When data sharing gets close to 100%. What human paleogenetics can teach the open science movement

This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals’ editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers’ awareness of the importance of openness and transparency for scientific progress may complement stakeholders’ policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges

Detecting Genetic Isolation in Human Populations: A Study of European Language Minorities

The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a Bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four "linguistic islands" of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations. © 2013 Capocasa et al

Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman

The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps – putatively in genetic continuity with the Tyrolean Iceman—and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.This study was financed by the Provincia Autonoma di Bolzano – Alto Adige, Ripartizione Diritto allo studio, università e ricerca scientifica, funds to VCS

Functional diversity of the glutathione peroxidase gene family among human populations: implications for genetic predisposition to disease and drug response

To analyze the human genetic variation of glutathione peroxidases (GPX), estimating the functional differences among human populations and suggesting interethnic differences in predisposition to disease and drug response

A report of four different unusual 6-PGD electrotypes in Caucasian and Negro populations

Four different unusual 6-phosphogluconate dehydrogenase (6-PGD) electrophoretic patterns found among the Italian (Rome), Bamileke (Cameroon), and North Bateke and Babenga Pygmy (Congo) populations are described

Multiple Delayed Verbal Reactions (MDRV) as Vulnerability Indicators for Schizophrenia

Proceedings of the 9th International Multidisciplinary Conference «Stress and Behavior» Saint-Petersburg, Russia, 16–19 May 2005.Multiple Delayed Verbal Reactions (MDRV) methods allow us to identify early cerebral impairments in different phases of brain cognitive functions, such as pre-programming and programming, Working Memory task-independent and task-dependent processes, and transfer between perceptive and executive system and modulation of the final output. MDRV yields information on the two domains of brain function: 1) the processes involved in verbal processing, developing from the language cortical areas to the corresponding phasic motor system, and 2) the general processes of sensomotor integration, programming and attention that are task- independent. The neural substrate involved is the prefrontal network. The brain elementary function is represented by the Central Executive System of Working Memory and more specifically by the delayed reaction.MDRV method: the task stimuli consist of a monosyllable, a dysillabic word and a sentence, all with the same pronounciation, each presented on the screen of the monitor 12 times in random succession. The subject is asked to pronounce the word immediately with a loudspeaker placed near his mouth, while some pairs of surface electrodes record the EMG from oromandibular muscles. In a second series of reactions he is asked to answer only after 0.5–4 s interval has elapsed following the appearance of the task-stimulus; in that moment a go-signal (asterisks) appears on the screen. The main parameters studied were: 1) the latency time of the immediate reaction (tACG at FP = 0). The mean value of tACG at FP = 0 depends on: a) the functional state of the executive systems b) the programming, c) the timing processes. The difference tACG-tEMG as a cue of the relationship between preparatory and timing processes and the duration of ACG (D ACG) as a cue of the timing processes. A further, but not less significant parameter, is represented by the percentage of errors, particularly anticipation-errors. 2) The index of the effects of interfering stimuli. The IF-in, namely tACG at FP = 0.1/ t ACG at FP = 0 depends on lateral inhibition processes and on available cerebral associative channels. 3) The index of the latent learning occurring during the Temporal Bridging (TB) of delayed reactions (TB-in). TB indices, namely the ratios between tACG at FP = 0.5s, or tACG at FP = 1.5 s, or tACG at FP = 4 s as numerators, and tACG at FP = 0 at the denominator, reflect the course of facilitation processes associated with TB. We have examined 80 patients (30 males and 50 females) classified as schizophrenics according to the DSM III-R criteria and 40 normal patients for comparison: all s.p. were treated with atypical anti-psychotic drugs.Results. On the basis of the MDRV we divided the patients in 3 subgroups: 31 with TB-in >1 at FP 0.5 and 4s (paranoid schizophrenics), 16 with TB-in >1 at FP 1.5s (positive syndromes), 33 with TB-in >1 at FP 0.5, 1.5 and 4s (severe cases of disorganized schizophrenia). We have observed the most significance difference in paranoid schizophrenics vs. normal controls in TB-in at FP = 0.5 and at FP = 4s, with a trend to higher values in schizophrenics. We have found that positive syndromes with acute exacerbations shows the highest TB-in increase at FP = 1.5s in a range of 0.90 to 2.4. In severe cases of disorganized schizophrenia TB-in increased at all FPs with highest values at FP = 4s: 1.6 to 2.35.Discussion. A fundamental point inferred from the occurrence of TB-in inversion and impairment in both patients with frank symptoms of schizophrenia and relatives of schizophrenics without clinical symptoms of schizophrenia is that the impairment of WM and delayed reactions associated with a dorso-lateral prefrontal state independent hypoactivity, does not necessarily cause the dysfunctions that lead to the schizophrenic behavior. These prefrontal-dependent impairments could be hardly considered to reflect the cerebral dysfunction that actually produces dysphrenic alterations at the mental level, and dysexecution at the behavioral level. The schizophrenic disorder is in fact a heterogeneous and even the follow-up prognostic criterium of progressiveness adopted by Kraepelin for differentiating dementia praecox from manic-depressive psychosis, is under discussion. A general prefrontal dysfunction that is in itself latent at the level of the general cerebral performance ultimately responsible of the output seems to be a more likely interpretation. The picture in the twins is very interesting from the MDRV point of view because it shows another aspect of schizophrenia. Indeed, obsessive-compulsive symptoms in patients with schizophrenia occur in 8–10 % (Rosen, 1986), and the comorbidity totals 3–25 % (Ingram, 1961), in this case we have an abnormal acceleration in delayed reactions with an impairment of lateral inhibition detected in interfering-stimuli-reactions. These results are in agreement with those obtained by Park et al. (1995) on Working Memory, and Schreiber et al. (1998) on the P3 and N2 components of the Event-Related-Potentials, thus proving that TB-in inversion represent an index of vulnerability for schizophrenia