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Understanding the main drivers of species distributions is one of the main goals of ecology. However, the relationships between traits and elevational and longitudinal distributions in inland fishes, as well as their underlying evolutionary processes, have been less investigated. Thus, we aimed to quantify and assess the relationships among several types of traits resulting from species’ evolutionary histories by measuring their phylogenetic signal across inland fishes of the Iberian Peninsula. We also aimed to test for correlated evolution of these traits with elevation and stream size (i.e. stream order), to test whether a species’ suite of traits and their elevational and longitudinal niche tend to evolve together. We compiled data on 23 fish biological and ecological traits for 30 inland fish species present in the Iberian Peninsula. We quantified their phylogenetic signal using four complementary indices (Pagel’s λ, Blomberg’s K, and Abouheif’s Cmean for continuous and −D + 1 for binary traits). We used both phylogenetic and non-phylogenetic methods to evaluate the relationship among traits and their relationship with elevation and stream order. We found a significant phylogenetic signal for 65% of the studied traits. Phylogenetic signals were quite variable, but we did not detect clear differences between continuous and binary traits or among trait types (i.e. morphological, trophic, reproductive, and habitat use). Evolutionary models revealed that elevational and longitudinal distribution showed little evidence for directional trends of evolution. Hence, species elevational and longitudinal niches tend to resemble to those of the common ancestor. Many fish traits were inter-correlated as revealed by phylogenetic methods, indicating correlated evolution of pairs of traits. For example, reproductive traits such as maximum longevity, fecundity and age at maturity tended to evolve together with fish maximum length. Consequently, certain orders of fish showed shared suites of traits. Comparative methods revealed a significant positive relationship of parental care with elevation and stream order. By contrast, non-phylogenetic analyses and multivariate analyses indicated positive relationships between elevation and rheophily and lithophily, and a negative relationship between stream order and invertivory and rheophily. Overall, our results point to a notable phylogenetic signal in many traits of inland fishes and a strong phylogenetic structure in their functional traits along their elevational and longitudinal gradients. Thereby, our results contribute to an improved understanding of species’ adaptations to environmental changes with important conceptual and practical implications for minimising further species losses This research was financially supported by the Spanish Ministry of Science and Innovation (project CGL2016-80820-R). Further funding support was provided by the 2015-2016 BiodivERsA COFUND call and the Spanish Ministry of Science (projects: ODYSSEUS, BiodivERsA3-2015-26, PCIN-2016-168; PID2019-103936GB-C21; and RED2018-102571-T) and the Government of Catalonia (ref. 2017 SGR 548). CCB benefitted from a pre-doctoral fellowship of the Spanish Ministry of Science (ref. BES-2017-081999). The EDB laboratory was supported by ‘Investissement d’Avenir’ Grants (CEBA, ref. ANR-10-LABX-0025; TULIP, ref. ANR-10-LABX-41) Open Access funding provided thanks to the CRUE-CSIC agreement with Wiley

Galeaspids are extinct jawless relatives of living jawed vertebrates whose contribution to understanding the evolutionary assembly of the gnathostome bodyplan has been limited by absence of postcranial remains. Here, we describe Foxaspis novemura gen. et sp. nov., based on complete articulated remains from a newly discovered Konservat-Lagerstätte in the Early Devonian (Pragian, ∼410 Ma) of Guangxi, South China. F. novemura had a broad, circular dorso-ventrally compressed headshield, slender trunk and strongly asymmetrical hypochordal tail fin comprised of nine ray-like scale-covered digitations. This tail morphology contrasts with the symmetrical hypochordal tail fin of Tujiaaspis vividus, evidencing disparity in galeaspid postcranial anatomy. Analysis of swimming speed reveals galeaspids as moderately fast swimmers, capable of achieving greater cruising swimming speeds than their more derived jawless and jawed relatives. Our analyses reject the hypothesis of a driven trend towards increasingly active food acquisition which has been invoked to characterize early vertebrate evolution.

Biozones are routinely used for chronological purposes, but their nature is seldomly questioned. Here, we attempt to find the evolutionary-ecological basis for Iberian rodent biozones for the interval 8.5–2 Ma based on currently available paleontological, stratigraphic and paleoclimatic information. Our comparison of biozone boundary age uncertainty intervals to records of marine SST, δ18O and δ13C, terrestrial hydrological proxies and astronomical parameters suggests an orbitally forced climatic origin for the majority of biozones. Zone boundary ages during the late Miocene are mostly associated with humidity changes during 1.2-Myr obliquity nodes and 405-kyr eccentricity minima. Tectonics and strong regional cooling may additionally explain faunal change during the Messinian (7–5 Ma). A partly reversed pattern characterizes most Pliocene zone boundaries, which are mostly associated with wetter conditions during obliquity nodes and 405-kyr eccentricity maxima. A third configuration culminates in the early Pleistocene and consists of the combination of strong obliquity amplitude maxima and 2.4-Myr eccentricity minima. It is suggested that larger-scale, European Neogene mammal (MN) units have an astronomical basis as well, with an important role of 2.4-Myr eccentricity cycle and the 1.2-Myr obliquity cycle, with the latter becoming especially important after the mid-Miocene cooling (∼14 Ma). Whereas rodent events on the Iberian Peninsula during the late Miocene are shaped by replacements within resident communities dominated by dry-adapted clades of true mice (Murinae) and hamsters (Cricetinae), transitions during the cooler Pliocene involve invasions of newly emerging Eurasian clades of ‘microtoid hamsters’ and voles (Arvicolinae) preferring wetter and cooler environments. A new model of stepwise clade displacement is proposed in which the combination of long-period Milankovitch cycles and gradual long-term climatic change allows for the periodic functioning of migration corridors, along which increasingly pervasive dispersal events by members of new clades cause the gradual extinction of old clades.

Un dels aspectes més importants en biologia de la conservació és anticipar fins a quin punt les espècies es podran adaptar amb prou rapidesa als canvis que s'estan produint en el clima, deguts, en bona part o en la seva totalitat, a l'activitat humana. Per ser consistents, aquestes adaptacions han de comportar canvis evolutius permanents que tinguin una base genètica. ¿Amb quina rapidesa estan evolucionant les poblacions naturals de mamífers i d'ocells? Aquesta és la pregunta que s'han plantejat el biòleg Timothée Bonnet i els seus col·laboradors, una quarantena de científiques i científics de més d'una vintena d'universitats i centres de recerca d'arreu del món. La conclusió a què han arribat, que s'acaba de publicar a la revista Science, és que la taxa d'evolució adaptativa de les espècies analitzades és gairebé el doble de la que fins ara s'havia pressuposat, però tanmateix pot no ser suficient per garantir la seva supervivència en els hàbitats que ocupen actualment.

Ribosomal DNA (rDNA) is the genetic loci that encodes rRNA in eukaryotes. It is typically arranged as tandem repeats that vary in copy number within the same species. We have recently shown that rDNA repeats copy number in the yeast Saccharomyces cerevisiae is controlled by cell volume via a feedback circuit that senses cell volume by means of the concentration of the free upstream activator factor (UAF). The UAF strongly binds the rDNA gene promoter, but is also able to repress SIR2 deacetylase gene transcription that, in turn, represses rDNA amplification. In this way, the cells with a smaller DNA copy number than what is optimal evolve to increase that copy number until they reach a number that sequestrates free UAF and provokes SIR2 derepression that, in turn, blocks rDNA amplification. Here we propose a mathematical model to show that this evolutionary process can amplify rDNA repeats independently of the selective advantage of yeast cells having bigger or smaller rDNA copy numbers. We test several variants of this process and show that it can explain the observed experimental results independently of natural selection. These results predict that an autoregulated feedback circuit may, in some instances, drive to non Darwinian deterministic evolution for a limited time period., This work was supported by a grant from MCIN/AEI/10.13039/501100011033 (grant number PID2020-112853GB-C31 to J.E.P-O).

La nostra història és fascinant. No em refereixo només a la trajectòria vital de cadascú, perquè totes ho són. Ni tampoc als fets històrics que ens han conduït on som, el coneixent dels quals és indispensable per gestionar el futur col·lectiu. Em vull referir a una història encara més antiga, la que compartim com a espècie, que sens dubte ens agermana a tots. La història evolutiva de l'espècie humana és llarga i enrevessada, amb molts protagonistes que, com diu el poema que encapçala aquest escrit, no tornaran mai, però llurs vides van donar el seu fruit en nosaltres. Des de parents llunyans que van viure fa sis o set milions d'anys fins a l'Homo sapiens modern, passant pels australopitecs, els Homo habilis, els Homo erectus, els Homo heidelbergensis, els Homo neanderthalensis...

13 pages, extended data, supplementary information https://doi.org/10.1038/s41559-022-01838-4, The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life, Open access funding provided by Uppsala University. [...] Marine sampling was supported by the Spanish Ministry of Economy, Competitiveness projects Malaspina-2010 (CSD2008–00077) and ALLFLAGS (CTM2016-75083-R). [...] With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

The ecological context of early vertebrate evolution is envisaged as a long-term trend towards increasingly active food acquisition and enhanced locomotory capabilities culminating in the emergence of jawed vertebrates. However, support for this hypothesis has been anecdotal and drawn almost exclusively from the ecology of living taxa, despite knowledge of extinct phylogenetic intermediates that can inform our understanding of this formative episode. Here we analyse the evolution of swimming speed in early vertebrates based on caudal fin morphology using ancestral state reconstruction and evolutionary model fitting. We predict the lowest and highest ancestral swimming speeds in jawed vertebrates and microsquamous jawless vertebrates, respectively, and find complex patterns of swimming speed evolution with no support for a trend towards more active lifestyles in the lineage leading to jawed groups. Our results challenge the hypothesis of an escalation of Palaeozoic marine ecosystems and shed light into the factors that determined the disparate palaeobiogeographic patterns of microsquamous versus macrosquamous armoured Palaeozoic jawless vertebrates. Ultimately, our results offer a new enriched perspective on the ecological context that underpinned the assembly of vertebrate and gnathostome body plans, supporting a more complex scenario characterized by diverse evolutionary locomotory capabilities reflecting their equally diverse ecologies.

