Genealogical inferences based on comparison of modern and ancient DNA

The study of genetic variation within and between populations can help us understand aspects of human demographic history over the past thousands of years, i.e. well beyond the timescales of historical evidence. Demographic and evolutionary dynamics influence the distribution of the observed genetic diversity, and so one can retrospectively reconstruct episodes in population history on the basis of genetic diversity data. One way to do this is to make extensive use of simulations, considering evolution as a stochastic process in which the genetic data are modeled as random variables. The simulation of genetic data under various scenarios allows one to explore how demographic and evolutionary parameters can affect genetic variation, also making it possible to approximately estimate the historical parameters that produced the observed data. To this aim, many statistical approaches have been developed, but, when models are complex or datasets are large, they often become computationally expensive, or analytically intractable. Approximate Bayesian Computation (ABC) methods overcome these problems allowing, for the first time, to analyze large datasets and to interpret them in the light of realistic (i.e. complex) models, thus enabling the probabilistic comparison among different models of evolution, the simultaneous estimation of demographic and evolutionary parameters, and the quantitative evaluation of the results credibility. In this context, we analyzed datasets of modern and ancient genetic variation in order to understand the demographic histories of these populations, to highlight traces of past genetic variation in modern populations, and to evaluate whether, and to what extent, ancient and modern populations that have lived in the same place in different period of times can be considered genealogically related. We tried to address three anthropological questions, namely the interaction of anatomically modern humans with archaic forms (i.e. Neandertals in Europe), evidence for genealogical continuity in Sardinia since the Bronze-age, and the origins and evolution of the Etruscan population. Within the ABC framework, in each of the three studies, we explicitly compared several models, differing for the demographic processes and the genealogical relationship among population, to identify the model best accounting for the observed variation, and to estimate its demographic and evolutionary parameters. This way, it has been possible to shed light on past population history and to address questions about the nature and the extent of genealogical links between modern and ancient populations, clarifying aspects of human history that have long been controversial in population genetics and evolutionary biology

Genomic Evidence for an African Expansion of Anatomically Modern Humans by a Southern Route

There is general agreement among scientists about a recent (less than 200,000 yrs ago) African origin of anatomically modern humans, whereas there is still uncertainty about whether, and to what extent, they admixed with archaic populations, which thus may have contributed to the modern populations’ gene pools. Data on cranial morphology have been interpreted as suggesting that, before the main expansion from Africa through the Near East, anatomically modern humans may also have taken a Southern route from the Horn of Africa through the Arabian peninsula to India, Melanesia and Australia, about 100,000 yrs ago. This view was recently supported by archaeological findings demonstrating human presence in Eastern Arabia 90,000 yrs ago. In this study we analyzed genetic variation at 111,197 nuclear SNPs in nine populations (Kurumba, Chenchu, Kamsali, Madiga, Mala, Irula, Dalit, Chinese, Japanese), chosen because their genealogical relationships are expected to differ under the alternative models of expansion (single vs. multiple dispersals). We calculated correlations between genomic distances, and geographic distances estimated under the alternative assumptions of a single dispersal, or multiple dispersals, and found a significantly stronger association for the multiple dispersal model. If confirmed, this result would cast doubts on the possibility that some non-African populations (i.e., those whose ancestors expanded through the Southern route) may have had any contacts with Neandertals

Y chromosomal evidence on the origin of northern Thai people.

The Khon Mueang represent the major group of people present in today's northern Thailand. While linguistic and genetic data seem to support a shared ancestry between Khon Mueang and other Tai-Kadai speaking people, the possibility of an admixed origin with contribution from local Mon-Khmer population could not be ruled out. Previous studies conducted on northern Thai people did not provide a definitive answer and, in addition, have largely overlooked the distribution of paternal lineages in the area. In this work we aim to provide a comprehensive analysis of Y paternal lineages in northern Thailand and to explicitly model the origin of the Khon Mueang population. We obtained and analysed new Y chromosomal haplogroup data from more than 500 northern Thai individuals including Khon Mueang, Mon-Khmer and Tai-Kadai. We also explicitly simulated different demographic scenarios, developed to explain the Khon Mueang origin, employing an ABC simulation framework on both mitochondrial and Y microsatellites data. Our results highlighted a similar haplogroup composition of Khon Mueang and Tai-Kadai populations in northern Thailand, with shared high frequencies of haplogroups O-PK4, O-M117 and O-M111. Our ABC simulations also favoured a model in which the ancestors of modern Khon Mueang originated recently after a split from the other Tai-Kadai populations. Our different analyses concluded that the ancestors of Khon Mueang are likely to have originated from the same source of the other Tai-Kadai groups in southern China, with subsequent admixture events involving native Mon-Khmer speakers restricted to some specific populations

Health professionals learning qualitative research in their workplace: a focused ethnography

