Paolo Anagnostou, Marco Capocasa, Francesca Brisighelli, Cinzia Battaggia, Giovanni Destro Bisol
In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the "intelligent data openness" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.
近几十年来,科学界已经意识到科学有效开放对于加快科技进步的重要性。在此背景下,实现稳健、有效和负责任的数据共享形式已被广泛视为研究过程的基本组成部分。近年来,人类基因组数据的生产和分辨率稳步提高,这主要是由于技术进步以及 DNA 基因分型和测序成本的降低。然而,由于数据和相关元数据的复杂性大幅增加,这一过程也存在弊端。这意味着我们应该超越只关注数据可用性的传统共享分析形式。在此,我们介绍一项试点研究,该研究旨在通过对可查找性、可访问性、可使用性和可评估性(根据 "智能数据开放性 "计划)的分析,对同行评议出版物相关数据的可用性调查进行补充。结果发现,基因组人类学的共享率(73.0%)高于人类基因组学(32.4%),但低于密切相关的研究领域(古遗传学和进化遗传学的共享率分别为 96.8% 和 79.2%)。我们讨论了可能与这一发现有关的隐私和方法问题。对众多学科共享率的比较表明,人类基因组学作为开放数据运动先驱的观点应该受到质疑。最后,在基因组人类学和人类基因组学中,可查找性和可使用性都符合对智能数据开放的期望,而只有一小部分研究满足了使数据完全可评估的需求。
{"title":"The emerging complexity of Open Science: assessing Intelligent Data Openness in Genomic Anthropology and Human Genomics.","authors":"Paolo Anagnostou, Marco Capocasa, Francesca Brisighelli, Cinzia Battaggia, Giovanni Destro Bisol","doi":"10.4436/JASS.99016","DOIUrl":"10.4436/JASS.99016","url":null,"abstract":"<p><p>In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the \"intelligent data openness\" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.</p>","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"135-152"},"PeriodicalIF":1.8,"publicationDate":"2021-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39761580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carlos A Palancar, Daniel García-Martínez, David Cáceres-Monllor, Bernardo Perea-Pérez, Maria Teresa Ferreira, Markus Bastir
This study aims to carry out the first geometric morphometric analysis of the 3D size and shape of the full series of cervical vertebrae delving into variability related to sex and population background. For this reason, we analyzed the cervical vertebrae of both males and females belonging to Europeans, Africans, and Greenland Inuit. We 3D-scanned a total of 219 cervical vertebrae of males and females of three different modern human populations (European, African, and Inuit). A minimum of 72 landmarks and curve semilandmarks were positioned in each of the 3D vertebral models. Landmark configurations were analyzed following the standards of 3D Geometric Morphometrics to test for size and shape differences related to sex or population variation. Results show that male cervical vertebrae are consistently larger than in females while no regular shape differences are observed between males and females in any of the populations. Sex differences in cervical lordosis are thus not supported at the skeletal level of the 3D shape. On the other hand, there is no evidence for population-specific differences in size while shape does vary considerably, possibly also in relation to eco-geographic factors of overall trunk shape. Cervical vertebrae in cold-adapted Inuit were consistently shorter than in Europeans and Africans. The cervical spine may show a different pattern than the thoracic and lumbar spine, which might be related to stronger integration with the cranium, head mobility, and soft-tissue dependence. Our findings suggest that morpho-functional interpretations of the cervical spine based on vertebral skeletal morphology requires caution.
{"title":"Geometric Morphometrics of the human cervical vertebrae: sexual and population variations.","authors":"Carlos A Palancar, Daniel García-Martínez, David Cáceres-Monllor, Bernardo Perea-Pérez, Maria Teresa Ferreira, Markus Bastir","doi":"10.4436/JASS.99015","DOIUrl":"10.4436/JASS.99015","url":null,"abstract":"<p><p>This study aims to carry out the first geometric morphometric analysis of the 3D size and shape of the full series of cervical vertebrae delving into variability related to sex and population background. For this reason, we analyzed the cervical vertebrae of both males and females belonging to Europeans, Africans, and Greenland Inuit. We 3D-scanned a total of 219 cervical vertebrae of males and females of three different modern human populations (European, African, and Inuit). A minimum of 72 landmarks and curve semilandmarks were positioned in each of the 3D vertebral models. Landmark configurations were analyzed following the standards of 3D Geometric Morphometrics to test for size and shape differences related to sex or population variation. Results show that male cervical vertebrae are consistently larger than in females while no regular shape differences are observed between males and females in any of the populations. Sex differences in cervical lordosis are thus not supported at the skeletal level of the 3D shape. On the other hand, there is no evidence for population-specific differences in size while shape does vary considerably, possibly also in relation to eco-geographic factors of overall trunk shape. Cervical vertebrae in cold-adapted Inuit were consistently shorter than in Europeans and Africans. The cervical spine may show a different pattern than the thoracic and lumbar spine, which might be related to stronger integration with the cranium, head mobility, and soft-tissue dependence. Our findings suggest that morpho-functional interpretations of the cervical spine based on vertebral skeletal morphology requires caution.</p>","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"97-116"},"PeriodicalIF":1.8,"publicationDate":"2021-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39826040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Margherita Micheletti Cremasco, Giuseppe D'Amore, Vitale Stefano Sparacello, Margherita Mussi, Manon Galland, Antonio Profico, Melchiorre Masali, Sylvia Di Marco, Roberto Micciché, Martin Friess, Luca Sineo
In two publications from 1967 and 1971, M. Masali described human skeletal remains presumed to have been found in the Balzi Rossi caves (Ventimiglia, Italy), based on a signed note dated to 1908. Since then, the remains - dubbed "Conio's Finds" and preserved at the University of Torino - had not been further studied. We performed a multidisciplinary investigation aimed at clarifying the geographical and chronological attribution of these specimens. Collagen extraction for AMS dating was unsuccessful, but we obtained two direct dates on the best- preserved crania via 231Pa/235U direct gamma-ray spectrometry (10,500±2,000 years BP and 12,500±2,500 years BP). We analyzed the metrics and morphology of the crania and femora by comparing them with samples belonging to the Upper Paleolithic, Mesolithic, and Neolithic periods, and evidenced that the "Conio's Finds" are morphologically more compatible with a Late Pleistocene rather than Holocene attribution. We analyzed the literature regarding the history of excavations at Balzi Rossi, and we propose that - if any credence should be given to the note accompanying the material - the remains may have been found in front of Grotta dei Fanciulli or Grotta del Caviglione, in the redeposited soil dug up during the installation of lime kilns carried out between the late 18th and the early 19th centuries. These hypotheses may be tested in the future by comparing the speleothem deposited on one of the crania and the remaining deposit at the site.
