110 results on '"Riutort M"'
Search Results
2. CpG methylation frequency of TET2, GRIA2, and CDKN2A genes in the North Atlantic fin whale varies with age and between populations
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Garcia-Vernet, R, Martin, B, Peinado, MA, Vikingsson, G, Riutort, M, and Aguilar, A
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cetaceans ,Atlàntic, Oceà ,epigenetics ,Genes ,population biology ,Whales ,molecular biology ,marine mammals ,Metilació ,Methylation ,Atlantic Ocean ,Gens ,Balenes - Abstract
Recovery rates for baleen whales that were decimated by exploitation vary between species and populations. Age determination is critical for the understanding of recovery trends and population structure, but determining age in free-ranging individuals remains challenging. Recent research has suggested that the methylation level of some genes in skin samples may provide age determinations with accuracy. We selected nine CpG sites from three genes (TET2, CDKN2A, and GRIA2) and analyzed them in 40 skin samples from known-age individuals pertaining to two different populations of fin whales from the North Atlantic. We observed significant correlations with age in five CpG sites. We used three of these CpG sites to perform an epigenetic age estimation. Predictions had a standard deviation of 2.94, but regression between observed and predicted ages showed a clear underestimation for older fin whales. For further development, we suggest: (1) screening for new CpG sites associated with age that exhibit higher variability between individuals, and (2) including older animals whenever the sampling allows it. We also observed subtle, but significant differences between the two populations studied in one of the CpG sites (TET2_CpG + 21). We attributed these differences to genetic differences or to the dissimilar environments that affect both populations.
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- 2021
3. A new turbellarian parasite inflicting serious mortalities in red drum aquaculture
- Author
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Montero, Francisco Esteban, Estensoro, Itziar, Leria, L., Víllora-Montero, M., Planas, E., Riutort, M., and Sitjà-Bobadilla, Ariadna
- Abstract
Trabajo presentado en la International Conference & Exposition Aquaculture Europe, celebrada en Funchal, Maderia (Portugal) del 04 al 07 de octubre de 2021., [Introduction]: Turbellarian flatworms are controverted organisms with changing taxonomical adscription. Most of these platyhelminths are terrestrial and aquatic free-living organisms, but also include symbiotic species, and few cases of parasitic ones associated to fish, crustaceans and molluscs. Here, we report an epizootic due to a rhabdocoelan infection in cultured red drum (Sciaenops ocellatum) in a sea-cage farm in a tropical area. We describe the morphological, histological and molecular approaches for its identification., [Methods]: Two subsequent outbreaks in 2018-2019 affected red drum in the first year after entering the farm (weight ranging from 12g to 180 g). Water temperature ranged from 23 to 29.5°C and salinity was 36 ‰. Different types of samples of fish presenting acute mortalities and clinical signs were taken. Fresh smears of gills were observed at light microscope on site. Necropsied gills were fixed in 10% neutral buffered formalin (NBF), processed routinely, embedded in Technovit7100-resin, sectioned at 1 µm and stained with Giemsa, PAS, and alcian blue-PAS. Some NBF-fixed specimens were dehydrated, cleared with dimethyl phthalate and stained with iron acetic carmine. Another sample set was stored in 70% ethanol for molecular identification. The ribosomal genes 18S and 28S were PCR-amplified (Giribet et al., 1996; Jovelin & Justine, 2001) and used concatenated to infer a phylogeny by Bayesian inference. Other representatives of Rhabdocoela present in GenBank were included in the analyses. Bacterial samples were taken for basic bacteriological analysis., [Results]: Prevalence of infection was 100 % in some stocks, and mortality ranged from 5% to 60%. Clinical signs included anaemia, weight loss, pale and necrotic gills with mucous masses, desquamation and erosion of the skin, and asphyxiation. Bacteriological results were variable, from negative to opportunistic bacteria or septicaemia, often accompanied by splenomegaly. Microscopical observation of gill scrapings of affected fish revealed ciliated turbellarians with eyespots. When gravid adults were mounted in seawater under a glass coverslip, active swimming eyed juvenile emerged. Worms, with characteristic anterior eyes, were visible under low magnification (Fig. 1). The morphometric study of fixed worms showed that adults were elongated, piriform with pointed posterior end (854-1403 × 356-589 µm) and a short anterior distal projection. Eyespots were separated. Pharynx was subconical and anterior. Testes and ovary were small and follicular. Some large specimens exhibited numerous completely developed juveniles occupying most of the body. Based on the body shape, pharynx arrangement and the presence of juveniles, the worms were tentatively assigned to the family Graffillidae. Histologically, worms were placed in shallow epithelial tunnels on secondary and primary lamella, and even on the cartilages of gill arches, and some small specimens were found free among gill filaments (Fig.1). The infection caused destruction of the normal gill architecture with minor histopathological reaction, lacking signs of necrosis or inflammation. Among the epithelial host cells forming the tunnel walls, little or no focal hyperplasia was observed. The primary direct effect of the turbellarian gill infection was the loss of respiratory function by impairment of gas exchange in parasitized lamella. In some sections, long filamentous bacteria covered the tissue and worm surface, suggesting secondary bacterial infections involved in the epizootic case. The worms enclosed within epithelial tunnels appeared to be covered by a sheath of cellular and mucous material. The molecular study placed the parasite within the Order Rhabdocoela, Suborder Dalytyphloplanida and Infraorder Neodalyellida. However, it was highly divergent from all the deposited sequences of the group, indicating that it may belong to a new species not yet described. It did not match with the recent sequence of the old known Pseudografillaria arenicola (Meixner, 1938), and it could be similar to a turbellarian causing epitozootics (with mortalities > 60%) in the same fish species as well as in other cultured marine fish in China (Wang et al., 2002). Attempts to treat the infections with formalin baths were unsuccessful., [Conclusions]: The histological examination revealed the invasive nature of the worms infecting red drum, and the gill damage could easily explain the anaemia and the asphyxiation of the fish. According to the obtained molecular data, the available orphan sequences and morphological descriptions, the species could be new to science, but probably present in other far distant locations and hosts. Studies are ongoing for the full description of the species. The current study and the previous reports on turbellarians causing lesions on various marine fish from the Pacific, Caribbean, Chinese and Australian waters, suggest that these parasites may represent and emerging problem in aquaculture, as they are transmitted fish-to-fish, and topic treatments can be ineffective since they live within gill tissues. Future studies are needed to decipher if other reservoir hosts could be involved in its transmission to cultured fish, and which farming conditions favour its blooming.
