Publications by authors named "Daniel Corach"

57 Publications

Use of genetic tools to assess predation on reintroduced howler monkeys (Alouatta caraya) in Northeastern Argentina.

Primates 2021 May 20;62(3):521-528. Epub 2021 Feb 20.

Estación Biológica Corrientes-CCT Nordeste, Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Corrientes, Argentina.

Despite strong support from the media, the reintroduction of animals into natural environments does not always achieve its goal. Alouatta caraya is the primate species facing the greatest hunting pressure due to the illegal pet trade in Argentina. Confiscations of this species are common, as is the voluntary surrender of animals by owners no longer able or willing to care for them. These animals ultimately arrive at rehabilitation centers and, in many cases, are released into natural environments that may differ from the original sites where they were captured. Until recently, the lack of genetic analysis of the individuals involved led to biased relocation decisions. We followed the reintroduction of 12 A. caraya individuals in a protected area (Isla Palacio, Misiones, Argentina). The presence of potential predators such as pumas (Puma concolor) and jaguars (Panthera onca) in this area was confirmed by camera traps, footprints and feces. After the disappearance of four A. caraya at the reintroduction site, we investigated the applicability of genetic assignment tests based on genotypic data to accurately identify predated individuals. Genetic analyses allowed us to determine the predator species (P. onca) and to identify the predated individuals as two of the reintroduced animals. This procedure is promising for identifying the remains of predated individuals, and can contribute to the design of reintroduction policies based on scientific evidence.
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http://dx.doi.org/10.1007/s10329-021-00896-9DOI Listing
May 2021

Genetic diversity and phylogeographic analysis of human herpesvirus type 8 (HHV-8) in two distant regions of Argentina: Association with the genetic ancestry of the population.

Infect Genet Evol 2020 11 3;85:104523. Epub 2020 Sep 3.

Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. Electronic address:

Background: The genetic diversity of persistent infectious agents, such as HHV-8, correlates closely with the migration of modern humans out of East Africa which makes them useful to trace human migrations. However, there is scarce data about the evolutionary history of HHV-8 particularly in multiethnic Latin American populations.

Objectives: The aims of this study were to characterize the genetic diversity and the phylogeography of HHV-8 in two distant geographic regions of Argentina, and to establish potential associations with pathogenic conditions and the genetic ancestry of the population.

Study Design: A total of 101 HIV-1 infected subjects, 93 Kaposi's Sarcoma (KS) patients and 411 blood donors were recruited in the metropolitan (MET) and north-western regions of Argentina (NWA). HHV-8 DNA was detected by ORF-26 PCR in whole blood, saliva and FFPE tissues. Then, ORF-26 and ORF-K1 were analyzed for subtype assignment. Mitochondrial DNA and Y chromosome haplogroups, as well as autosomal ancestry markers were evaluated in samples in which subtypes could be assigned. Phylogeographic analysis was performed in the ORF-K1 sequences from this study combined with 388 GenBank sequences.

Results: HHV-8 was detected in 50.7%, 59.2% and 8% of samples from HIV-1 infected subjects, KS patients and blood donors, respectively. ORF-K1 phylogenetic analyses showed that subtypes A (A1-A5), B1, C (C1-C3) and F were present in 46.9%, 6.25%, 43.75% and 3.1% of cases, respectively. Analyses of ORF-26 fragment revealed that 81.95% of strains were subtypes A/C followed by J, B2, R, and K. The prevalence of subtype J was more commonly observed among KS patients when compared to the other groups. Among KS patients, subtype A/C was more commonly detected in MET whereas subtype J was the most frequent in NWA. Subtypes A/C was significantly associated with Native American maternal haplogroups (p = 0.004), whereas subtype J was related to non-Native American haplogroups (p < 0.0001). Sub-Saharan Africa, Europe and Latin America were the most probable locations from where HHV-8 was introduced to Argentina.

Conclusions: These results give evidence of the geographic circulation of HHV-8 in Argentina, suggest the association of ORF-26 subtype J with KS development and provide new insights about its relationship with ancient and modern human migrations and identify the possible origins of this virus in Argentina.
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http://dx.doi.org/10.1016/j.meegid.2020.104523DOI Listing
November 2020

DNA commission of the International Society of Forensic Genetics (ISFG): Recommendations on the interpretation of Y-STR results in forensic analysis.

Forensic Sci Int Genet 2020 09 4;48:102308. Epub 2020 Jun 4.

Institute of Legal Medicine and Forensic Sciences, Dept. Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany.

