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2. DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis.

Author

Gusmao, L., Butler, J.M., Carracedo, A., Gill, P., Kayser, M., Mayr, W.R., Morling, Niels, Prinz, M., Roewer, L., Tyler-Smith, Chris, and Schneider, Peter M.

Subjects
Mutation (Biology) -- Analysis -- Usage, Human population genetics -- Usage -- Analysis, Y chromosome -- Analysis -- Usage
Abstract

Abstract The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A [...]

Published
2006

3. Y-chromosome STR haplotypes in East Timor: forensic evaluation and population data.

Author

Souto, L., Gusmao, L., Ferreira, E., Amorim, Antonio, Corte-Real, F., and Vieira, D.N.

Subjects
Haplotypes -- Analysis -- Research, Human population genetics -- Research -- Analysis, Y chromosome -- Analysis -- Research
Abstract

Population: One hundred and thirty eight unrelated individuals from several districts of East Timor, including the Oecussi-Ambeno enclave and island of Atauro (Fig. 1). DNA extraction: The DNA was extracted [...]

Published
2006

4. Fungal Planet description sheets: 868-950

Author

Crous, P. W., Carnegie, A. J., Wingfield, M. J., Sharma, R., Mughini, G., Noordeloos, M. E., Santini, A., Shouche, Y. S., Bezerra, J. D. P., Dima, B., Guarnaccia, V., Imrefi, I., Jurjevic, Z., Knapp, D. G., Kovacs, G. M., Magista, D., Perrone, G., Rama, T., Rebriev, Y. A., Shivas, R. G., Singh, S. M., Souza-Motta, C. M., Thangavel, R., Adhapure, N. N., Alexandrova, A. V., Alfenas, A. C., Alfenas, R. F., Alvarado, P., Alves, A. L., Andrade, D. A., Andrade, J. P., Barbosa, R. N., Barili, A., Barnes, C. W., Baseia, I. G., Bellanger, J. -M., Berlanas, C., Bessette, A. E., Bessette, A. R., Biketova, A. Yu., Bomfim, F. S., Brandrud, T. E., Bransgrove, K., Brito, A. C. Q., Cano-Lira, J. F., Cantillo, T., Cavalcanti, A. D., Cheewangkoon, R., Chikowski, R. S., Conforto, C., Cordeiro, T. R. L., Craine, J. D., Cruz, R., Damm, U., de Oliveira, R. J. V., de Souza, J. T., de Souza, H. G., Dearnaley, J. D. W., Dimitrov, R. A., Dovana, F., Erhard, A., Esteve-Raventos, F., Felix, C. R., Ferisin, G., Fernandes, R. A., Ferreira, R. J., Ferro, L. O., Figueiredo, C. N., Frank, J. L., Freire, K. T. L. S., Garcia, D., Gene, J., Gesiorska, A., Gibertoni, T. B., Gondra, R. A. G., Gouliamova, D. E., Gramaje, D., Guard, F., Gusmao, L. F. P., Haitook, S., Hirooka, Y., Houbraken, J., Hubka, V., Inamdar, A., Iturriaga, T., Iturrieta-Gonzalez, I., Jadan, M., Jiang, N., Justo, A., Kachalkin, A. V., Kapitonov, V. I., Karadelev, M., Karakehian, J., Kasuya, T., Kautmanova, I., Kruse, J., Kusan, I., Kuznetsova, T. A., Landell, M. F., Larsson, K. -H., Lee, H. B., Lima, D. X., Lira, C. R. S., Machado, A. R., Madrid, H., Magalhaes, O. M. C., Majerova, H., Malysheva, E. F., Mapperson, R. R., Marbach, P. A. S., Martin, M. P., Martin-Sanz, A., Matocec, N., McTaggart, A. R., Mello, J. F., Melo, R. F. R., Mesic, A., Michereff, S. J., Miller, A. N., Minoshima, A., Molinero-Ruiz, L., Morozova, O. V., Mosoh, D., Nabe, M., Naik, R., Nara, K., Nascimento, S. S., Neves, R. P., Olariaga, I., Oliveira, R. L., Oliveira, T. G. L., Ono, T., Ordonez, M. E., Ottoni, A. de M., Paiva, L. M., Pancorbo, F., Pant, B., Pawlowska, J., Peterson, S. W., Raudabaugh, D. B., Rodriguez-Andrade, E., Rubio, E., Rusevska, K., Santiago, A. L. C. M. A., Santos, A. C. S., Santos, C., Sazanova, N. A., Shah, S., Sharma, J., Silva, B. D. B., Siquier, J. L., Sonawane, M. S., Stchigel, A. M., Svetasheva, T., Tamakeaw, N., Telleria, M. T., Tiago, P. V., Tian, C. M., Tkalcec, Z., Tomashevskaya, M. A., Truong, H. H., Vecherskii, M. V., Visagie, C. M., Vizzini, A., Yilmaz, N., Zmitrovich, I. V., Zvyagina, E. A., Boekhout, T., Kehlet, T., Laessoe, T., Groenewald, J. Z., Crous, P. W., Carnegie, A. J., Wingfield, M. J., Sharma, R., Mughini, G., Noordeloos, M. E., Santini, A., Shouche, Y. S., Bezerra, J. D. P., Dima, B., Guarnaccia, V., Imrefi, I., Jurjevic, Z., Knapp, D. G., Kovacs, G. M., Magista, D., Perrone, G., Rama, T., Rebriev, Y. A., Shivas, R. G., Singh, S. M., Souza-Motta, C. M., Thangavel, R., Adhapure, N. N., Alexandrova, A. V., Alfenas, A. C., Alfenas, R. F., Alvarado, P., Alves, A. L., Andrade, D. A., Andrade, J. P., Barbosa, R. N., Barili, A., Barnes, C. W., Baseia, I. G., Bellanger, J. -M., Berlanas, C., Bessette, A. E., Bessette, A. R., Biketova, A. Yu., Bomfim, F. S., Brandrud, T. E., Bransgrove, K., Brito, A. C. Q., Cano-Lira, J. F., Cantillo, T., Cavalcanti, A. D., Cheewangkoon, R., Chikowski, R. S., Conforto, C., Cordeiro, T. R. L., Craine, J. D., Cruz, R., Damm, U., de Oliveira, R. J. V., de Souza, J. T., de Souza, H. G., Dearnaley, J. D. W., Dimitrov, R. A., Dovana, F., Erhard, A., Esteve-Raventos, F., Felix, C. R., Ferisin, G., Fernandes, R. A., Ferreira, R. J., Ferro, L. O., Figueiredo, C. N., Frank, J. L., Freire, K. T. L. S., Garcia, D., Gene, J., Gesiorska, A., Gibertoni, T. B., Gondra, R. A. G., Gouliamova, D. E., Gramaje, D., Guard, F., Gusmao, L. F. P., Haitook, S., Hirooka, Y., Houbraken, J., Hubka, V., Inamdar, A., Iturriaga, T., Iturrieta-Gonzalez, I., Jadan, M., Jiang, N., Justo, A., Kachalkin, A. V., Kapitonov, V. I., Karadelev, M., Karakehian, J., Kasuya, T., Kautmanova, I., Kruse, J., Kusan, I., Kuznetsova, T. A., Landell, M. F., Larsson, K. -H., Lee, H. B., Lima, D. X., Lira, C. R. S., Machado, A. R., Madrid, H., Magalhaes, O. M. C., Majerova, H., Malysheva, E. F., Mapperson, R. R., Marbach, P. A. S., Martin, M. P., Martin-Sanz, A., Matocec, N., McTaggart, A. R., Mello, J. F., Melo, R. F. R., Mesic, A., Michereff, S. J., Miller, A. N., Minoshima, A., Molinero-Ruiz, L., Morozova, O. V., Mosoh, D., Nabe, M., Naik, R., Nara, K., Nascimento, S. S., Neves, R. P., Olariaga, I., Oliveira, R. L., Oliveira, T. G. L., Ono, T., Ordonez, M. E., Ottoni, A. de M., Paiva, L. M., Pancorbo, F., Pant, B., Pawlowska, J., Peterson, S. W., Raudabaugh, D. B., Rodriguez-Andrade, E., Rubio, E., Rusevska, K., Santiago, A. L. C. M. A., Santos, A. C. S., Santos, C., Sazanova, N. A., Shah, S., Sharma, J., Silva, B. D. B., Siquier, J. L., Sonawane, M. S., Stchigel, A. M., Svetasheva, T., Tamakeaw, N., Telleria, M. T., Tiago, P. V., Tian, C. M., Tkalcec, Z., Tomashevskaya, M. A., Truong, H. H., Vecherskii, M. V., Visagie, C. M., Vizzini, A., Yilmaz, N., Zmitrovich, I. V., Zvyagina, E. A., Boekhout, T., Kehlet, T., Laessoe, T., and Groenewald, J. Z.

Published
2019

5. Population data on 15 autosomal STRs in a sample from East Timor.

Author

Souto, L., Alves, Cintia, Gusmao, L., Ferreira, E., Amorim, Antonio, Corte-Real, F., and Vieira, D.N.

Subjects
Genetic markers -- Research, Human population genetics -- Research
Abstract

Abstract Allele frequencies for the fifteen STRs included in the AmpF/STR Identifiler (CSFIPO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) were estimated [...]

Published
2005

6. Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance

Author

Chacon-Duque, J., Adhikari, K., Fuentes-Guajardo, M., Mendoza-Revilla, J., Acuna-Alonzo, V., Barquera Lozano, R., Quinto-Sanchez, M., Gomez-Valdes, J., Everardo Martinez, P., Villamil-Ramirez, H., Hunemeier, T., Ramallo, V., Silva de Cerqueira, C., Hurtado, M., Villegas, V., Granja, V., Villena, M., Vasquez, R., Llop, E., Sandoval, J., Salazar-Granara, A., Parolin, M., Sandoval, K., Penaloza-Espinosa, R., Rangel-Villalobos, H., Winkler, C., Klitz, W., Bravi, C., Molina, J., Corach, D., Barrantes, R., Gomes, V., Resende, C., Gusmao, L., Amorim, A., Xue, Y., Dugoujon, J., Moral, P., Gonzalez-Jose, R., Schuler-Faccini, L., Salzano, F., Bortolini, M., Canizales-Quinteros, S., Poletti, G., Gallo, C., Bedoya, G., Rothhammer, F., Balding, D., Hellenthal, G., and Ruiz-Linares, A.

Subjects
parasitic diseases
Abstract

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods here we infer the sub-populations involved in admixture for over 6,500 Latin Americans and evaluate the impact of sub-continental ancestry on the physical appearance of these individuals. We find that pre-Columbian Native genetic structure is mirrored in Latin Americans and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that Central Andean ancestry impacts on variation of facial features in Latin Americans, particularly nose morphology, possibly relating to environmental adaptation during the evolution of Native Americans.

Published
2018

7. Fungal Planet description sheets : 785-867

Author

Crous, P. W., Luangsa-ard, J. J., Wingfield, M. J., Carnegie, A. J., Hernandez-Restrepo, M., Lombard, L., Roux, J., Barreto, R. W., Baseia, I. G., Cano-Lira, J. F., Martin, M. P., Morozova, O. V., Stchigel, A. M., Summerell, B. A., Brandrud, T. E., Dima, B., Garcia, D., Giraldo, A., Guarro, J., Gusmao, L. F. P., Khamsuntorn, P., Noordeloos, M. E., Nuankaew, S., Pinruan, U., Rodriguez-Andrade, E., Souza-Motta, C. M., Thangavel, R., van Iperen, A. L., Abreu, V. P., Accioly, T., Alves, J. L., Andrade, J. P., Bahram, Mohammad, Baral, H. -O, Barbier, E., Barnes, C. W., Bendiksen, E., Bernard, E., Bezerra, J. D. P., Bezerra, J. L., Bizio, Enrico, Blair, J. E., Bulyonkova, T. M., Cabral, T. S., Caiafa, M. V., Cantillo, T., Colman, A. A., Conceicao, L. B., Cruz, S., Cunha, A. O. B., Darveaux, B. A., da Silva, A. L., da Silva, G. A., da Silva, G. M., da Silva, R. M. F., de Oliveira, R. J. V., Oliveira, R. L., De Souza, J. T., Duenas, M., Evans, H. C., Epifani, F., Felipe, M. T. C., Fernandez-Lopez, J., Ferreira, B. W., Figueiredo, C. N., Filippova, N. V., Flores, J. A., Gene, J., Ghorbani, G., Gibertoni, T. B., Glushakova, A. M., Healy, R., Huhndorf, S. M., Iturrieta-Gonzalez, I., Javan-Nikkhah, M., Juciano, R. F., Jurjevic, Z., Kachalkin, A. V., Keochanpheng, K., Krisai-Greilhuber, I., Li, Y. -C, Lima, A. A., Machado, A. R., Madrid, H., Magalhaes, O. M. C., Marbach, P. A. S., Melanda, G. C. S., Miller, A. N., Mongkolsamrit, S., Nascimento, R. P., Oliveira, T. G. L., Ordonez, M. E., Orzes, R., Palma, M. A., Pearce, C. J., Pereira, O. L., Perrone, G., Peterson, S. W., Pham, T. H. G., Piontelli, E., Pordel, A., Quijada, L., Raja, H. A., de Paz, E. Rosas, Ryvarden, L., Saitta, A., Salcedo, S. S., Sandoval-Denis, M., Santos, T. A. B., Seifert, K. A., Silva, B. D. B., Smith, M. E., Soares, A. M., Sommai, S., Sousa, J. O., Suetrong, S., Susca, A., Tedersoo, L., Telleria, M. T., Thanakitpipattana, D., Valenzuela-Lopez, N., Visagie, C. M., Zapata, M., Groenewald, J. Z., Crous, P. W., Luangsa-ard, J. J., Wingfield, M. J., Carnegie, A. J., Hernandez-Restrepo, M., Lombard, L., Roux, J., Barreto, R. W., Baseia, I. G., Cano-Lira, J. F., Martin, M. P., Morozova, O. V., Stchigel, A. M., Summerell, B. A., Brandrud, T. E., Dima, B., Garcia, D., Giraldo, A., Guarro, J., Gusmao, L. F. P., Khamsuntorn, P., Noordeloos, M. E., Nuankaew, S., Pinruan, U., Rodriguez-Andrade, E., Souza-Motta, C. M., Thangavel, R., van Iperen, A. L., Abreu, V. P., Accioly, T., Alves, J. L., Andrade, J. P., Bahram, Mohammad, Baral, H. -O, Barbier, E., Barnes, C. W., Bendiksen, E., Bernard, E., Bezerra, J. D. P., Bezerra, J. L., Bizio, Enrico, Blair, J. E., Bulyonkova, T. M., Cabral, T. S., Caiafa, M. V., Cantillo, T., Colman, A. A., Conceicao, L. B., Cruz, S., Cunha, A. O. B., Darveaux, B. A., da Silva, A. L., da Silva, G. A., da Silva, G. M., da Silva, R. M. F., de Oliveira, R. J. V., Oliveira, R. L., De Souza, J. T., Duenas, M., Evans, H. C., Epifani, F., Felipe, M. T. C., Fernandez-Lopez, J., Ferreira, B. W., Figueiredo, C. N., Filippova, N. V., Flores, J. A., Gene, J., Ghorbani, G., Gibertoni, T. B., Glushakova, A. M., Healy, R., Huhndorf, S. M., Iturrieta-Gonzalez, I., Javan-Nikkhah, M., Juciano, R. F., Jurjevic, Z., Kachalkin, A. V., Keochanpheng, K., Krisai-Greilhuber, I., Li, Y. -C, Lima, A. A., Machado, A. R., Madrid, H., Magalhaes, O. M. C., Marbach, P. A. S., Melanda, G. C. S., Miller, A. N., Mongkolsamrit, S., Nascimento, R. P., Oliveira, T. G. L., Ordonez, M. E., Orzes, R., Palma, M. A., Pearce, C. J., Pereira, O. L., Perrone, G., Peterson, S. W., Pham, T. H. G., Piontelli, E., Pordel, A., Quijada, L., Raja, H. A., de Paz, E. Rosas, Ryvarden, L., Saitta, A., Salcedo, S. S., Sandoval-Denis, M., Santos, T. A. B., Seifert, K. A., Silva, B. D. B., Smith, M. E., Soares, A. M., Sommai, S., Sousa, J. O., Suetrong, S., Susca, A., Tedersoo, L., Telleria, M. T., Thanakitpipattana, D., Valenzuela-Lopez, N., Visagie, C. M., Zapata, M., and Groenewald, J. Z.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora cotymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia cotymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniefia eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis, Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus

Published
2018
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8. A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

Author

Pereira, R., Alves, C., Aler, M., Amorim, A., Arevalo, C., Betancor, E., Braganholi, D., Bravo, M. L., Brito, P., Builes, J. J., Burgos, G., Carvalho, E. F., Castillon, A., Catanesi, C. I., Cicarelli, R. M. B., Coufalova, P., Dario, P., D'Amato, M. E., Davison, S., Ferragut, J., Fondevila, M., Furfuro, S., Garcia, O., Gaviria, A., Gomes, I., Gonzalez, E., Gonzalez-Linan, A., Gross, T. E., Hernandez, A., Huang, Q., Jimenez, S., Jobim, L. F., Lopez-Parra, A. M., Marino, M., Marques, S., Martinez-Cortes, G., Masciovecchio, V., Parra, D., Penacino, G., Pinheiro, M. F., Porto, M. J., Posada, Y., Restrepo, C., Ribeiro, T., Rubio, L., Sala, A., Santurtun, A., Solis, L. S., Souto, L., Streitemberger, E., Torres, A., Vilela-Lamego, C., Yunis, J. J., Yurrebaso, I., Gusmao, L., Pereira, R., Alves, C., Aler, M., Amorim, A., Arevalo, C., Betancor, E., Braganholi, D., Bravo, M. L., Brito, P., Builes, J. J., Burgos, G., Carvalho, E. F., Castillon, A., Catanesi, C. I., Cicarelli, R. M. B., Coufalova, P., Dario, P., D'Amato, M. E., Davison, S., Ferragut, J., Fondevila, M., Furfuro, S., Garcia, O., Gaviria, A., Gomes, I., Gonzalez, E., Gonzalez-Linan, A., Gross, T. E., Hernandez, A., Huang, Q., Jimenez, S., Jobim, L. F., Lopez-Parra, A. M., Marino, M., Marques, S., Martinez-Cortes, G., Masciovecchio, V., Parra, D., Penacino, G., Pinheiro, M. F., Porto, M. J., Posada, Y., Restrepo, C., Ribeiro, T., Rubio, L., Sala, A., Santurtun, A., Solis, L. S., Souto, L., Streitemberger, E., Torres, A., Vilela-Lamego, C., Yunis, J. J., Yurrebaso, I., and Gusmao, L.

Abstract

A collaborative effort was carried out by the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) to promote knowledge exchange between associate laboratories interested in the implementation of indel-based methodologies and build allele frequency databases of 38 indels for forensic applications. These databases include populations from different countries that are relevant for identification and kinship investigations undertaken by the participating laboratories. Before compiling population data, participants were asked to type the 38 indels in blind samples from annual GHEP-ISFG proficiency tests, using an amplification protocol previously described. Only laboratories that reported correct results contributed with population data to this study. A total of 5839 samples were genotyped from 45 different populations from Africa, America, East Asia, Europe and Middle East. Population differentiation analysis showed significant differences between most populations studied from Africa and America, as well as between two Asian populations from China and East Timor. Low F-ST values were detected among most European populations. Overall diversities and parameters of forensic efficiency were high in populations from all continents.