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- 2021
4. Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)
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Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G
- Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.
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- 2021
5. Dense sampling of bird diversity increases power of comparative genomics
- Author
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Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G
- Abstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
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- 2020
6. Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot
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Álvarez-Presas, M., Carbayo, F., Rozas, J., and Riutort, M.
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- 2011
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7. First report of the land planarian Diversibipalium multilineatum (Makino & Shirasawa, 1983) (Platyhelminthes, Tricladida, Continenticola) in Europe
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Mazza, G, Menchetti, M, Sluys, R, Sola, E, Riutort, M, Tricarico, E, Justine, Jl, Cavigioli, L, and Mori, E
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- 2016
8. Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms
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Escriva, H, Solà, E, Álvarez-Presas, M, Frías-López, C, Littlewood, T, Rozas, J, Riutort, M, Escriva, H, Solà, E, Álvarez-Presas, M, Frías-López, C, Littlewood, T, Rozas, J, and Riutort, M
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- 2015
9. Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot
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Riutort, M.
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BIODIVERSIDADE - Published
- 2011
10. Conscious recollection in autobiographical memory: an investigation in schizophrenia
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Danion , J.M., Cuervo , C., Piolino , P., Huron , C., Riutort , M., Peretti , C.-S., Eustache , F., Psychopathologie et pharmacologie de la cognition, Institut National de la Santé et de la Recherche Médicale (INSERM), Physiopathologie clinique et expérimentale de la schizophrénie, Université Louis Pasteur - Strasbourg I-IFR37-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Psychologie et Neurosciences Cognitives (LPNCog / UMR 8189), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Neuropsychologie, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École pratique des hautes études (EPHE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Cognition et Comportement (FRE 2987), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), Neuropsychologie cognitive et neuroanatomie fonctionnelles de la mémoire humaine, Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Louis Pasteur - Strasbourg I-IFR37-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Psychologie et Neurosciences Cognitives ( LPNCog ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -École pratique des hautes études ( EPHE ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire Cognition et Comportement, Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Lahaye, Eliane, Normandie Université (NU)-Normandie Université (NU)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Laboratoire Cognition et Comportement ( FRE 2987 )
- Subjects
[ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,[SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2005
11. Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism
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Álvarez-Presas, M, primary, Sánchez-Gracia, A, additional, Carbayo, F, additional, Rozas, J, additional, and Riutort, M, additional
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- 2014
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12. Structure and expression of Spk-1, an src-related gene product found in the planarian Dugesia (G) tigrina
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Burgaya, F., Jordi Garcia-Fernandez, Riutort, M., Baguna, J., and Salo, E.
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Genes, src ,src-Family Kinases ,Base Sequence ,Molecular Sequence Data ,Animals ,RNA ,Regeneration ,Amino Acid Sequence ,Planarians ,Protein-Tyrosine Kinases ,Blotting, Northern ,Biological Evolution ,Polymerase Chain Reaction - Abstract
A cDNA clone encoding a 497 amino acid protein 75% similar to most Src proteins has been isolated from the planarian Dugesia (Girardia) tigrina (Platyhelminthes; Turbellaria) by PCR followed by screening procedures. This gene product has been designated Spk-1 as it is the first Src-related kinase isolated in a planarian. The predicted amino acid sequence of Spk-1 suggest that it is anchored to the plasma membrane and that it interacts with other phosphotyrosine proteins. Spk-1 is expressed in both intact and regenerating organisms as an mRNA transcript of about 1.9 kb. Planarians, which conserve most features of the common ancestor to protostomian and deuterostomian phyla, are the most primitive triploblastic organisms from which a protein tyrosine kinase gene product has been isolated. The presence of this gene product in such a primitive organism, and its presumed role, are discussed.
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- 1994
13. Esclaus a Inca al llarg del S. XV
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Matas Riutort, M. Antònia and Vidal Mateu, Aina M.