Background The interest for qualitative research methodology has expanded beyond theoretical academic research on medical education, gathering interest from all healthcare professionals. Qualitative research has potentials in exploring the social, emotional, psychological aspects of care and in broadening professionals\u2019 scientific competencies. Nonetheless, qualitative research has still not been embraced within formal and academic curricula for future professionals, preventing newer generations from appreciating the value of its epistemological and methodological aspects and from using it in the development and implementation of clinical research. The purpose of this study was to comprehend the attitudes of health professionals learning and conducting qualitative studies within a practical training program developed in their workplace. Methods The present work consisted of a focused ethnography, including 14 professionals during their one-year attendance training on qualitative research methodology. Strategies used for collecting data included participant observations, field notes, semi-structured interviews, and a focus group. All the data were analyzed consistently with ethnographic indications. Results Analyses allowed us to evidence the educational, motivational, group-related and organizational factors influencing the attitudes and skill acquisition of healthcare professionals learning and conducting qualitative research within a practical training program developed in their workplace. Prior educational background was perceived as a sort of barrier. Nonetheless, the training boosted a change in attitude both in terms of appreciation of the research approach and trainees\u2019 emotional involvement with research participants. Doing a qualitative study in a multidisciplinary team raised in-group dynamics that hindered bringing the studies to conclusion. Trainees repeatedly lamented the difficulty in managing time to devote to research-related activities and questioned the feasibility of adopting this methodology for conducting research in their workplace. Conclusions Continual education training on the methodological aspects and practical implications of qualitative research may foster a renewed attitude towards one\u2019s professional education, while making inter-professional relationship issues emerge. Nonetheless, broadening the perspectives of professionals on their clinical practice by means of learning qualitative methodology may have an evident quality improvement return. Strategies for future qualitative research methodology hands-on training addressed to health professionals in continuing education are proposed

\u201cI go into crisis when \u2026\u201d: ethics of care and moral dilemmas in palliative care

Background: Recognising and knowing how to manage ethical issues and moral dilemmas can be considered an ethical skill. In this study, ethics of care is used as a theoretical framework and as a regulatory criterion in the relationship among healthcare professionals, patients with palliative care needs and family members. This study is a part of a larger project aimed at developing and implementing a training programme on \u201cethical communication\u201d addressed to professionals caring for patients with palliative care needs. The aim of this study was comprehending whether and how the ethics of care informs the way healthcare professionals make sense of and handle ethical issues in palliative care. Methods: Qualitative study employing a theoretically driven thematic analysis performed on semi-structured interviews. The research was conducted in a clinical cancer centre in northern Italy. Eligible participants were physicians and nurses from eleven hospital wards who assisted patients with chronic advanced disease daily and had previously attended a 4-h training on palliative care held by the hospital Palliative Care Unit. Results: The researchers identified five themes: morality is providing global care; morality is knowing how to have a relationship with patients; morality is recognizing moral principles; moral dimension and communication; and moral dilemmas are individual conflicts. Conclusions: Ethics of care seems to emerge as a theoretical framework that includes the belief systems of healthcare professionals, especially those assisting patients with palliative care needs; moreover, it allows the values of both the patients and professionals to come to light through the relationship of care. Ethics of care is also appropriate as a framework for ethical training

Undergoing head and neck cancer surgery: A grounded theory

Surgery is the treatment of choice in most head and neck cancers. Very often, the surgery is radical with high impact on the psychosocial, functional and aesthetic fields. The aim of this study is to gain a deeper understanding of the patient's, clinician's and key informant's point of view when surgery is proposed, to improve the quality of pathways in terms of patients' practical, psychological and relational needs. We followed a Grounded Theory approach with semi-structured interviews. Seventeen participants (six patients, nine healthcare professionals and two volunteers) were interviewed immediately before surgery. The study generated a process of "persuading the patient of an obligation" as the core category. The other principal categories that emerged highlighted the patients' doubts and fears regarding the surgery consequences and, in parallel, strategies employed by the healthcare professionals to rebut hindering issues impeding surgery. In particular, healthcare professionals involved patients in an affiliation process through simplified communication to sustain the choice of surgery; the family plays a supportive role in this process. The interplay between the organisational process and patients' experience results in "I will let you convince me" at the end of the decision-making process, where the main aim was to save and be saved

Palliative care training addressed to hospital healthcare professionals by palliative care specialists: a mixed-method evaluation

Despite the great advances in the concept of palliative care (PC) and its benefits, its application seems to be delayed, leaving unfulfilled the many needs of patients and family members. One way to overcome this difficulty could be to develop a new training programme by palliative care specialists to improve PC primary skills in healthcare professionals. The aim of this study was to evaluate the training's impact on trainees within a hospital setting using Kirkpatrick's and Moore's models

Formal linguistics as a cue to demographic history

Beyond its theoretical success, the development of molecular genetics has brought about the possibility of extraordinary progress in the study of classification and in the inference of the evolutionary history of many species and populations. A major step forward was represented by the availability of extremely large sets of molecular data suited to quantitative and computational treatments. In this paper, we argue that even in cognitive sciences, purely theoretical progress in a discipline such as linguistics may have analogous impact. Thus, exactly on the model of molecular biology, we propose to unify two traditionally unrelated lines of linguistic investigation: 1) the formal study of syntactic variation (parameter theory) in the biolinguistic program 2) the reconstruction of relatedness among languages (phylogenetic taxonomy) The results of our linguistic analysis have thus been plotted against data from population genetics and the correlations have turned out to be largely significant: given a non-trivial set of languages/populations, the description of their variation provided by the comparison of systematic parametric analysis and molecular anthropology informatively recapitulates their history and relationships. As a result, we can claim that the reality of some parametric model of the language faculty and language acquisition/transmission (more broadly of generative grammar) receives strong and original support from its historical heuristic power. Then, on these grounds, we can begin testing Darwin's prediction that, when properly generated, the trees of human populations and of their languages should eventually turn out to be significantly parallel

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes

Helicobacter pylori's historical journey through Siberia and the Americas.

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait