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7. Papuan mitochondrial genomes and the settlement of Sahul

Author

Pedro, Nicole, Brucato, Nicolas, Fernandes, Veronica, André, Mathilde, Saag, Lauri, Pomat, William, Besse, Céline, Boland, Anne, Deleuze, Jean-François, Clarkson, Chris, Sudoyo, Herawati, Metspalu, Mait, Stoneking, Mark, Cox, Murray P., Leavesley, Matthew, Pereira, Luisa, and Ricaut, François-Xavier

Published
2020
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9. High-resolution characterization of genetic markers in the Arabian Peninsula and Near East

Author

Neves da Nova Fernandes, Veronica Cristina, Richards, Martin, and Pereira, Luisa

Subjects
570
Abstract

In this work, I analysed the maternally transmitted mtDNA and biparentally inherited genome-wide polymorphisms to shed light on successive migrations into and from the Arabian Peninsula, at the crossroads between Africa, Europe and Asia. I focused on three main issues: 1- The first descendants of the out-of-Africa migration: My phylogeographic analysis on 385 complete mtDNA N1, N2 and X sequences showed their common origin in the Gulf Oasis region at ~57-65 ka. Instead of isolation, I identified a continuous gene flow between Arabia and Near East. Genome-wide data supported the strong clustering of Arabian and Near Eastern populations. 2- Major population expansions in the Arabian Peninsula: My data on the rare N(xR) lineages supported a continuous settlement of the Peninsula, while my founder analysis of other N lineages suggested Near Eastern lineages arriving continuously from the Late Glacial (31%-46%; some U and N1 lineages), Younger Dryas (24-28%; R0a and HV), Neolithic (20-25%; J and T; supported by my new complete 44 sequences) and till recently (10-15%; derived lineages). These results again challenge the hypothesis of long-term isolation between these two regions. 3- Genetic exchanges across the Red Sea: Phylogeographic analysis of L4 and L6 mtDNA complete sequences and HVS-I founder analysis from Africa into Arabia/Near East indicated that the Arab maritime dominance and slave trade (0.5-2.5 ka) were the main contributors (~60-70%) to the African input, but the entrance began with the establishment of maritime networks in the Red Sea by 8 ka. Genome-wide analyses supported this recent introduction (ROLLOFF estimates of 30-40 generations) suggesting that Arabia has 6% eastern African and 3% western African input. The HVS-I founder analysis for the back-to-Africa migrations showed that the Late Glacial period dominated introductions into eastern Africa, while the Neolithic was more important for migrations towards North Africa.

Published
2013

11. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America

Author

Patin, Etienne, Lopez, Marie, Grollemund, Rebecca, Verdu, Paul, Harmant, Christine, Quach, Hélène, Laval, Guillaume, Perry, George H., Barreiro, Luis B., Froment, Alain, Heyer, Evelyne, Massougbodji, Achille, Fortes-Lima, Cesar, Migot-Nabias, Florence, Bellis, Gil, Dugoujon, Jean-Michel, Pereira, Joana B., Fernandes, Verónica, Pereira, Luisa, Van der Veen, Lolke, Mouguiama-Daouda, Patrick, Bustamante, Carlos D., Hombert, Jean-Marie, and Quintana-Murci, Lluís

Published
2017

13. Profiling the Adrenergic System in Breast Cancer and the Development of Metastasis

Author

Sousa, Daniela M., primary, Fernandes, Veronica, additional, Lourenço, Catarina, additional, Carvalho-Maia, Carina, additional, Estevão-Pereira, Helena, additional, Lobo, João, additional, Cantante, Mariana, additional, Couto, Marina, additional, Conceição, Francisco, additional, Jerónimo, Carmen, additional, Pereira, Luisa, additional, and Lamghari, Meriem, additional

Published
2022
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14. Circum-Saharan Prehistory through the Lens of mtDNA Diversity

Author

Diallo, Mame Yoro, primary, Čížková, Martina, additional, Kulichová, Iva, additional, Podgorná, Eliška, additional, Priehodová, Edita, additional, Nováčková, Jana, additional, Fernandes, Veronica, additional, Pereira, Luísa, additional, and Černý, Viktor, additional

Published
2022
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16. Origin and spread of human mitochondrial DNA haplogroup U7