The evolution of grouping behaviour involves a complex trade-off of benefits and costs. Among the latter, an increase in the risk of parasitic transmission is a well-documented phenomenon that has likely promoted the evolution of defensive mechanisms in aquatic vertebrates. Here, we explore the relationship between grouping behaviour, parasitic richness (∼parasitic pressure), and the evolution of potential defensive traits in the squamation of sharks through phylogenetic, standard and zero-inflation regression models. Our results demonstrate that sharks that frequently aggregate show increased parasitic pressure, which may constitute an agent of selection. Accordingly, their squamation is characterized by large-scale crown insertion angles and low-scale coverage, which are interpreted as traits that compromise parasite attachment and survival. These traits are less evident in regions of the body and ecological groups that are subjected to high abrasive stress or increased drag. Thus, the squamation of sharks responds to a compromise between various functions, where protective and hydrodynamic roles prevail over the rest (e.g. ectoparasitic defence and bioluminescence aiding). This work establishes a quantitative framework for inferring parasitic pressure and social interaction from squamation traits and provides an empirical basis from which to explore these phenomena through early vertebrate and chondrichthyan evolution.

Placoderms are an extinct group of early jawed vertebrates that play a key role in understanding the evolution of the gnathostome body plan, including the origin of novelties such as jaws, teeth, and pelvic fins. As placoderms have a poorly ossified axial skeleton, preservation of the mainly cartilaginous axial and fin elements is extremely rare, contrary to the heavily mineralized bones of the skull and thoracic armor. Therefore, the gross anatomy of the animals and body shape is only known from a few taxa, and reconstructions of the swimming function and ecology are speculative. Here, we describe articulated specimens preserving skull roofs, shoulder girdles, most fins, and body outlines of a newly derived arthrodire. Specimens of the selenosteid Amazichthys trinajsticae gen. et sp. nov. display a skull roof with reticular ornamentation and raised sensory lines like Driscollaspis, a median dorsal plate with a unique sharp posterior depression, the pelvic girdle, the proportions and shape of the pectoral, dorsal, and caudal fins as well as a laterally enlarged region resembling the lateral keel of a few modern sharks and bony fishes. Our new phylogenetic analyses support the monophyly of the selenosteid family and place the new genus in a clade with Melanosteus, Enseosteus, Walterosteus, and Draconichthys. The shape of its body and heterocercal caudal fin in combination with the pronounced 'lateral keel' suggest Amazichthys trinajsticae was an active macropelagic swimmer capable of reaching high swimming speeds.

Els ocells sempre han estat objecte d'admiració i estudi. Les descripcions més antigues que es coneixen sobre la vida i les característiques dels ocells possiblement són les que recullen els Vedes hindús, de fa uns 3.500 anys. Aristòtil també va dedicar alguns escrits a analitzar diversos aspectes del comportament dels ocells, com ara les migracions i la manera com incuben els ous, i totes les cultures els han representat en les seves obres d'art.

Genomic data allowed for a detailed resolution of the tree of life. Yet, tricky nodes such as the root of the animal, plants, eukaryotes, bacterial and archaeal trees remain unresolved. Genomic datasets are heterogeneous as genes and species evolve under different selective pressures, impending the efficacy of evolutionary analyses. Amino acid recodings were developed to reduce heterogeneity, but clear evidence to justify their use is missing. We use simulated genomic-scale datasets and show that recodings can substantially improve phylogenetic accuracy when tackling tricky nodes. We apply our findings to address the root of the animal tree where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) branched out first. We show that results from real data follow predictions from simulated data and indicate that a placement of the ctenophores as the first branching animal lineage is most likely artifactual.

Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metallothionein (MT) proteins in O. dioica. MTs are a heterogeneous group of modular proteins defined by their cysteine (C)-rich domains, which confer the capacity of coordinating different transition metal ions. O. dioica has two MTs, a bi-modular OdiMT1 consisting of two domains (t-12C and 12C), and a multi-modular OdiMT2 with six t-12C/12C repeats. By means of mass spectrometry and spectroscopy of metal-protein complexes, we have shown that the 12C domain is able to autonomously bind four divalent metal ions, although the t-12C/12C pair –as it is found in OdiMT1– is the optimized unit for divalent metal binding. We have also shown a direct relationship between the number of the t-12C/12C repeats and the metal-binding capacity of the MTs, which means a stepwise mode of functional and structural evolution for OdiMT2. Finally, after analyzing four different O. dioica populations worldwide distributed, we have detected several OdiMT2 variants with changes in their number of t-12C/12C domain repeats. This finding reveals that the number of repeats fluctuates between current O. dioica populations, which provides a new perspective on the evolution of domain repeat proteins.

Reproducció del document publicat a: https://theconversation.com/la-evolucion-es-un-hecho-tan-indiscutible-como-que-la-tierra-no-es-plana-162135, Nos ha sorprendido leer un artículo donde un conocido escritor niega la evolución biológica, ignorando la evidencia científica. No es nuestra intención antagonizar con dicho autor ni discutir uno por uno los muchos errores que contiene su texto

Metallothioneins (MTs) are proteins devoted to the control of metal homeostasis and detoxification, and therefore, MTs have been crucial for the adaptation of the living beings to variable situations of metal bioavailability. The evolution of MTs is, however, not yet fully understood, and to provide new insights into it, we have investigated the MTs in the diverse classes of Mollusks. We have shown that most molluskan MTs are bimodular proteins that combine six domains—α, β1, β2, β3, γ, and δ—in a lineage-specific manner. We have functionally characterized the Neritimorpha β3β1 and the Patellogastropoda γβ1 MTs, demonstrating the metal-binding capacity of the new γ domain. Our results have revealed a modular organization of mollusk MT, whose evolution has been impacted by duplication, loss, and de novo emergence of domains. MTs represent a paradigmatic example of modular evolution probably driven by the structural and functional requirements of metal binding.

Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000-944 000), points toward an island colonization during the Günz-Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals., For technical support, we thank the research service facilities of IJC and IGTP, the Crystallization Facility of the Max Planck Institute of Biochemistry, the ICTS NMR facility from the Scientific and Technological Centres of the University of Barcelona and Biophysics Core Facility of BMC-LMU. I.G. was a fellow of the Marie Skłodowska Curie Training network ‘ChroMe’ (H2020-MSCA-ITN-2015-675610, awarded to M.B. and A.G.L.). The project was further supported by national grants (nos. RTI2018-094005-B-I00 and BFU2015-66559-P from FEDER/Ministerio de Ciencia e Innovación—Agencia Estatal de Investigación to M.B.). Research in the participating labs was further supported by the following grants: the Marie Skłodowska Curie Training network ‘INTERCEPT-MDS’ no. H2020-MSCA-ITN-2020-953407 (to M.B.), MINECO-ISCIII no. PIE16/00011 (to M.B.); the Deutsche José Carreras Leukämie Stiftung DJCLS (no. 14R/2018 to M.B.), AGAUR (no. 2017-SGR-305 to M.B.), Fundació La Marató de TV3 (no. 257/C/2019 to M.B.), German Research Foundation Project (ID 213249687—SFB 1064 and Project ID 325871075—SFB 1309 to A.G.L.), the Spanish Ministry of Science (PID2019-110183RB-C21 to A.R.M.), Community of Madrid (P2018/BAA-4343-ALIBIRD2020-CM to A.R.M), Ramón Areces Foundation (to A.R.M.), National Science Foundation (EF-1921402 to J.M.E.L.), 2015 International Doctoral Fellowship La Caixa-Severo Ochoa (to M.F.V.), Marie Skłodowska-Curie Individual Fellowship (no. 747789 to M.M.L.), Juan de la Cierva-Incorporación (IJC2018-036657-I to M.M.L., ERC-2012-CoG-616960 to I.R.T.), MINECO (BFU2017-90114-P to I.R.T.), AGAUR (2017-SGR-324 to X.S.) and MINECO (BIO2015-70092-R and ERC-2014-CoG-648201 to X.S.). Research at the IJC is supported by the ‘La Caixa’ Foundation, Fundació Internacional Josep Carreras, Celgene Spain and the CERCA Programme/Generalitat de Catalunya.

L'evolució dels animals ha fascinat investigadors de molts camps des que Charles Darwin va proposar la teoria de la selecció natural. En un dels passatges del seu llibre parla de la importància del desenvolupament embrionari per a l'evolució, perquè durant aquest període es formen les estructures dels organismes adults. El que no va poder explicar era de quina manera es produeixen els canvis sobre els quals actua la selecció natural. Ara sabem que el material genètic conté les instruccions perquè els organismes es formin, per la qual cosa els canvis o mutacions en el DNA són la font de les innovacions evolutives. De manera intuïtiva pot semblar que els organismes complexos han de tenir més gens. Actualment se sap que la complexitat no depèn tant del nombre de gens com de la manera com se'n regula el funcionament. El que poques persones sospitarien és que, de vegades, la pèrdua de gens pot implicar un increment de complexitat evolutiva. Això és el que han demostrat Cristian Cañestro i els seus col·laboradors, del grup de recerca en evolució i desenvolupament (Evo-Devo) de la Universitat de Barcelona. Han descobert que una sèrie de pèrdues gèniques sobtades va alliberar un grup d'animals sèssils, que vivien enganxats al fons marí, d'aquesta dependència, i van esdevenir organismes de vida lliure. Segons afirmen a l'article que la revista Nature ha destacat a la portada, aquest fet ha introduït un tomb important en la visió evolutiva que fins ara es tenia de l'origen del nostre llinatge, i al mateix temps ha obert la porta a noves recerques biomèdiques.

