Pedro Soares

Pedro Soares

pedrosoares@bio.uminho.pt

People Detail

Researcher ID : G-9422-2011

Researchgate : https://www.researchgate.net/profile/Pedro_Soares

Research Area : Biodiversity

Position : Integrated members

Qualifications

Member and group leader in CBMA since 2014. PhD in Human Genetics in the University of Leeds in 2009. Degree in Biology in the University of Porto in 2003.

Research

Research focuses on a) human evolution and tracing the history of human past migration and history; b) development and application of bioinformatics’ tools in the fields of Biodiversity and biotechnology.

Ongoing Projects

“Testing the hypothesis of late Neolithic dispersals from Iberia using both ancient and contemporary mitochondrial genomes”
PTDC/EPH-ARQ/4164/2014

“From Portugal back to Africa: uncovering the African roots of present-day Portuguese”
PTDC/SOC-ANT/30316/2017
With Professor Antonio Brehm, University of Madeira, Portugal

Concluded Projects

“Genetic history and population structure in Southeast Asia”
PTDC/IVC-ANT/4917/2012

Students

Current PhD students
Marina Silva (University of Huddersfield)

Current Master students
Jorge Reis (Master in Bioinformatics, School of Engineering, the University of Minho)
João Guimarães, Erica Matos, Nídia Miranda, Luísa Sá, Anisse Medane (Master in Molecular Genetics, School of Sciences, University of Minho)

Former PhD students
Andreia Brandão, Petr Triska (Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto)

Former Master students
Marina Silva (Master in Biodiversity, Genetics and Evolution, Faculty of Sciences, University of Porto)
Daniel Vieira, Raquel Silva, Joana Ferreira, Daniela Pereira (Master in Bioinformatics, School of Engineering, the University of Minho)
Luís Oliveira (Master in Ecology, School of Sciences, University of Minho)
Simão Rodrigues, Mafalda Almeida, Hugo Oliveira (Master in Molecular Genetics, School of Sciences, University of Minho)
Christina Branco (Master in Applied Biochemistry, School of Sciences, University of Minho)
Soraia Esteves (Master in Forensic Genetics, Faculty of Sciences, University of Porto)

Publications

Papers:

Rito T, Vieira D, Silva M, Conde-Sousa E, Pereira L, Mellars P, Richards MB, Soares P (2019). A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration. Scientific Reports 9, 4728

Vieira PE, Desiderato A, Holdich DM, Soares P, Creer S, Carvalho G, Costa FO, Queiroga H (2019). Deep segregation in the open ocean: Macaronesia as an evolutionary hotspot for low dispersal marine invertebrates. Molecular Ecology 28: 1784– 1800

Brucato N, Fernandes V, Kusuma P, Černý V, Mulligan CJ, Soares P, Rito T, Besse C, Boland A, Deleuze J-F, Cox MP, Sudoyo H, Stoneking M, Pereira L, Ricaut F-X (2019). Evidence of Austronesian genetic lineages in East Africa and South Arabia: complex dispersal from Madagascar and Southeast Asia. Genome Biology and Evolution 11:748-758