Author

Sahakyan, Hovhannes, Hooshiar Kashani, Baharak, Tamang, Rakesh, Kushniarevich, Alena, Francis, Amirtharaj, Costa, Marta D, Pathak, Ajai Kumar, Khachatryan, Zaruhi, Sharma, Indu, van Oven, Mannis, Parik, Jüri, Hovhannisyan, Hrant, Metspalu, Ene, Pennarun, Erwan, Karmin, Monika, Tamm, Erika, Tambets, Kristiina, Bahmanimehr, Ardeshir, Reisberg, Tuuli, Reidla, Maere, Achilli, Alessandro, Olivieri, Anna, Gandini, Francesca, Perego, Ugo A., Al-Zahery, Nadia, Houshmand, Massoud, Sanati, Mohammad Hossein, Soares, Pedro, Rai, Ekta, Šarac, Jelena, Šarić, Tena, Sharma, Varun, Pereira, Luisa, Fernandes, Veronica, Černý, Viktor, Farjadian, Shirin, Singh, Deepankar Pratap, Azakli, Hülya, Üstek, Duran, Ekomasova (Trofimova), Natalia, Kutuev, Ildus, Litvinov, Sergei, Bermisheva, Marina, Khusnutdinova, Elza K., Rai, Niraj, Singh, Manvendra, Singh, Vijay Kumar, Reddy, Alla G., Tolk, Helle-Viivi, Cvjetan, Svjetlana, Lauc, Lovorka Barac, Rudan, Pavao, Michalodimitrakis, Emmanuel N., Anagnou, Nicholas P., Pappa, Kalliopi I., Golubenko, Maria V., Orekhov, Vladimir, Borinskaya, Svetlana A, Kaldma, Katrin, Schauer, Monica A., Simionescu, Maya, Gusar, Vladislava, Grechanina, Elena, Govindaraj, Periyasamy, Voevoda, Mikhail, Damba, Larissa, Sharma, Swarkar, Singh, Lalji, Semino, Ornella, Behar, Doron M., Yepiskoposyan, Levon, Richards, Martin B., Metspalu, Mait, Kivisild, Toomas, Thangaraj, Kumarasamy, Endicott, Phillip, Chaubey, Gyaneshwer, Torroni, Antonio, and Villems, Richard

Published
2017
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31. Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western desert

Author

Kujanova, Martina, Pereira, Luisa, Fernandes, Veronica, Pereira, Joana B., and Cerny, Viktor

Subjects
Deserts -- Analysis, Mitochondrial DNA -- Analysis, Genetic research -- Analysis, Anthropology/archeology/folklore
Abstract

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 [+ or -] 3,633 YBE Similarly, the Y-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b line-ages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa. KEY WORDS Egyptian Western Desert; complete mtDNA sequences; T haplogroup; Y-chromosome; Neolithic

Published
2009

33. Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia

Author

Cherni, Lotfi, Fernandes, Veronica, Pereira, Joana B., Costa, Marta D., Goios, Ana, Frigi, Sabeh, Yacoubi-Loueslati, Besma, Amor, Mohamed Ben, Slama, Abdelhakim, Amorim, Antonio, Gaaied, Amel Ben Ammar El, and Pereira, Luisa

Subjects
Iberian Peninsula -- Natural history, Northern Africa -- Natural history, Tunisia -- Natural history, Haplotypes -- Identification and classification, Last Glacial Maximum -- Environmental aspects, Mitochondrial DNA -- Properties, Population genetics -- Research, Anthropology/archeology/folklore
Abstract

The first large-scale fine characterization of Tunisian H lineages clarifies that the post-Last glacial maximum expansion originating in Iberia hot only led to the resettlement of Europe but also of North Africa. We found that 46% of 81 Tunisian H lineages subscreened for 1,580 bp in mtDNA coding region were affiliated with H1 and H3 subhaplogroups, which are known to have originated in Iberia. Although no signs of local expansion were detected, which would allow a clear dating of their introduction, the younger and less diverse Tunisian H1 and H3 lineages indicate Iberia as the radiating centre. Major contributions from historical migrations to this Iberian genetic imprint in Tunisia were ruled out by the mtDNA gene pool similarity between Berber/Arab/cosmopolitan samples and some 'Andalusian' communities, settled by the descendents of the 'Moors' who once lived in Iberia for 10 centuries (between 8th and 17th centuries), before being expelled to Tunisia. KEY WORDS mtDNA; haplogroup H; Tunisia; Andalusians

Published
2009

35. Association of Pro‐B‐Type Natriuretic Peptide With Cardiac Magnetic Resonance–Measured Global and Regional Cardiac Function and Structure Over 10 Years: The MESA Study

Author

Rahsepar, Amir Ali, primary, Bluemke, David A., additional, Habibi, Mohammadali, additional, Liu, Kiang, additional, Kawel‐Boehm, Nadine, additional, Ambale‐Venkatesh, Bharath, additional, Fernandes, Veronica R. S., additional, Rosen, Boaz D., additional, Lima, Joao A. C., additional, and Carr, James C., additional

Published
2021
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38. Deep-sea taxonomic standardization: Strategic approaches for collaboration

