Mateusz Baca

Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community

BackgroundA detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves.ResultsThe remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y–chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave.ConclusionsGenetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities.

Locals, Resettlers, and Pilgrims: A Genetic Portrait of Three Pre-Columbian Andean Populations

The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities.

Genetic analysis of cave bear specimens from Niedźwiedzia Cave, Sudetes, Poland

The vast majority of fossil remains in Late Pleistocene deposits from Niedźwiedzia Cave in Kletno, Sudetes, Poland, belong to the cave bear. Phylogenetic analyses based on a fragment of the mitochondrial D-loop region extracted from two cave bear samples unambiguously showed their close relationship with the Ursus ingressus haplogroup. This taxonomic affiliation of the cave bear remains from Niedźwiedzia Cave was further confirmed by biometrical analyses of molar teeth and skulls. Our results represent the first record of U. ingressus north of the Carpathian Arch, while radiocarbon dating (> 49,000 yr BP) of the samples indicates that they represent some of the oldest specimens of this cave bear taxon known so far. Multi-method phylogenetic analyses including numerous publicly available cave bear sequences allowed analysing the relationships among these samples in details, including the significance of particular clades, and discussing some aspects of cave bear phylogeography. The sequences of U. ingressus from Poland are most closely related to specimens from the Ural Mountains and next to Slovenia, which may indicate migrations between Central and Eastern European populations. The internal placement of Ural samples among European specimens in phylogenetic trees and the older age of Polish samples than those from Urals suggest that the eastward expansion of U. ingressus may have started from Central Europe. Mateusz Baca (corresponding author). Center for Precolumbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland. bacamat@gmail.com Anna Stankovic. Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland. anams@ibb.waw.pl Krzysztof Stefaniak. Department of Palaeozoology, Zoological Institute, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland. stefanik@biol.uni.wroc.pl Adrian Marciszak. Department of Palaeozoology, Zoological Institute, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland. caspian8@wp.pl Michael Hofreiter. Department of Biology (Area 2), The University of York, Wentworth Way, Heslington York, YO10 5DD, United Kingdom. michi@palaeo.eu Adam Nadachowski. Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland. nadachowski@isez.pan.krakow.pl Piotr Węgleński. Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, PE Article Number: 15.2.21A Copyright: Palaeontological Association July 2012 Submission: 8 September 2011. Acceptance: 5 June 2012 Baca, Mateusz, Stankovic, Anna, Stefaniak, Krzysztof, Marciszak, Adrian, Hofreiter, Michael, Nadachowski, Adam, Węgleński, Piotr, and Mackiewicz, Paweł. 2012. Genetic analysis of cave bear specimens from Niedźwiedzia Cave, Sudetes, Poland. Palaeontologia Electronica Vol. 15, Issue 2;21A,16p; palaeo-electronica.org/content/2012-issue-2-articles/263-cave-bears-from-poland BACA ET AL.: CAVE BEARS FROM POLAND 02-106 Warsaw, Poland. wegle@adm.uw.edu.pl Paweł Mackiewicz (corresponding author). Department of Genomics, Faculty of Biotechnology, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wrocław, Poland. pamac@smorfland.uni.wroc.pl

Human-mediated dispersal of cats in the Neolithic Central Europe

Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.

Impact of climatic changes in the Late Pleistocene on migrations and extinction of mammals in Europe: four case studies

Climate changes that occurred during the Late Pleistocene have profound effects on the distribution of many plant and animal species and influenced the formation of contemporary faunas and floras of Europe. The course and mechanisms of responses of species to the past climate changes are now being intensively studied by the use of direct radiocarbon dating and genetic analyses of fossil remains. Here, we review the advances in understanding these processes by the example of four mammal species: woolly mammoth (Mammuthus primigenius), cave bear (Ursus spelaeus s. l.), saiga antelope (Saiga tatarica) and collared lemmings (Dicrostonyx ssp.). The cases discussed here as well as others show that the migrations, range shifts and local extinctions were the main responses to climate changes and that the dynamics of these climate driven processes were much more profound than it was previously thought. Each species reacted by its individual manner, which depended on its biology and adaptation abilities to the changing environment and climate conditions. The most severe changes in European ecosystems that affected the largest number of species took place around 33–31 ka BP, during the Last Glacial Maximum 22–19 ka BP and the Late Glacial warming 15–13 ka BP.

Complete mitochondrial genome sequences of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, Gulf sturgeon, A. o. desotoi and European sturgeon A. sturio (Acipenseriformes: Acipenseridae) obtained through next generation sequencing

Abstract Complete mitochondrial genome sequences of European sturgeon and two subspecies of the North American, Atlantic and Gulf sturgeons were determined using MiSeq Illumina technology. All three genomes show typical vertebrate organization. They possess 22 tRNA genes, 13 protein-coding genes, 2 rRNA (ribosomal RNA) genes and a non-coding control region. Excluding ND6, all protein-coding genes are on the heavy strand. The whole mitogenome sequences have been deposited in GenBank under accession numbers KP997216–KP997218.

Restitution of vimba (Vimba vimba, Cyprinidae) in Poland: genetic variability of existing and restored populations

Until 1960s, vimba was found abundantly in Polish rivers and was an important species for the fishing industry. Overfishing, water pollution and dam constructions brought most of the vimba populations close to extinction. We analyzed the genetic variability of several remnant vimba populations in the Vistula and Oder river basins. The 305-bp fragment encompassing the 5′-end of the mtDNA control region was sequenced in a total of 202 wild specimens derived from six populations. Six different haplotypes were distinguished. The population of Barycz River was found to be the most polymorphic and was chosen as a source of breeding material for the vimba restitution program. In the years 2000–2008 fishes from this river were caught, spawned in captivity and released to the same river. The number of fishes returning to the Barycz River spawning grounds was monitored in the following years. In 2008, it was almost 70 times higher than the number of fishes recorded in 2003, when the lowest population size was observed. The haplotype and nucleotide diversities of the restored population were similar to those of the original population.