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The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here, we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (

[eng] Mercury is a strong neurotoxin. It has adverse effects on the nervous and cardiovascular systems, it is also deleterious for several organs, and may act as immunotoxic and hormonal disruptor. This compound is released to the environment by several processes which have generated a widespread contamination throughout the whole planet. However, because of the physical-chemical properties of this metal, semi-volatility and water insolubility, the sink of most of it are the sediments of water bodies, namely marine and lacustrine systems. Bacterial processes transform mercury into methylmercury which is much more deleterious for the organisms and human beings. Methylmercury enters into the food chain and accumulates in fish and from fish into humans. Fish consumption is the main source of mercury for the general population. The Mediterranean Sea is a hot spot of mercury pollution, but the origin of this metal has not been elucidated. The present PhD dissertation is devoted assessing what is the origin of this metal and which human pollution burden is involved in fish consumption. To assess the impact of a chlor-alkali plant on a confined environment, fish, sediment and a mammal were collected downstream from the location of a chlor-alkali plant that used a technology that directly releases mercury. Mercury and other metals were examined in the area surrounding the Ebro River and in the marine area located near the mouth of this river. The study has shown that the effects of metal contamination are visible nearby the industrial complex, downriver and in the fish of the Mediterranean area located nearby the Ebro mouth, more than 110 kilometres downriver. This study has also allowed to characterize the specific mercury isotopic composition of chlor-alkali plants. Subsequently, the study of the fish devoted to human consumption in L’Ampolla, Ametlla de Mar, Alacant, Mallorca, Menorca, Eivissa, Marseille, Genoa, Civitavecchia and Alghero has allowed the contribution characterization of the atmospheric deposition plus the background level and chlor-alkali plants in the fish from Western Mediterranean. The inputs from the chlor-alkali plants represented about 63-100% of total mercury while the inputs from background + atmospheric fallout ranged between 0% and 37%. The study of 1345 specimens of commercial value sold for human consumption in the above- mentioned locations allowed the characterization of the mercury concentrations in 58 species of lean and cartilaginous fish. 316 samples (23.5% of the total) showed Hg concentrations above the EU recommended limits for human consumption, 0.5 mg kg-1 wet weight (ww) or 1 mg kg-1 ww. The extrapolation of the mercury concentrations observed in Mediterranean fish to the tolerable provisional weekly intakes of methylmercury showed intakes above the thresholds recommended by EFSA for the three countries where the fish was collected, 152%, 151% and 144% for the populations of Spain, France and Italy, respectively. Comparison of the mercury content in the different species allowed to define one group of twelve species whose specimens always fulfilled the EU recommended values for human consumption: sardine, anchovie, squid, surmullet, painted comber, blackspot seabream, blue whiting, salema, brown meagre, picarel, pearly razorfish and common dolphinfish. On the contrary, the species showing a high percentage of individuals not fulfilling the EU recommendations were dusky grouper, european barracuda, common dentex, norway lobster, greater forkbeard, common seabream, porbeagle and thornback ray., [spa] El mercurio es un contaminante potente que se libera tanto a partir de fuentes industriales como naturales. Se encuentra en todas partes pero tiende a acumularse en los sistemas acuáticos debido a sus propiedades fisicoquímicas. La fuente principal de mercurio en los seres humanos es el consumo de pescado y marisco. La ingesta de dicho metal da lugar a efectos adversos a nivel neuronal, endocrino e inmunológico. Este contaminante es particularmente abundante en los organismos marinos del