La infancia constituye el periodo más prolongado y sensible en la vida de los seres humanos. En los principios de nuestra especie, la supervivencia de los recién nacidos y de los niños estuvo íntimamente ligada a las habilidades de sus progenitores y de su pequeño grupo social para garantizar su seguridad. Que los niños sobrevivieran y llegaran a la adolescencia para poder transmitir los genes de sus padres a una nueva generación, era una cuestión esencial para la continuidad de la especie. Resulta sencillo pensar, por tanto, hasta qué punto los vínculos afectivos y las habilidades para desarrollar estrategias de protección por parte de los adultos hacia sus niños fueron seleccionadas por la evolución como funciones mentales humanas esenciales y características de nuestra especie.

Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.

10 pages, 5 figures, supporting information https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2020955118/-/DCSupplemental.-- Data Availability: DNA sequences and metadata from the Malaspina expedition are publicly available at the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena; accession numbers PRJEB23913 (66) [18S rRNA genes] and PRJEB25224 (68) [16S rRNA genes]). DNA sequences from Tara Oceans are also stored at ENA with the accession numbers PRJEB6603 (76) for the SAGs, PRJEB6609 (101) for the metatranscriptomes, and PRJEB4352 (100) for the metagenomes (reference Datasets S1 and S4). Genome coassemblies, coding sequence predictions, and amino acid predictions have been deposited in FigShare (DOI: 10.6084/m9.figshare.13072322) (89). All other study data are included in the article and/or supporting information, Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs, F.L. was supported by the Spanish National Program Formación de Personal Investigador 2016 (BES-2016-076317, Ministerio de Ciencia e Innovación, Spain). R.L. was supported by a Ramón y Cajal fellowship (RYC-2013-12554, Ministerio de Economía y Empresa, Spain). This work was supported by the projects INTERACTOMICS (Unveiling Core Ecological Interactions in Marine Microbial Communities Using Omics Approaches) (CTM2015-69936-P, MINECO, Spain, to R.L.), MicroEcoSystems (240904, Research Council of Norway, to R.L.), and MINIME (Microbial Evolution and Population Genomics in a Changing Ocean) (PID2019-105775RB-I00, Agencia Estatal de Investigación Spain, to R.L.). I.M.D. and A.L. were supported by the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie Grant Agreement No. 675752 (SINGEK [Promoting Single Cell Genomics to Explore the Ecology and Evolution of Hidden Microeukaryotes]: http://www.singek.eu). We thank the Consejo Superior de Investigaciones Científicas (CSIC) Open Access Publication Support Initiative through the Unit of Information Resources for Research for helping to cover publication fees, With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Summary The evolutionary assembly of the vertebrate bodyplan has been characterized as a long-term ecological trend toward increasingly active and predatory lifestyles, culminating in jawed vertebrates that dominate modern vertebrate biodiversity [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 ]. This contrast is no more stark than between the earliest jawed vertebrates and their immediate relatives, the extinct jawless, dermal armor-encased osteostracans, which have conventionally been interpreted as benthic mud-grubbers with poor swimming capabilities and low maneuverability [ 9 , 10 , 11 , 12 ]. Using computational fluid dynamics, we show that osteostracan headshield morphology is compatible with a diversity of hydrodynamic efficiencies including passive control of water flow around the body; these could have increased versatility for adopting diverse locomotor strategies. Hydrodynamic performance varies with morphology, proximity to the substrate, and angle of attack (inclination). Morphotypes with dorsoventrally oblate headshields are hydrodynamically more efficient when swimming close to the substrate, whereas those with dorsoventrally more prolate headshields exhibit maximum hydrodynamic efficiency when swimming free from substrate effects. These results suggest different hydrofoil functions among osteostracan headshield morphologies, compatible with ecological diversification and undermining the traditional view that jawless stem-gnathostomes were ecologically constrained [ 9 , 10 , 11 , 12 ] with the origin of jaws as the key innovation that precipitated the ecological diversification of the group [ 13 , 14 ].

L'Evo-Devo, o Evolució del Desenvolupament, és una disciplina formalment nascuda el 1994. No obstant, ja en Darwin creia que l'Embriologia Comparada, i la semblança entre embrions eren claus per determinar parentius evolutius, malgrat els adults fossin molt diferents. No obstant, el Segle XX va viure el divorci entre l'Evo (pels seus descendents directes, els genetistes) i la Devo. No va ser fins els anys 80 del segle passat, amb el descobriment dels gens del desenvolupament, que es va produir la reconciliació, en donar-se compte que els gens del desenvolupament estaven molt conservats en organismes molt diferents. Desprès d'un època dorada d'anar descobrint més i més gens conservats, va sorgir la nova pregunta, la del Segle XXI: si estan tant conservats, cóm es que un cuc, una mosca, o nosaltres mateixos, som tant diferents? Aquesta és la gran pregunta de l'Evo-Devo actual, resposta només parcialment, i per a exemples molt concrets, com l'absència d'extremitats a les serps, l'evolució dels becs dels pinsans, o hipòtesis molt generals sobre l'origen dels vertebrats, o dels mamífers euteris. Subtils canvis en regions reguladores, petits canvis en el procés de maduració del RNA, fenòmens poc entesos com el RNA editing.... tots ells, en el fons, el que provoquen son petits canvis en xarxes gèniques reguladores, fent-les diferents, més complexes, asincròniques.... en altres paraules, 'jugant' amb la caixa d'eines del desenvolupament, que és comú a tot o quasi tots el Regne Animal. Jugueteix que sovint s'esmenta amb la paraula 'tinkering'. Un capítol apart, del que en parlarem, i més en aquest 2020, són les troballes Evo-Devo en un dels grups de mamífers més estès i de més èxit evolutiu, els ratpenats.

Development requires an increment of cell growth and cell number, concomitant to a tightly control of cell differentiation. Thanks to cell communication, cells can be spatiotemporal patterned to acquire the required fate. Planarians are a unique model to study developmental processes due to their ability to regenerate and modulate their body size according to the nutrient availability. This body plasticity is based on the presence of pluripotent adult stem cells (neoblasts) and the continuous activation of the intercellular communication mechanisms. This active regulation of stem cells fate make them perfect models to study processes as growth, patterning, differentiation cell proliferation or cell death. In this thesis we have studied different molecular mechanisms that control planarian growth and pattern. We have described a novel gene family, blitzschnell (bls), formed by de novo and taxonomically restricted genes, which control cell number trough the regulation of cell proliferation and cell death. Nutrient intake controls its expression suggesting that bls family have evolved in planarians as a mechanism by which to restrict cell number in nutrient-fluctuating environments. During growth and regeneration, planarians are not only able regulate their body and organ size accordingly but they also maintain a proper pattern. This regulation is mediated by different signalling centres that specify different regions along the 3 body axes (AP, DV and ML). Particularly, after an amputation, the anterior and the posterior planarian tips behave as organizers (signalling centre), specifying the fate of each planarian pole. The anterior organizer is defined by notum (a Wnt inhibitor) and the posterior by wnt1 expression. The inhibition of any of those elements leads to a shift in polarity. During the first hours of regeneration both notum and wnt1 are expressed in both poles, and it’s around 36 hours that their expression becomes restricted to their respective tip. To decipher the molecular interactions that restrict the expression of wnt1 to the posterior tip and confer the organizing activity we used genome wide approaches. ATAC-seq and RNA-seq analysis of regenerating wild-type and wnt1 (RNAi) planarians allowed the identification of specific Cis-Regulatory Elements (CREs) of posterior regeneration. We found that already at 12 hours of regeneration the accessible CREs in posterior and anterior blastemas have essentially changed, indicating that specific posterior chromatin changes induced by amputation occur much earlier than the formation of the organizers. Furthermore, we have identified specific transcription factors (TF) of the Otx and Fox families, which are enriched in posterior CREs. Particularly, pitx and foxG regulates wnt1+ cells and are essential for the specification of the posterior cells. TFs regulate patterning events and developmental specification, particularly the Fox Family exerts crucial roles defining cell types of all germ cell layers or regulating cell cycle. Before this Thesis, poorly was known about the Fox family in Schmidtea mediterranea (Smed) neither in the Lophocotrozoan clade. In this study we have identified 27 Fox genes in Smed, classified in 13 families: A, At, C, D, E, G, L1t, QD, J1, N2/3, Nt, O and P. We have performed an extensive phylogenetic study of the family to understand the evolution of the Fox family in this clade. Furthermore, we have studied the sequence, expression and function of several planarian Fox genes. Overall, we studied different molecular mechanisms that regulate planarian growth and regeneration, and that provide novel data concerning development and evolution.

In this study, we seek to understand and to correlate the genetic patterns observed in the population of the island of Ibiza in the Western Mediterranean basin with past events. Genome-wide genotypes of 189 samples representing 13 of 17 regions in Spain have been analyzed, in addition to 105 samples from the Levant, 157 samples from North Africa, and one ancient sample from the Phoenician Cas Molí site in Ibiza. Before the Catalans conquered the island in 1235 CE, Ibiza (Eivissa) had already been influenced by several cultures, starting with the Phoenicians, then the Carthaginians, followed by the Umayyads. The impact of these various cultures on the genetic structure of the islanders is still unexplored. Our results show a clear distinction between Ibiza and the rest of Spain. To investigate whether this was due to the Phoenician colonization or to more recent events, we compared the genomes of current Ibizans to that of an ancient Phoenician sample from Ibiza and to both modern Levantine and North African genomes. We did not identify any trace of Phoenician ancestry in the current Ibizans. Interestingly, the analysis of runs of homozygosity and changes in the effective population size through time support the idea that drift has shaped the genetic structure of current Ibizans. In addition to the small carrying capacity of the island, Ibiza experienced a series of dramatic demographic changes due to several instances of famine, war, malaria and plague that could have significantly contributed to its current genetic differentiation., Funding was provided by the Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866, and “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370). SAB was supported by the Agencia Estatal de Investigación FPI grant BES-2014-069224.

