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The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments. ; This work was supported by a research grant from the Fundación BBVA (Spain). DP is also supported by the Ramón y Cajal programme of the Spanish Government. ; Peer reviewed

Oceanic archipelagos are excellent systems for studying speciation, yet inference of evolutionary process requires that the colonization history of island organisms be known with accuracy. Here, we used phylogenomics and patterns of genetic diversity to infer the sequence and timing of colonization of Macaronesia by mainland common chaffinches (Fringilla coelebs), and assessed whether colonization of the different archipelagos has resulted in a species-level radiation. To reconstruct the evolutionary history of the complex we generated a molecular phylogeny based on genome-wide SNP loci obtained from genotyping-by-sequencing, we ran ancestral range biogeographic analyses, and assessed fine-scale genetic structure between and within archipelagos using admixture analysis. To test for a species-level radiation, we applied a probabilistic tree-based species delimitation method (mPTP) and an integrative taxonomy approach including phenotypic differences. Results revealed a circuitous colonization pathway in Macaronesia, from the mainland to the Azores, followed by Madeira, and finally the Canary Islands. The Azores showed surprisingly high genetic diversity, similar to that found on the mainland, and the other archipelagos showed the expected sequential loss of genetic diversity. Species delimitation methods supported the existence of several species within the complex. We conclude that the common chaffinch underwent a rapid radiation across Macaronesia that was driven by the sequential colonization of the different archipelagos, resulting in phenotypically and genetically distinct, independent evolutionary lineages. We recommend a taxonomic revision of the complex that takes into account its genetic and phenotypic diversity. ; The research was funded by Spain's Ministry of Science grants CGL2015-66381P, PGC-2018-098897-B-I00, and PGC2018-097575-B-I00. MR was supported by a doctoral fellowship from the Spanish Ministry of Education, Culture, and Sport (FPU16/05724), and JCI was funded by a GRUPIN research grant from the Regional Government of Asturias (Ref.: IDI/2018/000151). ; Peer reviewed

The mud snails endemic to the East Atlantic/Mediterranean region (genus Tritia; subfamily Nassariinae) account for the second highest diversity within the family Nassariidae (Gastropoda: Buccinoidea). In order to understand how the diversity of species, shell morphologies and ecological traits evolved within this genus, a robust phylogenetic framework is needed, yet still unavailable due to high levels of homoplasy in shell morphology, the main trait used for their taxonomic classification. Here, the near-complete mitogenomes of 20 species representing more than half of the diversity of Tritia were sequenced. All mitogenomes of Tritia shared the same gene order, which is identical to the consensus reported for caenogastropods. The reconstructed phylogeny indicates that all analysed Tritia species formed a natural group except Tritia vaucheri, which was sister to an early diverging clade within subfamily Nassariinae that includes species of genus Reticunassa sister to Nassarius jacksonianus and Nassarius sp. Within Tritia, the North-west Atlantic species Tritia obsoleta was placed as the sister group of three mostly East Atlantic/Mediterranean clades (I-III), prompting the reinstatement of the genus Ilyanassa. The latter three clades corresponded to different shell features (I, shell mostly with marked sculpture; II, shell with strong nodules and small size; and III, smooth shell). For Tritia incrassata, the analysed specimens from Norway and from the Spanish Mediterranean coasts showed notable genetic divergence, which may indicate the existence of cryptic species. The ancestral character state reconstruction of protoconch inferred that the ancestor of Tritia had planktotrophic larvae and that a transition to lecithotrophy occurred independently at least three times within Nassariinae. The reconstructed chronogram dated the origin of Tritia in the Oligocene and main diversification events during the Miocene to Pleistocene, correlated with drastic shifts in local paleoecosystems caused by cooling events, eustatic sea level changes and the Messinian Salinity Crisis that favoured temperate taxa. ; This work was funded by the Spanish Ministry of Economy, Industry and Competitiveness (CGL2016-75255-C2-1-P [AEI/FEDER, UE] to R.Z.; BES-2014-069575 to S.A). Yi Yang was supported by a scholarship from the China Scholarship Council (CSC-201806330034) for studying and living abroad. The project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 865101) to NP. ; Peer reviewed