Published
2018

9. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Author

Chacon-Duque, J-C, Adhikari, K, Fuentes-Guajardo, M, Mendoza-Revilla, J, Acuna-Alonzo, V, Barquera, R, Quinto-Sanchez, M, Gomez-Valdes, J, Everardo Martinez, P, Villamil-Ramirez, H, Hunemeier, T, Ramallo, V, Silva de Cerqueira, CC, Hurtado, M, Villegas, V, Granja, V, Villena, M, Vasquez, R, Llop, E, Sandoval, JR, Salazar-Granara, AA, Parolin, M-L, Sandoval, K, Penaloza-Espinosa, RI, Rangel-Villalobos, H, Winkler, CA, Klitz, W, Bravi, C, Molina, J, Corach, D, Barrantes, R, Gomes, V, Resende, C, Gusmao, L, Amorim, A, Xue, Y, Dugoujon, J-M, Moral, P, Gonzalez-Jose, R, Schuler-Faccini, L, Salzano, FM, Bortolini, M-C, Canizales-Quinteros, S, Poletti, G, Gallo, C, Bedoya, G, Rothhammer, F, Balding, D, Hellenthal, G, Ruiz-Linares, A, Chacon-Duque, J-C, Adhikari, K, Fuentes-Guajardo, M, Mendoza-Revilla, J, Acuna-Alonzo, V, Barquera, R, Quinto-Sanchez, M, Gomez-Valdes, J, Everardo Martinez, P, Villamil-Ramirez, H, Hunemeier, T, Ramallo, V, Silva de Cerqueira, CC, Hurtado, M, Villegas, V, Granja, V, Villena, M, Vasquez, R, Llop, E, Sandoval, JR, Salazar-Granara, AA, Parolin, M-L, Sandoval, K, Penaloza-Espinosa, RI, Rangel-Villalobos, H, Winkler, CA, Klitz, W, Bravi, C, Molina, J, Corach, D, Barrantes, R, Gomes, V, Resende, C, Gusmao, L, Amorim, A, Xue, Y, Dugoujon, J-M, Moral, P, Gonzalez-Jose, R, Schuler-Faccini, L, Salzano, FM, Bortolini, M-C, Canizales-Quinteros, S, Poletti, G, Gallo, C, Bedoya, G, Rothhammer, F, Balding, D, Hellenthal, G, and Ruiz-Linares, A

Abstract

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.