Understanding the effects of male and female age on reproductive success is vital to explain the evolution of life history traits and sex‐specific aging. A general prediction is that pre‐/postmeiotic aging processes will lead to a decline in the pre‐ and postcopulatory abilities of both males and females. However, in as much the sexes have different strategies to optimize their fitness, the decline of reproductive success late in life can be modulated by social context, such as sex ratio, in a sex‐specific manner. In this study, we used Drosophila melanogaster to investigate whether sex ratio at mating modulates age effects on male and female reproductive success. As expected, male and female age caused a decrease in reproductive success across male‐biased and female‐biased social contexts but, contrary to previous findings, social context did not modulate age‐related fitness decline in either of the two sexes. We discuss these results in the light of how sex ratio might modulate pre‐/postcopulatory abilities and the opportunity for inter‐ and intrasexual competition in D. melanogaster, and generally suggest that social context effects on these processes are likely to be species specific.

Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).

Evolutionary medicine applies the principles of evolutionary biology to understand why we get sick rather than how, and it has undergone an exponential growth since the early 1990s [...]. This work was supported by a BFU2015-68759-P (MINECO/FEDER) grant and the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 937). O.L was also supported by a Ramón y Cajal grant from the Spanish Ministerio de Economia y Competitividad (MINECO) with reference RYC-2013-14797

Evolutionary distance formulas that take into account effects due to ancestral polymorphisms and purifying selection are obtained on the basis of the full solution of Jukes–Cantor and Kimura DNA substitution models. In the case of purifying selection two different methods are developed. It is shown that avoiding the dimensional reduction implicitly carried out in the conventional model solving is instrumental to incorporate the quoted effects into the formalism. The problem of estimating the numerical values of the model parameters, as well as those of the correction terms, is not addressed.

Phylogeographical studies can reveal hidden patterns in the evolutionary history of species. Comparative analyses of closely related species can further help disentangle the relative contributions of processes responsible for such patterns. In this work, the phylogeography of two aristeid species, Aristeus antennatus and Aristaeomorpha foliacea, was compared through multiple genetic markers. These marine shrimp species are of high commercial importance, and are exploited in the Mediterranean Sea (MED) and in Mozambique Channel (MOZ) where they occur in partial sympatry. Aristeus antennatus (N = 50) from Western and Eastern Mediterranean (WM and EM, respectively), Atlantic Ocean (AO) and MOZ, and Aristaeomorpha foliacea (N = 40) from WM, EM, MOZ North-Western Australia (AUS) were analyzed with two nuclear genes (PEPCK and NaK) and one mitochondrial (COI) gene. Within the study area differences were found between the two species in their phylogeographical patterns, suggesting distinct responses to environmental changes. Monophyly of Aristeus antennatus was found across its distributional range. This pattern contrasted by a deep evolutionary split within Aristaeomorpha foliacea where genetic diversity followed geography distinguishing MED-MOZ and AUS. We propose that the AUS lineage of A. foliacea warrants consideration as a distinct species, with consequent implications in systematics and resource management.

Tots els éssers vius coneguts comparteixen algunes característiques, com ara la manera d'organitzar el material genètic en l'ADN, la qual cosa assenyala directament cap a un origen evolutiu comú de tots ells. A partir d'un organisme ancestral, per evolució, s'han originat totes les espècies actuals. El medi on es desenvolupa la vida és dinàmic i canviant, la qual cosa obliga totes les espècies a adaptar-s'hi constantment. Una de les maneres que tenen d'adaptar-se és a través del sexe, o de fenòmens sexuals. El sexe és consubstancial a la vida, inherent als processos vitals. En aquest article, que es basa en diversos llibres publicats per l'autor on es fan aportacions noves sobre el tema, es parla de què és el sexe i de quina importància evolutiva té, per a la supervivència i l'adaptació de les espècies. La seva universalitat i indisociabilitat amb la vida fan que es proposi i es justifiqui l'existència d'una sexosfera, la capa de la Terra que es caracteritza per l'existència de sexe. I, en el cas de l'espècie humana, que es proposi també l'existència d'un nou tipus de sexe, el sexe intel·lectual.

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fevo.2018.00097/full#supplementary-material, Feather mites are useful models for studying speciation due to their high diversity and strong degree of host specialization. However, studies to date have focused on the evolution of higher-level mite taxa while much hidden diversity likely occurs at the level of host genera and species. In this study, we examined the diversity and evolution of feather mites infesting six sympatric seabird species from six genera, breeding in the Cape Verde archipelago. We report 32 feather mite morphospecies categorized into 10 genera and three families, of which nine correspond to new, undescribed species. Molecular data corroborated morphological species descriptions, except for two morphologically-cryptic, but genetically distinct mite lineages related to Zachvatkinia oceanodromae and Laminalloptes simplex. Using these communities, we then applied a co-structure approach to test the contribution of ectosymbiont and host factors in driving feather mite evolution. Most seabird species hosted specific and unique feather mite species, even under sympatric conditions, and in general, feather mite species exhibited strong host-driven genetic structure. However, patterns of genetic differentiation were variable. That is, some mite species are more generalist than others and mite lineages/haplotypes can be shared by related seabird species. Interestingly, host-specific mites (e.g., Zachvatkinia spp.) tend to display much higher intra-specific diversity compared to more generalist mites (e.g., Microspalax and Plicatalloptes spp.). We discuss ectosymbiont and host life-history traits that might generate these patterns, such as host dispersal and breeding behavior and/or mite spatial and trophic specialization. Our findings highlight both the vast and largely unrecognized diversity of avian feather mites on seabirds, and the intrinsic complexity of the ecological processes underlying the evolution of these ectosymbionts., We thank T. Militão, R. Ramos, P. Rodrigues, J.M. de los Reyes, P. Lopez., L. F. López-Jurado, E. Vendrell, S. Martins, A. Rendall, M. Brooke and H. Dinis for their help during fieldwork at different stages and mite sample collection and Valérie Noël for molecular assistance. Permits to capture and examine live procellariiform birds were issued by Direcção Geral do Ambiente and the Instituto Nacional de Investigação e Desenvolvimento Agrário from Cape Verde. The present investigation was performed during the postgraduate project of LMS supported by the University of Barcelona. EG-D was supported by JdC and RyC contracts from the MINECO, Spain. Financial support was provided by CGL2009-11278/BOS from the Ministerio de Ciencia e Innovación (Spain) and Fondos FEDER for LMS, by French ANR project ESPEVEC (ANR-13-BSV7-0018) and the CNRS, France for KM and by a Marie Curie Reintegration Grant to EG-D (ERG-2010-276838).

Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan across primate species. We used two different approaches. First, we searched for parallel amino-acid mutations that co-occur with increases in longevity across the primate linage. Twenty-five such amino-acid variants were identified, several of which have been previously reported by studies with different experimental setups and in different model organisms. The genes harboring these mutations are mainly enriched in functional categories such as wound healing, blood coagulation, and cardiovascular disorders. We demonstrate that these pathways are highly enriched for pleiotropic effects, as predicted by the antagonistic pleiotropy theory of aging. A second approach was focused on changes in rates of protein evolution across the primate phylogeny. Using the phylogenetic generalized least squares, we show that some genes exhibit strong correlations between their evolutionary rates and longevity-associated traits. These include genes in the Sphingosine 1-phosphate pathway, PI3K signaling, and the Thrombin/protease-activated receptor pathway, among other cardiovascular processes. Together, these results shed light into human senescence patterns and underscore the power of comparative genomics to identify pathways related to aging and longevity. This work was supported by Ministerio de Ciencia e Innovación, Spain (BFU2012-38236 and BFU2015-68649-P (MINECO/FEDER, UE) to AN), by Direcció General de Recerca, Generalitat de Catalunya (2014SGR1311 and 2014SGR866 to A.N., and 2014BP-B00157 to G.M.), by the Spanish National Institute of Bioinfomatics of the Instituto de Salud Carlos III (PT13/0001/0026), by “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370), and by FEDER (Fondo Europeo de Desarrollo Regional)/FSE (Fondo Social Europeo)

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes. This work was supported by the Swiss Federal Government through the Federal Office of Education and/nScience (B.B.). Funding for open access charge: Swiss Institute of Bioinformatics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. T.G. group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), a Grant from the Qatar National Research Fund (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC (grant agreement no. ERC-2012-StG-310325). M.M. acknowledges support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory.

L'evolució de les espècies és un fet que s'observa a la natura. Els canvis evolutius que afecten la morfologia dels organismes es poden detectar fàcilment quan s'analitzen períodes llargs de temps, però sovint costa reconèixer-los en períodes més curts. També acostuma a ser complicat associar aquests canvis a gens concrets i a factors de selecció específics, especialment quan s'estudien espècies complexes com els vertebrats, atès que sovint hi ha diversos gens que actuen sobre una mateixa característica. L'investigador Jon Slate i els seus col·laboradors, de diverses universitats i centres de recerca anglesos i holandesos, han observat l'existència de canvis evolutius recents en el bec de les mallerengues carboneres angleses ( Parus major ), i els han pogut relacionar amb mutacions concretes i també amb factors de selecció específics.