Forensic genetic laboratories perform a large amount of STR analyses of the Y chromosome, in particular to analyze the male part of complex DNA mixtures. However, the statistical interpretation of evidence retrieved from Y-STR haplotypes is challenging. Due to the uni-parental inheritance mode, Y-STR loci are connected to each other and thus haplotypes show patterns of relationship on the familial and population level. This precludes the treatment of Y-STR loci as independently inherited variables and the application of the product rule. Instead, the dependency structure of Y-STRs needs to be included in the haplotype frequency estimation process affecting also the current paradigm of a random match probability that is in the autosomal case approximated by the population frequency assuming unrelatedness of sampled individuals. Information on the degree of paternal relatedness in the suspect population as well as on the familial network is however needed to interpret Y-chromosomal results in the best possible way. The previous recommendations of the DNA commission of the ISFG on the use of Y-STRs in forensic analysis published more than a decade ago [1] cover the interpretation issue only marginally. The current recommendations address a number of topics (frequency estimators, databases, metapopulations, LR formulation, triage, rapidly mutating Y-STRs) with relevance for the Y-STR statistics and recommend a decision-based procedure, which takes into account legal requirements as well as availability of population data and statistical methods.
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http://dx.doi.org/10.1016/j.fsigen.2020.102308DOI Listing
September 2020

Genetic assignment of illegally trafficked neotropical primates and implications for reintroduction programs.

Sci Rep 2020 02 28;10(1):3676. Epub 2020 Feb 28.

Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología Inmunología Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Junín 956, C1113AAD, Buenos Aires, Argentina.

The black and gold howler monkey (Alouatta caraya) is a neotropical primate threatened by habitat loss and capture for illegal trade in Argentina. Using multilocus microsatellite genotypes from 178 A. caraya individuals sampled from 15 localities in Argentina, we built a genotype reference database (GRDB). Bayesian assignment methods applied to the GRDB allowed us to correctly re-assign 73% of individuals to their true location of origin and 93.3% to their cluster of origin. We used the GRDB to assign 22 confiscated individuals (17 of which were reintroduced), and 3 corpses to both localities and clusters of origin. We assigned with a probability >70% the locality of origin of 14 individuals and the cluster of origin of 21. We found that most of the confiscated individuals were assigned to one cluster (F-Ch-C) and two localities included in the GRDB, suggesting that trafficked A. caraya primarily originated in this area. Our results reveal that only 4 of 17 reintroduced individuals were released in sites corresponding to their cluster of origin. Our findings illustrate the applicability of genotype databases for inferring hotspots of illegal capture and for guiding future reintroduction efforts, both of which are essential elements of species protection and recovery programs.
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http://dx.doi.org/10.1038/s41598-020-60569-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048725PMC
February 2020

Genetic structure of Mataco-Guaycurú speakers from Argentina and the extent of their genetic admixture with neighbouring urban populations.

Sci Rep 2019 11 26;9(1):17559. Epub 2019 Nov 26.

Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina.

Argentina hosts more than 30 Native American groups, who are widely distributed throughout the country. Mataco-Guaycurú speakers settled in the ecoregion of Gran Chaco and represent 26.7% of the extant aboriginal population of the country. To further investigate the genetic attributes of these speakers, we focused our attention on four aboriginal groups, namely, Wichí, Toba, Pilagá and Mocoví, belonging to the Mataco-Guaycurú linguistic group. Our main goal was to evaluate the interrelationships among the groups and the relationships of these groups with admixed urban populations and to assess correspondences between molecular analysis and historical information. A total of 890 samples (282 Native Americans and 608 inhabitants of admixed urban areas) were analysed. Genetic information was gathered from 15 autosomal STRs, 17 Y-STRs, entire mtDNA control region sequences, 24 AIM-SNPs and 46 AIM-DIPs. Native American signatures were detected in 97.9% of mtDNA lineages, 89.1% of Y-haplotypes and 90.3% to 96.9% of autosomal markers. Wichí exhibited the genetic composition with the largest Native American contribution among the groups and a weak signal of gene flow. This work provides extended genetic information of potential interest in the fields of molecular anthropology and forensic genetics.
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http://dx.doi.org/10.1038/s41598-019-54146-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879578PMC
November 2019

Mitochondrial bioenergetics links inflammation and cardiac contractility in endotoxemia.

Basic Res Cardiol 2019 08 19;114(5):38. Epub 2019 Aug 19.

Instituto de Bioquímica y Medicina Molecular (IBIMOL), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.

