GHEP-ISFG collaborative exercise on mixture profiles of autosomal STRs (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03): results and evaluation

One of the main objectives of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the area of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, three exercises have been organized (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03), with 32, 24 and 17 participant laboratories respectively. The exercise aims to give a general vision by addressing, through the proposal of mock cases, aspects related to the edition of mixture profiles and the statistical treatment. The main conclusions obtained from these exercises may be summarized as follows. Firstly, the data show an increased tendency of the laboratories toward validation of DNA mixture profiles analysis following international recommendations (ISO/IEC 17025:2005). Secondly, the majority of discrepancies are mainly encountered in stutters positions (53.4%, 96.0% and 74.9%, respectively for the three editions). On the other hand, the results submitted reveal the importance of performing duplicate analysis by using different kits in order to reduce errors as much as possible. Regarding the statistical aspect (GHEP-MIX02 and 03), all participants employed the likelihood ratio (LR) parameter to evaluate the statistical compatibility and the formulas employed were quite similar. When the hypotheses to evaluate the LR value were locked by the coordinators (GHEP-MIX02) the results revealed a minor number of discrepancies that were mainly due to clerical reasons. However, the GHEP-MIX03 exercise allowed the participants to freely come up with their own hypotheses to calculate the LR value. In this situation the laboratories reported several options to explain the mock cases proposed and therefore significant differences between the final LR values were obtained. Complete information concerning the background of the criminal case is a critical aspect in order to select the adequate hypotheses to calculate the LR value. Although this should be a task for the judicial court to decide, it is important for the expert to account for the different possibilities and scenarios, and also offer this expertise to the judge. In addition, continuing education in the analysis and interpretation of mixture DNA profiles may also be a priority for the vast majority of forensic laboratories.Fil: Sala, Adriana Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Crespillo, M.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Barrio, P. A.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Luque, J. A.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Alves, Cíntia. Universidad de Porto; PortugalFil: Aler, M.. Servicio de Laboratorio. Sección de Genética Forense y Criminalística; EspañaFil: Alessandrini, F.. Università Politecnica delle Marche. Department of Biomedical Sciences and Public Health; ItaliaFil: Andrade, L.. Instituto Nacional de Medicina Legal e Ciências Forenses, Delegação do Centro. Serviço de Genética e Biologia Forenses; PortugalFil: Barretto, R. M.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Bofarull, A.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Costa, S.. Instituto Nacional de Medicina Legal y Ciencias Forenses; PortugalFil: García, M. A.. Servicio de Criminalística de la Guardia Civil. Laboratorio Central de Criminalística. Departamento de Biología; EspañaFil: García, O.. Basque Country Police. Forensic Genetics Section. Forensic Science Unit; EspañaFil: Gaviria, A.. Cruz Roja Ecuatoriana. Laboratorio de Genética Molecular; EcuadorFil: Gladys, A.. Corte Suprema de Justicia de la Nación; ArgentinaFil: Gorostiza, A.. Grupo Zeltia. Genomica S. A. U.. Laboratorio de Identificación Genética; EspañaFil: Hernández, A.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Herrera, M.. Laboratorio Genda S. A.; ArgentinaFil: Hombreiro, L.. Jefatura Superior de Policía de Galicia. Brigada de Policía Científica. Laboratorio Territorial de Biología – ADN; EspañaFil: Ibarra, A. A.. Universidad de Antioquia; ColombiaFil: Jiménez, M. J.. Policia de la Generalitat – Mossos d’Esquadra. Divisió de Policia Científica. Àrea Central de Criminalística. Unitat Central de Laboratori Biològic; EspañaFil: Luque, G. M.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Madero, P.. Centro de Análisis Genéticos; EspañaFil: Martínez Jarreta, B.. Universidad de Zaragoza; EspañaFil: Masciovecchio, M. Verónica. IACA Laboratorios; ArgentinaFil: Modesti, Nidia Maria. Provincia de Córdoba. Poder Judicial; ArgentinaFil: Moreno, F.. Servicio Médico Legal. Unidad de Genética Forense; ChileFil: Pagano, S.. Dirección Nacional de Policía Técnica. Laboratorio de Análisis de ADN para el CODIS; UruguayFil: Pedrosa, S.. Navarra de Servicios y Tecnologías S. A. U.; EspañaFil: Plaza, G.. Neodiagnostica S. L.; EspañaFil: Prat, E.. Comisaría General de Policía Científica. Laboratorio de ADN; EspañaFil: Puente, J.. Laboratorio de Genética Clínica S. L.; EspañaFil: Rendo, F.. Universidad del País Vasco; EspañaFil: Ribeiro, T.. Instituto Nacional de Medicina Legal e Ciências Forenses, Delegação Sul. Serviço de Genética e Biologia Forenses; PortugalFil: Santamaría, E.. Instituto Nacional de Toxicología y Ciencias Forenses; EspañaFil: Saragoni, V. G.. Servicio Médico Legal. Departamento de Laboratorios. Unidad de Genética Forense; ChileFil: Whittle, M. R.. Genomic Engenharia Molecular; Brasi