[eng] The study of intraspecific diversity is essential in ecology and evolution as they reveal fine-scale patterns and it is crucial in conservation planning. The main aim of this thesis is to study the evolutionary history of two Iberian Soricomorpha: The Pyrenean desman (Galemys pyrenaicus) and the Mediterranean water shrew (Neomys anomalus). Both mammals are semi-aquatic and endemic to the Iberian Peninsula. To this end, different approaches were applied, such as genomics, phylogeography and species distribution modelling (SDM), in the three chapters of this thesis. In Chapter 1, the main aim was to study the population structure of the Pyrenean desman using genomic markers. In order to achieve this objective, we optimized a genomic reduction protocol, double-digestion RAD sequencing (ddRAD), for the low DNA quantities needed when working with endangered species, like the Pyrenean desman. Moreover, we filtered and evaluated the library and determined the sex of the specimens used. Then, we estimated the heterozygosity rate and we determined population structure and evolutionary units performing a Principal Component Analysis (PCA), a Structure analysis and a genomic phylogenetic tree. As result, the heterozygosity rate turned out to be one of the lowest in mammals and five clades were delimited in the population structure. These results have important conservation implications. In Chapter 2, our main aim was to infer the mitochondrial genetic structure and the postglacial dispersal patterns of the north-western clade of the Pyrenean desman, using non-invasive samples. We delimited a contact zone in the Cantabrian Mountains and we studied the structure of nucleotide diversity through an interpolation map, the genetic structure through an Analysis of Molecular Variance (AMOVA) and the dispersal patterns through an Isolation-by-Distance approach. The results revealed areas of very high genetic diversity and areas of extremely low genetic diversity. Moreover, half of the genetic structure can be explained by the isolation of river basin, meaning that the desmans were not completely isolated in these basins, which is consistent with postglacial overland dispersal between the basins. This result was confirmed by the Isolation-by-Distance approach, which also revealed a high relative importance of overland dispersal during the Holocene but a similiar relative importance of overland and river dispersal for short distances. This study has also conservation implications, as it suggests that terrestrial corridors within the desman distribution range should also be restored and preserved. Finally, in Chapter 3, we studied the phylogeography of the Mediterranean water shrew, which was recently delimited as a species. We studied its phylogenetic structure using a Maximum Likelihood and Bayesian Inference phylogenetic trees. Moreover, we interpolated the nucleotide diversity and performed a species distribution modelling. The results revealed two main clades correlated with geographic structure. Moreover, the study suggests certain coincidence of high genetic diversity areas with optimal areas in the Last Glacial Maximum, which is consistent with the location of the glacial refugia., [spa] La diversidad dentro de especies es clave desde el punto de vista ecológico y evolutivo y, además, para la conservación. El principal objetivo de esta tesis es estudiar la historia evolutiva de dos mamíferos ibéricos: el Desmán de los Pirineos (Galemys pyrenaicus) y el Musgaño de Cabrera (Neomys anomalus). Para ello, se han utilizado diversas metodologías, entre ellas genómica, filogeografía y modelos de distribución de especies, a lo largo de los tres capítulos que conforman esta tesis. En el capítulo 1, se busca estudiar la estructura genética del desmán usando marcadores genómicos. Para ello, se optimizó un protocolo de reducción genómica (ddRADSeq) y se realizaron análisis genómicos con los datos resultantes de la librería. Los resultados revelaron una heterozigosidad extremadamente baja y cinco clados como unidades evolutivas. Estos resultados tienen repercusión en la conservación de la especie. En el capítulo 2, se estudia la estructura genética mitocondrial y los patrones de dispersión postglacial del desmán en el clado nor-occidental. Los resultados sugieren que los desmanes no estuvieron completamente aislados en las cuencas de los ríos y se dispersaron durante el Holoceno por tierra para realizar desplazamientos largos. Por el contrario, para desplazamientos cortos, los resultados sugieren que se pudieron desplazar tanto por el río como por tierra. Finalmente, en el capítulo 3, se estudia la filogeografía e historia evolutiva del Musgaño de Cabrera y se ha descubierto una estructura genética dividida en dos clados correlacionados con la estructura geográfica. Además, los resultados sugieren la existencia de refugios glaciares y una compleja historia postglacial.

The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature. This work was supported by grants to W.C.W. (NIH: 2R24OD011198-04A1), M.W.H. (NSF DBI-1564611), M.S. (German Research Foundation DFG projects Scha408/10-1 and Scha408/12-1), M.St. (Heisenberg-Fellowship STO 493/2-2 of the German Science Foundation/DFG), T.M.B.(MINECO BFU2014-55090-P (FEDER), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social ‘La Caixa’ and Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya) and R.B.W. (NIH: R24OD011120). The genome annotation work carried out by NCBI was supported by the Intramural Research Program of the NIH, National Library of Medicine. The genome annotation work by Ensembl was supported by funding from the Wellcome Trust (WT108749/Z/15/Z and WT098051), the National Institutes of Health (R24 RR032658-01) and the European Molecular Biology Laboratory

Hominin dietary specialization is crucial to understanding the evolutionary changes of craniofacial biomechanics and the interaction of food processing methods’ effects on teeth. However, the diet-related dental wear processes of the earliest European hominins remain unknown because most of the academic attention has focused on Neandertals. Non-occlusal dental microwear provides direct evidence of the effect of chewed food particles on tooth enamel surfaces and reflects dietary signals over time. Here, we report for the first time the direct effect of dietary abrasiveness as evidenced by the buccal microwear patterns on the teeth of the Sima del Elefante-TE9 and Gran Dolina-TD6 Atapuerca hominins (1.2–0.8 million years ago − Myr) as compared with other Lower and Middle Pleistocene populations. A unique buccal microwear pattern that is found in Homo antecessor (0.96–0.8 Myr), a well-known cannibal species, indicates dietary practices that are consistent with the consumption of hard and brittle foods. Our findings confirm that the oldest European inhabitants ingested more mechanically-demanding diets than later populations because they were confronted with harsh, fluctuating environmental conditions. Furthermore, the influence of grit-laden food suggests that a high-quality meat diet from butchering processes could have fueled evolutionary changes in brain size. This work was supported by the research grants, from the Dirección General de Investigación of Ministerio Ciencia y Tecnología (Spain), numbers CGL2007-60802/BTE, CGL2011-22999, CGL2012-38434-C03-01/02/03 and CGL2014-52611-C2-1-P, as well as by the grant 2009SGR884 Group of Study on the Evolution of Hominins and other Primates and grant 2014SGR900 Group of Analyses on Socio-Ecological Processes, Cultural Changes and Population Dynamics during Prehistory (GAPS) and CERCA Programme of the Generalitat de Catalunya.

[cat] L’origen de la multicel·lularitat en animals és un esdeveniment clau en l’evolució que vingué acompanyat de canvis profunds en els genomes, la biologia cel·lular i el desenvolupament dels ancestres unicel·lulars dels animals. En aquesta tesi analitzo l’origen dels animals mitjançant genòmica comprada i filogenòmica, amb l’objectiu de reconstruir les innovacions que sustentaren la transició a la multicel·lularitat mitjançant anàlisis de genomes animals i els seus parents unicel·lulars dins del llinatge Holoza. Els nostres anàlisis filogenòmics han establert quatre clades d’holozous: Teretosporea (Corallochytrium limacisporum i protistes ictiosporis), Filasterea (2 amebes, incloent-hi Capsaspora owczarzaki) i Choanoflagellata (protistes flagel·lats, ocasionalment colonials), a banda dels metazous multicel·lulars. Aquest marc filogenètic ens ha permès d’explotar la genòmica comparada per tal d’assenyalar els canvis genòmics concrets que ocorregueren a l’origen dels Metazoa. Hem reconstruït el contingut gènic ancestral de la via de senyalització de l’ubiquitina— famílies gèniques involucrades en el marcatge post-traduccional de proteïnes—, les miosines i factors de transcripció homeobox. Aquests anàlisis revelen un estat continuat d’innovació en aquests sets gènics, mitjançant origen de gens de novo, diversificació de dominis proteics i paralogia – la qual cosa suggereix que l’Urmetazoa fou un organisme genèticament complex i que la coopció de gens jugà un paper clau en l’origen de la multicel·lularitat. En segon lloc, vàrem examinar l’evolució de l’arquitectura genòmica en els premetazous. Hem seqüenciat i analitzat els genomes de 6 ictiosporis (Creolimax fragrantissima, Chromosphaera perkinsii, Sphaeroforma arctica, Ichthyophonus hoferi, Abeoforma whisleri i Pirum gemmata) i C. limacisporum; i els hem comparat als altres holozous unicel·lulars (C. Owczarzaki i els coanoflagel·lats) i als animals. Anteriorment, s’havia establert l’origen premetazou de diversos gens amb funcions en la multicel·lularitat, com per exemple factors de transcripció relacionats amb el desenvolupament, o proteïnes d’adhesió cel·lular. En aquest estudi, expandim anteriors resultats i demostrem que l’arquitectura genòmica també passà per importants innovacions evolutives: a banda de la invenció i diversificació gènica a l’origen dels holozous, identifiquem processos de disrupció i establiment de sintènia, guany d’introns i expansions genòmiques en els llinatges uni i multicel·lulars. Finalment, correlacionem l’evolució de l’estructura gènica amb els modes de splicing alternatiu presents en animals i eucariotes. Identifiquem un codi de determinació dels patrons de splicing alternatiu que afecta la freqüència d’ús d’exons-casette, a la manera típica dels animals, en organismes unicel·lulars com els ictiosporis (amb genomes grans i densos en introns). En global, demostrem que la genòmica comparada i les reconstruccions ancestrals són una poderosa eina per als anàlisis evolutius: per un cantó permeten inferir la composició primària dels genomes ancestrals; i per l’altre permeten estudiar l’evolució d’altres fonts d’innovació genòmica com ara la regulació transcripcional., [eng] The origin of multicellularity in animals is a hallmark event in evolution, that was accompanied by profound changes in the genomes, development and cell biology processes of the animal ancestors. I analyze the origin of animals from the point of view of comparative genomics and phylogenomics, aiming to reconstruct the innovations behind the transition to multicellularity by analyzing animals and their closest unicellular relatives within Holozoa. Our initial phylogenomic analyses established four holozoan clades: Teretosporea (Corallochytrium limacisporum and ichthyosporean protists), Filasterea (2 amoebas, including Capsaspora owczarzaki) and Choanoflagellata (flagellated protists, sometimes colonial), as well as multicellular Metazoa. Then, we used this robust phylogenetic framework in combination with comparative genomics, aiming to pinpoint the specific changes underscoring the origin of Metazoa. We reconstructed the ancestral gene contents were focused of the ubiquitin signaling tool-kit—gene families involved in post-translational protein modification—, myosin molecular motors and homeobox transcription factors. In pre-metazoan lineages, we uncovered a continued state of innovation in terms of de novo gene origin, protein diversification and paralogy – thus suggesting a genetically complex Urmetazoa, and a prominent role of gene co-option at the origin of multicellularity. Next, we aimed to examine genome architecture evolution in premetazoans. Thus, we sequenced and analyzed the genomes of 6 ichthyosporeans (Creolimax fragrantissima, Chromosphaera perkinsii, Sphaeroforma arctica, Ichthyophonus hoferi, Abeoforma whisleri and Pirum gemmata) and C. limacisporum; and compared them to other unicellular holozoans (C. owczarzaki and choanoflagellates) and animals. We uncovered the premetazoan origin of many genes with multicellularity-related functions, e.g. developmental transcription factors or cell adhesion proteins. Here we show that genome architecture evolution was equally innovative: the early burst of gene diversity in the holozoans was followed by episodes of synteny disruption, intron gain, and genome expansions in unicellular and multicellular lineages. Finally, we correlated the evolution of alternative splicing- based transcriptome regulation with exon/intron gene structure in holozoans. We unraveled a universal code of alternative splicing that determines the frequency of animal-like exon skipping profile in large, intron-dense ichthyosporean genomes. We demonstrate that comparative genomics and ancestral reconstructions constitute a powerful tool for evolutionary analysis of ancestral eukaryotes: not only it allows to uncover the primary composition of ancestral genomes; it can also fuel inferences regarding their transcriptomic regulation and the role played by non-genomic sources of evolutionary innovation.