There is current awareness about the central role of mitochondrial dysfunction in the development of cardiac dysfunction in systemic inflammatory syndromes, especially in sepsis and endotoxemia. The aim of this work was to elucidate the mechanism that governs the link between the severity of the systemic inflammatory insult and mitochondrial function, analysing the consequences on heart function, particularly in cardiac contractile state. Female Sprague-Dawley rats were subjected to low-grade endotoxemia (i.p. injection LPS 0.5 mg kg body weight) and severe endotoxemia (i.p. injection LPS 8 mg kg body weight) for 6 h. Blood NO, as well as cardiac TNF-α and IL-1β mRNA, were found increased as the severity of the endotoxemia increases. Cardiac relaxation was altered only in severe endotoxemia, although contractile and lusitropic reserves were found impaired in both treatments in response to work-overload. Cardiac ultrastructure showed disorientation of myofibrillar structure in both endotoxemia degrees, but mitochondrial swelling and cristae disruption were only observed in severe endotoxemia. Mitochondrial ATP production, O consumption and mitochondrial inner membrane potential decreases were related to blood NO levels and mitochondrial protein nitration, leading to diminished ATP availability and impairment of contractile state. Co-treatment with the NOS inhibitor L-NAME or the administration of the NO scavenger c-PTIO leads to the observation that mitochondrial bioenergetics status depends on the degree of the inflammatory insult mainly determined by blood NO levels. Unravelling the mechanisms involved in the onset of sepsis and endotoxemia improves the interpretation of the pathology, and provides new horizons for novel therapeutic targets.
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http://dx.doi.org/10.1007/s00395-019-0745-yDOI Listing
August 2019

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

Nat Commun 2018 12 19;9(1):5388. Epub 2018 Dec 19.

Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina.

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.
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http://dx.doi.org/10.1038/s41467-018-07748-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300600PMC
December 2018

Reconstructing the Deep Population History of Central and South America.

Cell 2018 11 8;175(5):1185-1197.e22. Epub 2018 Nov 8.

Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
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http://dx.doi.org/10.1016/j.cell.2018.10.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327247PMC
November 2018

Historical records under the genetic evidence: "Chiriguano" tribe genesis as a test case.

Mol Biol Rep 2018 Oct 12;45(5):987-1000. Epub 2018 Jul 12.

Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.

Historical records suggest that Chiriguano tribe is the result of a genetic admixture event. The process involved the arrival of Guaraní tribesmen descending from Amazonian region of Brazil along with groups of Arawak origin that inhabited the foothill plains of Bolivia. Later they arrived in Argentina at the beginning of the twentieth century. Aiming to test the historical records, we analysed a set of 46 samples collected at San Ramon de la Nueva Orán, Province of Salta, Argentina. A wide set of uni- and biparentally transmitted genetic markers were analysed, including 23 autosomal STRs; 46 AIM-DIPs and 24 AIM-SNPs all located at diverse autosomal chromosome locations; 23 Y-STRs and the entire mtDNA D-Loop sequence. Ancestry informative markers allowed for the detection of a strong Native American component in the genomes (> 94%), while all mtDNA haplotypes showed Native American characteristic motives, and 93% of Y-haplotypes belonged to the Q1a3a Y-haplogroup. The analysis of mitochondrial haplotypes and Y chromosome, although they did not match other populations, revealed a relationship between the Chiriguano and other groups of Guaraní and Arawak origin inhabiting Brazil and Bolivia, confirming, at least in part, the historical records describing the origins of Chiriguano tribal settlements in northwestern Argentina.
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http://dx.doi.org/10.1007/s11033-018-4246-0DOI Listing
October 2018

Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples.

PLoS One 2017 3;12(11):e0187190. Epub 2017 Nov 3.

Department of Forensic Genetics and DNA Fingerprinting Service, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, Buenos Aires, Argentina.

Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5' region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187190PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669423PMC
November 2017

Genetic structure in the southernmost populations of black-and-gold howler monkeys (Alouatta caraya) and its conservation implications.

PLoS One 2017 2;12(10):e0185867. Epub 2017 Oct 2.

Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA) - CONICET, Ciudad Autónoma de Buenos Aires, Argentina.

Black-and-gold howler monkeys Alouatta caraya, are arboreal primates, inhabitants of Neotropical forests, highly susceptible to the yellow fever virus, considered early 'sentinels' of outbreaks, and thus, of major epidemiological importance. Currently, anthropogenic habitat loss and modifications threatens their survival. Habitat modification can prevent, reduce or change dispersal behavior, which, in turn, may influence patterns of gene flow. We explored past and contemporary levels of genetic diversity, elucidated genetic structure and identified its possible drivers, in ten populations (n = 138) located in the southernmost distribution range of the species in South America, in Argentina and Paraguay. Overall, genetic variability was moderate (ten microsatellites: 3.16 ± 0.18 alleles per locus, allelic richness of 2.93 ± 0.81, 0.443±0.025 unbiased expected heterozygosity; 22 haplotypes of 491-bp mitochondrial Control Region, haplotypic diversity of 0.930 ± 0.11, and nucleotide diversity of0.01± 0.007). Significant evidence of inbreeding was found in a population that was, later, decimated by yellow fever. Population-based gene flow measures (FST = 0.13; θST = 018), hierarchical analysis of molecular variance and Bayesian clustering methods revealed significant genetic structure, grouping individuals into four clusters. Shared haplotypes and lack of mitochondrial differentiation (non-significant θST) among some populations seem to support the hypothesis of historical dispersal via riparian forests. Current resistance analyses revealed a significant role of landscape features in modeling contemporary gene flow: continuous forest and riparian forests could promote genetic exchange, whereas disturbed forests or crop/grassland fields may restrict it. Estimates of effective population size allow anticipating that the studied populations will lose 75% of heterozygosity in less than 50 generations. Our findings suggest that anthropogenic modifications on native forests, increasingly ongoing in Northeastern Argentina, Southern Paraguay and Southeastern Brazil, might prevent the dispersal of howlers, leading to population isolation. To ensure long-term viability and maintain genetic connectivity of A. caraya remnant populations, we recommend preserving and restoring habitat continuity. To conserve the species genetic pool, as well, the four genetic clusters identified here should be considered separate Management Units and given high conservation priority. In light of our findings and considering complementary non-genetic information, we suggest upgrading the international conservation status of A. caraya to "Vulnerable".
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185867PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624639PMC
October 2017

