Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization

OBJECTIVE

This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.

MATERIALS AND METHODS

We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.

RESULTS

We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP.

DISCUSSION

The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.

Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina

OBJECTIVES

The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene.

METHODS

We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of Córdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes.

RESULTS

Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly.

CONCLUSIONS

The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of Córdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.

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.

Detection of Vibrio cholerae aDNA in human burials from the fifth cholera pandemic in Argentina (1886-1887 AD)

OBJECTIVE

Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic.

MATERIALS

Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina.

METHODS

Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed.

RESULTS

By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed.

CONCLUSIONS

The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic.

SIGNIFICANCE

Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past.

LIMITATIONS

Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number.

SUGGESTIONS FOR FUTURE RESEARCH

Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains.

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.

Diversidad genética en restos humanos de contextos arqueológicos tardíos de la provincia de Santiago del Estero a partir del estudio de ADN mitocondrial

En este artículo se presentan los primeros resultados del secuenciamiento de la Región Hipervariable I del ADN mitocondrial de restos óseos humanos arqueológicos de la provincia de Santiago del Estero, con el objeto de contribuir al conocimiento sobre la diversidad genética de las poblaciones de la llanura santiagueña y los procesos de interacción con grupos de otras regiones de Argentina en tiempos prehispánicos tardíos. Se obtuvieron resultados positivos en 5 de las 10 muestras estudiadas que permitieron la identificación de 5 haplotipos diferentes. Una de las muestras, proveniente del norte del Río Dulce, presenta las mutaciones características del subhaplogrupo D1j, mientras que los demás individuos fueron asignados a linajes derivados de C1. La comparación de los haplotipos obtenidos en este trabajo con secuencias prehispánicas compiladas de la literatura no muestra una conexión con las poblaciones que habitaron el NOA en tiempos tardíos ni tampoco con los grupos chaco-litoraleños. En cambio, se observa claramente un vínculo biológico entre las poblaciones de la llanura santiagueña y los grupos de la región central de Argentina (fundamentalmente de la actual provincia de Córdoba) y de los valles del centro-oeste argentino. A pesar de su reducido número, los haplotipos obtenidos dan cuenta de este fenómeno: de las cinco secuencias obtenidas, tres fueron asignadas a los linajes D1j, C1d1b y C1b+146 que han sido señalados como indicadores de un estrecho vínculo entre las poblaciones del centro y el oeste argentino, y evidenciadel mantenimiento de flujo génico entre ellas.

DIVERSIDAD GENÉTICA EN RESTOS HUMANOS ARQUEOLÓGICOS DEL SITIO EL DIQUECITO (COSTA SUR, LAGUNA MAR CHIQUITA, PROVINCIA DE CÓRDOBA)

En este trabajo presentamos resultados del análisis de haplogrupos y secuencias de la Región Hipervariable I del ADN mitocondrial (RHV-I) en restos humanos del sitio El Diquecito, en la región sur de la Laguna Mar Chiquita, provincia de Córdoba, con antigüedades comprendidas entre 2562 ± 47 y 537 ± 57 14C años AP. De los 14 individuos analizados, 13 pudieron ser tipificados por APLP. Siete fueron asignados al haplogrupo C, cuatro al haplogrupo D y el restante no pudo ser amplificado por PCR. Se obtuvieron secuencias de 10 individuos, y todos ellos pudieron ser asignados con certeza a un linaje mitocondrial de origen continental americano, que coincidió con el determinado previamente por APLP. Entre las 7 secuencias correspondientes al haplogrupo C1 se reconocen 2 haplotipos diferentes, aunque sólo una no presenta el haplotipo nodal. Entre las 4 secuencias pertenecientes al haplogrupo D1 se distinguen 3 haplotipos diferentes: uno corresponde al haplotipo nodal, otro al subhaplogrupo D1j y los dos restantes al subhaplogrupo D1g. Si bien las conclusiones que pueden realizarse a partir del estudio de un solo sitio son limitadas, el estudio de la diversidad de linajes mitocondriales de los pobladores antiguos de la costa sur de la Laguna Mar Chiquita representa un nuevo aporte para comprender los procesos microevolutivos que sufrieron las poblaciones originarias del centro de Argentina.

Variación temporal y espacial en poblaciones prehispánicas de Córdoba. Análisis de ADN antiguo

Se presentan nuevas evidencias sobre la evolución de las poblaciones prehispánicas del actual territorio de Córdoba a partir del análisis de ADN mitocondrial de restos humanos de procedencia arqueológica de distintos contextos culturales, geográficos y temporales. La muestra estudiada incluyó 53 individuos de los cuales 48 pudieron ser genotipificados para alguno de los cuatro haplogrupos mitocondriales fundadores americanos. La totalidad de los restos analizados (excepto uno) fueron previamente datados por AMS, presentando un rango de antigüedad de entre 4525 ± 20 y 345 ± 20 años AP. Los resultados obtenidos muestran diferencias genéticas significativas entre los grupos que habitaron las serranías y los que vivieron en la llanura extraserrana. Esta diferenciación, caracterizada por un fuerte incremento en la frecuencia del haplogrupo B en la zona serrana, habría surgido recién alrededor del 1200 AP, modificando sensiblemente el pool génico de la población antigua, que presenta un neto predominio del haplogrupo C. También se advierte para esa época un incremento en la frecuencia del haplogrupo A en la llanura, pero sin llegar a alterar substancialmente el perfil genético de la población antigua. Las altas prevalencias relativas en la llanura de los haplogrupos C y D, similares a la que presentan las poblaciones de Patagonia y Tierra del Fuego, coinciden, de manera sugestiva y ciertamente difícil de desentrañar, en la población contemporánea que habita la provincia de Córdoba, y sugieren un posible origen común con los habitantes del extremo sur del continente.