El estudio de la localidad clásica de El Chorrillo del Mioceno Medio (Serravaliense) en la Provincia de Alicante, ha permitido la recuperación de una interesante asociación de microrestos de tiburones caracterizada por al menos siete taxones (Deania calcea, ¿Isistius triangulus, ¿Squaliolus cf. schaubi, ¿Paraetmopterus sp., Pristiophorus sp., Scyliorhinus sp. y un Squaliforme indeterminado) pertenecientes a tres órdenes diferentes (Squaliformes, Pristiophoriformes y Carcharhiniformes). Asociados a estos microrestos se han identificado también macrodientes pertenecientes a Cosmopolitodus hastalis, Isurus sp., Hemipristis serra, Odontaspis sp., Carcharhinus spp. y ¿Otodus (Megaselachus) megalodon. El conjunto contiene especies con preferencias ambientales dispares, que incluyen no sólo tiburones neríticos y epipelágicos (aguas someras o abiertas), sino también un número importante de representantes meso y batipelágicos (tiburones de profundidad). Esta asociación 'mezclada' es interpretada no como consecuencia de factores tafonómicos, sino por aspectos biológicos intrínsecos a la fauna que los componen. En este sentido, la migración de taxones de aguas profundas a aguas más superficiales a través de cañones submarinos para alimentarse (como sucede en la actualidad), pudo ser la causa más plausible para explicar el origen de tal asociación. Por otro lado, es importante destacar que la composición de los taxones de aguas profundas aquí descritas contrasta con el conjunto de condríctios del Plioceno, Pleistoceno y del de las comunidades mediterráneas actuales. Estos datos indican que la crisis de salinidad del Mesiniense afectó de forma importante a la evolución posterior de los ecosistemas abisales mediterráneos, pero que las diferencias detectadas con los faunas actuales debieron deberse además a otros factores, como la existencia de eventos anóxicos en los fondos abisales durante el Cuaternario. | The study of the classical locality of El Chorrillo, (Serravallian, Middle Miocene) from the Alicante Province has yielded a shark assemblage characterized by microremains of at least seven taxa (Deania calcea, ¿Isistius triangulus, ¿Squaliolus cf. S. schaubi, ¿Paraetmopterus sp., Pristiophorus sp., Scyliorhinus sp. and a cf. Squaliformes indet) of three different orders (Squaliformes, Pristiophoriformes and Carcharhinuformes). In addition, associated macroremains have also been found, including teeth of ¿Cosmopolitodus hastalis, Isurus sp., Hemipristis serra, Odontaspis sp., Carcharhinus spp. and ¿Otodus (Megaselachus) megalodon. The assemblage contains taxa with disparate environmental preferences including not only neritic and epipelagic sharks but also an important number of meso- and bathypelagic representatives. The migration of deep water taxa to shallower waters through submarine canyons is proposed as the most plausible cause for explaining the origin of such assemblage. Interestingly, the composition of the deep-water taxa here reported contrast with the chondrichthyans assemblages from the Pliocene and extant Mediterranean communities. This entails a complex biogeographic history, where the Messinian salinity crisis strongly affected the posterior evolution of the Mediterranean ecosystems but some other factors, such us the existence of anoxic events during the Quaternary, could have also played an important role.