Author

Amaro, Teresa, Amon, Diva, Aramayo, Víctor, Appeltans, Ward, Arteaga-Florez, Catalina, Jinwook Back, Benlakhdim, Ahmed, Best, Merlin, Bezerra, Tania Nara, Bhaumik, Amrita, Błażewicz, Magdalena, Broggiato, Arianna, Sydnei Cartwright, Castello-Branco, Cristiana, Cedeño-Posso, Cristina, Chen, Chong, Josh Choi, Christodoulou, Magdalini, Cunha, Marina, Currie, Bronwen, Damare, Samir, De Moura Neves, Bárbara, Eggleton, Jacqueline, Escoba, Elva, Esquete, Patricia, Feickert, Jessica, Fernandes, Veronica, Frutos, Inmaculada, Fukushima, Tomohiko, Gao, Xiang, Gao, Yan, Glover, Adrian, Gollner, Sabine, Gracia, Adolfo, Horton, Tammy, Howell, Kerry, Iguchi, Akira, Ikeuchi, Eri, Yukimitsu Imahara, Ingels, Jeroen, Baban Ingole, Jiang, Jun, Jolly, Claire, Se-Jong Ju, Jute, Alana, Kadiri, Omar, Kaiser, Stefanie, Kenchington, Ellen, Khodami, Sahar, Terue Kihara, Kim, Kyeong Mi, Kozlowska-Roman, Agata, Jimin Lee, Nanyoung Lee, Sang-Hui Lee, Moeketsi Lekobane, Yixuan Li, Liu, Qian, Manchih, Khalid, Gopikrishna Mantha, Arbizu, Pedro Martinez, McQuaid, Kirsty, Melnik, Viacheslav, Mianowicz, Kamila, Won-Gi Min, Miya, Masaki, Youngdawng Moh, Molodtsova, Tina, Moon, Hye-Won, Neto, Clovis Motta, Newbold, Rochelle, Lin, Peter Ng Kee, Nishijima, Miyuki, Nottage, Kenia, O'hara, Tim, Okanishi, Masanori, Oliver, Graham, Sang-Joon Pak, Pape, Ellen, Pasotti, Francesca, Paterson, Gordon, Rabone, Muriel, Radziejewska, Teresa, Dineshram Ramadoss, Ramalho, Sofia, Rhoden, Stephen, Riehl, Torben, Sanchez, Daniela Rojas, Samadi, Sarah, Sanchez-Flores, Alejandro, Sabyasachi Sautya, Wenge Shi, Shimabukuro, Mauricio, Sigwart, Julia, Simon-Lledo, Erik, Suh, Yeon Jee, Rupesh Kumar Sinha, Koh-Siang Tan, Smith, Jason, Smith, Samantha, Taverna, Anabela, Taylor, Michelle, Tomczak, Michal, Uysal, Irfan, Vanreusel, Ann, Victorero, Lissette, De Wachter, Tom, Chunsheng Wang, Wagner, Daniel, Les Watling, Williams, Christopher, Seonock Woo, Xavier, Joana, Qinzeng Xu, Xu, Xue-Wei, Yu, Ok Hwan, Yzewyn, Tim, Xiaojun Zhuo, Zeppilli, Daniela, Abdulqadir Ziyad, Jihyun Lee, Génio, Luciana, Wanfei Qiu, Changsung Lim, and Bonifácio, Paulo

Published
2020
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39. Eddy-mediated biological productivity in the Bay of Bengal during fall and spring intermonsoons

Author

Kumar, S. Prasanna, Nuncio, M., Ramaiah, N., Sardesai, S., Narvekar, Jayu, Fernandes, Veronica, and Paul, Jane T.