Hepatitis C virus pharmacogenomics in Latin American populations: implications in the era of direct-acting antivirals.

Pharmgenomics Pers Med 2017 28;10:79-91. Epub 2017 Mar 28.

Scientific and Technological National Research Council (CONICET); Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.

In recent years, great progress has been made in the field of new therapeutic options for hepatitis C virus (HCV) infection. The new direct-acting antiviral agents (DAAs) represent a great hope for millions of chronically infected individuals because their use may lead to excellent cure rates with fewer side effects. In Latin America, the high prevalence of HCV genotype 1 infection and the significant association of Native American ancestry with risk predictive single-nucleotide polymorphisms (SNPs) in and genes highlight the need to implement new treatment regimens in these populations. However, the universal accessibility to DAAs is still not a reality in the region as their high cost is one of the major, although not the only, limiting factors for their broad implementation. Therefore, under these circumstances, could the assessment of host genetic markers be a useful tool to prioritize DAA treatment until global access to these new drugs can be achieved? This review will summarize the scientific evidences and the potential implications of HCV pharmacogenomics in this rapidly evolving era of anti-HCV drug development.
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http://dx.doi.org/10.2147/PGPM.S125452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378445PMC
March 2017

Role of HLA-DP and HLA-DQ on the clearance of hepatitis B virus and the risk of chronic infection in a multiethnic population.

Liver Int 2017 10 30;37(10):1476-1487. Epub 2017 Mar 30.

Scientific and Technological Research Council (CONICET), Buenos Aires, Argentina.

Background & Aims: HBV infection exhibits geographical variation in its distribution in South America. While HBV rates are low in central Argentina, the north-western region exhibits intermediate HBV rates. Unfortunately, the reasons that could explain this difference are still unknown.

Methods: A total of 1440 Argentines were recruited and grouped into HBV patients, HBV-resolved individuals and healthy controls. Genetic ancestry was assessed by analysis of biparental lineages and ancestry autosomal typing. SNPs of HLA-DPA1 (rs3077), HLA-DPB1 (rs9277542), HLA-DQB1 (rs2856718) and HLA-DQB2 (rs7453920) were determined, and HBV genotyping was performed by phylogenetic analysis in HBV patients.

Results: Native American ancestry prevailed in the north-western region when compared with central Argentina (P<.0001). However, no differences were observed among the three groups of each region. The distribution of HBV genotypes revealed significant differences (P<.0001). Three SNPs (rs3077, rs9277542 and rs7453920) showed a significant association with protection against chronic HBV and viral clearance in both regions. The remaining SNP showed a significant association with susceptibility to chronic HBV. The frequency rates of rs3077-T, related to protection against chronic HBV and viral clearance, were lower in north-western Argentina when compared with central Argentina. The same uneven frequency rates were observed for SNP rs9277542.

Conclusions: This is the first study addressing the associations between the HLA-DP and HLA-DQ loci and the protection against chronic HBV and viral clearance in a multiethnic South American population. The uneven distribution of HLA-DP and HLA-DQ supports the HBV epidemiological differences observed in these two regions of Argentina with dissimilar ancestry genetic background.
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http://dx.doi.org/10.1111/liv.13405DOI Listing
October 2017

Investigator HDplex (Qiagen) reference population database for forensic use in Argentina.

Forensic Sci Int Genet 2017 01 18;26:91-95. Epub 2016 Oct 18.