CHAPTER 1: Reconstructing ancient Mediterranean crossroads in Deronectes diving beetles Aim: To reconstruct the evolutionary history of a genus of freshwater beetle with a pan- Mediterranean distribution, to test classic hypotheses which proposed a Miocene origin for groups with high biodiversity in the Iberian and Anatolian peninsulas. Location: Mediterranean basin. Methods: We sequenced four mitochondrial and one nuclear gene from 51 specimens of 30 of the c. 60 extant species of Deronectes (Dytiscidae), all typical of mid-mountain streams from North Africa and Iberia over most of Europe to the Middle East. We used maximum likelihood, Bayesian probabilities with an a priori evolutionary rate and a dispersal–extinction–cladogenesis model to reconstruct their biogeographical history. Results: Deronectes has two major lineages which originated in the mid Miocene; one including mostly eastern and another mainly western and central Mediterranean species. From these two areas, range expansions, mainly at the end of the Miocene and beginning of the Pliocene, resulted in the many species groups and some of the extant species of the genus. Most of the current diversity and distributions are, however, of Plio-Pleistocene origin, particularly in widespread European species. Main conclusions: In line with traditional hypotheses, we found an ancient division between eastern and western Mediterranean lineages of Deronectes, likely resulting from the isolation of Europe west of the Alps from the Balkans and Anatolia during the early-middle Miocene. The history of the genus was strongly influenced by major geological and climatic events, with successive cycles of fragmentation and subsequent eastward and westward range expansions, resulting in a steady accumulation of species across the basin. Most of these range movements took place through the north side of the Mediterranean, with only local displacements in the south during the Messinian salinity crisis and a recent (Pleistocene) colonization of the Italian Peninsula, which remained largely submerged through most of the genus’ evolutionary history. CHAPTER 2: The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes) In most lineages most species have restricted geographic ranges, with only few reaching widespread distributions. How these widespread species reached their current ranges is an intriguing biogeographic and evolutionary question, especially in groups known to be poor dispersers. We reconstructed the biogeographic and temporal origin of the widespread species in a lineage with particularly poor dispersal capabilities, the diving beetle genus Deronectes (Dytiscidae). Most of the ca. 60 described species of Deronectes have narrow ranges in the Mediterranean area, with only four species with widespread European distributions. We sequenced four mitochondrial and two nuclear genes of 297 specimens of 109 different populations of the four lineages of Deronectes including widespread species, together with their closest narrow range relatives, covering their entire distributions. Using Bayesian probabilities with an a priori evolutionary rate we performed (1) a global phylogeny/phylogeography to estimate the relationships of the main lineages within each group and root them, and (2) demographic analyses of the best population coalescent model for each species group, including a reconstruction of the geographical history estimated from the distribution of the sampled localities. We also selected 56 specimens to test for the presence of Wolbachia, a maternally transmitted parasite that can alter the patterns of mtDNA variability. All species of the four studied groups originated in the southern Mediterranean peninsulas and were estimated to be of Pleistocene origin. In three of the four widespread species the central and northern European populations were nested within those in the northern areas of the Anatolian, Balkan and Iberian peninsulas respectively, suggesting a range expansion at the edge of the southern refugia. In the Mediterranean peninsulas the widespread European species were replaced by vicariant taxa of recent origin. The fourth species (D. moestus) was proven to be a composite of unrecognised lineages with more restricted distributions around the Western and Central Mediterranean. The analysis of Wolbachia showed a high prevalence of infection among Deronectes, especially in the D. aubei group, where all sequenced populations were infected with the only exception of the Cantabrian Mountains, the westernmost area of distribution of the lineage. In this group there is a phylogenetic incongruence between the mitochondrial and the nuclear sequence, although not clear pattern links this discordance to the Wolbachia infection. Our results suggest that in different glacial cycles populations that happened to be at the edge of the newly deglaciated areas took advantage of the optimal ecological conditions to expand their ranges to central and northern Europe. Once this favourable ecological window ended populations become isolated, resulting in the presence of closely related but distinct species in the Mediterranean peninsulas. CHAPTER 3: Pleistocene range expansions in Western Palaearctic aquatic Coleoptera The Quaternary glacial cycles lead to large changes in the size and location of the geographic distribution of many species. During glacial maxima large areas of central and northern Europe become inhospitable to temperate species, which are generally assumed to have been recolonized by range expansions from Mediterranean refugia in the interglacials. An alternative possibility is that the recolonization was from non-Mediterranean sources, from glacial refugia in central Europe or western Asia, but data are still scarce concerning the origin of the central and north European species with very large geographic distributions, especially for insects. In this work we studied some species of three wide distributed lineages of freshwater beetles (Platambus maculatus complex, H. gracilis complex, and the genus Oreodytes), all typical of running waters and including both narrowly distributed southern endemics and widespread European species, some with distributions spanning the whole Palearctic. The main goal was to understand the role of the Pleistocene glaciations in the diversification and current distribution of these species. For this we sequenced four mitochondrial and two nuclear genes of 212 specimens of 107 different populations of the different lineages and used Bayesian probabilities and Maximum Likelihood to reconstruct the phylogenetic relationships, age and geographical origin of the western Palaearctic species of these three widely distributed lineages. All species of the three studied groups were estimated to be of Pleistocene origin. In the H. gracilis complex, a secondary fast range expansion from northern Anatolian populations to western and northern Europe resulted in the current widespread European H. gracilis. However, in the other two groups we found widespread central and northern European species the origin of which was not the Mediterranean area but central Asia, but with peripheral isolated forms in the southern Mediterranean peninsulas. These peripheral forms could have been confined as remnants of earlier diversification cycles or be result of incipient isolation of the most recent post-glacial expansion. The accumulation of narrow endemics of these lineages in the Mediterranean may thus be the result of successive cycles of range expansions with subsequent speciation (and local extinction in glaciated areas) through the multiple Pleistocene glacial cycles. CHAPTER 4: Range expansion and ancestral niche reconstruction in the Mediterranean diving beetle genus Meladema (Coleoptera, Dytiscidae) Species of the genus Meladema (Dytiscidae, Colymbetinae) are some of the largest macroinvertebrates in the western Palearctic region, being top predators in fishless streams. Two of the three described species, M. imbricata (Wollaston, 1871) and M. lanio (Fabricius, 1775) are Macaronesian endemics from the Canary Islands and Madeira respectively, while the third, M. coriacea Laporte, 1835, is widely distributed from Morocco and the Iberian Peninsula to Turkey, including the Canary Islands. Previous phylogenetic analysis using only mitochondrial markers revealed the existence of two cryptic lineages within M. coriacea, one restricted to Corsica and the other including the rest of sampled populations. We reconstruct here the evolutionary history of the species of Meladema using a more comprehensive sampling covering its whole geographical range, adding nuclear markers and Bayesian molecular dating. Using environmental niche modelling we test for possible differences in climatic preferences among lineages, and reconstruct their ancestral climatic niche. Our results strongly supported the existence of four monophyletic lineages represented by the three recognised species plus a fourth cryptic lineage with populations of M. coriacea from the Tyrrhenian islands (Corsica, Sardinia and Montecristo). This pattern is not likely to be the result of mitochondrial artefacts due to Wolbachia infection, as all 11 tested individuals were negative for this parasite. Dating analysis placed the origin of Meladema in the Middle Miocene although diversification among extant Meladema lineages started in the early Pleistocene and took place in a relatively short time period. Phylogeographic analysis inferred a continental origin of Meladema, with an independent colonization of the Macaronesian and Mediterranean islands. From the southwestern Mediterranean region the continental M. coriacea expanded its range up to Turkey in the northern basin, and to Tunisia in the southern. Results of niche modelling showed that seasonality is the critical factor in shaping the current distribution of Meladema. Island lineages (M. imbricata, M. lanio and the Thyrrenian lineage of M. coriacea) occur in sites with low seasonality, within the range of the reconstructed ancestral climatic niche of the genus. On the contrary, continental M. coriacea expanded its range to localities outside the ancestral climatic range of the genus, with a higher seasonality and aridity., Una pregunta básica sobre los rangos geográficos es comprender por qué unas especies están ampliamente distribuidas mientras otras, estrechamente emparentadas tienen distribuciones restringidas. En este estudio pretendo comprender los factores que llevaron a algunas especies a expandir su rango original y sugerir posibles hipótesis que expliquen las enormes diferencias de rango entre especies emparentadas. Para ello, reconstruyo la historia evolutiva de varios linajes de coleópteros acuáticos del Paleártico Occidental bajo el contexto de la compleja historia geológica y climática de este área, con el fin de aclarar los procesos que han contribuido a la actual distribución de especies en estos grupos. Estos linajes son típicos de aguas corrientes (es decir, con baja capacidad dispersiva) e incluyen tanto endemismos distribuidos en pequeñas áreas, como especies de amplia distribución, mostrando su potencial de expansión de rango. Las reconstrucciones biogeográficas llevadas a cabo sugieren la existencia de varios eventos de expansión de rango entre la zona oriental y occidental de la Cuenca Mediterránea bajo condiciones favorables, seguidos de fragmentación cuando las condiciones empeoraban. Estas expansiones debieron producirse principalmente a lo largo de la costa norte del Mediterráneo, ya que por la sur hay ausencia de especies al este de Túnez. A pesar de que no es posible establecer un origen temporal común para los grupos estudiados, el Mioceno con sus múltiples conexiones entre el Mediterráneo occidental y oriental seguidas de aislamiento, parece estar implicado en el origen y disyunción este-oeste en varios grupos. Sin embargo, la mayor parte de las especies actuales se originaron durante el Pleistoceno, incluyendo aquellas que han alcanzado amplias distribuciones, siendo por tanto la época mas influyente en la distribución actual de especies. Las sucesivas rondas de expansión y fragmentación de rango resultaron principalmente en la acumulación de especies restringidas en el área Mediterránea, especialmente en Anatolia y la Península Ibérica. A pesar de la evidencia en muchos casos de especiación con estabilidad de rango dentro del área Mediterránea, algunas especies lograron expandir su rango original hasta alcanzar amplias distribuciones en áreas mas al norte, probablemente aprovechando una posición geográfica ventajosa cuando las condiciones ambientales fueron ventajosas. No obstante, diferencias en tolerancia fisiológica y/o ecológica también pudieron favorecer las expansiones de rango en unas especies y limitarlo en otras, aunque futuras investigaciones experimentales se requieren para poder testar esta hipótesis.

Feather mites are among the most abundant and commonly occurring bird ectosymbionts. They live permanently on the host body, are adapted to inhabit well-defined host microhabitats and are found in almost all avian groups. Although feather mites have been extensively studied at the taxonomic level, much diversity remains undescribed and there are many open questions on the biology, ecology and evolution of feather mites. There is also an ongoing debate on the type of symbiosis, that is, whether bird-feather mite interactions are parasitic, commensalistic or even mutualistic. Therefore, better knowledge of feather mite communities at different levels of their biological organization (i.e., among host individuals, host populations and host species) can contribute to our understanding of the evolutionary ecology of feather mite-bird interactions, and of the evolution of parasite biodiversity in general. In this context, the main goal of this thesis was to investigate the evolutionary and ecological factors driving the diversity and community structure of feather mites inhabiting seabirds of the north-eastern Atlantic Ocean and Mediterranean Sea. More specifically, using a multi-host and multi-mite species community approach, I quantify feather mite morphological and genetic diversity within different seabird species and populations; evaluate the relative importance of host versus geographic structure in influencing the evolution and population structure of seabird feather mites; investigate the spatial distribution and trophic structure within a host individual to identify the driving mechanisms and proximate factors shaping symbiont infra-community structure. Based on morphological criteria, the results show that seabird species harbour a diverse and unique mite fauna composed of 38 species belonging to 10 genera and three families. All seabird species hosted at least three feather mite species, while the richest community was composed of nine mite species. Each seabird genus harboured a distinct feather mite community and only three mite species were shared by two related shearwater genera. Seventeen of the 38 mite species found were new, undescribed species; official descriptions of six are included in this thesis. Overall, molecular data correlated well with morphological species descriptions, but also revealed the presence of six putative cryptic species belonging to four mite genera. The patterns of mite genetic structure were variable both among different sympatric hosts and among the same host species in different geographic regions. Thus, the great majority of mite species from sympatric seabirds exhibited strong host-associated patterns of genetic structure. When comparing mite communities among sibling host species from the same genus, some mite species were genetically unstructured among hosts and localities, whereas other mite species showed higher degree of genetic diversity and among population differentiation. These observed differences correspond to microhabitat use on the host body. No genetic differentiation among localities was found for feather mites, suggesting that mite dispersal regularly occurs between host populations. The distribution of two widely abundant mite species that co-occur on the flight feathers of a single seabird species, Calonectris borealis, showed clear spatial segregation among feathers; one species preferred the central primaries, whereas the other was restricted to the outermost primaries. This pattern resulted from a combination of habitat-specific adaptations and ongoing competition. In addition, isotopic analyses of mite diet indicated that the two mite species share the same host food resources, probably preen gland oil complemented with exogenous material. Altogether, this thesis highlights the vast and largely unrecognized diversity of feather mites harboured by seabirds, provides a comprehensive characterization of the patterns of seabird-feather mite species/lineages associations and contributes to a better understanding of the ecological and evolutionary processes that have lead to their high diversity., Los ácaros de las plumas son unos de los ectosimbiontes más abundantes y comunes que se encuentran en casi todos los grupos de aves. Aunque han sido ampliamente estudiados a nivel taxonómico, mucha diversidad permanece sin ser descrita y todavía hay muchas preguntas abiertas sobre la biología, ecología y evolución de estos ectosimbiontes. Un mejor conocimiento de las comunidades de los ácaros de las plumas en diferentes niveles de su organización biológica puede contribuir a nuestra comprensión de la ecología evolutiva de las interacciones entre aves y ácaros, y de la evolución de la biodiversidad de los parásitos en general. El objetivo principal de esta tesis ha sido investigar los factores evolutivos y ecológicos que influyen la diversidad y la estructura de la comunidad de los ácaros de las plumas en aves marinas del Océano Atlántico y del Mediterráneo. Las especies de aves albergan una fauna de ácaros diversa y única compuesta por 38 especies perteneciendo a 10 géneros y tres familias. Cada género de ave albergaba una comunidad distinta de ácaros y solo tres especies de ácaros fueron compartidos por dos géneros cercanos de pardelas. Diecisiete de las 38 especies encontradas eran nuevas, no descritas; descripciones formales de seis especies están incluidas en esta tesis. Los datos moleculares correlacionaron bien con las descripciones morfológicas, pero también revelaron la presencia de seis especies cripticas pertenecientes a cuatro géneros de ácaros. Los patrones de la estructura genética de los ácaros fueron variables tanto entre los diferentes huéspedes simpátricos y entre la misma especie de huésped en diferentes regiones geográficas. La gran mayoría de las especies de ácaros de aves marinas simpátricas exhibió fuertes patrones de estructura genética asociados al huésped. Al comparar las comunidades de ácaros entre especies hermanas del mismo género de huésped, algunas especies de ácaros no estaban genéticamente estructuradas tanto entre huéspedes como entre localidades, mientras que otras especies presentaron diferenciación entre poblaciones. Estas diferencias observadas corresponden con el uso de microhabitats en el cuerpo del huésped. No se encontró ninguna diferenciación genética entre las localidades para los ácaros, sugiriendo que la dispersión de los ácaros se produce regularmente entre las poblaciones de huéspedes. La distribución de dos especies de ácaros que coocurren en las plumas del vuelo de Calonectris borealis mostró una clara segregación espacial entre plumas resultada de una combinación de adaptaciones específicas de hábitat y la competición en curso. Los análisis isotópicos de la dieta de los ácaros indicaron que las dos especies de ácaros comparten los mismos recursos alimenticios provenientes del huésped, probablemente aceite de la glándula uropígeal y material exógeno. En conjunto, esta tesis destaca la gran y poco conocida diversidad de los ácaros de las plumas albergada por las aves marinas y contribuye a una mejor comprensión de los procesos ecológicos y evolutivos que conlleva dicha alta diversidad.

