to demonstrate the positive effects of the pMPC on the Stratum corneum function, namely the interaction with lamellar lipids and the plasticizing effects, which are both supposed to spell out the moisturizing effect. This study demonstrates the efficiency of a original hydrating agent, pMPC, entrapped with Hyaluronic acid in a new type of microcapsules by the use of a novel tool developed for both in vitro and in vivo approaches. This indicates a new step to evaluate and improve new moisturizers in response to the cosmetics or dermatologic demands.     

Technical note: A new method for measuring long bone curvature using 3D landmarks and semi‐landmarks

Here we describe and evaluate a new method for quantifying long bone curvature using geometric morphometric and semi‐landmark analysis of the human femur. The technique is compared with traditional ways of measuring subtense and point of maximum curvature using either coordinate calipers or projection onto graph paper. Of the traditional methods the graph paper method is more reliable than using coordinate calipers. Measurement error is consistently lower for measuring point of maximum curvature than for measuring subtense. The results warrant caution when comparing data collected by the different traditional methods. Landmark data collection proves reliable and has a low measurement error. However, measurement error increases with the number of semi‐landmarks included in the analysis of curvature. Measurements of subtense can be estimated more reliably using 3D landmarks along the curve than using traditional techniques. We use equidistant semi‐landmarks to quantify the curve because sliding the semi‐landmarks masks the curvature signal. Principal components analysis of these equidistant semi‐landmarks provides the added benefit of describing the shape of the curve. These results are promising for functional and forensic analysis of long bone curvature in modern human populations and in the fossil record. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Comparison of two methods for noninvasive determination of carotenoids in human and animal skin: Raman spectroscopy versus reflection spectroscopy

Based on compelling in vivo and in vitro studies on human skin, carotenoids are thought to be of great interest as powerful antioxidants acting to prevent free‐radical‐induced damages, including premature skin ageing and the development of skin diseases such as cancer. Among the available techniques that are suitable for noninvasive determination of carotenoids in human skin, are resonance Raman spectroscopy (RRS) and reflection spectroscopy (RS). For RS, a LED‐based miniaturized spectroscopic system (MSS) was developed for noninvasive measurement of carotenoids in human skin. The optimization and subsequent calibration of the MSS was performed with the use of RRS. A strong correlation between the carotenoid concentration determined by the RS and for the RRS system was achieved for human skin in vivo (R = 0.88) and for bovine udder skin in vitro (R = 0.81). (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Slc45a2 and V‐ATPase are regulators of melanosomal pH homeostasis in zebrafish,providing a mechanism for human pigment evolution and disease

We present here the positional cloning of the Danio rerio albino mutant and show that the affected gene encodes Slc45a2. The human orthologous gene has previously been shown to be involved in human skin color variation, and mutations therein have been implicated in the disease OCA4. Through ultrastructural analysis of the melanosomes in albino alleles as well as the tyrosinase‐deficient mutant sandy, we add new insights into the role of Slc45a2 in the production of melanin. To gain further understanding of the role of Slc45a2 and its possible interactions with other proteins involved in melanization, we further analyzed the role of the V‐ATPase as a melanosomal acidifier. We show that it is possible to rescue the melanization potential of the albino melanosomes through genetic and chemical inhibition of V‐ATPase, thereby increasing internal melanosome pH.     

Historical and non‐invasive samples: a study case of genotyping errors in newly isolated microsatellites for the lesser anteater (Tamandua tetradactyla L., Pilosa)

Tamandua tetradactyla (Pilosa), the lesser anteater, is a medium‐size mammal from South America. Its wide distribution through different landscapes, solitary and nocturnal habits, and the difficulty to capture and contain specimens limit the amount of individuals and populations sampled during fieldworks. These features along with the lack of specific molecular markers for the lesser anteater might be the causes for paucity in population genetic studies for the species. Historical samples from museum specimens, such as skins, and non‐invasive samples, such as plucked hair, can be supplementary sources of DNA samples. However, the DNA quantity and quality of these samples may be limiting factors in molecular studies. In this study, we describe nine microsatellite loci for T. tetradactyla and test the amplification success, data reliability and estimate errors on both historical and non‐invasive sample sets. We tested nine polymorphic microsatellites and applied the quality index approach to evaluate the relative performance in genotype analysis of 138 historical samples (study skin) and 19 non‐invasive samples (plucked hair). The observed results show a much superior DNA quality of non‐invasive over historical samples and support the quality index analysis as a practical tool to exclude samples with doubtful performance in genetic studies. We also found a relationship between the age of non‐invasive samples and DNA quality, but lack of evidence of this pattern for historical samples.