Published
2018

10. Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Author

Zamora, J. C. (Juan Carlos), Svensson, M. (Mans), Kirschner, R. (Roland), Olariaga, I. (Ibai), Ryman, S. (Svengunnar), Alberto Parra, L. (Luis), Geml, J. (Jozsef), Rosling, A. (Anna), Adamcik, S. (Slavomir), Ahti, T. (Teuvo), Aime, M. C. (M. Catherine), Ainsworth, A. M. (A. Martyn), Albert, L. (Laszlo), Alberto, E. (Edgardo), Garcia, A. A. (Alberto Altes), Ageev, D. (Dmitry), Agerer, R. (Reinhard), Aguirre-Hudson, B. (Begona), Ammirati, J. (Joe), Andersson, H. (Harry), Angelini, C. (Claudio), Antonin, V. (Vladimir), Aoki, T. (Takayuki), Aptroot, A. (Andre), Argaud, D. (Didier), Sosa, B. I. (Blanca Imelda Arguello), Aronsen, A. (Arne), Arup, U. (Ulf), Asgari, B. (Bita), Assyov, B. (Boris), Atienza, V. (Violeta), Bandini, D. (Ditte), Baptista-Ferreira, J. L. (Joao Luis), Baral, H.-O. (Hans-Otto), Baroni, T. (Tim), Barreto, R. W. (Robert Weingart), Baker, H. (Henry), Bell, A. (Ann), Bellanger, J.-M. (Jean-Michel), Bellu, F. (Francesco), Bemmann, M. (Martin), Bendiksby, M. (Mika), Bendiksen, E. (Egil), Bendiksen, K. (Katriina), Benedek, L. (Lajos), Beresova-Guttova, A. (Anna), Berger, F. (Franz), Berndt, R. (Reinhard), Bernicchia, A. (Annarosa), Biketova, A. Y. (Alona Yu), Bizio, E. (Enrico), Bjork, C. (Curtis), Boekhout, T. (Teun), Boertmann, D. (David), Bohning, T. (Tanja), Boittin, F. (Florent), Boluda, C. G. (Carlos G.), Boomsluiter, M. W. (Menno W.), Borovicka, J. (Jan), Brandrud, T. E. (Tor Erik), Braun, U. (Uwe), Brodo, I. (Irwin), Bulyonkova, T. (Tatiana), Burdsall, H. H. (Harold H., Jr.), Buyck, B. (Bart), Burgaz, A. R. (Ana Rosa), Calatayud, V. (Vicent), Callac, P. (Philippe), Campo, E. (Emanuele), Candusso, M. (Massimo), Capoen, B. (Brigitte), Carbo, J. (Joaquim), Carbone, M. (Matteo), Castaneda-Ruiz, R. F. (Rafael F.), Castellano, M. A. (Michael A.), Chen, J. (Jie), Clerc, P. (Philippe), Consiglio, G. (Giovanni), Corriol, G. (Gilles), Courtecuisse, R. (Regis), Crespo, A. (Ana), Cripps, C. (Cathy), Crous, P. W. (Pedro W.), da Silva, G. A. (Gladstone Alves), da Silva, M. (Meiriele), Dam, M. (Marjo), Dam, N. (Nico), Dammrich, F. (Frank), Das, K. (Kanad), Davies, L. (Linda), De Crop, E. (Eske), De Kesel, A. (Andre), De Lange, R. (Ruben), Bonzi, B. D. (Barbara De Madrignac), dela Cruz, T. E. (Thomas Edison E.), Delgat, L. (Lynn), Demoulin, V. (Vincent), Desjardin, D. E. (Dennis E.), Diederich, P. (Paul), Dima, B. (Balint), Dios, M. M. (Maria Martha), Divakar, P. K. (Pradeep Kumar), Douanla-Meli, C. (Clovis), Douglas, B. (Brian), Drechsler-Santos, E. R. (Elisandro Ricardo), Dyer, P. S. (Paul S.), Eberhardt, U. (Ursula), Ertz, D. (Damien), Esteve-Raventos, F. (Fernando), Salazar, J. A. (Javier Angel Etayo), Evenson, V. (Vera), Eyssartier, G. (Guillaume), Farkas, E. (Edit), Favre, A. (Alain), Fedosova, A. G. (Anna G.), Filippa, M. (Mario), Finy, P. (Peter), Flakus, A. (Adam), Fos, S. (Simon), Fournier, J. (Jacques), Fraiture, A. (Andre), Franchi, P. (Paolo), Molano, A. E. (Ana Esperanza Franco), Friebes, G. (Gernot), Frisch, A. (Andreas), Fryday, A. (Alan), Furci, G. (Giuliana), Marquez, R. G. (Ricardo Galan), Garbelotto, M. (Matteo), Garcia-Martin, J. M. (Joaquina Maria), Otalora, M. A. (Monica A. Garcia), Sanchez, D. G. (Dania Garcia), Gardiennet, A. (Alain), Garnica, S. (Sigisfredo), Benavent, I. G. (Isaac Garrido), Gates, G. (Genevieve), Gerlach, A. d. (Alice da Cruz Lima), Ghobad-Nejhad, M. (Masoomeh), Gibertoni, T. B. (Tatiana B.), Grebenc, T. (Tine), Greilhuber, I. (Irmgard), Grishkan, B. (Bella), Groenewald, J. Z. (Johannes Z.), Grube, M. (Martin), Gruhn, G. (Gerald), Gueidan, C. (Cecile), Gulden, G. (Gro), Gusmao, L. F. (Luis F. P.), Hafellner, J. (Josef), Hairaud, M. (Michel), Halama, M. (Marek), Hallenberg, N. (Nils), Halling, R. E. (Roy E.), Hansen, K. (Karen), Harder, C. B. (Christoffer Bugge), Heilmann-Clausen, J. (Jacob), Helleman, S. (Stip), Henriot, A. (Alain), Hernandez-Restrepo, M. (Margarita), Herve, R. (Raphael), Hobart, C. (Caroline), Hoffmeister, M. (Mascha), Hoiland, K. (Klaus), Holec, J. (Jan), Holien, H. (Hakon), Hughes, K. (Karen), Hubka, V. (Vit), Huhtinen, S. (Seppo), Ivancevic, B. (Boris), Jagers, M. (Marian), Jaklitsch, W. (Walter), Jansen, A. (AnnaElise), Jayawardena, R. S. (Ruvishika S.), Jeppesen, T. S. (Thomas Stjernegaard), Jeppson, M. (Mikael), Johnston, P. (Peter), Jorgensen, P. M. (Per Magnus), Karnefelt, I. (Ingvar), Kalinina, L. B. (Liudmila B.), Kantvilas, G. (Gintaras), Karadelev, M. (Mitko), Kasuya, T. (Taiga), Kautmanova, I. (Ivona), Kerrigan, R. W. (Richard W.), Kirchmair, M. (Martin), Kiyashko, A. (Anna), Knapp, D. G. (Daniel G.), Knudsen, H. (Henning), Knudsen, K. (Kerry), Knutsson, T. (Tommy), Kolarik, M. (Miroslav), Koljalg, U. (Urmas), Kosuthova, A. (Alica), Koszka, A. (Attila), Kotiranta, H. (Heikki), Kotkova, V. (Vera), Koukol, O. (Ondrej), Kout, J. (Jiri), Kovacs, G. M. (Gabor M.), Kriz, M. (Martin), Kruys, A. (Asa), Kudera, V. (Viktor), Kudzma, L. (Linas), Kuhar, F. (Francisco), Kukwa, M. (Martin), Kumar, T. K. (T. K. Arun), Kunca, V. (Vladimir), Kusan, I. (Ivana), Kuyper, T. W. (Thomas W.), Lado, C. (Carlos), Laessoe, T. (Thomas), Laine, P. (Patrice), Langer, E. (Ewald), Larsson, E. (Ellen), Larsson, K.-H. (Karl-Henrik), Laursen, G. (Gary), Lechat, C. (Christian), Lee, S. (Serena), Lendemer, J. C. (James C.), Levin, L. (Laura), Lindemann, U. (Uwe), Lindstrom, H. (Hakan), Liu, X. (Xingzhong), Hernandez, R. C. (Regulo Carlos Llarena), Llop, E. (Esteve), Locsmandi, C. (Csaba), Lodge, D. J. (Deborah Jean), Loizides, M. (Michael), Lokos, L. (Laszlo), Luangsa-ard, J. (Jennifer), Luderitz, M. (Matthias), Lumbsch, T. (Thorsten), Lutz, M. (Matthias), Mahoney, D. (Dan), Malysheva, E. (Ekaterina), Malysheva, V. (Vera), Manimohan, P. (Patinjareveettil), Mann-Felix, Y. (Yasmina), Marques, G. (Guilhermina), Martinez-Gil, R. (Ruben), Marson, G. (Guy), Mata, G. (Gerardo), Matheny, P. B. (P. Brandon), Mathiassen, G. H. (Geir Harald), Matocec, N. (Neven), Mayrhofer, H. (Helmut), Mehrabi, M. (Mehdi), Melo, I. (Ireneia), Mesic, A. (Armin), Methven, A. S. (Andrew S.), Miettinen, O. (Otto), Romero, A. M. (Ana M. Millanes), Miller, A. N. (Andrew N.), Mitchell, J. K. (James K.), Moberg, R. (Roland), Moreau, P.-A. (Pierre-Arthur), Moreno, G. (Gabriel), Morozova, O. (Olga), Morte, A. (Asuncion), Muggia, L. (Lucia), Gonzalez, G. M. (Guillermo Munoz), Myllys, L. (Leena), Nagy, I. (Istvan), Nagy, L. G. (Laszlo G.), Neves, M. A. (Maria Alice), Niemela, T. (Tuomo), Nimis, P. L. (Pier Luigi), Niveiro, N. (Nicolas), Noordeloos, M. E. (Machiel E.), Nordin, A. (Anders), Noumeur, S. R. (Sara Raouia), Novozhilov, Y. (Yuri), Nuytinck, J. (Jorinde), Ohenoja, E. (Esteri), Fiuza, P. O. (Patricia Oliveira), Orange, A. (Alan), Ordynets, A. (Alexander), Ortiz-Santana, B. (Beatriz), Pacheco, L. (Leticia), Pal-Fam, F. (Ferenc), Palacio, M. (Melissa), Palice, Z. (Zdenek), Papp, V. (Viktor), Partel, K. (Kadri), Pawlowska, J. (Julia), Paz, A. (Aurelia), Peintner, U. (Ursula), Pennycook, S. (Shaun), Pereira, O. L. (Olinto Liparini), Daniels, P. P. (Pablo Perez), Capella, M. A. (Miguel A. Perez-De-Gregorio), del Amo, C. M. (Carlos Manuel Perez), Gorjon, S. P. (Sergio Perez), Perez-Ortega, S. (Sergio), Perez-Vargas, I. (Israel), Perry, B. A. (Brian A.), Petersen, J. H. (Jens H.), Petersen, R. H. (Ronald H.), Pfister, D. H. (Donald H.), Phukhamsakda, C. (Chayanard), Piatek, M. (Marcin), Piepenbring, M. (Meike), Pino-Bodas, R. (Raquel), Esquivel, J. P. (Juan Pablo Pinzon), Pirot, P. (Paul), Popov, E. S. (Eugene S.), Popoff, O. (Orlando), Alvaro, M. P. (Maria Prieto), Printzen, C. (Christian), Psurtseva, N. (Nadezhda), Purahong, W. (Witoon), Quijada, L. (Luis), Rambold, G. (Gerhard), Ramirez, N. A. (Natalia A.), Raja, H. (Huzefa), Raspe, O. (Olivier), Raymundo, T. (Tania), Reblova, M. (Martina), Rebriev, Y. A. (Yury A.), Garcia, J. d. (Juan de Dios Reyes), Ripoll, M. A. (Miguel Angel Ribes), Richard, F. (Franck), Richardson, M. J. (Mike J.), Rico, V. J. (Victor J.), Robledo, G. L. (Gerardo Lucio), Barbosa, F. R. (Flavia Rodrigues), Rodriguez-Caycedo, C. (Cristina), Rodriguez-Flakus, P. (Pamela), Ronikier, A. (Anna), Casas, L. R. (Luis Rubio), Rusevska, K. (Katerina), Saar, G. (Gunter), Saar, I. (Irja), Salcedo, I. (Isabel), Martinez, S. M. (Sergio M. Salcedo), Montoya, C. A. (Carlos A. Salvador), Sanchez-Ramirez, S. (Santiago), Sandoval-Sierra, J. V. (J. Vladimir), Santamaria, S. (Sergi), Monteiro, J. S. (Josiane Santana), Schroers, H. J. (Hans Josef), Schulz, B. (Barbara), Schmidt-Stohn, G. (Geert), Schumacher, T. (Trond), Senn-Irlet, B. (Beatrice), Sevcikova, H. (Hana), Shchepin, O. (Oleg), Shirouzu, T. (Takashi), Shiryaev, A. (Anton), Siepe, K. (Klaus), Sir, E. B. (Esteban B.), Sohrabi, M. (Mohammad), Soop, K. (Karl), Spirin, V. (Viacheslav), Spribille, T. (Toby), Stadler, M. (Marc), Stalpers, J. (Joost), Stenroos, S. (Soili), Suija, A. (Ave), Sunhede, S. (Stellan), Svantesson, S. (Sten), Svensson, S. (Sigvard), Svetasheva, T. Y. (Tatyana Yu), Swierkosz, K. (Krzysztof), Tamm, H. (Heidi), Taskin, H. (Hatira), Taudiere, A. (Adrien), Tedebrand, J.-O. (Jan-Olof), Lahoz, R. T. (Raul Tena), Temina, M. (Marina), Thell, A. (Arne), Thines, M. (Marco), Thor, G. (Goren), Thus, H. (Holger), Tibell, L. (Leif), Tibell, S. (Sanja), Timdal, E. (Einar), Tkalcec, Z. (Zdenko), Tonsberg, T. (Tor), Trichies, G. (Gerard), Triebel, D. (Dagmar), Tsurykau, A. (Andrei), Tulloss, R. E. (Rodham E.), Tuovinen, V. (Veera), Sosa, M. U. (Miguel Ulloa), Urcelay, C. (Carlos), Valade, F. (Francois), Garza, R. V. (Ricardo Valenzuela), van den Boom, P. (Pieter), Van Vooren, N. (Nicolas), Vasco-Palacios, A. M. (Aida M.), Vauras, J. (Jukka), Santos, J. M. (Juan Manuel Velasco), Vellinga, E. (Else), Verbeken, A. (Annemieke), Vetlesen, P. (Per), Vizzini, A. (Alfredo), Voglmayr, H. (Hermann), Volobuev, S. (Sergey), von Brackel, W. (Wolfgang), Voronina, E. (Elena), Walther, G. (Grit), Watling, R. (Roy), Weber, E. (Evi), Wedin, M. (Mats), Weholt, O. (Oyvind), Westberg, M. (Martin), Yurchenko, E. (Eugene), Zehnalek, P. (Petr), Zhang, H. (Huang), Zhurbenko, M. P. (Mikhail P.), Ekmani, S. (Stefan), Zamora, J. C. (Juan Carlos), Svensson, M. (Mans), Kirschner, R. (Roland), Olariaga, I. (Ibai), Ryman, S. (Svengunnar), Alberto Parra, L. (Luis), Geml, J. (Jozsef), Rosling, A. (Anna), Adamcik, S. (Slavomir), Ahti, T. (Teuvo), Aime, M. C. (M. Catherine), Ainsworth, A. M. (A. Martyn), Albert, L. (Laszlo), Alberto, E. (Edgardo), Garcia, A. A. (Alberto Altes), Ageev, D. (Dmitry), Agerer, R. (Reinhard), Aguirre-Hudson, B. (Begona), Ammirati, J. (Joe), Andersson, H. (Harry), Angelini, C. (Claudio), Antonin, V. (Vladimir), Aoki, T. (Takayuki), Aptroot, A. (Andre), Argaud, D. (Didier), Sosa, B. I. (Blanca Imelda Arguello), Aronsen, A. (Arne), Arup, U. (Ulf), Asgari, B. (Bita), Assyov, B. (Boris), Atienza, V. (Violeta), Bandini, D. (Ditte), Baptista-Ferreira, J. L. (Joao Luis), Baral, H.