Holocene climate variability, vegetation dynamics and fire regime in the central Pyrenees: the Basa de la Mora sequence (NE Spain)

High resolution multiproxy data (pollen, sedimentology, geochemistry, chironomids and charcoal) from the Basa de la Mora (BSM) lake sequence (42° 32′ N, 0° 19′ E, 1914 m a.s.l.) show marked climate variability in the central southern Pyrenees throughout the Holocene. A robust age model based on 15 AMS radiocarbon dates underpins the first precise reconstruction of rapid climate changes during the Holocene from this area. During the Early Holocene, increased winter snowpack and high snowmelt during summer, as a consequence of high seasonality, led to higher lake levels, a chironomid community dominated by non-lacustrine taxa (Orthocladiinae) related to higher inlet streams, and a forested landscape with intense run-off processes in the watershed. From 9.8 to 8.1 cal ka BP, climate instability is inferred from rapid and intense forest shifts and high fluctuation in surface run-off. Shifts among conifers and mesophytes reveal at least four short-lived dry events at 9.7, 9.3, 8.8 and 8.3 cal ka BP. Between 8.1 and 5.7 cal ka BP a stable climate with higher precipitation favoured highest lake levels and forest expansion, with spread of mesophytes, withdrawal of conifers and intensification of fires, coinciding with the Holocene Climate Optimum. At 5.7 cal ka BP a major change leading to drier conditions contributed to a regional decline in mesophytes, expansion of pines and junipers, and a significant lake level drop. Despite drier conditions, fire activity dropped as consequence of biomass reduction. Two arid intervals occurred between 2.9 and 2.4 cal ka BP and at 1.2–0.7 cal ka BP (800–1300 AD). The latter coincides with the Medieval Climate Anomaly and is one of the most arid phases of the Holocene in BSM sequence. Anthropogenic disturbances were small until 700 AD, when human pressure over landscape intensified, with Olea cultivation in the lowlands and significant deforestation in highlands. Colder and unfavourable weather conditions during the second part of the Little Ice Age caused a temporary cease of high-land management. The most intense anthropogenic disturbances occurred during the second half of 19th century. Last decades are characterized by recovery of the vegetation cover as a result of land abandonment, and lowered lake levels, probably due to higher temperatures

Biomic Specialization and Speciation Rates in Ruminants (Cetartiodactyla, Mammalia): A Test of the Resource-Use Hypothesis at the Global Scale

The resource-use hypothesis proposed by E.S. Vrba predicts that specialist species have higher speciation and extinction rates than generalists because they are more susceptible to environmental changes and vicariance. In this work, we test some of the predictions derived from this hypothesis on the 197 extant and recently extinct species of Ruminantia (Cetartiodactyla, Mammalia) using the biomic specialization index (BSI) of each species, which is based on its distribution within different biomes. We ran 10000 Monte Carlo simulations of our data in order to get a null distribution of BSI values against which to contrast the observed data. Additionally, we drew on a supertree of the ruminants and a phylogenetic likelihood-based method (QuaSSE) for testing whether the degree of biomic specialization affects speciation rates in ruminant lineages. Our results are consistent with the predictions of the resource-use hypothesis, which foretells a higher speciation rate of lineages restricted to a single biome (BSI = 1) and higher frequency of specialist species in biomes that underwent high degree of contraction and fragmentation during climatic cycles. Bovids and deer present differential specialization across biomes; cervids show higher specialization in biomes with a marked hydric seasonality (tropical deciduous woodlands and schlerophyllous woodlands), while bovids present higher specialization in a greater variety of biomes. This might be the result of divergent physiological constraints as well as a different biogeographic and evolutionary history

Tempo and mode in the influence of global climatic changes on mammalian evolution