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History ,Slavery Spain Inca 15th century - Published
- 1994
14. Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal Acoelomorpha
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Paps, J., primary, Baguna, J., additional, and Riutort, M., additional
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- 2009
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15. Effectiveness of community health agents' actions in situations of social vulnerability
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Zanchetta, M. S., primary, McCrae Vander Voet, S., additional, Galhego-Garcia, W., additional, Smolentzov, V. M. N., additional, Talbot, Y., additional, Riutort, M., additional, Galhego, A. M. M. F., additional, de Souza, T. J., additional, Caldas, R. S., additional, Costa, E., additional, Kamikihara, M. M., additional, and Smolentzov, S., additional
- Published
- 2008
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16. Reduced levels of specific autobiographical memories in schizophrenia
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Danion, J., primary, Riutort, M., additional, Cuervo, C.V., additional, Peretti, C.S., additional, and Salame´, P., additional
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- 2003
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17. Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences
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Carranza, S., primary, Baguna, J., additional, and Riutort, M., additional
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- 1997
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18. Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida)
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Carranza, S., primary, Giribet, G., additional, Ribera, C., additional, and Riutort, M., additional
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- 1996
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19. First molecular evidence for the existence of a Tardigrada + Arthropoda clade
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Giribet, G., primary, Carranza, S., additional, Baguna, J., additional, Riutort, M., additional, and Ribera, C., additional
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- 1996
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20. Enzyme electrophoresis, 18S rRNA sequences, and levels of phylogenetic resolution among several species of freshwater planarians (Platyhelminthes, Tricladida, Paludicola)
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Riutort, M., primary, Field, K. G., additional, Turbeville, J. M., additional, Raff, R. A., additional, and Baguña, J., additional
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- 1992
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21. Effectiveness of community health agents' actions in situations of social vulnerability.
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Zanchetta MS, McCrae Vander Voet S, Galhego-Garcia W, Smolentzov VM, Talbot Y, Riutort M, Galhego AM, de Souza TJ, Caldas RS, Costa E, Kamikihara MM, and Smolentzov S
- Published
- 2009
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22. A reappraisal of the phylogenetic and taxonomic position of land planarians (Platyhelminthes, Turbellaria, Tricladida) inferred from 18S rDNA sequences
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Carranza, S., Ruiz-Trillo, I., Littlewood, D.T.J., Riutort, M., and Baguñà, J.
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- 1998
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23. Cartes a un obrer II
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Riutort, M.
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Multidisciplinar - Abstract
not available
- Published
- 1917
24. First molecular evidence for the existence of a Tardigrada plus arthropoda clade
- Author
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Giribet, G., Salvador Carranza, Baguna, J., Riutort, M., and Ribera, C.
25. A reappraisal of the phylogenetic and taxonomic position of land planarians (Platyhelminthes, Turbellaria, Tricladida) inferred from 18S rDNA sequences
- Author
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Salvador Carranza, Ruiz-Trillo, I., Littlewood, D. T. J., Riutort, M., and Baguna, J.
26. Schmidtea mediterranea phylogeography: an old species surviving on a few Mediterranean islands?
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Pala Maria, Stocchino Giacinta A, Harrath Abdul, Lázaro Eva M, Baguñà Jaume, and Riutort Marta
- Subjects
Evolution ,QH359-425 - Abstract
Abstract Background Schmidtea mediterranea (Platyhelminthes, Tricladida, Continenticola) is found in scattered localities on a few islands and in coastal areas of the western Mediterranean. Although S. mediterranea is the object of many regeneration studies, little is known about its evolutionary history. Its present distribution has been proposed to stem from the fragmentation and migration of the Corsica-Sardinia microplate during the formation of the western Mediterranean basin, which implies an ancient origin for the species. To test this hypothesis, we obtained a large number of samples from across its distribution area. Using known and new molecular markers and, for the first time in planarians, a molecular clock, we analysed the genetic variability and demographic parameters within the species and between its sexual and asexual populations to estimate when they diverged. Results A total of 2 kb from three markers (COI, CYB and a nuclear intron N13) was amplified from ~200 specimens. Molecular data clustered the studied populations into three groups that correspond to the west, central and southeastern geographical locations of the current distribution of S. mediterranea. Mitochondrial genes show low haplotype and nucleotide diversity within populations but demonstrate higher values when all individuals are considered. The nuclear marker shows higher values of genetic diversity than the mitochondrial genes at the population level, but asexual populations present lower variability than the sexual ones. Neutrality tests are significant for some populations. Phylogenetic and dating analyses show the three groups to be monophyletic, with the west group being the basal group. The time when the diversification of the species occurred is between ~20 and ~4 mya, although the asexual nature of the western populations could have affected the dating analyses. Conclusions S. mediterranea is an old species that is sparsely distributed in a harsh habitat, which is probably the consequence of the migration of the Corsica-Sardinia block. This species probably adapted to temperate climates in the middle of a changing Mediterranean climate that eventually became dry and hot. These data also suggest that in the mainland localities of Europe and Africa, sexual individuals of S. mediterranea are being replaced by asexual individuals that are either conspecific or are from other species that are better adapted to the Mediterranean climate.
- Published
- 2011
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27. 18S rRNA Sequences and Phylogeny of Platyhelminthes
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Riutort, M., Field, K. G., Raff, R. A., and a, J. Bagu
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- 1993
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28. Women's attitudes towards intimate partner violence in Guyana: a population-based study.