-O. (Hans-Otto), Baroni, T. (Tim), Barreto, R. W. (Robert Weingart), Baker, H. (Henry), Bell, A. (Ann), Bellanger, J.-M. (Jean-Michel), Bellu, F. (Francesco), Bemmann, M. (Martin), Bendiksby, M. (Mika), Bendiksen, E. (Egil), Bendiksen, K. (Katriina), Benedek, L. (Lajos), Beresova-Guttova, A. (Anna), Berger, F. (Franz), Berndt, R. (Reinhard), Bernicchia, A. (Annarosa), Biketova, A. Y. (Alona Yu), Bizio, E. (Enrico), Bjork, C. (Curtis), Boekhout, T. (Teun), Boertmann, D. (David), Bohning, T. (Tanja), Boittin, F. (Florent), Boluda, C. G. (Carlos G.), Boomsluiter, M. W. (Menno W.), Borovicka, J. (Jan), Brandrud, T. E. (Tor Erik), Braun, U. (Uwe), Brodo, I. (Irwin), Bulyonkova, T. (Tatiana), Burdsall, H. H. (Harold H., Jr.), Buyck, B. (Bart), Burgaz, A. R. (Ana Rosa), Calatayud, V. (Vicent), Callac, P. (Philippe), Campo, E. (Emanuele), Candusso, M. (Massimo), Capoen, B. (Brigitte), Carbo, J. (Joaquim), Carbone, M. (Matteo), Castaneda-Ruiz, R. F. (Rafael F.), Castellano, M. A. (Michael A.), Chen, J. (Jie), Clerc, P. (Philippe), Consiglio, G. (Giovanni), Corriol, G. (Gilles), Courtecuisse, R. (Regis), Crespo, A. (Ana), Cripps, C. (Cathy), Crous, P. W. (Pedro W.), da Silva, G. A. (Gladstone Alves), da Silva, M. (Meiriele), Dam, M. (Marjo), Dam, N. (Nico), Dammrich, F. (Frank), Das, K. (Kanad), Davies, L. (Linda), De Crop, E. (Eske), De Kesel, A. (Andre), De Lange, R. (Ruben), Bonzi, B. D. (Barbara De Madrignac), dela Cruz, T. E. (Thomas Edison E.), Delgat, L. (Lynn), Demoulin, V. (Vincent), Desjardin, D. E. (Dennis E.), Diederich, P. (Paul), Dima, B. (Balint), Dios, M. M. (Maria Martha), Divakar, P. K. (Pradeep Kumar), Douanla-Meli, C. (Clovis), Douglas, B. (Brian), Drechsler-Santos, E. R. (Elisandro Ricardo), Dyer, P. S. (Paul S.), Eberhardt, U. (Ursula), Ertz, D. (Damien), Esteve-Raventos, F. (Fernando), Salazar, J. A. (Javier Angel Etayo), Evenson, V. (Vera), Eyssartier, G. (Guillaume), Farkas, E. (Edit), Favre, A. (Alain), Fedosova, A. G. (Anna G.), Filippa, M. (Mario), Finy, P. (Peter), Flakus, A. (Adam), Fos, S. (Simon), Fournier, J. (Jacques), Fraiture, A. (Andre), Franchi, P. (Paolo), Molano, A. E. (Ana Esperanza Franco), Friebes, G. (Gernot), Frisch, A. (Andreas), Fryday, A. (Alan), Furci, G. (Giuliana), Marquez, R. G. (Ricardo Galan), Garbelotto, M. (Matteo), Garcia-Martin, J. M. (Joaquina Maria), Otalora, M. A. (Monica A. Garcia), Sanchez, D. G. (Dania Garcia), Gardiennet, A. (Alain), Garnica, S. (Sigisfredo), Benavent, I. G. (Isaac Garrido), Gates, G. (Genevieve), Gerlach, A. d. (Alice da Cruz Lima), Ghobad-Nejhad, M. (Masoomeh), Gibertoni, T. B. (Tatiana B.), Grebenc, T. (Tine), Greilhuber, I. (Irmgard), Grishkan, B. (Bella), Groenewald, J. Z. (Johannes Z.), Grube, M. (Martin), Gruhn, G. (Gerald), Gueidan, C. (Cecile), Gulden, G. (Gro), Gusmao, L. F. (Luis F. P.), Hafellner, J. (Josef), Hairaud, M. (Michel), Halama, M. (Marek), Hallenberg, N. (Nils), Halling, R. E. (Roy E.), Hansen, K. (Karen), Harder, C. B. (Christoffer Bugge), Heilmann-Clausen, J. (Jacob), Helleman, S. (Stip), Henriot, A. (Alain), Hernandez-Restrepo, M. (Margarita), Herve, R. (Raphael), Hobart, C. (Caroline), Hoffmeister, M. (Mascha), Hoiland, K. (Klaus), Holec, J. (Jan), Holien, H. (Hakon), Hughes, K. (Karen), Hubka, V. (Vit), Huhtinen, S. (Seppo), Ivancevic, B. (Boris), Jagers, M. (Marian), Jaklitsch, W. (Walter), Jansen, A. (AnnaElise), Jayawardena, R. S. (Ruvishika S.), Jeppesen, T. S. (Thomas Stjernegaard), Jeppson, M. (Mikael), Johnston, P. (Peter), Jorgensen, P. M. (Per Magnus), Karnefelt, I. (Ingvar), Kalinina, L. B. (Liudmila B.), Kantvilas, G. (Gintaras), Karadelev, M. (Mitko), Kasuya, T. (Taiga), Kautmanova, I. (Ivona), Kerrigan, R. W. (Richard W.), Kirchmair, M. (Martin), Kiyashko, A. (Anna), Knapp, D. G. (Daniel G.), Knudsen, H. (Henning), Knudsen, K. (Kerry), Knutsson, T. (Tommy), Kolarik, M. (Miroslav), Koljalg, U. (Urmas), Kosuthova, A. (Alica), Koszka, A. (Attila), Kotiranta, H. (Heikki), Kotkova, V. (Vera), Koukol, O. (Ondrej), Kout, J. (Jiri), Kovacs, G. M. (Gabor M.), Kriz, M. (Martin), Kruys, A. (Asa), Kudera, V. (Viktor), Kudzma, L. (Linas), Kuhar, F. (Francisco), Kukwa, M. (Martin), Kumar, T. K. (T. K. Arun), Kunca, V. (Vladimir), Kusan, I. (Ivana), Kuyper, T. W. (Thomas W.), Lado, C. (Carlos), Laessoe, T. (Thomas), Laine, P. (Patrice), Langer, E. (Ewald), Larsson, E. (Ellen), Larsson, K.-H. (Karl-Henrik), Laursen, G. (Gary), Lechat, C. (Christian), Lee, S. (Serena), Lendemer, J. C. (James C.), Levin, L. (Laura), Lindemann, U. (Uwe), Lindstrom, H. (Hakan), Liu, X. (Xingzhong), Hernandez, R. C. (Regulo Carlos Llarena), Llop, E. (Esteve), Locsmandi, C. (Csaba), Lodge, D. J. (Deborah Jean), Loizides, M. (Michael), Lokos, L. (Laszlo), Luangsa-ard, J. (Jennifer), Luderitz, M. (Matthias), Lumbsch, T. (Thorsten), Lutz, M. (Matthias), Mahoney, D. (Dan), Malysheva, E. (Ekaterina), Malysheva, V. (Vera), Manimohan, P. (Patinjareveettil), Mann-Felix, Y. (Yasmina), Marques, G. (Guilhermina), Martinez-Gil, R. (Ruben), Marson, G. (Guy), Mata, G. (Gerardo), Matheny, P. B. (P. Brandon), Mathiassen, G. H. (Geir Harald), Matocec, N. (Neven), Mayrhofer, H. (Helmut), Mehrabi, M. (Mehdi), Melo, I. (Ireneia), Mesic, A. (Armin), Methven, A. S. (Andrew S.), Miettinen, O. (Otto), Romero, A. M. (Ana M. Millanes), Miller, A. N. (Andrew N.), Mitchell, J. K. (James K.), Moberg, R. (Roland), Moreau, P.-A. (Pierre-Arthur), Moreno, G. (Gabriel), Morozova, O. (Olga), Morte, A. (Asuncion), Muggia, L. (Lucia), Gonzalez, G. M. (Guillermo Munoz), Myllys, L. (Leena), Nagy, I. (Istvan), Nagy, L. G. (Laszlo G.), Neves, M. A. (Maria Alice), Niemela, T. (Tuomo), Nimis, P. L. (Pier Luigi), Niveiro, N. (Nicolas), Noordeloos, M. E. (Machiel E.), Nordin, A. (Anders), Noumeur, S. R. (Sara Raouia), Novozhilov, Y. (Yuri), Nuytinck, J. (Jorinde), Ohenoja, E. (Esteri), Fiuza, P. O. (Patricia Oliveira), Orange, A. (Alan), Ordynets, A. (Alexander), Ortiz-Santana, B. (Beatriz), Pacheco, L. (Leticia), Pal-Fam, F. (Ferenc), Palacio, M. (Melissa), Palice, Z. (Zdenek), Papp, V. (Viktor), Partel, K. (Kadri), Pawlowska, J. (Julia), Paz, A. (Aurelia), Peintner, U. (Ursula), Pennycook, S. (Shaun), Pereira, O. L. (Olinto Liparini), Daniels, P. P. (Pablo Perez), Capella, M. A. (Miguel A. Perez-De-Gregorio), del Amo, C. M. (Carlos Manuel Perez), Gorjon, S. P. (Sergio Perez), Perez-Ortega, S. (Sergio), Perez-Vargas, I. (Israel), Perry, B. A. (Brian A.), Petersen, J. H. (Jens H.), Petersen, R. H. (Ronald H.), Pfister, D. H. (Donald H.), Phukhamsakda, C. (Chayanard), Piatek, M. (Marcin), Piepenbring, M. (Meike), Pino-Bodas, R. (Raquel), Esquivel, J. P. (Juan Pablo Pinzon), Pirot, P. (Paul), Popov, E. S. (Eugene S.), Popoff, O. (Orlando), Alvaro, M. P. (Maria Prieto), Printzen, C. (Christian), Psurtseva, N. (Nadezhda), Purahong, W. (Witoon), Quijada, L. (Luis), Rambold, G. (Gerhard), Ramirez, N. A. (Natalia A.), Raja, H. (Huzefa), Raspe, O. (Olivier), Raymundo, T. (Tania), Reblova, M. (Martina), Rebriev, Y. A. (Yury A.), Garcia, J. d. (Juan de Dios Reyes), Ripoll, M. A. (Miguel Angel Ribes), Richard, F. (Franck), Richardson, M. J. (Mike J.), Rico, V. J. (Victor J.), Robledo, G. L. (Gerardo Lucio), Barbosa, F. R. (Flavia Rodrigues), Rodriguez-Caycedo, C. (Cristina), Rodriguez-Flakus, P. (Pamela), Ronikier, A. (Anna), Casas, L. R. (Luis Rubio), Rusevska, K. (Katerina), Saar, G. (Gunter), Saar, I. (Irja), Salcedo, I. (Isabel), Martinez, S. M. (Sergio M. Salcedo), Montoya, C. A. (Carlos A. Salvador), Sanchez-Ramirez, S. (Santiago), Sandoval-Sierra, J. V. (J. Vladimir), Santamaria, S. (Sergi), Monteiro, J. S. (Josiane Santana), Schroers, H. J. (Hans Josef), Schulz, B. (Barbara), Schmidt-Stohn, G. (Geert), Schumacher, T. (Trond), Senn-Irlet, B. (Beatrice), Sevcikova, H. (Hana), Shchepin, O. (Oleg), Shirouzu, T. (Takashi), Shiryaev, A. (Anton), Siepe, K. (Klaus), Sir, E. B. (Esteban B.), Sohrabi, M. (Mohammad), Soop, K. (Karl), Spirin, V. (Viacheslav), Spribille, T. (Toby), Stadler, M. (Marc), Stalpers, J. (Joost), Stenroos, S. (Soili), Suija, A. (Ave), Sunhede, S. (Stellan), Svantesson, S. (Sten), Svensson, S. (Sigvard), Svetasheva, T. Y. (Tatyana Yu), Swierkosz, K. (Krzysztof), Tamm, H. (Heidi), Taskin, H. (Hatira), Taudiere, A. (Adrien), Tedebrand, J.-O. (Jan-Olof), Lahoz, R. T. (Raul Tena), Temina, M. (Marina), Thell, A. (Arne), Thines, M. (Marco), Thor, G. (Goren), Thus, H. (Holger), Tibell, L. (Leif), Tibell, S. (Sanja), Timdal, E. (Einar), Tkalcec, Z. (Zdenko), Tonsberg, T. (Tor), Trichies, G. (Gerard), Triebel, D. (Dagmar), Tsurykau, A. (Andrei), Tulloss, R. E. (Rodham E.), Tuovinen, V. (Veera), Sosa, M. U. (Miguel Ulloa), Urcelay, C. (Carlos), Valade, F. (Francois), Garza, R. V. (Ricardo Valenzuela), van den Boom, P. (Pieter), Van Vooren, N. (Nicolas), Vasco-Palacios, A. M. (Aida M.), Vauras, J. (Jukka), Santos, J. M. (Juan Manuel Velasco), Vellinga, E. (Else), Verbeken, A. (Annemieke), Vetlesen, P. (Per), Vizzini, A. (Alfredo), Voglmayr, H. (Hermann), Volobuev, S. (Sergey), von Brackel, W. (Wolfgang), Voronina, E. (Elena), Walther, G. (Grit), Watling, R. (Roy), Weber, E. (Evi), Wedin, M. (Mats), Weholt, O. (Oyvind), Westberg, M. (Martin), Yurchenko, E. (Eugene), Zehnalek, P. (Petr), Zhang, H. (Huang), Zhurbenko, M. P. (Mikhail P.), and Ekmani, S. (Stefan)