[Background] The European mink (Mustela lutreola, L. 1761) is a critically endangered mustelid, which inhabits several main river drainages in Europe. Here, we assess the genetic variation of existing populations of this species, including new sampling sites and additional molecular markers (newly developed microsatellite loci specific to European mink) as compared to previous studies. Probabilistic analyses were used to examine genetic structure within and between existing populations, and to infer phylogeographic processes and past demography. ; [Results] According to both mitochondrial and nuclear microsatellite markers, Northeastern (Russia, Estonia and Belarus) and Southeastern (Romania) European populations showed the highest intraspecific diversity. In contrast, Western European (France and Spain) populations were the least polymorphic, featuring a unique mitochondrial DNA haplotype. The high differentiation values detected between Eastern and Western European populations could be the result of genetic drift in the latter due to population isolation and reduction. Genetic differences among populations were further supported by Bayesian clustering and two main groups were confirmed (Eastern vs. Western Europe) along with two contained subgroups at a more local scale (Northeastern vs. Southeastern Europe; France vs. Spain). ; [Conclusions] Genetic data and performed analyses support a historical scenario of stable European mink populations, not affected by Quaternary climate oscillations in the Late Pleistocene, and posterior expansion events following river connections in both North- and Southeastern European populations. This suggests an eastern refuge during glacial maxima (as already proposed for boreal and continental species). In contrast, Western Europe was colonised more recently following either natural expansions or putative human introductions. Low levels of genetic diversity observed within each studied population suggest recent bottleneck events and stress the urgent need for conservation measures to counteract the demographic decline experienced by the European mink. ; This work was partially funded by three LIFE projects ("Conservación del visón europeo (Mustela lutreola) en "Castilla León" LIFE 00/NAT/E7229, La Rioja" LIFE 00/NAT/E7331 and "Álava" LIFE 00/NAT/E7335), and grants from the Diputación Foral de Álava and the University of the Basque Country (GIU 06/09) awarded to BJGM. The Basque Government (BG) also financed this study (project numbers IT317-10; IT575-13). ; We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI). ; Peer Reviewed

Times Cited: 0Gillet, F. Garrido, M. T. Cabria Blanc, F. Fournier-Chambrillon, C. Nemoz, M. Sourp, E. Vial-Novella, C. Zardoya, R. Aulagnier, S. Michaux, J. R.Conservatoire d'Espaces Naturels de Midi-Pyrenees (CEN-MP) [LIFE13NAT/FR/000092]; European Union Funding Network (ERDF); European Union Funding Network (LIFE+); Agence de l'eau Adour-Garonne; Agence de l'eau Rhone-Mediterranee-Corse; DREAL Aquitaine, Midi-Pyrenees, and Languedoc-Roussillon; Conseil Regional Aquitaine, Midi-Pyrenees and Languedoc-Roussillon; Conseil General des Pyrenees-Atlantiques, de l'Aude et des Pyrenees-Orientales; EDF; SHEM; Patagonia; Parc National des Pyrenees; ANRT (Association Nationale de la Recherche et de la Technologie); ANRT (CIFRE) [2011/1571]We thank the following people who collected tissue samples: EDF agents, Pyrenees National Park agents, M. Bayon, A. Bertrand, J.-P. Besson, J.-P. Quere, A. Charbonnel, F. Elzear, L. Fabre, P. Fantin, B. Le Roux, V. Lacaze, M. Lagardere, F. Lasserre, B. Le Corre, M. Mas, P. Maunas, G. Nogue, F. Prud'Homme, T. Quintilla, B. Salmeron, T. Tico, S. Torreilles, and S. Vernet. We also thank representatives of the following organizations who collected feces samples: Association des Naturalistes de l'Ariege, Conservatoire d'Espaces Naturels d'Aquitaine, Conservatoire d'Espaces Naturels de Midi-Pyrenees, Federation Aude Claire, Federation des Reserves Naturelles Catalanes, Groupe de Recherche et d'Etude pour la Gestion de l'Environnement, Office National de la Chasse et de la Faune Sauvage, Office National des Forets, and Parc National des Pyrenees. This study is part of the "Plan National d'Actions en faveur du Desman des Pyrenees" and the LIFE+ Desman project (LIFE13NAT/FR/000092) which are coordinated by the Conservatoire d'Espaces Naturels de Midi-Pyrenees (CEN-MP) and financially supported by the following structures: European Union Funding Network (ERDF and LIFE+), Agence de l'eau Adour-Garonne, Agence de l'eau Rhone-Mediterranee-Corse, DREAL Aquitaine, Midi-Pyrenees, and ...