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Joseph G, Branas CC, Rupnarain S, Riutort M, and Morrison CN
- Abstract
Background: Intimate partner violence (IPV) against women is a global health issue and a breach of human rights. However, the literature lacks understanding of how socioeconomic and geographic disparities influence women's attitudes toward IPV in Guyana over time. This study aimed to assess trends in women's attitudes about IPV in Guyana., Methods: Data from three nationally representative surveys from 2009, 2014 to 2019 were analysed. The prevalence of women's attitudes about IPV was assessed, specifically in response to going out without telling their partners, neglecting their children, arguing with their partner, refusing sex with their partner, or burning food prepared for family meals. A series of stratified subgroup analyses were also completed. We assessed trends in IPV using the slope index of inequality (SII) and the concentration index of inequality (CIX). We used multilevel mixed-effects logistic regression to assess factors associated with women's attitudes justifying IPV., Findings: The prevalence of women's attitudes justifying IPV for any of the five reasons declined from 16.4% (95% CI: 15.1-17.8) in 2009 to 10.8% (95% CI: 9.7-12.0) in 2019. Marked geographic and socioeconomic inequalities were observed among subgroups. The SII for any of the five reasons decreased from -20.02 to -14.28, while the CIX remained constant over time. Key factors associated with women's attitudes about IPV were area of residence, sex of the household head, marital status, respondent's level of education, wealth index quintile, and the frequency of reading newspapers/magazines., Interpretation: From 2009 to 2019, Guyana was able to reduce women's attitudes justifying IPV against women by 34.1% and shortened subgroup inequalities. However, the prevalence remained high in 2019, with persisted inequalities among subgroups. Effective strategies, including the use of media to raise awareness, promotion of community-based approaches, and educational campaigns focusing on geographic and socioeconomic disparities, are essential for continuing to reduce the prevalence of IPV and associated inequalities., Funding: The study was funded in part by the National Institutes of Health, Fogarty International Center grant number D43TW012189., Competing Interests: We declare no competing interests., (© 2024 The Author(s).)
- Published
- 2024
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29. The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics.
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Corominas M, Marquès-Bonet T, Arnedo MA, Bayés M, Belmonte J, Escrivà H, Fernández R, Gabaldón T, Garnatje T, Germain J, Niell M, Palero F, Pons J, Puigdomènech P, Initiative For The Earth BioGenome Project TC, Arroyo V, Cuevas-Caballé C, Obiol JF, Gut I, Gut M, Hidalgo O, Izquierdo-Arànega G, Pérez-Sorribes L, Righi E, Riutort M, Vallès J, Rozas J, Alioto T, and Guigó R
- Abstract
The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories (Catalan Linguistic Area, CLA). These territories represent a biodiversity hotspot. While covering less than 1% of Europe, they are home to about one fourth of all known European eukaryotic species. These include a high proportion of endemisms, many of which are threatened. This trend is likely to get worse as the effects of global change are expected to be particularly severe across the Mediterranean Basin, particularly in freshwater ecosystems and mountain areas. Following the EBP model, the CBP is a networked organization that has been able to engage many scientific and non-scientific partners. In the pilot phase, the genomes of 52 species are being sequenced. As a case study in biodiversity conservation, we highlight the genome of the Balearic shearwater Puffinus mauretanicus , sequenced under the CBP umbrella., (© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
- Published
- 2024
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30. Correction: Epigenetic, psychological, and EEG changes after a 1-week retreat based on mindfulness and compassion for stress reduction in healthy adults: Study protocol of a cross-over randomized controlled trial.
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Diez GG, Martin-Subero I, Zangri RM, Kulis M, Andreu C, Blanco I, Roca P, Cuesta P, García C, Garzón J, Herradón C, Riutort M, Baliyan S, Venero C, and Vázquez C
- Abstract
[This corrects the article DOI: 10.1371/journal.pone.0283169.]., (Copyright: © 2024 Diez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2024
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31. Epigenetic, psychological, and EEG changes after a 1-week retreat based on mindfulness and compassion for stress reduction in healthy adults: Study protocol of a cross-over randomized controlled trial.
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Diez GG, Martin-Subero I, Zangri RM, Kulis M, Andreu C, Blanco I, Roca P, Cuesta P, García C, Garzón J, Herradón C, Riutort M, Baliyan S, Venero C, and Vázquez C
- Subjects
- Humans, Adult, Empathy, Hydrocortisone, Electroencephalography, Stress, Psychological psychology, Treatment Outcome, Randomized Controlled Trials as Topic, Mindfulness methods, Meditation methods
- Abstract
Introduction: The main objective of the study will be to evaluate the effects of two widely used standardized mindfulness-based programs [Mindfulness-Based Stress Reduction (MBSR) and Compassion Cultivation Training (CCT)], on epigenetic, neurobiological, psychological, and physiological variables., Methods: The programs will be offered in an intensive retreat format in a general population sample of healthy volunteer adults. During a 7-day retreat, participants will receive MBSR and CCT in a crossover design where participants complete both programs in random order. After finishing their first 3-day training with one of the two programs, participants will be assigned to the second 3-day training with the second program. The effects of the MBSR and CCT programs, and their combination, will be measured by epigenetic changes (i.e., DNA methylation biomarkers), neurobiological and psychophysiological measures (i.e., EEG resting state, EKG, respiration patterns, and diurnal cortisol slopes), self-report questionnaires belonging to different psychological domains (i.e., mindfulness, compassion, well-being, distress, and general functioning), and stress tasks (i.e., an Arithmetic Stress Test and the retrieval of negative autobiographical memories). These measures will be collected from both groups on the mornings of day 1 (pre-program), day 4 (after finishing the first program and before beginning the second program), and day 7 (post-second program). We will conduct a 3-month and a 12-month follow-up using only the set of self-report measures., Discussion: This study aims to shed light on the neurobiological and psychological mechanisms linked to meditation and compassion in the general population. The protocol was registered at clinicaltrials.gov (Identifier: NCT05516355; August 23, 2022)., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Diez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
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32. Corrigendum to "Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds" [Mol. Phylogenet. Evol. 179 (2023) 107671].