Subjects
Chlorophyll, Earth sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.dsr.2007.06.002 Byline: S. Prasanna Kumar, M. Nuncio, N. Ramaiah, S. Sardesai, Jayu Narvekar, Veronica Fernandes, Jane T. Paul Keywords: Cold-core eddies; Biological productivity; Subsurface chlorophyll maxima; Nutrient pumping; Water column stability; Eddy-pumping; Bay of Bengal Abstract: The signature of cold-core eddies and their role in altering the biological productivity of the Bay of Bengal was examined using two recent sets of hydrographic data collected along the central and western Bay of Bengal during fall (14 September-12 October, 2002) and spring (12 April-7 May, 2003) intermonsoons under the Bay of Bengal process studies (BOBPS) programme. Based on the thermohaline structure and the satellite-derived sea-level anomaly maps nine cyclonic eddies were identified. Out of this, four cyclonic eddies -- two each along the central Bay and along the western boundary -- occurred during fall intermonsoon 2002, while five occurred -- three along the central Bay and two along the western boundary -- during spring intermonsoon. The eddy depressed the temperature, which varied from 3[degrees]C to 7[degrees]C at 120m depth. Maximum depression of temperature was associated with spring-time eddies in the northern Bay, where subsurface stability was low. The reduced water column stability in spring leads to greater eddy-pumping, thereby cooling the water to a greater extent. However, the cyclonic eddies were unable to break the stratification of the top 20m layer, thereby curtailing their effects below this depth during both seasons. Eddy-pumping not only cooled the water column but also enhanced the nutrient concentrations. This in turn increased the biological productivity of the Bay to 11/2-2 times. In addition, the subsurface chlorophyll maximum (SCM), which is generally located between 40 and 70m in fall and 60 and 90m in spring intermonsoons, shallowed under the influence of the eddies and also enhanced the chlorophyll concentration in the SCM to more than double. Thus, eddy-pumping of nutrients controls the biological productivity of the Bay of Bengal during both the seasons. In the fall intermonsoon, however, the riverine input of nutrients and sediments in the northern Bay also plays a role in altering the biological productivity. This has an overall implication to the basin-wide new production and export flux and, at least partly, resolves the reason for the comparable annual fluxes of organic carbon between the high-productivity Arabian Sea and low-productivity Bay of Bengal. Author Affiliation: National Institute of Oceanography, Dona Paula, Goa-403 004, India Article History: Received 19 January 2007; Revised 4 June 2007; Accepted 7 June 2007

Published
2007

50. Acineta foetida Maupas 1881

Author

Chatterjee, Tapas, Dovgal, Igor, Nanajkar, Mandar, and Fernandes, Veronica

Subjects
Acineta, Tracheophyta, Liliopsida, Asparagales, Biodiversity, Plantae, Orchidaceae, Acineta foetida, Taxonomy
Abstract

Acineta foetida Maupas, 1881 (Fig. 2E) Material examined: Several specimens on pelagic ostracods Cypridina dentata (Müller, 1906) from station 16. Brief Description: Suctorian ciliate with a triangular or trapezoidal, somewhat asymmetric body attached to the bottom of the lorica. The lorica is triangular or trapezoidal, asymmetric, often with transverse folds of irregular shape, usually located in its lower part. Stalk short, its length does not exceed the length of the body. There is the stalk extension (basal disk) in the zone of stalk-lorica connection, which can be immersed in the base of the lorica. The stalk is attached to the substrate by means of an attachment disk. Tentacles arranged in two apical bundles, actinophores poorly developed, sometimes absent. Macronucleus is rounded, central. Above the macronucleus single contractile vacuole positioned. Measurements from present find: (measurements taken from 3 individuals; in μm) lorica length 32–40; lorica width 32–34; lorica thickness 16; size of macronucleus 10–16×11–13; length of tentacles 7–37; stalk length 6–15; stalk diameter 4; basal disk diameter 11. Host and substrate specificity: Ubiquitous marine and brackish-water species, observed on inanimate substrates, algae, but often found on representatives of crustacean (Dovgal 2013). The species was observed on representatives of crusracean orders, eg. (Dovgal 2013), on Amphipoda— Gammarus olivii Milne-Edwards, 1830, G. subtipicus Stock, 1966, Pontogammarus maeoticus (Sowinsky, 1894) and Orchestia bottae Milne-Edwards, 1840; Isopoda— Sphaeroma serratum (Fabricius, 1787), S. pulchellum (Colosi, 1921) and Idotea baltica basteri (Pallas, 1772); Decapoda— Palaemon elegans Rathke, 1837, Crangon crangon (Linnaeus, 1758), Diogenes pugilator (Roux, 1829), Astacus leptodactylus Eschscholtz, 1823 and Eriphia verrucosa (Forskal, 1775); Ostracoda— Cypridina dentata (Müller, 1906) (present report). Distribution: Widespread found in the Mediterranean, North, Baltic, Black Sea and the Sea of Azov, on the Pacific coast of Canada and the Atlantic coast of Mexico (Dovgal 2013); the Arabian Sea (Present report). Remarks: Acineta foetida was registered as epibiont on benthic or meiobenthic organisms only. Our finding is a first registration of this species on planktonic marine Ostracoda., Published as part of Chatterjee, Tapas, Dovgal, Igor, Nanajkar, Mandar & Fernandes, Veronica, 2019, Report of epibiont ciliates (Cilliophora: Suctorea) on pelagic ostracods (Crustacea: Ostracoda) from the Arabian Sea, pp. 378-384 in Zootaxa 4695 (4) on pages 381-382, DOI: 10.11646/zootaxa.4695.4.5, http://zenodo.org/record/3534816, {"references":["Dovgal, I. V. (2013) Fauna of Ukraine: in 40 Vols. Vol. 36. Ciliates-Ciliophora. Issue 1. Class Suctorea. Naukova Dumka, Kiev, 267 pp. [in Russian with English summary]"]}

Published
2019
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