Olalde I, Mallick S, Patterson N, Rohland N, Villalba-Mouco V, Silva M, Dulias K, Edwards CJ, Gandini F, Pala M, Soares P, Ferrando-Bernal M, Adamski N, Broomandkhoshbacht N, Cheronet O, Culleton BJ, Fernandes D, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zhang Z, Arenas JMJ, Moyano IJT, Salazar-García DC, Castanyer P, Santos M, Tremoleda J, Lozano M, Borja PG, Fernández-Eraso J, Mujika-Alustiza JA, Barroso C, Bermúdez FJ, Mínguez EV, Burch J, Coromina N, Vivó D, Cebrià A, Fullola JM, García-Puchol O, Morales JI, Oms FX, Majó T, Vergès JM, Díaz-Carvajal A, Ollich-Castanyer I, López-Cachero FJ, Silva AM, Alonso-Fernández C, Castro GD, Echevarría JJ, Moreno-Márquez A, Berlanga GP, Ramos-García P, Muñoz JR, Vila EV, Arzo GA, Arroyo AE, Lillios KT, Mack J, Velasco-Vázquez J, Waterman A, Enrich LBL, Sánchez MB, Agustí B, Codina F, Prado G, Estalrrich A, Flores AF, Finlayson C, Finlayson G, Finlayson S, Giles-Guzmán F, Rosas A, González VB, Atiénzar GG, Pérez MSH, Llanos A, Marco YC, Beneyto IC, López-Serrano D, Tormo MS, Valera AC, Blasco C, Liesau C, Ríos P, Daura J, Michó MJP, Diez-Castillo AA, Fernández AF, Farré JF, Garrido-Pena R, Gonçalves VS, Guerra-Doce E, Herrero-Corral AM, Juan-Cabanilles J, López-Reyes D, McClure SB, Pérez MM, Foix AO, Borràs MS, Sousa AC, Encinas JMV, Kennett DJ, Richards MB, Alt KW, Haak W, Pinhasi R, Lalueza-Fox C, Reich D (2019). The genomic history of the Iberian Peninsula over the past 8000 years. Science 6432: 1230-1234

Macaulay V, Soares P, Richards MB (2019). Rectifying long-standing misconceptions about the ρ statistic for molecular dating. Plos One 14(2): e0212311

Ribas D, Soares-Silva I, Vieira D, Sousa-Silva M, Sá-Pessoa J, Azevedo-Silva J, Viegas SC, Arraiano CM, Diallinas G, Paiva S, Soares P, Casal M (2019). The acetate uptake transporter family motif “NPAPLGL(M/S)” is essential for substrate uptake. Fungal Genetics and Biology 120: 1-10

Olivieri A, Sidore C, Achilli A, Angius A, Posth C, Furtwängler A, Brandini S, Capodiferro MR, Gandini F, Zoledziewska M, Pitzalis M, Maschio A, Busonero F, Lai L, Skeates R, Gradoli MG, Beckett J, Marongiu M, Mazzarello V, Marongiu P, Rubino S, Rito T, Macaulay V, Semino O, Pala M, Abecasis GR, Schlessinger D, Conde-Sousa E, Soares P, Richards MB, Cucca F, Torroni A. (2017) Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past. Molecular Biology and Evolution 34 (5): 1230-1239

Sahakyan H, Kashani BH, Tamang R, Kushniarevich A, Francis A, Costa MD, Pathak AK, Khachatryan Z, Sharma I, Oven Mv, Parik J, Hovhannisyan H, Metspalu E, Pennarun E, Karmin M, Tamm E, Tambets K, Bahmanimehr A, Reisberg T, Reidla M, Achilli A, Olivieri A, Gandini F, Perego UA, Al-Zahery N, Houshmand M, Sanati MH, Soares P, Rai E, Šarac J, Šarić T, Sharma V, Pereira L, Fernandes V, Černý V, Farjadian S, Singh DP, Azakli H, Üstek D, Ekomasova N, Kutuev I, Litvinov S, Bermisheva M, Khusnutdinova EK, Rai N, Singh M, Singh VK, Reddy AG, Tolk H-V, Cvjetan S, Lauc LB, Rudan P, Michalodimitrakis EN, Anagnou NP, Pappa KI, Golubenko MV, Orekhov V, Borinskaya SA, Kaldma K, Schauer MA, Simionescu M, Gusar V, Grechanina E, Govindaraj P, Voevoda M, Damba L, Sharma S, Singh L, Semino O, Behar DM, Yepiskoposyan L, Richards MB, Metspalu M, Kivisild T, Thangaraj K, Endicott P, Chaubey G, Torroni A, Villems R. (2017) Origin and spread of human mitochondrial DNA haplogroup U7. Scientific Reports 7:46044