RXRalpha regulates the pregnancy-specific glycoprotein 5 gene transcription through a functional retinoic acid responsive element

Human pregnancy-specific glycoproteins (PSG) are major placental polypeptides encoded by eleven highly conserved genes expressed by the syncytiotrophoblast. The minimal promoter region of all PSG genes contains a putative Retinoic Acid Responsive Element (RARE) though the ability of retinoids to regulate PSG gene expression has not been established. Retinoid signaling pathway plays a key role for overall placenta biology and is essential for trophoblast differentiation. In this work, we investigated the participation of the RARE motif in the regulation of PSG5 gene transcription by retinoic acid and its receptors. The minimal promoter region of PSG5 gene was activated by RXRalpha but not by RARalpha, in a ligand-dependent manner. The RARE sequence of PSG5 gene promoter was recognized by endogenous RXRalpha present in placental nuclear extracts as well as by RXRalpha either over expressed in cultured non-placental cells or in vitro translated. Mutations at specific nucleotides within the RARE motif abrogated both RXRalpha DNA binding and transcriptional activation of PSG5 promoter mediated by RXRalpha. Moreover, endogenous PSG expression was significantly induced in trophoblast-derived Jeg-3 cells upon 9-cis retinoic acid treatment. Interestingly, the induction level was higher following methotrexate-induced differentiation of Jeg-3 cells to syncytiotrophoblast-like structures. Altogether, these data provide the first evidences demonstrating that transcriptional activity of PSG5 gene is responsive to an external signal involving the retinoids-RXRalpha axis through a conserved RARE motif shared by all PSG gene family members.

Activation of the human pregnancy-specific glycoprotein PSG-5 promoter by KLF4 and Sp1

Pregnancy-specific glycoproteins (PSGs) are major placental proteins thought to be essential for the maintenance of gestation. Little is known about the regulation of expression of the 11 genes encoding these proteins. It was previously demonstrated that Krüppel-like factor 6 (KLF6) and specific-protein 1 (Sp1) bind to conserved sequence within the PSG-5 gene promoter. Informatics analysis revealed the presence of one potential binding site for Krüppel-like factor 4 (KLF4), in the PSG-5 promoter, suggesting a potential transcriptional regulator role for KLF4. Using gene promoter-reporter transfections and X-ChIP assays, we demonstrated that KLF4 is an activator of the PSG-5 promoter by binding to a KLF consensus like binding which includes the Core Promoter Element region (-147/-140). Furthermore, we used previous data showing the binding of Sp1 transcription factor to a GT-box (-443/-437) and co-transfection assays with KLF4 and Sp1 to demonstrate the strong synergic activity of these two factors on the PSG-5 promoter.

Transcriptional control of the human pregnancy-specific glycoprotein 5 gene is dependent on two GT-boxes recognized by the ubiquitous specificity protein 1 (Sp1) transcription factor

Pregnancy-specific glycoprotein 5 gene (PSG-5) belongs to the human pregnancy-specific glycoprotein family, encoded by eleven highly similar and transcriptionally active genes. High levels of PSG biosynthesis are restricted to the placenta syncytiotrophoblast and are essential for the maintenance of normal gestation in mammalian species. We have investigated here the nature of the transcription factors that recognize the FP1 (-455/-433) and the CPE (-147/-140) regulatory sequences that significantly contribute to basal PSG-5 promoter activity. Both elements bear a similar GT-box motif; and DNA-protein complex formation, as well as promoter activity, is largely dependent on the integrity of these GT-box sequences. Gel shift, super gel shift and UV-crosslinking experiments clearly demonstrate that the ubiquitous specificity protein 1 (Sp1) is the major transcription factor involved in complex formation with both cis-acting elements in normal term placenta tissue and in PSG-non-expressing COS-7 cells. Furthermore, transfection experiments indicate that Sp1 activates PSG-5 promoter constructs. In addition, we show that Sp1 is indeed co-expressed with PSG genes in the syncytiotrophoblast cells, stressing its potential role in the in vivo regulation of PSG expression.

Transcription of genes encoding pregnancy-specific glycoproteins is regulated by negative promoter-selective elements

The human pregnancy-specific glycoprotein (PSG) genes comprise a family of 11 highly conserved members whose expression is maximal in placental cells and marginal in other cell types. We have investigated here the molecular basis of PSG regulation by analysing a large regulatory region of the PSG-5 gene in cells that do and do not express these genes. The promoter region (-254 to -43), which does not contain a TATA-box, large GC-rich sequences or a classical initiator, was active in all cell types analysed. Additional upstream sequences up to position -3204 repressed promoter activity. Two independent repressor regions were identified and found to operate effectively in HeLa, COS-7 and HTR8/SVneo placental cells. More significantly, these negatively acting modules failed to repress a heterologous TATA-containing thymidine kinase promoter. Detailed transcriptional and DNA-protein analyses of the proximal repressor region (-605 to -254) revealed the presence of both negative and positive cis-acting elements. Disruption of the repressive functions resulted in an enhanced transcription of the reporter constructs. In conclusion, these results demonstrate that PSG-5 gene transcription is highly repressed by promoter-selective negative regulatory regions and the relief of repression allows enhanced PSG-5 gene transcription irrespective of the cell type. Furthermore, our findings suggest that PSG genes are expressed mainly through a derepression mechanism.