Abstract

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN., Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. Harry Andersson Eichhahnweg 29a, 38108 Braunschweig, Germany Claudio Angelini Jardín Botánico Nacional Dr. Rafael Ma. Moscoso, Apartado 21-9, Santo Domingo, Dominican Republic Vladimír Antonín Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Takayuki Aoki Genetic Reso

Published
2018

11. Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes

Author

Roewer, L., Krawczak, M., Willuweit, S., Nagy, M., Alves, C., Amorim, A., Anslinger, K., Augustin, C., Betz, A., Bosch, E., Cagliá, A., Carracedo, A., Corach, D., Dekairelle, A.-F., Dobosz, T., Dupuy, B.M., Füredi, S., Gehrig, C., Gusmaõ, L., Henke, J., Henke, L., Hidding, M., Hohoff, C., Hoste, B., Jobling, M.A., Kärgel, H.J., de Knijff, P., Lessig, R., Liebeherr, E., Lorente, M., Martı́nez-Jarreta, B., Nievas, P., Nowak, M., Parson, W., Pascali, V.L., Penacino, G., Ploski, R., Rolf, B., Sala, A., Schmitt, C., Schmidt, U., Schneider, P.M., Szibor, R., Teifel-Greding, J., and Kayser, M.

Published
2001
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13. DNA Commission of the International Society for Forensic Genetics: Recommendations on the validation of software programs performing biostatistical calculations for forensic genetics applications

Author

Coble, M. D., Buckleton, J., Butler, J. M., Egeland, T., Fimmers, R., Gill, P., Gusmao, L., Guttman, B., Krawczak, M., Morling, N., Parson, W., Pinto, N., Schneider, P. M., Sherry, S. T., Willuweit, S., Prinz, M., Coble, M. D., Buckleton, J., Butler, J. M., Egeland, T., Fimmers, R., Gill, P., Gusmao, L., Guttman, B., Krawczak, M., Morling, N., Parson, W., Pinto, N., Schneider, P. M., Sherry, S. T., Willuweit, S., and Prinz, M.

Abstract

The use of biostatistical software programs to assist in data interpretation and calculate likelihood ratios is essential to forensic geneticists and part of the daily case work flow for both kinship and DNA identification laboratories. Previous recommendations issued by the DNA Commission of the International Society for Forensic Genetics (ISFG) covered the application of bio-statistical evaluations for STR typing results in identification and kinship cases, and this is now being expanded to provide best practices regarding validation and verification of the software required for these calculations. With larger multiplexes, more complex mixtures, and increasing requests for extended family testing, laboratories are relying more than ever on specific software solutions and sufficient validation, training and extensive documentation are of upmost importance. Here, we present recommendations for the minimum requirements to validate bio-statistical software to be used in forensic genetics. We distinguish between developmental validation and the responsibilities of the software developer or provider, and the internal validation studies to be performed by the end user. Recommendations for the software provider address, for example, the documentation of the underlying models used by the software, validation data expectations, version control, implementation and training support, as well as continuity and user notifications. For the internal validations the recommendations include: creating a validation plan, requirements for the range of samples to be tested, Standard Operating Procedure development, and internal laboratory training and education. To ensure that all laboratories have access to a wide range of samples for validation and training purposes the ISFG DNA commission encourages collaborative studies and public repositories of STR typing results. Published by Elsevier Ireland Ltd.

Published
2016

15. DNA Commission of the International Society for Forensic Genetics: Revised and extended guidelines for mitochondrial DNA typing

Author

Parson, W., Gusmao, L., Hares, D. R., Irwin, J. A., Mayr, W. R., Morling, N., Pokorak, E., Prinz, M., Salas, A., Schneider, P. M., Parsons, T. J., Parson, W., Gusmao, L., Hares, D. R., Irwin, J. A., Mayr, W. R., Morling, N., Pokorak, E., Prinz, M., Salas, A., Schneider, P. M., and Parsons, T. J.

Abstract

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the question of human identification. Previous recommendations published in 2000 addressed the analysis and interpretation of mitochondrial DNA (mtDNA) in forensic casework. While the foundations set forth in the earlier recommendations still apply, new approaches to the quality control, alignment and nomenclature of mitochondrial sequences, as well as the establishment of mtDNA reference population databases, have been developed. Here, we describe these developments and discuss their application to both mtDNA casework and mtDNA reference population databasing applications. While the generation of mtDNA for forensic casework has always been guided by specific standards, it is now well-established that data of the same quality are required for the mtDNA reference population data used to assess the statistical weight of the evidence. As a result, we introduce guidelines regarding sequence generation, as well as quality control measures based on the known worldwide mtDNA phylogeny, that can be applied to ensure the highest quality population data possible. For both casework and reference population databasing applications, the alignment and nomenclature of haplotypes is revised here and the phylogenetic alignment proffered as acceptable standard. In addition, the interpretation of heteroplasmy in the forensic context is updated, and the utility of alignment-free database searches for unbiased probability estimates is highlighted. Finally, we discuss statistical issues and define minimal standards for mtDNA database searches. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

Published
2014

16. Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa

Author

Pereira, F., Queiros, S., Gusmao, L., Nijman, I.J., Cuppen, E., Lenstra, J.A., Consortium, E., Davis, S.J.M., Nejmeddine, F., Amorim, A., Algemeen Onderzoek DGK, Developmental Biology, Dep Biologie, and Dep IRAS

Subjects
Econometric and Statistical Methods: General, International (English), Geneeskunde (GENK), Bescherming en bevordering van de menselijke gezondheid, Geneeskunde(GENK), Medical sciences
Abstract

Valuable insights into the history of human populations have been obtained by studying the genetic composition of their domesticated species. Here we address some of the long-standing questions about the origin and subsequent movements of goat pastoralism in Northern Africa. We present the first study combining results from mitochondrial DNA (mtDNA) and Y chromosome loci for the genetic characterization of a domestic goat population. Our analyses indicate a remarkably high diversity of maternal and paternal lineages in a sample of indigenous goats from the northwestern fringe of the African continent. Median-joining networks and a multidimensional scaling of ours and almost 2000 published mtDNA sequences revealed a considerable genetic affinity between goat populations from the Maghreb (Northwest Africa) and the Near East. It has been previously shown that goats have a weak phylogeographic structure compatible with high levels of gene flow, as demonstrated by the worldwide dispersal of the predominant mtDNA haplogroup A. In contrast, our results revealed a strong correlation between genetic and geographical distances in 20 populations from different regions of the world. The distribution of Y chromosome haplotypes in Maghrebi goats indicates a common origin for goat patrilines in both Mediterranean coastal regions. Taken together, these results suggest that the colonization and subsequent dispersal of domestic goats in Northern Africa was influenced by the maritime diffusion throughout the Mediterranean Sea and its coastal regions of pastoralist societies whose economy included goat herding. Finally, we also detected traces of gene flow between goat populations from the Maghreb and the Iberian Peninsula corroborating evidence of past cultural and commercial contacts across the Strait of Gibraltar.