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Obiol JF, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, and González-Solís J
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- 2023
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33. Molecular phylogenetics facilitates the first historical biogeographic analysis of the hammerhead worms (Platyhelminthes: Tricladida: Bipaliinae), with the description of twelve new species and two new genera.
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Sol E, Sluys R, Riutort M, and Kawakatsu M
- Subjects
- Animals, Phylogeny, Biodiversity, Ecosystem, Planarians
- Abstract
The hammerhead worms constitute a land planarian subfamily (Platyhelminthes: Tricladida: Bipaliinae) that is popular among natural historians as well as citizen scientists due to their characteristic semi-lunar-shaped head, the striking colours of many species, and the worldwide presence of introduced species, which has raised much concern about their putative impact on the receiving ecosystems. Despite such current awareness, the majority of Bipaliinae species was described before the second half of the 20th century. Over the past few decades, description of new species has been rather scarce. In the present paper, we describe twelve new species and two new genera from Madagascar, Borneo, and Japan, mainly using specimens that form part of the collections of Naturalis Biodiversity Center, Leiden. Species identification has been based on morphology, inner anatomy, and, when available, molecular information. Our molecular phylogenetic tree suggests that either Malagasy or Bornean representatives form the sister-group to the rest of Bipaliinae. The phylogeny suggests also that the Bipaliinae comprises several new and, as yet, undescribed genera. Although the geographical origin of the subfamily is uncertain and may involve either Madagascar or the Bornean region, a molecular time-calibration of the phylogenetic tree indicated that the origin of the Bipaliinae may date back to about 253 Mya, placing its origin near the Permian-Triassic transition and, thus, on Pangea.
- Published
- 2023
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34. Phylogenetic relationships of the Geoplaninae land planarians (Platyhelminthes, Tricladida) assessed with a total evidence approach, with the description of a new species of Gigantea.
- Author
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Lago-Barcia D, Álvarez-Presas M, Riutort M, Oceguera-Figueroa A, and Carbayo F
- Subjects
- Animals, Phylogeny, Planarians genetics
- Abstract
Several studies have focused on the phylogenetic relationships within the Geoplaninae land planarians (Tricladida). In those studies, ancient phylogenetic relationships remained obscure. In this work, the phylogeny of Geoplaninae is assessed through three different datasets, namely morphological, molecular, and both datasets combined, i.e, a total evidence approach (TE). The data matrix consisted of six DNA regions, including a newly developed marker (DOM5), and a morphological matrix with 37 characters. The study produced the best-resolved hypothesis so far for the phylogeny of Geoplaninae, although ancient clades still remain elusive. The effect of the morphological data on the TE tree topology and clade support is seemingly negligible. The phylogenetic tree also suggests that most of the diagnostic morphological characters of the genera are homoplastic, while unambiguous unique synapomorphies can characterize some supra-generic informal groupings., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)
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- 2023
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35. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds.
- Author
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Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, and González-Solís J
- Subjects
- Animals, Phylogeny, Species Specificity, Birds genetics, Genome, Genomics
- Abstract
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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36. Phylotranscriptomics interrogation uncovers a complex evolutionary history for the planarian genus Dugesia (Platyhelminthes, Tricladida) in the Western Mediterranean.
- Author
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Benítez-Álvarez L, Leria L, Fernández R, Mateos E, El Ouanighi Y, Bennas N, El Alami M, Yacoubi-Khebiza M, Ayt Ougougdal H, and Riutort M
- Subjects
- Animals, Phylogeny, Evolution, Molecular, Biodiversity, Europe, Planarians
- Abstract
The Mediterranean is one of the most biodiverse areas of the Paleartic region. Here, basing on large data sets of single copy orthologs obtained from transcriptomic data, we investigated the evolutionary history of the genus Dugesia in the Western Mediterranean area. The results corroborated that the complex paleogeological history of the region was an important driver of diversification for the genus, speciating as microplates and islands were forming. These processes led to the differentiation of three main biogeographic clades: Iberia-Apennines-Alps, Corsica-Sardinia, and Iberia-Africa. The internal relationships of these major clades were analysed with several representative samples per species. The use of large data sets regarding the number of loci and samples, as well as state-of-the-art phylogenomic inference methods allowed us to answer different unresolved questions about the evolution of particular groups, such as the diversification path of D. subtentaculata in the Iberian Peninsula and its colonization of Africa. Additionally, our results support the differentiation of D. benazzii in two lineages which could represent two species. Finally, we analysed here for the first time a comprehensive number of samples from several asexual Iberian populations whose assignment at the species level has been an enigma through the years. The phylogenies obtained with different inference methods showed a branching topology of asexual individuals at the base of sexual clades. We hypothesize that this unexpected topology is related to long-term asexuality. This work represents the first phylotranscriptomic analysis of Tricladida, laying the first stone of the genomic era in phylogenetic studies on this taxonomic group., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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37. Building Phylogenies from Transcriptomic Data.