PRICAI-Fundación Favaloro, Buenos Aires, Argentina. Electronic address:

Currently, autosomal Short Tandem Repeat (STR) markers represent the method of election in forensic human identification. Commercial kits of most common use nowadays -e.g. PowerPlexFusion, Promega Corp.; AmpFlSTR GlobalFiler, Thermofisher scientific; Investigator 24Plex QS,Qiagen-, allow the co-amplification of 23 highly polymorphic STR loci providing a high discrimination power in human identity testing. However, in complex kinship analysis and familial database searches involving distant relationships, additional DNA typing is often required in order to achieve well-founded conclusions. The recently developed kit Investigator HDplex (Qiagen) co-amplify twelve autosomal STRs markers (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D18S51, D21S2055, D10S2325, SE33), nine of which are not present in the above mentioned kits, providing a set of efficient supplementary markers for human identification purposes. In this study we genotyped a sample of 980 individuals from urban areas of ten Argentinean provinces using the Investigator HDplex kit, aiming to provide forensic estimates for use in forensic casework and parentage testing in Argentina. We report reference allelic frequency databases for each of the provinces studied as well as for the combined samples. No deviation of Hardy-Weinberg equilibrium was observed. A reasonable discrimination capacity and power of exclusion was estimated which allowed predicting an acceptable forensic behavior of this kit, either to be used as the main STR panel for simple cases or as an auxiliary tool in complex cases. Additionally, population comparison tests showed that the studied samples are relatively homogeneous across the country for these STR set.
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http://dx.doi.org/10.1016/j.fsigen.2016.10.009DOI Listing
January 2017

Development of a quantitation approach for total human and male DNA based on real time PCR followed by high resolution melting analysis.

Electrophoresis 2016 10 7;37(21):2734-2741. Epub 2016 Sep 7.

Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Junín 956, Buenos Aires, Argentina.

We developed and validated a total human DNA quantitation technique that simultaneously allows male DNA detection. This assay, called Amel-Y, is a duplex Real Time PCR followed by HRM (high resolution melting) analysis using the intercalating dye SYTO9. Amel-Y duplex produces two amplicons, one for the amelogenin gene (106/112 bp, female/male) and another (84 bp) corresponding to human Y chromosome-specific fragment to detect male DNA. After HRM analysis, two melting peaks differing in 5.3°C-5.5°C are detected if both male and female DNA are present and only one if only female DNA is present. For specificity assessment, the inclusion of high concentrations of bacterial and fungal DNA in the quantitation reactions allowed discarding species cross-reactivity. A set of crime scene evidence from forensic casework has been quantified with commercial kits and compared with Amel-Y duplex. Our method detected male DNA from a concentration of 18 pg/μL and supports autosomal/Y DNA detection ratio up to 200:1. A limitation of the technique is its inability to quantify male and female donnors in a mixed sample. The Amel-Y duplex demonstrated to be an efficient system for quantifying total human DNA being a specific, rapid, sensitive, and cost-effective method suitable for mixed DNA samples and applicable to any field where human DNA quantification is required, such as molecular diagnosis, population genetics, and forensic identification.
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http://dx.doi.org/10.1002/elps.201600185DOI Listing
October 2016

Increased prevalence of human herpesvirus type 8 (HHV-8) genome among blood donors from North-Western Argentina.

J Med Virol 2017 03 31;89(3):518-527. Epub 2016 Aug 31.

Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina.

The prevalence of HHV-8 infection varies widely in South American populations, displaying geographical variations in its distribution. The heterogeneous genetic contributions provided by the transatlantic parental populations that modified the Native American genomes may explain this epidemiological observation. Aiming to determine the prevalence of HHV-8 genome among healthy South American blood donors and its potential association with genetic ancestry, 772 individuals were screened by a highly sensitive PCR protocol and ancestry was assessed in 414 samples. HHV-8 DNA was significantly more prevalent among North-western Argentines than among those from the metropolitan region (P = 0.001) and Bolivians (P = 0.0008), but no differences were found when compared with Peruvians and Paraguayans. Although significant differences were observed in the ancestry components of the studied populations, no association was found in the genetic admixture between HHV-8 [+] and HHV-8 [-] samples from the same place. These results support the hypothesis of the existence of geographical factors related to HHV-8 prevalence which could be explained by the presence of specific risk factors, cultural characteristics or behaviors, probably related to contaminated saliva and/or sexual transmission. The presence of HHV-8 in South American blood units available for transfusion and an increased risk of infection in some provinces of North-western Argentina represent a hazard for immunosuppressed recipients. J. Med. Virol. 89:518-527, 2017. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jmv.24656DOI Listing
March 2017

Influence of ethnicity on the distribution of genetic polymorphisms associated with risk of chronic liver disease in South American populations.

BMC Genet 2015 Jul 29;16:93. Epub 2015 Jul 29.

National Scientific and Technical Research Council (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina.

Background: The global burden of chronic liver disease is rising. Besides environmental, behavioral, viral and metabolic factors, genetic polymorphisms in patatin-like phospholipase-3 (PNPLA3) and vitamin D receptor (VDR) genes have been related to the development of chronic liver disease and progression towards liver cancer. Although their prevalence differs remarkably among ethnic groups, the frequency of these polymorphisms in South American populations -whose genetic background is highly admixed- has been poorly studied. Hence, the aim of this study was to characterize polymorphisms related to chronic liver disease and their association with the genetic ancestry of South American populations.