Published
2009

17. DIALYSIS ANAEMIA

Author

Locatelli, F., primary, Choukroun, G., additional, Fliser, D., additional, Moecks, J., additional, Wiggenhauser, A., additional, Gupta, A., additional, Swinkels, D. W., additional, Lin, V., additional, Guss, C., additional, Pratt, R., additional, Carrilho, P., additional, Martins, A. R., additional, Alves, M., additional, Mateus, A., additional, Gusmao, L., additional, Parreira, L., additional, Assuncao, J., additional, Rodrigues, I., additional, Stamopoulos, D., additional, Mpakirtzi, N., additional, Afentakis, N., additional, Grapsa, E., additional, Zitt, E., additional, Sturm, G., additional, Kronenberg, F., additional, Neyer, U., additional, Knoll, F., additional, Lhotta, K., additional, Weiss, G., additional, Robinson, B. M., additional, Larkina, M., additional, Bieber, B., additional, Kleophas, W., additional, Li, Y., additional, Locatelli, F., additional, McCullough, K., additional, Nolen, J. G., additional, Port, F. K., additional, Pisoni, R. L., additional, Kalicki, R. M., additional, Uehlinger, D. E., additional, Ogawa, C., additional, Kanda, F., additional, Tomosugi, N., additional, Maeda, T., additional, Kuji, T., additional, Fujikawa, T., additional, Shino, M., additional, Shibata, K., additional, Kaneda, T., additional, Nishihara, M., additional, Satta, H., additional, Kawata, S.-I., additional, Koguchi, N., additional, Tamura, K., additional, Hirawa, N., additional, Toya, Y., additional, Umemura, S., additional, Chanliau, J., additional, Martin, H., additional, Stamatelou, K., additional, Gonzalez-Tabares, L., additional, Manamley, N., additional, Farouk, M., additional, Addison, J., additional, Donck, J., additional, Schneider, A., additional, Gutjahr-Lengsfeld, L., additional, Ritz, E., additional, Scharnagl, H., additional, Gelbrich, G., additional, Pilz, S., additional, Macdougall, I. C., additional, Wanner, C., additional, Drechsler, C., additional, Kuntsevich, V., additional, Charen, E., additional, Kobena, D., additional, Sheth, N., additional, Siktel, H., additional, Levin, N. W., additional, Winchester, J. F., additional, Kotanko, P., additional, Kaysen, G., additional, Kuragano, T., additional, Kida, A., additional, Yahiro, M., additional, Nanami, M., additional, Nagasawa, Y., additional, Hasuike, Y., additional, Nakanishi, T., additional, Dimitratou, V., additional, Griveas, I., additional, Lianos, E., additional, Sasaki, Y., additional, Yamazaki, S., additional, Fujita, K., additional, Kurasawa, M., additional, Yorozu, K., additional, Shimonaka, Y., additional, Suzuki, N., additional, Yamamoto, M., additional, Zwiech, R., additional, Szczepa ska, J., additional, Bruzda-Zwiech, A., additional, Rao, A., additional, Gilg, J., additional, Caskey, F., additional, Kirkpantur, A., additional, Balci, M. M., additional, Turkvatan, A., additional, Afsar, B., additional, Alkis, M., additional, Mandiroglu, F., additional, Kim, Y. O., additional, Yoon, S. A., additional, Kim, Y. S., additional, Choi, S. J., additional, Min, J. W., additional, Cheong, M. A., additional, Oue, M., additional, Yamamoto, K., additional, Kimura, T., additional, Fukao, W., additional, Kaibe, S., additional, Djuric, P. S., additional, Ikonomovski, J., additional, Tosic, J., additional, Jankovic, A., additional, Majster, Z., additional, Stankovic Popovic, V., additional, Dimkovic, N., additional, Aicardi Spalloni, V., additional, Del Vecchio, L., additional, Longhi, S., additional, Violo, L., additional, La Milia, V., additional, Pontoriero, G., additional, Macdougall, I., additional, Rumjon, A., additional, Mangahis, E., additional, Goldstein, L., additional, Ryzlewicz, T., additional, Becker, F., additional, Kilgallon, W., additional, Fukasawa, M., additional, Otake, Y., additional, Yamagishi, T., additional, Kamiyama, M., additional, Kobayashi, H., additional, Takeda, M., additional, Toida, T., additional, Sato, Y., additional, and Fujimoto, S., additional

Published
2014
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18. Reconstructing the Population History of European Romani from Genome-wide Data

Author

Mendizabal, I., Lao, O., Marigorta, U.M., Wollstein, A., Gusmao, L., Ferak, V., Ioana, M., Jordanova, A., Kaneva, R., Kouvatsi, A., Kucinskas, V., Makukh, H., Metspalu, A., Netea, M.G., de Pablo, R., Pamjav, H., Radojkovic, D., Rolleston, S.J., Sertic, J., Macek, M., Jr., Comas, D., Kayser, M., Mendizabal, I., Lao, O., Marigorta, U.M., Wollstein, A., Gusmao, L., Ferak, V., Ioana, M., Jordanova, A., Kaneva, R., Kouvatsi, A., Kucinskas, V., Makukh, H., Metspalu, A., Netea, M.G., de Pablo, R., Pamjav, H., Radojkovic, D., Rolleston, S.J., Sertic, J., Macek, M., Jr., Comas, D., and Kayser, M.

Abstract

Item does not contain fulltext, The Romani, the largest European minority group with approximately 11 million people [1], constitute a mosaic of languages, religions, and lifestyles while sharing a distinct social heritage. Linguistic [2] and genetic [3-8] studies have located the Romani origins in the Indian subcontinent. However, a genome-wide perspective on Romani origins and population substructure, as well as a detailed reconstruction of their demographic history, has yet to be provided. Our analyses based on genome-wide data from 13 Romani groups collected across Europe suggest that the Romani diaspora constitutes a single initial founder population that originated in north/northwestern India approximately 1.5 thousand years ago (kya). Our results further indicate that after a rapid migration with moderate gene flow from the Near or Middle East, the European spread of the Romani people was via the Balkans starting approximately 0.9 kya. The strong population substructure and high levels of homozygosity we found in the European Romani are in line with genetic isolation as well as differential gene flow in time and space with non-Romani Europeans. Overall, our genome-wide study sheds new light on the origins and demographic history of European Romani.

Published
2012

19. DNA commission of the International Society of Forensic Genetics: Recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods

Author

Gill, P., Gusmao, L., Haned, H., Mayr, W. R., Morling, N., Parson, W., Prieto, L., Prinz, M., Schneider, H., Schneider, P. M., Weir, B. S., Gill, P., Gusmao, L., Haned, H., Mayr, W. R., Morling, N., Parson, W., Prieto, L., Prinz, M., Schneider, H., Schneider, P. M., and Weir, B. S.

Abstract

DNA profiling of biological material from scenes of crimes is often complicated because the amount of DNA is limited and the quality of the DNA may be compromised. Furthermore, the sensitivity of STR typing kits has been continuously improved to detect low level DNA traces. This may lead to (1) partial DNA profiles and (2) detection of additional alleles. There are two key phenomena to consider: allelic or locus 'drop-out', i.e. 'missing' alleles at one or more genetic loci, while 'drop-in' may explain alleles in the DNA profile that are additional to the assumed main contributor(s). The drop-in phenomenon is restricted to 1 or 2 alleles per profile. If multiple alleles are observed at more than two loci then these are considered as alleles from an extra contributor and analysis can proceed as a mixture of two or more contributors. Here, we give recommendations on how to estimate probabilities considering drop-out, Pr(D), and drop-in, Pr(C). For reasons of clarity, we have deliberately restricted the current recommendations considering drop-out and/or drop-in at only one locus. Furthermore, we offer recommendations on how to use Pr(D) and Pr(C) with the likelihood ratio principles that are generally recommended by the International Society of Forensic Genetics (ISFG) as measure of the weight of the evidence in forensic genetics. Examples of calculations are included. An Excel spreadsheet is provided so that scientists and laboratories may explore the models and input their own data. (C) 2012 Elsevier Ireland Ltd. All rights reserved.

Published
2012

21. ISFG: Recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations

Author

Linacre, A., Gusmao, L., Hecht, W., Hellmann, A. P., Mayr, W. R., Parson, W., Prinz, M., Schneider, P. M., Morling, N., Linacre, A., Gusmao, L., Hecht, W., Hellmann, A. P., Mayr, W. R., Parson, W., Prinz, M., Schneider, P. M., and Morling, N.

Abstract

The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Published
2011

22. The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269

Author

Busby, Gbj, Brisighelli, Francesca, Sanchez Diz, P, Ramos Luis, E, Martinez Cadenas, C, Thomas, Mg, Bradley, Dg, Gusmao, L, Winney, B, Bodmer, W, Vennemann, M, Coia, V, Scarnicci, F, Tofanelli, S, Vona, G, Ploski, R, Vecchiotti, C, Zemunik, T, Rudan, I, Karachanak, S, Toncheva, D, Anagnostou, P, Ferri, G, Rapone, C, Hervig, T, Moen, T, Wilson, Jf, Capelli, C., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Busby, Gbj, Brisighelli, Francesca, Sanchez Diz, P, Ramos Luis, E, Martinez Cadenas, C, Thomas, Mg, Bradley, Dg, Gusmao, L, Winney, B, Bodmer, W, Vennemann, M, Coia, V, Scarnicci, F, Tofanelli, S, Vona, G, Ploski, R, Vecchiotti, C, Zemunik, T, Rudan, I, Karachanak, S, Toncheva, D, Anagnostou, P, Ferri, G, Rapone, C, Hervig, T, Moen, T, Wilson, Jf, Capelli, C., and Brisighelli, Francesca (ORCID:0000-0001-5469-4413)

Abstract

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution

Published
2011

23. Two pairs of proven monozygotic twins discordant for familial amyloid neuropathy (FAP) TTR Met 30

Author

MUNAR‐QUES, M., PEDROSA, J.L., COELHO, T., GUSMAO, L., SERUCA, R., AMORIM, A., and SEQUEIROS, J.