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Benítez-Álvarez L, Leria L, Dols-Serrate D, and Riutort M
- Subjects
- Phylogeny, Biological Evolution, Genomics, Transcriptome, Evolution, Molecular
- Abstract
Transcriptomic data (obtained from RNA sequencing) has become a very powerful source of information to reconstruct the evolutionary relationships among organisms. Although phylogenetic inference using transcriptomes retains the same core steps as when working with few molecular markers (viz., nucleic acid extraction and sequencing, sequence treatment, and tree inference), all of them show significant differences. First, the needed quantity and quality of the extracted RNA has to be very high. Although this may not represent a challenge when working with certain organisms, it may well be a headache with others, especially for those with small body sizes. Second, the tremendous increase in the quantity of sequences obtained requires a high computational power for both treating the sequences and inferring the subsequent phylogenies. This means that transcriptomic data can no longer be analyzed using personal computers nor local programs with a graphical interface. This, in turn, implies the requirement of an increased set of bioinformatic skills from the researchers. Finally, the genomic peculiarities of each group of organisms, such as the level of heterozygosity or the percentage of base composition, also need to be considered when inferring phylogenies using transcriptomic data., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2023
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38. Suicidality and psychotic episodes after starting aripiprazole: two case reports.
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Meyer G, Gitahy Falcao Faria C, Beck M, Riutort M, Michel B, and Javelot H
- Subjects
- Aripiprazole adverse effects, Humans, Male, Paliperidone Palmitate, Risperidone adverse effects, Antipsychotic Agents adverse effects, Suicide
- Abstract
Switching antipsychotic medication must be done carefully to ensure patient safety and a successful response. Here, we present two major psychotic decompensations that occurred following a switch to aripiprazole in two patients with schizophrenia. Mr. X was treated with paliperidone and experienced residual anxiety. Thus, a switch to aripiprazole was planned with risperidone and a gradual decrease in paliperidone. Initially, an increase in aripiprazole resulted in remission of his residual symptoms. However, two weeks later, he presented an anxiety relapse with persecutory ideas which required hospitalization. Mr. Y, who was treated for many years with risperidone, presented with a treatment resistant psychotic episode. A switch to aripiprazole enhanced his clinical condition. Despite the initial improvement, soon after discharge from the hospital, the patient presented psychotic symptoms requiring home intervention. Ultimately, the patient in the midst of a delusional recrudescence, had killed himself when the health care team arrived. A strong dopamine antagonist may lead to the development of dopaminergic upregulation. The addition of a partial agonist to these hypersensitive neurotransmitter pathways could explain these episodes. We agree with previous reports and recommend careful management when switching from strong dopamine antagonists to aripiprazole., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)
- Published
- 2022
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39. The expansion continues: Girardia arrives in Africa. First record of Girardia sinensis (Platyhelminthes, Tricladida, Continenticola, Dugesiidae) in Morocco.
- Author
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Bentez-Lvarez L, Mateos E, Ouanighi YE, Bennas N, Alami ME, and Riutort M
- Subjects
- Animals, Morocco, Planarians
- Published
- 2022
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40. Island-specific evolution of a sex-primed autosome in a sexual planarian.
- Author
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Guo L, Bloom JS, Dols-Serrate D, Boocock J, Ben-David E, Schubert OT, Kozuma K, Ho K, Warda E, Chui C, Wei Y, Leighton D, Lemus Vergara T, Riutort M, Sánchez Alvarado A, and Kruglyak L
- Subjects
- Animals, Chromosome Mapping, Female, Genome genetics, Inbreeding, Male, Evolution, Molecular, Islands, Planarians genetics, Reproduction, Sex Chromosomes genetics
- Abstract
The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite
1,2 . Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5-13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome., (© 2022. The Author(s).)- Published
- 2022
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41. The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle.
- Author
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Cuevas-Caballé C, Ferrer Obiol J, Vizueta J, Genovart M, Gonzalez-Solís J, Riutort M, and Rozas J
- Subjects
- Animals, Demography, Genomics, Humans, Mammals, Predatory Behavior, Birds genetics, Endangered Species
- Abstract
The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater population size. Currently, populations of the species continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, with some studies predicting its extinction by 2070. Here, using a combination of short and long reads, we generate the first high-quality reference genome for the Balearic shearwater, with a completeness amongst the highest across available avian species. We used this reference genome to study critical aspects relevant to the conservation status of the species and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194-135 ka). Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision, and the development of natriuresis. The reference genome obtained will be the crucial in the future development of genetic tools in conservation efforts for this Critically Endangered species., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2022
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42. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds.
- Author
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Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González-Solís J, Rozas J, Riutort M, and Welch AJ
- Subjects
- Animals, Base Sequence, Phylogeny, Sequence Analysis, DNA, Biological Evolution, Birds genetics
- Abstract
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales. [Aves; incomplete lineage sorting; introgression; PE-ddRAD-Seq; phylogenomics; radiations; shearwaters; UCEs.]., (© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.)