Prado-Martinez, Javier et al., Most great ape genetic variation remains uncharacterized1,2; however, its study is critical for understanding population history3–6, recombination7, selection8 and susceptibility to disease9,10.Herewe sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/ eastern populations.Wefind extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over timein different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genomediversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations., We thank the following funding agencies: ERC Starting Grant (260372) to T.M.-B.; NIH grants HG002385 to E.E.E., R01_HG005226 to K.R.V., A.E.W., M.F.H., L.S. and J.D.W., GM100233 and NSF HOMINID grant 1032255 to D.R. and He.Li.;MICINN(Spain)BFU2011-28549to T.M.-B.,BFU2010-19443to Ja.Be.,Spanish Government and FEDER for grants BFU2009-13409-C02-02 and BFU2012-38236 to A.N. and J.P.-M., Direccio´ General de Recerca, Generalitat de Catalunya (Grup de Recerca Consolidat 2009 SGR 1101) to Ja.Be., D.C., A.N. and T.M.-B.; ERC Advanced Grant (233297) and Max Planck Society to S. Paabo; Danish Council for Independent Research Natural Sciences to H.S.; Spanish Grant (CGL-2010-20170) and Zoo de Barcelona (Beca PRIC) to A.R.-H.; EUPRIM-Net to BPRC; DP1ES022577-04 NIH grant to S.A.T.; NSF Grant 0755823 to M.K.G.; P.G. is supported by the G. Harold and Leila Y. Mathers Foundation. A.N. and T.M.-B. are ICREA Research Investigators (Institut Catala d’Estudis i RecercaAvancats delaGeneralitat deCatalunya). J.P.-M. is supported by the Zoo de Barcelona and l’Ajuntament de Barcelona.

[eng] Feather mites are among the most abundant and commonly occurring bird ectosymbionts. They live permanently on the host body, are adapted to inhabit well-defined host microhabitats and are found in almost all avian groups. Although feather mites have been extensively studied at the taxonomic level, much diversity remains undescribed and there are many open questions on the biology, ecology and evolution of feather mites. There is also an ongoing debate on the type of symbiosis, that is, whether bird-feather mite interactions are parasitic, commensalistic or even mutualistic. Therefore, better knowledge of feather mite communities at different levels of their biological organization (i.e., among host individuals, host populations and host species) can contribute to our understanding of the evolutionary ecology of feather mite-bird interactions, and of the evolution of parasite biodiversity in general. In this context, the main goal of this thesis was to investigate the evolutionary and ecological factors driving the diversity and community structure of feather mites inhabiting seabirds of the north-eastern Atlantic Ocean and Mediterranean Sea. More specifically, using a multi-host and multi-mite species community approach, I quantify feather mite morphological and genetic diversity within different seabird species and populations; evaluate the relative importance of host versus geographic structure in influencing the evolution and population structure of seabird feather mites; investigate the spatial distribution and trophic structure within a host individual to identify the driving mechanisms and proximate factors shaping symbiont infra-community structure. Based on morphological criteria, the results show that seabird species harbour a diverse and unique mite fauna composed of 38 species belonging to 10 genera and three families. All seabird species hosted at least three feather mite species, while the richest community was composed of nine mite species. Each seabird genus harboured a distinct feather mite community and only three mite species were shared by two related shearwater genera. Seventeen of the 38 mite species found were new, undescribed species; official descriptions of six are included in this thesis. Overall, molecular data correlated well with morphological species descriptions, but also revealed the presence of six putative cryptic species belonging to four mite genera. The patterns of mite genetic structure were variable both among different sympatric hosts and among the same host species in different geographic regions. Thus, the great majority of mite species from sympatric seabirds exhibited strong host-associated patterns of genetic structure. When comparing mite communities among sibling host species from the same genus, some mite species were genetically unstructured among hosts and localities, whereas other mite species showed higher degree of genetic diversity and among population differentiation. These observed differences correspond to microhabitat use on the host body. No genetic differentiation among localities was found for feather mites, suggesting that mite dispersal regularly occurs between host populations. The distribution of two widely abundant mite species that co-occur on the flight feathers of a single seabird species, Calonectris borealis, showed clear spatial segregation among feathers; one species preferred the central primaries, whereas the other was restricted to the outermost primaries. This pattern resulted from a combination of habitat-specific adaptations and ongoing competition. In addition, isotopic analyses of mite diet indicated that the two mite species share the same host food resources, probably preen gland oil complemented with exogenous material. Altogether, this thesis highlights the vast and largely unrecognized diversity of feather mites harboured by seabirds, provides a comprehensive characterization of the patterns of seabird-feather mite species/lineages associations and contributes to a better understanding of the ecological and evolutionary processes that have lead to their high diversity., [spa] Los ácaros de las plumas son unos de los ectosimbiontes más abundantes y comunes que se encuentran en casi todos los grupos de aves. Aunque han sido ampliamente estudiados a nivel taxonómico, mucha diversidad permanece sin ser descrita y todavía hay muchas preguntas abiertas sobre la biología, ecología y evolución de estos ectosimbiontes. Un mejor conocimiento de las comunidades de los ácaros de las plumas en diferentes niveles de su organización biológica puede contribuir a nuestra comprensión de la ecología evolutiva de las interacciones entre aves y ácaros, y de la evolución de la biodiversidad de los parásitos en general. El objetivo principal de esta tesis ha sido investigar los factores evolutivos y ecológicos que influyen la diversidad y la estructura de la comunidad de los ácaros de las plumas en aves marinas del Océano Atlántico y del Mediterráneo. Las especies de aves albergan una fauna de ácaros diversa y única compuesta por 38 especies perteneciendo a 10 géneros y tres familias. Cada género de ave albergaba una comunidad distinta de ácaros y solo tres especies de ácaros fueron compartidos por dos géneros cercanos de pardelas. Diecisiete de las 38 especies encontradas eran nuevas, no descritas; descripciones formales de seis especies están incluidas en esta tesis. Los datos moleculares correlacionaron bien con las descripciones morfológicas, pero también revelaron la presencia de seis especies cripticas pertenecientes a cuatro géneros de ácaros. Los patrones de la estructura genética de los ácaros fueron variables tanto entre los diferentes huéspedes simpátricos y entre la misma especie de huésped en diferentes regiones geográficas. La gran mayoría de las especies de ácaros de aves marinas simpátricas exhibió fuertes patrones de estructura genética asociados al huésped. Al comparar las comunidades de ácaros entre especies hermanas del mismo género de huésped, algunas especies de ácaros no estaban genéticamente estructuradas tanto entre huéspedes como entre localidades, mientras que otras especies presentaron diferenciación entre poblaciones. Estas diferencias observadas corresponden con el uso de microhabitats en el cuerpo del huésped. No se encontró ninguna diferenciación genética entre las localidades para los ácaros, sugiriendo que la dispersión de los ácaros se produce regularmente entre las poblaciones de huéspedes. La distribución de dos especies de ácaros que coocurren en las plumas del vuelo de Calonectris borealis mostró una clara segregación espacial entre plumas resultada de una combinación de adaptaciones específicas de hábitat y la competición en curso. Los análisis isotópicos de la dieta de los ácaros indicaron que las dos especies de ácaros comparten los mismos recursos alimenticios provenientes del huésped, probablemente aceite de la glándula uropígeal y material exógeno. En conjunto, esta tesis destaca la gran y poco conocida diversidad de los ácaros de las plumas albergada por las aves marinas y contribuye a una mejor comprensión de los procesos ecológicos y evolutivos que conlleva dicha alta diversidad.