Silva M, Oliveira M; Vieira D, Brandão A, Rito T, Pereira JB, Fraser RM; Hudson B, Gandini F, Edwards C, Pala M, Koch J, Wilson JF, Pereira L, Richards MB, Soares P. (2017) A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. BMC Evolutionary Biology 17 (1), 88

Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harrich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P*, Pereira L*, Richards MB* (2017) Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proceedings of the Royal Society of London B: Biological Sciences 284 (1851), 20161976 *Joint senior authors

Sierra B, Triska P, Soares P, Garcia G, Perez AB, Aguirre E, Oliveira M, Cavadas B, Regnault B, Alvarez M, Ruiz D, Samuels DC, Sakuntabhai A, Pereira M, Guzman MG. (2017) OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed CUBANS. PLoS Pathogens 13 (2), e1006220

Gandini F, Achilli A, Pala M, Bodner M, Brandini S, Huber G, Egyed B, Ferretti L, Gómez-Carballa A, Salas A, Scozzari R, Cruciani F, Coppa A, Parson W, Semino O, Soares P, Torroni A, Richards MB, Olivieri A. (2016) Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Scientific Reports 6: 25472

Richards MB, Soares P, Torroni A (2016). Palaeogenomics: Mitogenomes and Migrations in Europe’s Past. Current Biology 26(6): R243-R246

Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko T-M, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P. (2016) Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Human Genetics 135(4): 363-376

Soares PA, Trejaut JA, Rito T, Cavadas B, Hill C, Eng KK, Mormina M, Brandão A, Fraser RM, Wang T-Y, Loo J-H, Snell C, Ko T-M, Amorim A, Pala M, Macaulay V, Bulbeck D, Wilson JF, Gusmão L, Pereira L, Oppenheimer S, Lin M, Richards MB (2016). Resolving the ancestry of Austronesian-speaking populations. Human Genetics 135(3): 309-326

Triska P, Soares P, Patin E, Fernandes V, Cerny V, Pereira L. (2015) Extensive Admixture and Selective Pressure Across the Sahel Belt. Genome Biology and Evolution 7(12):evv236

Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L; Calderón R (2015). Early Holocenic and historic mtDNA African signatures in the Iberian Peninsula: the Andalusian region as a paradigm. Plos One 10: e0139784

Silva M, Alshamali F, Silva P, Carrilho C, Mandlate F, Trovoada MJ, Černý V, Pereira L, Soares P. (2015) 60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Scientific Reports 5:12526

Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L (2015). Fine time-scaling of purifying selection on human non-synonymous mtDNA mutations based on worldwide population tree and mother-child pairs. Human Mutation 36: 1100-1111

Gomes V, Pala M, Salas A, Álvarez-Iglesias V, Amorim A, Gómez-Carballa A, Carracedo A, Clarke DJ, Hill C, Mormina M, Shaw MA, Dunne DW, Pereira R, Pereira V, Prata MJ, Sánchez-Diz P, Rito T, Soares P, Gusmão L, Richards MB (2015). Mosaic maternal ancestry in the Great Lakes region of East Africa. Human Genetics 134(9): 1013-1027

Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, Černý V, Soares P, Richards MB, Pereira L (2015). Genetic stratigraphy of key demographic events in Arabia. Plos One 10: e0118625

Pereira L, Soares P, Triska P, Rito T, Li B, Radivojac P, Samuels DC. (2014) Global human frequencies of predicted nuclear pathogenic variants conditioning mitochondrial diseases and the role played by protein hydrophobicity in the pathogenicity. Scientific Reports 4:7155

Martins RG, Nunes JB, Máximo V, Soares P, Peixoto J, Catarino T, Rito T, Soares P, Pereira L, Sobrinho-Simões M, Santos AP, Couto J, Henrique R, Matos-Loureiro J, Dias P, Torres I, Lima J (2013). A founder SDHB mutation in Portuguese paraganglioma patients. Endocrine-related cancer 20:L23-L26

Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P (2013). The First Modern Human Dispersals Across Africa. Plos One 8:e80031

Podgorna E, Soares P, Pereira L, Cerny V (2013). The Genetic Impact of the Lake Chad Basin Population in North Africa as Documented by Mitochondrial Diversity and Internal Variation of the L3e5 Haplogroup. Annals of Human Genetics 77:513-523

Costa MD, Pereira JB, Pala M, Fernandes V, Olivieri A, Achilli A, Perego UA, Rychkov S, Naumova O, Hatina J, Woodward SR, Eng S, Carr M, Macaulay V, Soares P, Pereira L, Richards MB (2013). A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature Communications 4:2543

Mellars P, Gori KC, Carr M, Soares PA, Richards MB (2013). Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proceedings of the National Academy of Sciences USA 110:10699-10704

Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L. (2013). Evaluating purifying selection in the mitochondrial DNA of various mammalian species. Plos One 8: e58993

Al-Abri A, Podgorná E, Rose JI, Pereira L, Mulligan CJ, Silva NM, Bayoumi R, Soares P, Černý V. (2012). Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation. American Journal of Physical Anthropology 149:291-8

Pala M, Olivieri A, Achilli A, Accetturo M, Metspalu E, Reidla M, Tamm E, Karmin M, Reisberg T, Kashani BH, Perego UA, Carossa V, Gandini F, Pereira JB, Soares P, Angerhofer N, Rychov S, Al-Zahery N, Carelli V, Sanati MH, Houshmand M, Hatina J, Macaulay V, Pereira L, Woodward SR, Davies W, Gamble C, Baird D, Semino O, Villems R, Torroni A, Richards MB. (2012). Mitochondrial DNA signals of Late Glacial re-colonisation of Europe from Near Eastern refugia. American Journal of Human Genetics 90: 915-924

Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilová E, Macaulay V, Richards MB, Cerny V, Pereira L. (2012). The Expansion of mtDNA Haplogroup L3 within and out of Africa. Molecular Biology and Evolution 29: 915-927

Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, Cherni L, Harich N, Cerny V, Soares P, Richards MB, Pereira L. (2012). The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa. American Journal of Human Genetics 90: 347-355

Pereira L, Soares P, Máximo V, Samuels DC. (2012). Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors. BMC Cancer 12: 53

Achilli A, Olivieri A, Soares P, Lancioni H, Kashani BH, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MCT, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt H-J, Torroni A. (2012). Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proceedings of the National Academy of Sciences USA 109: 2449-2454

Cerny V, Pereira L, Musilová E, Kujanová M, Vasíková A, Blasi P, Garofalo L, Soares P, Diallo I, Brdicka R, Novelletto A. (2011). Genetic structure of pastoral and farmer populations in the African Sahel. Molecular Biology and Evolution 28: 2491-2500

Musilová E, Fernandes, V, Silva, NM, Soares P, Alshamali, F, Harich, N, Cherni, L, Gaaied, ABAE, Al-Meeri, A, Pereira, L, Cerný, V. (2011). Population history of the Red Sea - genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup. American Journal of Physical Anthropology 145: 592-598

Pereira L, Soares P, Radivojac P, Li B, Samuels DC. (2011). Comparing Phylogeny and the Predicted Pathogenicity of Protein Variations Reveals Equal Purifying Selection across the Global Human mtDNA Diversity. American Journal of Human Genetics 88: 433-9

Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, Braid M, Clarke DJ, Loo JH, Thomson N, Denham T, Donohue M, Macaulay V, Lin M, Oppenheimer S, Richards MB. (2011). Ancient Voyaging and Polynesian Origins. American Journal of Human Genetics 88: 239-247