Results: DNA samples from 258 healthy unrelated male volunteers were analyzed. The frequencies of G and C alleles of rs738409 polymorphism (PNPLA3 gene) were 74 % and 26 %, respectively; whereas the bAt (CCA) haplotype (VDR gene) was observed in 32.5 % of the samples. The GG genotype of PNPLA3 rs738409 and the bAt (CCA) haplotype -associated with an increased risk of chronic liver disease and progression towards liver cancer- were significantly more frequent among samples exhibiting maternal and paternal Native American haplogroups (63.7 % and 64.6 %), intermediate among admixed samples (45.1 % and 44.9 %; p = 0.03) and the lowest for Non-native American ancestry (30.1 % and 29.6 %; p = 0.001 and p = 0.0008).

Conclusions: These results suggest that individuals with Native American ancestry might have a high risk of chronic liver disorders and cancer. Furthermore, these data not only support the molecular evaluation of ancestry in multi-ethnic population studies, but also suggest that the characterization of these variants in South American populations may be useful for establishing public health policies aimed at high risk ethnic communities.
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http://dx.doi.org/10.1186/s12863-015-0255-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518515PMC
July 2015

Analysis of locus D9S1120 and its genetic admixture correlation in seven argentina native american ethnic groups.

Am J Hum Biol 2016 Jan-Feb;28(1):57-66. Epub 2015 Jun 19.

Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, Buenos Aires, Argentina.

Objective: Genetic data have complemented archaeological and linguistic investigations for understanding the peopling of the Americas. Aiming to investigate the Native South American genetic background in Argentina, seven Amerindian and one urban population were selected. The analysis focused on locus D9S1120 due to its potential anthropological information about Native American origins.

Methods: The sample set included 603 individuals belonging to nine isolated Argentinean aboriginal communities from seven tribes (N = 296), 100 individuals living in Buenos Aires city, and three potentially parental population references samples (N = 207). We computed allele and genotype frequency distributions, genetic distances, and pairwise differences among and within them. Admixture proportion was determined by means of typing 13 autosomal short tandem repeats plus D9S1120 in all populations, and comparing the data with those from three parental groups including Native American, European and Sub Saharan West African.

Results: The Native American-specific allele 9RA was found at an average frequency of 0.26 in aboriginal groups. Statistically significant differences were observed among the Native American groups when compared with the Buenos Aires urban population using analysis of molecular variance (AMOVA) (Fst = 0.05669; P < 0.0001). Admixture analysis denoted different results between the cohorts of Amerindian samples displaying the specific 9RA allele, compared with those lacking it. A linear correlation was established between positive 9RA and Native American ancestry.

Conclusions: Autosomal-based genetic admixture showed that the studied communities have considerable European and Native America contributions. Our results concerning D9S1120 further contribute to a better understanding of the admixture process between Sub Saharan African, Native American, and European individuals that shaped the genetic background of Argentinean extant population.
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http://dx.doi.org/10.1002/ajhb.22755DOI Listing
October 2016

Sample selection bias in an international DNA panel: does Native American haplogroup Q-M3 has the b2/b3 deletion?

Genomics 2015 May 19;105(5-6):273-4. Epub 2015 Feb 19.

Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2015.02.004DOI Listing
May 2015

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Nature 2014 Sep;513(7518):409-13

Center for Global Health and Child Development, Kisumu 40100, Kenya.

We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
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http://dx.doi.org/10.1038/nature13673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574PMC
September 2014

Cardiac mitochondrial biogenesis in endotoxemia is not accompanied by mitochondrial function recovery.

Free Radic Biol Med 2014 Dec 16;77:1-9. Epub 2014 Sep 16.

Institute of Biochemistry and Molecular Medicine, School of Pharmacy and Biochemistry, University of Buenos Aires-CONICET, Junín 956, C1113AAD Buenos Aires, Argentina. Electronic address:

Mitochondrial biogenesis emerges as a compensatory mechanism involved in the recovery process in endotoxemia and sepsis. The aim of this work was to analyze the time course of the cardiac mitochondrial biogenesis process occurring during endotoxemia, with emphasis on the quantitative analysis of mitochondrial function. Female Sprague-Dawley rats (45 days old) were ip injected with LPS (10 mg/kg). Measurements were performed at 0-24 h after LPS administration. PGC-1α and mtTFA expression for biogenesis and p62 and LC3 expression for autophagy were analyzed by Western blot; mitochondrial DNA levels by qPCR, and mitochondrial morphology by transmission electron microscopy. Mitochondrial function was evaluated as oxygen consumption and respiratory chain complex activity. PGC-1α and mtTFA expression significantly increased in every time point analyzed, and mitochondrial mass was increased by 20% (P<0.05) at 24 h. p62 expression was significantly decreased in a time-dependent manner. LC3-II expression was significantly increased at all time points analyzed. Ultrastructurally, mitochondria displayed several abnormalities (internal vesicles, cristae disruption, and swelling) at 6 and 18 h. Structures compatible with fusion/fission processes were observed at 24 h. A significant decrease in state 3 respiration was observed in every time point analyzed (LPS 6h: 20%, P<0.05). Mitochondrial complex I activity was found decreased by 30% in LPS-treated animals at 6 and 24h. Complex II and complex IV showed decreased activity only at 24 h. The present results show that partial restoration of cardiac mitochondrial architecture is not accompanied by improvement of mitochondrial function in acute endotoxemia. The key implication of our study is that cardiac failure due to bioenergetic dysfunction will be overcome by therapeutic interventions aimed to restore cardiac mitochondrial function.
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http://dx.doi.org/10.1016/j.freeradbiomed.2014.08.009DOI Listing
December 2014

Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.

Hum Mutat 2014 Aug 14;35(8):1021-32. Epub 2014 Jul 14.

Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Victoria, Australia.

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.
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http://dx.doi.org/10.1002/humu.22599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145662PMC
August 2014

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Forensic Sci Int Genet 2014 Sep 28;12:12-23. Epub 2014 Apr 28.

Forensische Genetik, Kantonsspital Aarau AG, Switzerland.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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http://dx.doi.org/10.1016/j.fsigen.2014.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127773PMC
September 2014

High-throughput screening for spermatogenesis candidate genes in the AZFc region of the Y chromosome by multiplex real time PCR followed by high resolution melting analysis.

PLoS One 2014 14;9(5):e97227. Epub 2014 May 14.

Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.

Microdeletions in the AZF region of the Y chromosome are among the most frequent genetic causes of male infertility, although the specific role of the genes located in this region is not fully understood. AZFa and AZFb deletions impair spermatogenesis since no spermatozoa are found in the testis. Deletions of the AZFc region, despite being the most frequent in azoospermic patients, do not correlate with spermatogenic failure. Therefore, the aim of this work was to develop a screening method to ascertain the presence of the main spermatogenesis candidate genes located in the AZFc region in the light of the identification of those responsible for spermatogenic failure. DAZ, CDY, BPY2, PRY, GOLGA2LY and CSGP4LY genes were selected on the basis of their location in the AZFc region, testis-only expression, and confirmed or predicted protein codification. AMEL and SRY were used as amplification controls. The identification of Real Time PCR products was performed by High Resolution Melting analysis with SYTO 9 as intercalating dye. The herein described method allows a rapid, simple, low-cost, high-throughput screening for deletions of the main AZFc genes in patients with spermatogenic failure. This provides a strategy that would accelerate the identification of spermatogenesis candidate genes in larger populations of patients with non-obstructive idiopathic azoospermia.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097227PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020812PMC
January 2015

Ethnic characterization of a population of children exposed to high doses of arsenic via drinking water and a possible correlation with metabolic processes.

Int J Mol Epidemiol Genet 2014 17;5(1):1-10. Epub 2014 Feb 17.

Servicio de Huellas Digitales Genéticas and Cátedra de Genética y Biología Molecular, Faculty of Pharmacy and Biochemistry, University of Buenos Aires Argentina.

Because the ratio between the two major arsenic metabolites is related to the adverse health effects of arsenic, numerous studies have been performed to establish a relationship between the ability to metabolically detoxify arsenic and other variables, including exposure level, gender, age and ethnicity. Because ethnicity may play a key role and provide relevant information for heterogeneous populations, we characterized a group of 70 children from rural schools in the Argentinean provinces of Chaco and Santiago del Estero who were exposed to high levels of arsenic. We used genetic markers for maternal, paternal and bi-parental ancestry to achieve this goal. Our results demonstrate that the Amerindian maternal linages are present in 100% of the samples, whereas the Amerindian component transmitted through the paternal line is less than 10%. Informative markers for autosomal ancestry show a predominantly European ancestry, in which 37% of the samples contained between 90 and 99% European ancestry. The native American component ranged from 50 to 80% in 15.7% of the samples, and in all but four samples, the African component was less than 10%. Correlation analysis demonstrated that the ethnicity and the ratio of the excreted arsenic metabolites monomethyl arsenic and dimethyl arsenic are not associated, dismissing a relationship between ethnic origin and differential metabolism.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939002PMC
March 2014

Analysis of admixture and genetic structure of two Native American groups of Southern Argentinean Patagonia.

Mol Biol Rep 2014 Mar 14;41(3):1533-43. Epub 2014 Jan 14.