- Published
- 2021
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43. Fructosyltransferase production by Aspergillus oryzae BM-DIA using solid-state fermentation and the properties of its nucleotide and protein sequences.
- Author
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Michel MR, Gallegos ACF, Villarreal-Morales SL, Aguilar-Zárate P, Aguilar CN, Riutort M, and Rodríguez-Herrera R
- Subjects
- Nucleotides chemistry, Proteins chemistry, Aspergillus oryzae enzymology, Aspergillus oryzae genetics, Fermentation, Hexosyltransferases biosynthesis, Hexosyltransferases chemistry, Industrial Microbiology methods
- Abstract
Fructosyltransferase (FTase) catalyzes the transfer of a fructosyl group to a sucrose molecule or a fructooligosaccharide (FOS) when a FOS with a longer chain is formed. Production of FTase by two Aspergillus species and its mixture was exploited using solid-state fermentation (SSF) and employing agave sap as substrate. The maximum FTase activity (1.59 U/mL) by Aspergillus oryzae was obtained after 24 h, using a temperature of 30 °C, with an inoculum of 2 × 10
7 spores/mL. The nucleotide sequence coding for the fructosyltransferase showed 1494 bp and encodes for a protein of 498 amino acids. The hypothetical molecular tertiary structure of Aspergillus oryzae BM-DIA FTase showed the presence of structural domains, such as a five-bladed beta-propeller domain characteristic of GH (glycoside hydrolase) and C terminal, which forms a beta-sandwich module. This study contributes to the knowledge of stability, compatibility, and genetic expression of Aspergillus oryzae BM-DIA under SSF bioprocess conditions for industrial production of fructosyltransferase.- Published
- 2021
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44. Author Correction: Dense sampling of bird diversity increases power of comparative genomics.
- Author
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Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, and Zhang G
- Published
- 2021
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45. Dense sampling of bird diversity increases power of comparative genomics.
- Author
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Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, and Zhang G
- Subjects
- Animals, Chickens genetics, Conservation of Natural Resources, Datasets as Topic, Finches genetics, Humans, Selection, Genetic genetics, Synteny genetics, Birds classification, Birds genetics, Genome genetics, Genomics methods, Genomics standards, Phylogeny
- Abstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity
1-4 . Sparse taxon sampling has previously been proposed to confound phylogenetic inference5 , and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.- Published
- 2020
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46. A new species of alien terrestrial planarian in Spain: Caenoplana decolorata .
- Author
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Mateos E, Jones HD, Riutort M, and Álvarez-Presas M
- Abstract
Terrestrial planarians found in a plant nursery in Spain in 2012 are described as a new species, Caenoplana decolorata . Dorsally they are mahogany brown with a cream median line. Ventrally they are pastel turquoise fading to brown laterally. Molecular data indicate that they are a member of the genus Caenoplana , but that they differ from other Caenoplana species found in Europe. One mature specimen has been partially sectioned, and the musculature and copulatory apparatus is described, confirming the generic placement but distinguishing the species from other members of the genus. It is probable that the species originates from Australia., Competing Interests: Marta Riutort is an Academic Editor for PeerJ., (© 2020 Mateos et al.)
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- 2020
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47. Five new pseudocryptic land planarian species of Cratera (Platyhelminthes: Tricladida) unveiled through integrative taxonomy.
- Author
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Araujo APG, Carbayo F, Riutort M, and Álvarez-Presas M
- Abstract
Background: Cratera is a genus of land planarians endemic to the Brazilian Atlantic forest. The species of this genus are distinguished from each other by a series of external and internal characters, nonetheless they represent a challenging taxonomic issue due to the extreme alikeness of the species analysed in the present work. To resolve these difficulties, we have performed morphological analyses and used three nuclear markers (ribosomal 18S and 28S, Elongation Factor, a new anonymous marker named Tnuc813) and two mitochondrial fragments (Cytochrome c oxidase subunit I gene, and a fragment encompasing NADH deshydrogenase subunit 4 gene, trnF and the beginning of the Cytochrome c oxidase I gene) in an integrative taxonomic study., Methods: To unveil cryptic species, we applied a molecular species delimitation approach based on molecular discovery methods, followed by a validation method. The putative species so delimited were then validated on the basis of diagnostic morphological features., Results: We discovered and described four new species, namely Cratera assu, C. tui, C. boja, and C. imbiri . A fifth new species, C. paraitinga was not highly supported by molecular evidence, but was described because its morphological attributes are unique. Our study documents for the genus Cratera the presence of a number of highly similar species, a situation that is present also in other genera of land planarians. The high number of poorly differentiated and presumably recent speciation events might be explained by the recent geological history of the area., Competing Interests: Marta Riutort is an Academic Editor for PeerJ., (©2020 Araujo et al.)
- Published
- 2020
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48. Phylogeny and biogeography of the Cavernicola (Platyhelminthes: Tricladida): Relicts of an epigean group sheltering in caves?