Chaubey G, Metspalu M, Choi Y, Mägi R, Romero IG, Soares P, Oven M, Behar DM, Rootsi S, Hudjashov G, Mallick CB, Karmin M, Nelis M, Parik J, Reddy AG, Metspalu E, Driem G, Xue Y, Tyler-Smith C, Thangaraj K, Singh L, Remm M, Richards MB, Lahr MM, Kayser M, Villems R, Kivisild T. (2011). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture. Molecular Biology and Evolution 28: 1013-1024

Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V. (2010). Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology 10: 390

Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt HJ, Torroni A, Richards MB. (2010). The Archaeogenetics of Europe. Current Biology 20: R174-R183

Soares P, Ermini L, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards M. (2009). Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock. American Journal of Human Genetics 84: 740-759

Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Nallari P, Rai TS, Khullar M, Soares P, Bahl A, Tharkan JM, Vaideeswar P, Rathinavel A, Rani DS, Narasimhan C, Ayapati DR, Qasim A, Mehdi S, Oppenheimer S, Richards M, Singh L,, Tyler-Smith C, Thangaraj K. (2009). A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature Genetics 41:187-191

Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra J.A, Gusmão L, Amorim A. (2008). A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny. Molecular Phylogenetics and Evolution 49: 663-668

Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A. (2008). Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Molecular Biology and Evolution 25: 2759-2770

Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, Rollo F. (2008). Complete Mitochondrial Genome Sequence of the Tyrolean Iceman. Current Biology 18: 1687-1693

Soares P, Trejaut JA, Loo J.-H, Hill C, Mormina M, Lee C-L, Chen Y.-M, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB. (2008). Climate change and post-glacial human dispersals in Southeast Asia. Molecular Biology and Evolution 25: 1209-1218

Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M. (2007). A mitochondrial stratigraphy for Island Southeast Asia. American Journal of Human Genetics 80: 29–43

Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, Clarke D, Raja JM, Ismail P, Bulbeck D, Oppenheimer S, Richards M. (2006). Phylogeography and ethnogenesis of aboriginal Southeast Asians. Molecular Biology and Evolution 23: 2480-2491

Azevedo L, Soares PA, Quental R, Vilarinho L, Teles EL, Martins E, Diogo L, Garcia P, Cenni B, Wermuth B, Amorim A. (2006). Mutational spectrum and linkage disequilibrium patterns at the ornithine transcarbamylase gene (OTC). Annals of Human Genetics 70: 797-801

Book Chapters:

Silva M, Dulias K, Oteo-Garcia G, Gandini F, Edwards C, Pala M, Soares P, Wilson JF, Richards MB (2019). Once Upon a Time in the West: The Archaeogenetics of Celtic Origins. in “Exploring Celtic Origins: New ways forward in archaeology, linguistics, and genetics” edited by Barry Cunliffe and John Koch. Oxbow Books, Oxford. p:153-191

Richards MB, Torroni A, Soares P. Phylogeography. (2018) in “The International Encyclopedia of Biological Anthropology” edited by Wenda Trevathan. John Wiley and Sons, Inc., New Jersey.

Pala M, Soares P, Richards MB (2016). Archaeogenetic and palaeogenetic evidence for Metal Age mobility in Europe. “Celtic from the West 3: Atlantic Europe in the Metal Ages — questions of shared language”, edited by John T. Koch, Barry Cunliffe, Oxbow Books. p:321-344

Soares P, Rito T, Pereira L, Richards MB. (2016). A Genetic Perspective on African Prehistory. “Africa from MIS 6-2: Population Dynamics and Paleoenvironments”, edited by Sacha C. Jones and Brian A. Stewart. Springer Netherlands p: 383-405

Richards MB, Chaubey G, Soares P, Pala M. (2015). Chapter 2: Archaeogenetics. “The Cambridge History of the World Volume 2: A World with Agriculture” edited by Graeme Barker and Candice Goucher. Cambridge University Press. p:26-54

Pala M, Chaubey G, Soares P, Richards MB. (2014). The Archaeogenetics of European Ancestry. Encyclopedia of Life Science (eLS). John Wiley and Sons, Chichester