Análisis de linajes maternos en poblaciones indígenas americanas

Tesis presentada para optar al Grado de Doctor en Ciencias NaturalesFil: Bravi, Claudio M.. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; Argentin

Desnaturalización de alta resolución para estudio de marcadores moleculares asociados a obesidad

El objetivo del presente trabajo fue determinar la utilidad de la técnica de “High Resolution Melting” (HRM) como método para identificar variantes en genes asociados al desarrollo de obesidad en niños

Primer genoma mitocondrial en restos humanos de la Costa de Santa Cruz, Argentina

En este trabajo se presenta la secuencia completa de ADN mitocondrial, obtenida a partir de restos óseos de un hombre adulto, hallado en el sitio Cañadón Misioneros (provincia de Santa Cruz, Argentina), con una antigüedad de 70 ± 30 años antes del presente. La secuencia corresponde al haplogrupo (hg) D4h3a5, nativo de América y exclusivo del sur de Patagonia, donde ha sido descripto tanto en muestras antiguas como actuales. Esta secuencia constituye el primer dato de ADN mitocondrial en la costa atlántica de Patagonia con la resolución suficiente para definir a nivel de subhaplogrupo. Se discuten las implicancias en cuanto a los vínculos biológicos de las poblaciones que habitaron esa porción del espacio patagónico en el marco de la información genética y arqueológica disponible.We describe the complete mitochondrial genome sequence of an adult male skeleton, discovered at Cañadón Misioneros (Santa Cruz Province, Argentina), and dated 70 ± 30 years before present. The DNA sequence corresponded to haplogroup D4h3a5, native to the Americas and exclusive to the south of Patagonia, where it has been observed both in ancient and present-day individuals. This is the first mitochondrial DNA data of the Atlantic coast of Patagonia of sufficient resolution to permit classification at the subhaplogroup level. The implications for the genetic affinities of populations of this region of Patagonia will be discussed in the context of available genetic and archaeological information

Síndrome de despoblamiento de colmenas: estudio de caso en la provincia de Buenos Aires

Las abejas melíferas (Apis mellifera) cumplen un rol importante como polinizadores de diversos cultivos y contribuyen con los ecosistemas, su disminución amenaza a la polinización tanto de plantas silvestres como cultivadas, poniendo en peligro la biodiversidad, el alimento y la producción agrícola (Simon-Delso et al. 2014). El Síndrome de despoblamiento de colmenas (SDC) es un fenómeno que afecta a las poblaciones de abejas y que se caracteriza por la pérdida masiva de sus colonias, en especial durante la temporada invernal (vanEngelsdorp et al., 2009). En 2017 se registró un posible caso de SDC en el que 170 colmenas pertenecientes al partido de General Alvear, provincia de Buenos Aires, nucleadas en 3 colmenares, habían sufrido la pérdida masiva de sus abejas. El objetivo del presente trabajo fue determinar las posibles causas de dicho episodio a partir del estudio de presencia de patógenos en esas colmenas

Ancient and modern mitogenomes from Central Argentina: New insights into population continuity, temporal depth and migration in South America

The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.This work was supported by Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (PICT 2007-1549, PICT 2012-711 and PICT 2015-3155), Secretaría de Ciencia y Tecnología (Universidad Nacional de Córdoba), Ministerio de Ciencia y Tecnología de la Provincia de Córdoba (PID 2018-79) and Consejo Nacional de Investigaciones Científicas y Técnicas (2015-11220150100953CO). M.P. is a postdoctoral fellow and A.G., R.N., J.M.B.M, C.M.B., M.F. and D.A.D. are research career members of CONICET, Argentina

GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data

Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth.Facultad de Ciencias Naturales y MuseoInstituto Multidisciplinario de Biología Celula

GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data

Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth.Facultad de Ciencias Naturales y MuseoInstituto Multidisciplinario de Biología Celula

An homoplasmic large deletion in mtDNA control region: case report

We report a new case of a large, homoplasmic Control Region deletion in human mitochondrial DNA. A missing 154 bp fragment spanning positions 16154?16307 was found in an apparently healthy blood donor from Salta (NW Argentina) whose maternal lineage was attributable to Native American haplogroup D1. The same mutation, to the best of our knowledge, has been independently reported before only twice, in both homoplasmic and heteroplasmic states.Fil: Motti, Josefina María Brenda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Alfaro, E. L.. Universidad Nacional de Jujuy. Instituto de Biología de la Altura; ArgentinaFil: Dipierri, Jose Edgardo. Universidad Nacional de Jujuy. Instituto de Biología de la Altura; ArgentinaFil: Muzzio, Marina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Santos, María Rita. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Irwin, J. A.. Armed Forces Dna Identification Laboratory; Estados UnidosFil: Scheible, M.. Armed Forces Dna Identification Laboratory; Estados UnidosFil: Saunier, J. L.. Armed Forces Dna Identification Laboratory; Estados UnidosFil: Coble, M. B.. Armed Forces Dna Identification Laboratory; Estados UnidosFil: Bailliet, Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Bravi, Claudio Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; Argentin

Continental Origin for Q Haplogroup Patrilineages in Argentina and Paraguay

Haplogroup Q originated in Eurasia around 30,000 years ago. It is present in Y-chromosomes from Asia and Europe at rather low frequencies. Since America is undoubtedly one of the continents where this haplogroup is highly represented, it has been defined as one of the founding haplogroups. Its M3 clade has been early described as the most frequent, with Pan-American representation. However, it was also possible to find several other haplogroup Q clades at low frequencies. Numerous mutations have been described for haplogroup Q, allowing the analysis of its variability and the assignment of its geographic origin. We have analyzed 442 samples belonging to haplogroup Q of unrelated men from Argentina and Paraguay, but this work is specifically referred to 27 Q (xM3) lineages. We tested 3 SNPs by APLP, 3 for RFLP, 15 SNPs by Sanger sequencing, and 17 STRs. Our approach allowed us to identify 5 sub-haplogroups. Q-M3 and Q-CTS2730/Z780 are undoubtedly autochthonous lineages and represent the most frequent sub-haplogroups. With significant representation in self-defined aboriginal populations, their autochthonous status has been previously described. The aim of present work is to identify the continental origin of the remaining Q lineages. Thus, we analyzed the STR haplotypes for the samples of our series and compared them with haplotypes described by other authors for the rest of the world. Even when haplogroup Qs have been extensively studied in America, some of them could have their origin in post Columbian human migration from Europe and Middle East