- Author
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Benítez-Álvarez L, Maria Leal-Zanchet A, Oceguera-Figueroa A, Lopes Ferreira R, de Medeiros Bento D, Braccini J, Sluys R, and Riutort M
- Subjects
- Animals, Bayes Theorem, Biological Evolution, Caves, Ecosystem, Phylogeny, Phylogeography, Platyhelminths genetics, Platyhelminths physiology, RNA, Ribosomal, 18S chemistry, RNA, Ribosomal, 18S classification, RNA, Ribosomal, 18S metabolism, RNA, Ribosomal, 28S chemistry, RNA, Ribosomal, 28S classification, RNA, Ribosomal, 28S metabolism, Platyhelminths classification
- Abstract
The planarian suborder Cavernicola Sluys, 1990 was originally created to house five species of triclad flatworms with special morphological features and a surprisingly discontinuous and broad geographic distribution. These five species could not be accommodated with any degree of certainty in any of the three taxonomic groups existing at that moment, viz., Paludicola Hallez, 1892, Terricola Hallez, 1892, and Maricola Hallez, 1892. The scarce representation of the group and the peculiarities of the morphological features of the species, including several described more recently, have complicated new tests of the monophyly of the Cavernicola, the assessment of its taxonomic status, as well as the resolution of its internal relationships. Here we present the first molecular study including all genera currently known for the group, excepting one. We analysed newly generated 18S and 28S rDNA data for these species, together with a broad representation of other triclad flatworms. The resulting phylogenetic trees supported the monophyly of the Cavernicola, as well as its sister-group relationship to the Maricola. The sister-group relationship to the Maricola and affinities within the Cavernicola falsify the morphology-based phylogeny of the latter that was proposed previously. The relatively high diversity of some cavernicolan genera suggests that the presumed rarity of the group actually may in part be due to a collecting artefact. Ancestral state reconstruction analyses suggest that the ancestral habitat of the group concerned epigean freshwater conditions. Our results point to an evolutionary scenario in which the Cavernicola (a) originated in a freshwater habitat, (b) as the sister clade of the marine triclads, and (c) subsequently radiated and colonized both epigean and hypogean environments. Competition with other planarians, notably members of the Continenticola, or changes in epigean habitat conditions are two possible explanations -still to be tested- for the loss of most epigean diversity of the Cavernicola, which is currently reflected in their highly disjunct distributions., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2020
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49. The identity of the invasive yellow-striped terrestrial planarian found recently in Europe: Caenoplana variegata (Fletcher amp; Hamilton, 1888) or Caenoplana bicolor (Graff, 1899)?
- Author
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Jones HD, Mateos E, Riutort M, and Álvarez-Presas M
- Subjects
- Animals, Europe, Planarians
- Abstract
Terrestrial planarians with a dorsal yellow stripe and dark lateral surfaces and up to 15-20 cm long have been found in several countries in Europe, the earliest in 2008. They are similar to two species originally from Australia, Caenoplana variegata (Fletcher Hamilton, 1888) and C. bicolor (Graff, 1899), both described on external characters only, with no anatomical information. Careful reading suggests that there is no significant difference between the original descriptions. Further: observations on live specimens show considerable variation between individuals and in individuals over time and before and after feeding, negating any distinction between descriptions. Examination of three sectioned specimens shows considerable difference in sexual maturity, though one seems almost fully mature and the reproductive system is described. Molecular results show that specimens from the United Kingdom and Spain are of the same species. It is concluded that the planarians should be referred to as C. variegata, C. bicolor being a junior synonym.
- Published
- 2020
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50. Cryptic species delineation in freshwater planarians of the genus Dugesia (Platyhelminthes, Tricladida): Extreme intraindividual genetic diversity, morphological stasis, and karyological variability.
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Leria L, Vila-Farré M, Álvarez-Presas M, Sánchez-Gracia A, Rozas J, Sluys R, and Riutort M
- Subjects
- Animals, Fresh Water, Phylogeny, Planarians anatomy & histology, Reproduction, Asexual, Genetic Variation, Karyotype, Planarians classification, Planarians genetics
- Abstract
The keystone of planarian taxonomy traditionally has been the anatomy of the copulatory apparatus. However, many planarian species comprise asexual fissiparous populations, with the fissiparous animals not developing a copulatory apparatus, thus precluding their morphological identification. Incorporation of molecular data into planarian systematics has been of great value, not only in the identification of fissiparous individuals but also as an additional source of information for determining species boundaries. Nevertheless, the discrepancy between morphological and molecular data has highlighted the need for extra sources of taxonomic information. Moreover, a recent study has pointed out that fissiparous reproduction may lead to high levels of intraindividual genetic diversity in planarians, which may mislead molecular analyses. In the present study we aim to test a new up-to-date integrative taxonomic procedure for planarians, including intraindividual genetic data and additional sources of taxonomic information, besides morphology and DNA, using Dugesia subtentaculata sensu lato as a model organism, a species with an intricate taxonomic history. First, we used three different methods for molecular species delimitation on single locus datasets, both with and without intraindividual information, for formulating Primary Species Hypotheses (PSHs). Subsequently, Secondary Species Hypotheses (SSHs) were formulated on the basis of three types of information: (1) a coalescent-based species delimitation method applied to multilocus data, (2) morphology of the copulatory apparatus, and (3) karyological metrics. This resulted in the delimitation of four morphologically cryptic species within the nominal species D. subtentaculata. Our results provide evidence that the analysis of intraindividual genetic data is essential for properly developing PSHs in planarians. Our study reveals also that karyological differentiation, rather than morphological differentiation, may play an important role in speciation processes in planarians, thus suggesting that the currently known diversity of the group could be highly underestimated., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2020
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