{"title":"Multi-proxy analysis suggests Late Pleistocene affinities of human skeletal remains attributed to Balzi Rossi.","authors":"Margherita Micheletti Cremasco, Giuseppe D'Amore, Vitale Stefano Sparacello, Margherita Mussi, Manon Galland, Antonio Profico, Melchiorre Masali, Sylvia Di Marco, Roberto Micciché, Martin Friess, Luca Sineo","doi":"10.4436/JASS.99014","DOIUrl":"10.4436/JASS.99014","url":null,"abstract":"<p><p>In two publications from 1967 and 1971, M. Masali described human skeletal remains presumed to have been found in the Balzi Rossi caves (Ventimiglia, Italy), based on a signed note dated to 1908. Since then, the remains - dubbed \"Conio's Finds\" and preserved at the University of Torino - had not been further studied. We performed a multidisciplinary investigation aimed at clarifying the geographical and chronological attribution of these specimens. Collagen extraction for AMS dating was unsuccessful, but we obtained two direct dates on the best- preserved crania via 231Pa/235U direct gamma-ray spectrometry (10,500±2,000 years BP and 12,500±2,500 years BP). We analyzed the metrics and morphology of the crania and femora by comparing them with samples belonging to the Upper Paleolithic, Mesolithic, and Neolithic periods, and evidenced that the \"Conio's Finds\" are morphologically more compatible with a Late Pleistocene rather than Holocene attribution. We analyzed the literature regarding the history of excavations at Balzi Rossi, and we propose that - if any credence should be given to the note accompanying the material - the remains may have been found in front of Grotta dei Fanciulli or Grotta del Caviglione, in the redeposited soil dug up during the installation of lime kilns carried out between the late 18th and the early 19th centuries. These hypotheses may be tested in the future by comparing the speleothem deposited on one of the crania and the remaining deposit at the site.</p>","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"19-60"},"PeriodicalIF":1.8,"publicationDate":"2021-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39715747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Next questions in Molecular Anthropology.","authors":"Luca Pagani, Giovanni Destro Bisol","doi":"10.4436/JASS.99013","DOIUrl":"10.4436/JASS.99013","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"157-158"},"PeriodicalIF":1.8,"publicationDate":"2021-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39539909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biobank-scale datasets and their relevance to anthropology/popgen.","authors":"Francesco Montinaro","doi":"10.4436/JASS.99012","DOIUrl":"10.4436/JASS.99012","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"159-161"},"PeriodicalIF":1.8,"publicationDate":"2021-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39488015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Methodological challenges and opportunities for inferring human demography.","authors":"Garrett Hellenthal","doi":"10.4436/JASS.99010","DOIUrl":"10.4436/JASS.99010","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"175-177"},"PeriodicalIF":1.8,"publicationDate":"2021-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39481756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"From domestication genomics towards molecular ecology of human environments.","authors":"Anders Bergström","doi":"10.4436/JASS.99007","DOIUrl":"10.4436/JASS.99007","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"163-166"},"PeriodicalIF":1.8,"publicationDate":"2021-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39481755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Complexity in human ancestral demography.","authors":"Aylwyn Scally","doi":"10.4436/JASS.99009","DOIUrl":"10.4436/JASS.99009","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"179-182"},"PeriodicalIF":1.8,"publicationDate":"2021-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39481758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular Anthropology is dead, long live Molecular Anthropology.","authors":"Austin W Reynolds, Brenna M Henn","doi":"10.4436/JASS.99008","DOIUrl":"10.4436/JASS.99008","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"187-190"},"PeriodicalIF":1.8,"publicationDate":"2021-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39481757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Ancient Health Landscape: foundations and perspectives.","authors":"Christiana L Scheib","doi":"10.4436/JASS.99011","DOIUrl":"10.4436/JASS.99011","url":null,"abstract":"","PeriodicalId":48668,"journal":{"name":"Journal of Anthropological Sciences","volume":"99 ","pages":"167-170"},"PeriodicalIF":1.8,"publicationDate":"2021-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39481759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"社会学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}