Times Cited: 0Gillet, F. Garrido, M. T. Cabria Blanc, F. Fournier-Chambrillon, C. Nemoz, M. Sourp, E. Vial-Novella, C. Zardoya, R. Aulagnier, S. Michaux, J. R.Conservatoire d'Espaces Naturels de Midi-Pyrenees (CEN-MP) [LIFE13NAT/FR/000092]; European Union Funding Network (ERDF); European Union Funding Network (LIFE+); Agence de l'eau Adour-Garonne; Agence de l'eau Rhone-Mediterranee-Corse; DREAL Aquitaine, Midi-Pyrenees, and Languedoc-Roussillon; Conseil Regional Aquitaine, Midi-Pyrenees and Languedoc-Roussillon; Conseil General des Pyrenees-Atlantiques, de l'Aude et des Pyrenees-Orientales; EDF; SHEM; Patagonia; Parc National des Pyrenees; ANRT (Association Nationale de la Recherche et de la Technologie); ANRT (CIFRE) [2011/1571]We thank the following people who collected tissue samples: EDF agents, Pyrenees National Park agents, M. Bayon, A. Bertrand, J.-P. Besson, J.-P. Quere, A. Charbonnel, F. Elzear, L. Fabre, P. Fantin, B. Le Roux, V. Lacaze, M. Lagardere, F. Lasserre, B. Le Corre, M. Mas, P. Maunas, G. Nogue, F. Prud'Homme, T. Quintilla, B. Salmeron, T. Tico, S. Torreilles, and S. Vernet. We also thank representatives of the following organizations who collected feces samples: Association des Naturalistes de l'Ariege, Conservatoire d'Espaces Naturels d'Aquitaine, Conservatoire d'Espaces Naturels de Midi-Pyrenees, Federation Aude Claire, Federation des Reserves Naturelles Catalanes, Groupe de Recherche et d'Etude pour la Gestion de l'Environnement, Office National de la Chasse et de la Faune Sauvage, Office National des Forets, and Parc National des Pyrenees. This study is part of the "Plan National d'Actions en faveur du Desman des Pyrenees" and the LIFE+ Desman project (LIFE13NAT/FR/000092) which are coordinated by the Conservatoire d'Espaces Naturels de Midi-Pyrenees (CEN-MP) and financially supported by the following structures: European Union Funding Network (ERDF and LIFE+), Agence de l'eau Adour-Garonne, Agence de l'eau Rhone-Mediterranee-Corse, DREAL Aquitaine, Midi-Pyrenees, and Languedoc-Roussillon, Conseil Regional Aquitaine, Midi-Pyrenees and Languedoc-Roussillon, Conseil General des Pyrenees-Atlantiques, de l'Aude et des Pyrenees-Orientales, EDF, SHEM, Patagonia, Parc National des Pyrenees, and ANRT (Association Nationale de la Recherche et de la Technologie). FG is supported by a French research fellowship provided by ANRT (CIFRE No 2011/1571).01545-1542 ; The Pyrenean desman (Galemys pyrenaicus) is a small, semiaquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in cold and well-oxygenated flowing mountain streams. This species is currently classified as vulnerable on the IUCN Red List and has been undergoing habitat loss and fragmentation for decades, inevitably impacting its distribution. A recent genetic study, based on mitochondrial and intronic sequences, showed that the genetic variability of the Pyrenean desman is very low in the Pyrenees. In this study, we investigated the potential existence of genetic structure and gene flow at a smaller scale using 24 polymorphic microsatellite loci. As the Pyrenean desman is a very elusive species, we supplemented our tissue sample collection with samples of feces collected in the French range of this species. We successfully identified 70 individuals based on 355 fecal samples. Bayesian analyses revealed 3 genetic and geographic clusters (1 eastern, 1 central, and 1 western, including 3 genetic subclusters), with origins tracing back only 200 years. These clusters were characterized by low levels of genetic diversity and high inbreeding coefficients. Although gene flow among clusters appeared to be limited, populations seem to have exchanged alleles recently. Therefore, connectivity between watersheds should be enhanced to maintain genetic diversity and potentially improve the long-term survival of the Pyrenean desman in France.