Servicio de Huellas Digitales Genéticas (UBA) and Cátedra de Genética y Biología Molecular, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, Junin 956 (1113), Buenos Aires, Argentina,

Argentinean Patagonia is inhabited by people that live principally in urban areas and by small isolated groups of individuals that belong to indigenous aboriginal groups; this territory exhibits the lowest population density of the country. Mapuche and Tehuelche (Mapudungun linguistic branch), are the only extant Native American groups that inhabit the Argentinean Patagonian provinces of Río Negro and Chubut. Fifteen autosomal STRs, 17 Y-STRs, mtDNA full length control region sequence and two sets of Y and mtDNA-coding region SNPs were analyzed in a set of 434 unrelated individuals. The sample set included two aboriginal groups, a group of individuals whose family name included Native American linguistic root and urban samples from Chubut, Río Negro and Buenos Aires provinces of Argentina. Specific Y Amerindian haplogroup Q1 was found in 87.5% in Mapuche and 58.82% in Tehuelche, while the Amerindian mtDNA haplogroups were present in all the aboriginal sample contributors investigated. Admixture analysis performed by means of autosomal and Y-STRs showed the highest degree of admixture in individuals carrying Mapuche surnames, followed by urban populations, and finally by isolated Native American populations as less degree of admixture. The study provided novel genetic information about the Mapuche and Tehuelche people and allowed us to establish a genetic correlation among individuals with Mapudungun surnames that demonstrates not only a linguistic but also a genetic relationship to the isolated aboriginal communities, representing a suitable proxy indicator for assessing genealogical background.
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http://dx.doi.org/10.1007/s11033-013-2999-zDOI Listing
March 2014

Male reproductive strategies in black and gold howler monkeys (Alouatta caraya).

Am J Primatol 2014 Jan 6;76(1):43-55. Epub 2013 Sep 6.

CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina), Puerto Iguazú, Misiones, Argentina; IBS (Instituto de Biología Subtropical), Facultad de Ciencias Forestales, Universidad Nacional de Misiones, Puerto Iguazú, Misiones, Argentina; SDHG (Servicio de Huellas Digitales Genéticas), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.

Behavioral and demographic factors such as group size, social structure, dispersal patterns, and mating systems affect male reproductive success. In the present study, we analyze the relationship between social structure, genetic relatedness of adult males and offspring paternity in one population of Alouatta caraya inhabiting a continuous forest in Northern Argentina. After 14 months of behavioral studies and genotyping 11 microsatellites, we found that dominant or central males achieved greater mating success and fathered all the offspring conceived during our study in two multimale-multifemale groups (both including three adult males). Although skewed toward the dominant males, females copulated with almost all resident males and with extra group males. We found significantly fewer agonistic interactions between adult males in the group with fewer females and where males were more genetically related to each other (average relatedness r = 0.237; 0.015 int/ind/hr vs. r = 0.02; 0.029 int/ind/hr). Paternity was also analyzed in two other neighboring groups which also showed strong skew to one male over a 2-year period. These results reveal that even though female black and gold howlers mate with many males, infants are typically fathered by one dominant male.
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http://dx.doi.org/10.1002/ajp.22191DOI Listing
January 2014

A DNA extraction method of small quantities of bone for high-quality genotyping.

Forensic Sci Int Genet 2013 Sep 28;7(5):488-93. Epub 2013 Jun 28.

Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, Buenos Aires, Argentina.

DNA genotyping techniques have been used successfully in forensic science for almost three decades and represent the gold standard for individual identification. However, efficient protocols for obtaining DNA from exhumed bones suitable for genotyping are still scarce and most of them require a considerable amount of starting material, are time consuming and are inefficient for reducing inhibitor's effects. We sought to develop an optimised protocol for extracting DNA from bone samples obtained from exhumations. We tested two approaches for preparing bone samples: (a) fine powder and (b) thin slices of bone. The best ratio of bone amount to DNA yields was assessed by a titration experiment using bone powder ranging from 50 to 1000mg. We obtained optimal DNA yields (27pg mg(-1) on average) when 150-200mg of starting material were processed using a one-step demineralisation method. Better-quality profiles (determined by the number of genotyped loci) were obtained when DNA was extracted from bone slices compared to extraction from bone powder. From bone slices 83.9% and from bone powder 46.7% of the samples provided genotypes for 11 or more loci. Since bone preparation procedures were carried out at room temperature, the method developed in the present study might be an attractive alternative to the standard freeze-mill approach, being faster and more cost-efficient.
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http://dx.doi.org/10.1016/j.fsigen.2013.05.002DOI Listing
September 2013

Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans.

PLoS Genet 2013 Apr 11;9(4):e1003460. Epub 2013 Apr 11.

Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.
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http://dx.doi.org/10.1371/journal.pgen.1003460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623769PMC
April 2013

Where is the game? Wild meat products authentication in South Africa: a case study.

Investig Genet 2013 Mar 1;4(1). Epub 2013 Mar 1.

Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa.

Background: Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species.

Results: The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species.

Conclusions: The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
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http://dx.doi.org/10.1186/2041-2223-4-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621286PMC
March 2013
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