Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas

Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.This work was partially supported by grant AAEE246/2014 from the Direcció General de R + D + I (Comu-nitat Autònoma de les Illes Balears) and European Regional Development Fund (ERDF) and FCT, Portuguese Foundation for Science and Tecnology PTDC/ATP-DEM/4545/2012 project financed by European Social Funds (COMPETE-FEDER). We are grateful to Maria Trinidad Garcia (from the Serveis Cientificotècnics of the Uni-versitat de les Illes Balears) for her assistance and help with capillary electrophoresis procedures, María Luz Gómez-Barbeito for her help in mtDNA sequencing and Meryl Wyn Jones for the English language corrections. We would also like to sincerely thank all the people who volunteered to participate in this study

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

Background and AimsArchipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands.MethodsUsing allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale.Key ResultsGenetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure.ConclusionsOur results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands

Evolutionary history of Podarcis tiliguerta on Corsica and Sardinia.

BACKGROUND: Podarcis tiliguerta is a wall lizard endemic to the Mediterranean islands of Corsica and Sardinia. Previous findings of high mtDNA and morphological diversity have led to the suggestion that it may represent a species complex. Here, we analysed mitochondrial and nuclear markers (mtDNA, 3110 bp; 6 nDNA loci, 3961 bp) in P. tiliguerta sampled from thirty-two localities across Corsica and Sardinia. RESULTS: We find much greater intraspecific genetic divergence than between sister species of other Mediterranean island Podarcis, i.e., between P. lilfordi and P. pityusensis. We detected three mtDNA clusters in Corsica (North, South-East and South-West) and either two or three in Sardinia (North vs. South) depending on the clustering method. Only one or two nDNA groups were identified within each main island (again, depending on the method). A Bayesian time-calibrated multispecies coalescent tree was obtained from mtDNA and provided statistical support for a Miocene origin of the species (13.87 Ma, 95% HPD: 18.30-10.77 Ma). The posterior mean divergence time for the Corsican and Sardinian lineages was 12.75 Ma ago (95% HPD: 16.94-9.04 Ma). CONCLUSION: The results support the evolutionary distinctiveness of Corsican and Sardinian populations and also indicate a lack of post-divergence migration despite periods of contact being possible. Further to this, species delimitation analyses of Corsican and Sardinian lineages provided statistical support for their recognition as distinct (sister) taxa. Our results provide new insights into the biogeography of the Mediterranean biodiversity hotspot, and contribute important findings relevant to the systematics and evolution of this speciose lizard genus

Ancient crops provide first archaeological signature of the westward Austronesian expansion

The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island's early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa

Morphological and genetic diversity of the Balearic lizard,Podarcis lilfordi(Gunther, 1874): Is it relevant to its conservation?

Aims: To characterize the genetic and morphological diversification of the endangered Balearic lizard Podarcis lilfordi and to assess the relevance of this diversity, and how it is described, to conservation measures. Location: This study covers all the populations of the Balearic lizard, Podarcis lilfordi, present in its range of distribution at coastal islets of Menorca, Mallorca and Cabrera Archipelago. Methods: We analysed genetic and morphological variation across the 43 known extant populations of the Balearic lizard, using mitochondrial and nuclear markers. We examined morphometric and scalation characters using, in some cases, phylogenetically independent contrasts. We also incorporated the study of dorsal coloration and dorsal colour pattern including the analysis of melanism in several populations. Results: We detected clear genetic divergence between Menorcan populations and populations from Mallorca and Cabrera, in both nuclear and mtDNA markers, but genetic divergence is relatively low among different insular populations within these groups. In contrast, morphological divergence was substantial both between Menorcan and remaining populations and within these groups. Morphological traits, such as dorsal coloration, body size and the number and size of scales, seemed to be linked with differences in climatic conditions between populations. In addition, some traits, as melanism, showed a strong phylogenetic signal. Main conclusions: The morphological and genetic diversity of the Balearic lizard is incongruent with the subspecies described in the classical taxonomic literature. Moreover, current populations differ not only in some genetic and morphological features, but also in several ecological and ethological characteristics, in many cases unique to one population. Based on our results, we propose abandoning the use of subspecies to describe the extraordinary morphological diversity of the Balearic lizard and its replacement with the concept of evolutionary significant units (ESUs). ESUs are particularly suitable to describe and recognize such diversity and, especially, to ensure the continuity of the evolutionary process

Iterative variable selection for high-dimensional data: prediction of pathological response in triple-negative breast cancer