Mediterráneo occidental, desconociendose las causas que han dado lugar a las concentraciones elevadas y su distribución en dicha cuenca marina. Por ello, en la presente memoria de tesis se ha tomado esta cuenca como referencia y se ha investigado cuál es el origen y distribución de dicho contaminante y su posible acumulación en humanos mediante los temas siguientes: • descripción de la distribución de mercurio y su acumulación en sedimentos y organismos de un ambiente fluvial altamente contaminado por las emisiones de una planta cloro-álcali que utilizaba tecnología de mercurio en el cátodo. • composición isotópica del mercurio en diferentes tipos de muestras contaminadas por emisiones de plantas de cloro-álcali. • rastreo de la extensión geográfica de la contaminación utilizando las composiciones de los isótopos de mercurio de las diversas muestras contaminadas. • rastreo del origen del mercurio en muestras de pescado en el Mediterráneo occidental utilizando la composición isotópica del mercurio, discriminando entre diferentes fuentes y, específicamente, entre los aportes de plantas cloro-álcali, la deposición atmosférica y otras contribuciones. • desarrollo de un método para estimar la contribución de mercurio de diferentes fuentes. • descripción de la cantidad total de mercurio en el pescado del Mediterráneo occidental. • cálculo de las estimaciones de la ingesta semanal provisional tolerable de metilmercurio en las poblaciones de España, Francia e Italia. Estas estimaciones proporcionarán información preliminar para una evaluación futura de los riesgos para la salud asociados al consumo de pescado local. • evaluación de qué especies de peces comestibles en el mar Mediterráneo representan un riesgo o no para el consumo humano debido al mercurio. • identificación de las especies que tienen un nivel alto de mercurio en una región mediterránea específica., [ita] Il mercurio è un potente inquinante rilasciato sia da fonti industriali che naturali. Si trova ovunque, ma tende ad accumularsi nei sistemi acquatici a causa delle sue proprietà fisico-chimiche. La fonte primaria di mercurio nell'uomo è il consumo di pesce e frutti di mare. La maggiore preoccupazione per l'assorbimento del mercurio è dovuta agli effetti neuronali, endocrini e immunologici avversi che provoca. Nonostante le informazioni disponibili in letteratura, è necessario colmare diverse lacune in termini di valutazione dell'entità degli effetti di questo neuroinquinante, di previsione del contributo delle sorgenti che lo rilasciano e di considerazione della situazione del mercurio in un contesto come quello occidentale Mediterraneo perché si trova in grande abbondanza. Quindi in questa dissertazione si è cercato di colmare queste lacune trattando diverse tematiche che, nella fattispecie, sono: • la descrizione della distribuzione e l’estensione del mercurio in un ambiente altamente contaminato a causa del rilascio di questo inquinante da un impianto di produzione di cloro- alcali che utilizza una tecnologia a rilascio di mercurio. • la composizione isotopica del mercurio in diversi tipi di campioni contaminati dalle emissioni di impianti cloro-alcali. • il tracciamento dell'estensione geografica della contaminazione utilizzando le firme degli isotopi di mercurio dei diversi esemplari contaminati. • Il tracciamento dell'origine del mercurio in campioni di pesce nel Mar Mediterraneo occidentale utilizzando la composizione isotopica del mercurio, discriminando tra fonti diverse e, nello specifico, tra input di impianti cloro-alcalini e deposizione atmosferica più background. • lo sviluppo di un metodo per la stima del contributo del mercurio da diverse fonti. • la descrizione del quantitativo complessivo di mercurio nei pesci del Mediterraneo occidentale. • il calcolo delle stime di assunzione settimanale provvisoria tollerabile di metilmercurio nelle popolazioni di Spagna, Francia e Italia. Queste stime forniscono informazioni preliminari per una futura valutazione dei rischi per la salute associati al consumo locale di pesce. • la valutazione di specie ittiche edibili del Mar Mediterraneo che possono essere rischiose o sicure per il consumo umano. • identificare le specie che hanno un alto livello di mercurio in una specifica regione.

Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

Additional file 8: Supplementary Note 1. Relationship between mtDNA sequencing, coverage and genome size.

Additional file 12. Review history.

78 pages, 10 figures, 20 tables, Fem aquí un balanç dels darrers quaranta anys d'ús, en molts casos abús, dels recursos naturals a Catalunya, un país representatiu dels països europeus, en especial dels mediterranis. [...]

Figure S9. Female perspective (mtDNA) of the main migratory events between Beringia/Asia and North America. (PDF 342 kb)

Figure S2. Detailed version of the most parsimonious (MP) tree represented in Fig. 1 and estimated ages of the identified sub-haplogroups. Notes: The length of each branch is not proportional to its age estimate. For each branch, the name of the defining marker(s) and the number of mutations are reported. Markers in italics are outside the sequenced fragments and the relative branches are dotted. Nomenclature in blue colour is according to Jota et al. [25] while names in parentheses are according to Poznik et al. [29]. (a) Sample information in Additional file 1: Table S1. (PDF 962 kb)

Figure S3. Phylogeography of the branches Q-Y1150, Q-M378 and Q-F1096 (panels a, b and c, respectively). Each panel illustrates the phylogenetic relationships of the markers (in different colours) investigated per each branch and their pattern of frequency distribution (complete list of samples in Additional file 8: Table S6). Circles without any number refer to one subject. Larger circles refer to the number of specified subjects. Stars highlighted by a grey shading refer to ancient samples: (1) [74], (2) [75], (3) [76], (4) [28]; their relative dating, when available, is also reported in italics. Dates reported below branches refer to Bayesian estimates of node ages. (PDF 1420 kb)

Figure S1. Geographic origin of the subjects included in the phylogenetic analysis and listed in Additional file 1: Table S1. Circles and squares indicate modern samples from this study and from the literature, respectively. Stars indicate ancient samples: a-Kennewick; b-Anzick-1; c-Saqqaq. Colours identify different geographic macro-areas. When more than one subject is from the same area, the number of subjects is reported inside the symbol. (PDF 2653 kb)

Local breeds represent an important and often unique pool of endangered sources of genetic variability, particularly when confined to an isolated geographic area. The Maltese breed of cattle is considered to be of ancient origin. Late Pleistocene Oxen skeletal remains and Neolithic representations of primitive cattle have been suggested as proof of a possible local domestication. The objective of the present study is to explore the current mitochondrial DNA (mtDNA) diversity of this breed in order to reconstruct its maternal origins and to identify any residual genetic variants to be preserved. A mtDNA control-region analysis performed on the entire Maltese cattle population identified only two different mtDNAs (out of a total amount of 19 samples), one encompasses about 90% of the current population and confirms a strong founder effect on the mitochondrial gene pool; the remaining 10% seems to testify for the importation of British cattle, documented in historical records since 1809. The complete mtDNA has defined two novel clades T3c and T3d, both dated to ~9.5 thousand years ago, encompassing the Maltese breed and only a few other breeds of Northern European ancestry. This new piece of information does not support the hypothesis of a local domestication in Malta since the Maltese cattle mtDNAs are nested within the known domestic founding lineage T3, but confirms a strong maternal influence from Northern Europe rather than from the African coastline., N/A

Table S5. Goat haplogroup frequencies based on modern and ancient control-region mtDNA data from this study and downloaded from GenBanka. Table S6. Diagnostic mutational motifs of goat mtDNA haplogroups and sub-haplogroups. Table S7. A comparison of the phylogeographic features of goat, taurine and horse mtDNA haplogroups identified by analyzing domestic breeds from Eurasia. Table S8. Oligonucleotides used to amplify and to sequence (Sanger method) the goat mitochondrial genome. (PDF 652Â kb)

Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithic transition and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidence points to demic and cultural influences between Southern Italians and the Balkans, starting with the initial Palaeolithic occupation until historical and modern times. To shed light on the dynamics of these contacts, we analysed a genome-wide SNP dataset of more than 700 individuals from the South Mediterranean area (102 from Southern Italy), combined with ancient DNA from neighbouring areas. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with the presence of a Bronze Age component ultimately originating from the Caucasus and characterised by high frequencies of Iranian and Anatolian Neolithic ancestries. Furthermore, to reveal possible signals of natural selection, we looked for extremely differentiated allele frequencies among Northern and Southern Italy, uncovering putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits, such as ALDH2, NID1 and CBLB.