Comunicación presentada en: XVIII INQUA Congress, 21st–27th July, 2011, Bern, Switzerland.Due to their extraordinary fossil record during the Cenozoic, mammals are a key factor in order to understand how global climatic changes have shaped biotic evolution, especially in continental environments. During the last decades, climatic influence on the evolution of mammal faunas has been reflected mainly in two sets of studies. First, there are works focused in the use of observed variations in the structure of mammalian palaeocommunities through extensive time sequences in order to detect significant palaeoclimatic changes. These studies are based in the concepts of community convergence and uniformitarism, and make use of modern ecological analogues to infer the climatic conditions in which the extinct faunas lived. On the other hand, when data on faunal change through time are confronted with independent data on palaeoclimatic changes it may be statistically inferred whether there has been simultaneous occurrence of climatic changes, faunal turnover and modifications in the ecological structure of the palaeofaunas. The second set of studies is based on the statistical analysis of ecological data from modern faunas. Extant assemblages reflect in their ecological characteristics the past influence of global climate changes on the evolution of mammalian lineages living today, both in geographical and cladal basis. Finally, there are new works based on the study of the phylogenetic signal that can be found in modern clades, which are able to identify periods of enhanced or reduced cladogenesis. Although all these approaches cannot be used simultaneously because of latent problems derived of circular reasoning, the development of methodological protocols for the combined analysis of their results has the potential to shed new light on the question of how and when climate changes affect evolution of biotic communities.The authors also thank the Unit of Information Resources for Research (URICI-CSIC) for the co-financing of this publication in Open Access.Peer reviewe

Clinical characteristics of patients with central nervous system relapse in BCR-ABL1-positive acute lymphoblastic leukemia : the importance of characterizing ABL1 mutations in cerebrospinal fluid

We investigated the frequency, predictors, and evolution of acute lymphoblastic leukemia (ALL) in patients with CNS relapse and introduced a novel method for studying BCR-ABL1 protein variants in cDNA from bone marrow (BM) and cerebrospinal fluid (CSF) blast cells. A total of 128 patients were analyzed in two PETHEMA clinical trials. All achieved complete remission after imatinib treatment. Of these, 30 (23%) experienced a relapse after achieving complete remission, and 13 (10%) had an isolated CNS relapse or combined CNS and BM relapses. We compared the characteristics of patients with and without CNS relapse and further analyzed CSF and BM samples from two of the 13 patients with CNS relapse. In both patients, classical sequencing analysis of the kinase domain of BCR-ABL1 from the cDNA of CSF blasts revealed the pathogenic variant p.L387M. We also performed ultra-deep next-generation sequencing (NGS) in three samples from one of the relapsed patients. We did not find the mutation in the BM sample, but we did find it in CSF blasts with 45% of reads at the time of relapse. These data demonstrate the feasibility of detecting BCR-ABL1 mutations in CSF blasts by NGS and highlight the importance of monitoring clonal evolution over time

Ecological correlates of ghost lineages in ruminants

Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation.The authors also thank the Unit of Information Resources for Research (URICI-CSIC) for the co-financing of this publication in Open Access.Peer reviewe

CAREGIVERSPRO-MMD project: Customization Guidance Document - First Version

This deliverable is the first version of the Customisation Guidance Document (D2.2) which present activities and progress made on gamification (T2.2), personalisation (T2.4) and interface adaptation (T2.5) of the CAREGIVERSPRO-MMD platform

Macroevolution and climate changes: a global multi-family test supports the resource-use hypothesis in terrestrial mammals

Elisabeth S. Vrba’s resource-use hypothesis suggests that speciation in biomes subjected to successive expansion-contraction-fragmentation during periods of climatic change generates high frequency of species restricted to a single biome (stenobiomic species). We compiled biome occupation for all terrestrial mammals and, using Monte Carlo simulations, demonstrated that patterns of biome occupation are congruent with those predicted by the resource-use hypothesis. Biome specialists are much more speciose than expected by chance, while there are fewer moderate biome generalists than expected. Despite their scarcity, extreme eurybiomic lineages show significant overrepresentation, which suggests they are seldom affected by climate-related extinction processes. Additionally, stenobiomic species are concentrated in biomes placed at the extremes of the climatic gradient, such as equatorial rainforest, subtropical desert, steppe, and tundra. Although this pattern is fairly maintained across different mammalian families, highlighting its universality, our analysis also found great variability. Exceptions to the predictions of the resource-use hypothesis seem to be associated to biome climatic or geographical heterogeneity, which favours vicariance in some biomes not placed in extremes of the climatic gradient (tropical deciduous woodland, sclerophyllous woodland-shrubland), as well as life-history differences across taxa, which generates a stronger trend to specialisation in small body size lineages than in larger mammals