In the last decade, regularized regression methods have offered alternatives forperforming multi-marker analysis and feature selection in a whole genome context.The process of defining a list of genes that will characterize an expressionprofile, remains unclear. This procedure oscillates between selecting the genes or transcripts of interest based on previous clinical evidence, or performing a whole transcriptome analys is that rests on advanced statistics. This paper introduces a methodology to deal with the variable selection and model estimation problems in the high-dimensional set-up, which can be particularly useful in the whole genome context. Results are validated using simulated data, and a real dataset from a triple negative breast cancer study

Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard

Genomic divergence was studied in 10 small insular populations of the endangered Balearic Islands lizard (Podarcis lilfordi) using double digest restriction-site associated DNA sequencing. The objectives were to establish levels of divergence among populations, investigate the impact of population size on genetic variability and to evaluate the role of different environmental factors on local adaptation. Analyses of 72,846 SNPs supported a highly differentiated genetic structure, being the populations with the lowest population size (Porros, Foradada and Esclatasang islets) the most divergent, indicative of greater genetic drift. Outlier tests identified ~ 2% of loci as candidates for selection. Genomic divergence-Enviroment Association analyses were performed using redundancy analyses based on SNPs putatively under selection, detecting predation and human pressure as the environmental variables with the greatest explanatory power. Geographical distributions of populations and environmental factors appear to be fundamental drivers of divergence. These results support the combined role of genetic drift and divergent selection in shaping the genetic structure of these endemic island lizard populations

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

[Background]: Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular.[Results]: The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80.[Conclusions]: In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.M.M was supported by two research grants from Ministry of Economy and Competitiveness ISCIII-FIS grants (PI 12/02684): “Predictores genómicos de respuesta a la quimioterapia neoadyuvante con docetaxel-carboplatino en pacientes con cáncer de mama triple negativo”/“Genomic predictors of response to neoadjuvant chemotherapy with docetaxel-carboplatin in patients with triple negative breast cancer”; and (PI 15/00117): “Cáncer de mama triple negative: Predicción de respuesta a docetaxel-carboplatino neoadyuvante mediante caracterización de TILs y firmas inmunes basadas en secuenciación masiva de RNA”/” Triple negative breast cancer: Prediction of response to neoadjuvant docetaxel-carboplatin by characterization of TILs and immune signatures based on massive RNA sequencing”. C.M.P was supported by funds from the NCI Breast SPORE program (P50-CA58223).Peer reviewe

A composite approach to produce reference datasets for extratropical cyclone tracks: application to Mediterranean cyclones

Many cyclone detection and tracking methods (CDTMs) have been developed in the past to study the climatology of extratropical cyclones. However, all CDTMs have different approaches in defining and tracking cyclone centers. This naturally leads to cyclone track climatologies with inconsistent physical characteristics. More than that, it is typical for CDTMs to produce a non-negligible number of tracks of weak atmospheric features, which do not correspond to large-scale or mesoscale vortices and can differ significantly between CDTMs. Lack of consensus in CDTM outputs and the inclusion of significant numbers of uncertain tracks therein have long prohibited the production of a commonly accepted reference dataset of extratropical cyclone tracks. Such a dataset could allow comparable results on the analysis of storm track climatologies and could also contribute to the evaluation and improvement of CDTMs. To cover this gap, we present a new methodological approach that combines overlapping tracks from different CDTMs and produces composite tracks that concentrate the agreement of more than one CDTM. In this study we apply this methodology to the outputs of 10 well-established CDTMs which were originally applied to ERA5 reanalysis in the 42-year period of 1979-2020. We tested the sensitivity of our results to the spatiotemporal criteria that identify overlapping cyclone tracks, and for benchmarking reasons, we produced five reference datasets of subjectively tracked cyclones. Results show that climatological numbers of composite tracks are substantially lower than the ones of individual CDTMs, while benchmarking scores remain high (i.e., counting the number of subjectively tracked cyclones captured by the composite tracks). Our results show that composite tracks tend to describe more intense and longer-lasting cyclones with more distinguished early, mature and decay stages than the cyclone tracks produced by individual CDTMs. Ranking the composite tracks according to their confidence level (defined by the number of contributing CDTMs), it is shown that the higher the confidence level, the more intense and long-lasting cyclones are produced. Given the advantage of our methodology in producing cyclone tracks with physically meaningful and distinctive life stages, we propose composite tracks as reference datasets for climatological research in the Mediterranean. The Supplement provides the composite Mediterranean tracks for all confidence levels, and in the conclusion we discuss their adequate use for scientific research and applications