Abstract

J Med Genet. 1999 Aug;36(8):629-32. Two pairs of proven monozygotic twins discordant for familial amyloid neuropathy (FAP) TTR Met 30. Munar-Qués M, Pedrosa JL, Coelho T, Gusmão L, Seruca R, Amorim A, Sequeiros J. Grupo de Estudio de la PAF, Palma de Mallorca, Spain. Abstract Twin studies are an important tool in medical genetics for the evaluation of the relative roles of genetic and non-genetic factors in several diseases. Familial amyloidotic polyneuropathy type I (FAP-I), TTR Met 30, was present in two sets of proven monozygotic (MZ) twins, one from Majorca and the other from Portugal. Monozygosity was established by analysis of DNA polymorphisms. Both pairs were discordant for age at onset and some clinical manifestations of FAP-I. We reviewed the differences in age at onset and clinical features in both sets and in two other pairs of presumed MZ twins with FAP-I and compared them with those in MZ twin pairs with other Mendelian disorders, such as neurofibromatosis type 1, Huntington's disease, facioscapulohumeral muscular dystrophy, and myotonic dystrophy. We conclude that, in addition to the postulated modifying genes, there must be a significant contribution from non-genetic factors to the phenotypic variability of FAP-I (age at onset and clinical expression), either because of environmental differences or stochastic events during (or after) the twinning process. PMID: 10465115 [PubMed - indexed for MEDLINE]PMCID: PMC1762972

Published
1999

24. Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa

Author

Algemeen Onderzoek DGK, Developmental Biology, Dep Biologie, Dep IRAS, Pereira, F., Queiros, S., Gusmao, L., Nijman, I.J., Cuppen, E., Lenstra, J.A., Consortium, E., Davis, S.J.M., Nejmeddine, F., Amorim, A., Algemeen Onderzoek DGK, Developmental Biology, Dep Biologie, Dep IRAS, Pereira, F., Queiros, S., Gusmao, L., Nijman, I.J., Cuppen, E., Lenstra, J.A., Consortium, E., Davis, S.J.M., Nejmeddine, F., and Amorim, A.

Published
2009

25. Estrutura da Comunidade Zooplantcônica.

Author

Paranaguá, M. N., Vieira, D. A. N., Gusmao, L. M. O., Leitao, S. N., Schwamborn, Ralf, Paranaguá, M. N., Vieira, D. A. N., Gusmao, L. M. O., Leitao, S. N., and Schwamborn, Ralf

Published
2004

47. DNA Mitocondrial Como Ferramenta na Investigação da Ancestralidade Materna e da Estrutura Populacional no Espírito Santo

Author

REIS, R. S., CARVALHO, E. F., FAGUNDES, V., GOUVEA, S. A., PAULA, F., LOURO, I. D., and GUSMAO, L.

Subjects
estratificação, macrorregiões, mtDNA, Brasil, ancestralidade
Abstract

Made available in DSpace on 2019-03-19T02:10:11Z (GMT). No. of bitstreams: 1 tese_13063_Tese - Raquel Silva dos Reis.pdf: 5806087 bytes, checksum: 422c281e304bbd0407257b8c011ffb09 (MD5) Previous issue date: 2019-02-28 Além de sua valiosa utilidade na prática forense, a análise do DNA mitocondrial (mtDNA) é uma ferramenta confiável para desvendar as origens de populações miscigenadas, como as brasileiras. O Espírito Santo (ES), assim como os demais estados costeiros do país, possui uma população moldada por três principais raízes ancestrais: ameríndios, africanos e europeus. Entre estes últimos, os descendentes da antiga Pomerânia destacam-se pela preservação dos aspectos tradicionais de sua cultura, especialmente a língua pomerana. Embora a diversidade genética mitocondrial no ES tenha investigada por um estudo anterior, a base de dados disponibilizada apresenta reduzido número amostras (N=97) cuja composição étnica, origem geográfica e abrangência territorial são desconhecidas. Com o objetivo de aprofundar o conhecimento sobre a ancestralidade materna e investigar a estratificação genética da população, dados da região controle do mtDNA foram produzidos para população geral (N=214) e comunidades pomeranas (N=77), totalizando 291 haplótipos. A amostragem da população geral incluiu indivíduos das 4 macrorregiões do ES, a saber, Metropolitana (N=81), Sul (N=62), Central (N=54) e Norte (N=17). Em relação à população geral, os altos valores de diversidade haplotípica (H = 99,9%) e de diferenças entre pares de haplótipos (mean number of pairwise diferences - MNPD = 16,9) encontrados estão de acordo com os relatados para outras populações na região Sudeste do Brasil. Quanto à herança materna, o ES destacou-se pela predominância de haplogrupos europeus (49,1%), embora a macrorregião Norte tenha apresentado um perfil mais africano (47,1%). Embora não estatisticamente significantes, as análises de distâncias genéticas indicaram uma estratificação genética da população geral, o que comprometeria a adoção de uma base de dados única de linhagens de mtDNA com finalidade forense para todo o ES. Entre os pomeranos, o menor valor de MNPD (11,2) e o alto percentual de haplótipos compartilhados (15%) foram indicativos de eventos fundadores. A análise de FST demonstrou que os pomeranos (com 98,7% de linhagens europeias) são geneticamente isolados das outras populações do Brasil. Este estudo evidenciou que o Estado do ES apresenta singularidades em relação à diversidade intra e interpopulacional do mtDNA. Mesmo após cinco séculos de miscigenação, a população atual do Espírito Santo abriga marcas genéticas que remontam aspectos históricos de sua formação.

Published
2019

48. GHEP-ISFG proficiency test 2011: Paper challenge on evaluation of mitochondrial DNA results

Author

C.M. López-Cubría, G. Chemale, Victor G. Saragoni, Ana María López-Parra, Lourdes Prieto, G. Burgos, A. Sala, Walther Parson, Adriano Tagliabracci, Carlos Vullo, M. V. Masciovecchio, Arnaldo Manuel Rodríguez Hernández, S. Merigioli, E. Betancor, Cíntia Alves, M. Montesino, G. Plaza, M. Aler, Bettina Zimmermann, Manuel Paredes, Martin R. Whittle, David Comas, Nidia M. Modesti, C. A. Mora-Torres, Sergio Cardoso, V. Prieto, M.J. Anjos, S. Pedrosa, R. Angulo, Miguel Marino, Peter M. Schneider, M. Sánchez-Simón, Beatriz Heinrichs, Jorge Puente, • Montesino, M., Tagliabracci, A., Zimmermann, B, Gusmao, L., Burgos, G., Hinrichs, B, Prieto, V., Paredes, M., Hernandez, A., Cardoso, S., Vullo, C., Marino, M., Whittle, M., Velazquez, M., Sanchez Simon, M., Maxud, K., Anjos, M. J., Vargas Diaz, L. E., Lopez Parra, A. M., Bobillo, C., Garcia Segura, R., Puente, J., Pedrosa, S., Streintenberger, E. R., Moreno, F., Chemale, G., Pestano, J., Merigioli, Sara, Espinoza, M., Comas, D., Lopez Cubria, C. M., Bogus, M., Prieto, L., Parson, W., and Austrian Science Fund

Subjects
Mitochondrial DNA, CIENCIAS MÉDICAS Y DE LA SALUD, DATABASE, Computer science, Hair shaft, Proficiency test, LR, Bioinformatics, computer.software_genre, DNA, Mitochondrial, Pathology and Forensic Medicine, Database, GHEP-ISFG, Databases, Genetic, Genetics, Humans, Reference population, mt DNA interpretation, business.industry, Haplotype, Sampling error, Bioquímica y Biología Molecular, mtDNA interpretation, Medicina Básica, Haplotypes, Artificial intelligence, business, computer, Natural language processing, EMPOP
Abstract

Prieto Solla, Lourdes et al., The GHEP-ISFG Working Group performed a collaborative exercise to monitor the current practice of mitochondrial (mt)DNA reporting. The participating laboratories were invited to evaluate a hypothetical case example and assess the statistical significance of a match between the haplotypes of a case (hair) sample and a suspect. A total of 31 forensic laboratories participated of which all but one used the EMPOP database. Nevertheless, we observed a tenfold range of reported LR values (32-333.4), which was mainly due to the selection of different reference datasets in EMPOP but also due to different applied formulae. The results suggest the need for more standardization as well as additional research to harmonize the reporting of mtDNA evidence. © 2012 Elsevier Ireland Ltd., WP was partly supported by the Austrian Science Fund FWF (P22880).

Published
2011

49. Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe

Author

António Amorim, Gianmarco Ferri, Valerio Onofri, Adriano Tagliabracci, Leonor Gusmão, Francesca Brisighelli, Vincenzo Lorenzo Pascali, Francesca Scarnicci, Sergio Tofanelli, Maria Brion, Mirna Kirin, Francesco Calì, Cristian Capelli, Ilaria Boschi, Valentino Romano, Mara Masullo, Davide Merlitti, Francesco Gatto, Alejandro Blanco Verea, Capelli, C, Onofri, V, Brisighelli, F, Boschi, I, Scarnicci, F, Masullo, M, Ferri, G, Tofanelli, S, Tagliabracci, A, Gusmao, L, Amorim, A, Gatto, F, Kirin, M, Merlitti, D, Brion, M, Verea, AB, Romano, V, Cali, F, Pascali, V, and Genetics, European Society of Human

Subjects
Male, Y chromosome, north africa medieval legacy, Population, Short Report, North africa, Haplogroup, Zoological sciences, Evolution, Molecular, Moors, Africa, Northern, Peninsula, Settore BIO/13 - Biologia Applicata, Humans, genetics, education, Genetics (clinical), education.field_of_study, geography.geographical_feature_category, Chromosomes, Human, Y, Geography, Evolution (zoology), social sciences, Settore MED/43 - MEDICINA LEGALE, populations, eye diseases, Arabs, Europe, Genetics, Population, Haplotypes, Anthropology, Saracen, Ethnology, North african, geographic locations
Abstract

To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data, southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.

Published
2009

50. Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe.

Author

Capelli C, Onofri V, Brisighelli F, Boschi I, Scarnicci F, Masullo M, Ferri G, Tofanelli S, Tagliabracci A, Gusmao L, Amorim A, Gatto F, Kirin M, Merlitti D, Brion M, Verea AB, Romano V, Cali F, and Pascali V

Subjects
Africa, Northern ethnology, Europe, Evolution, Molecular, Geography, Haplotypes, Humans, Male, Arabs genetics, Chromosomes, Human, Y genetics, Genetics, Population
Abstract

To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data. southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.

Published
2009
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