Anna Stankovic

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.

Recent origin of sub-Antarctic notothenioids

Abstract. Comparison of partial mitochondrial 12S and 16S rDNA sequences from non-Antarctic notothenioid fishes – an icefish Champsocephalus esox and two members of the genus Patagonotothen – and their sister species from the Southern Ocean suggests that their divergence took place 1.7 and 6.6–7 million years ago, respectively, i.e. much later than the formation of the Antarctic Polar Front (20–25 million years ago).

Bacterial diversity in Adélie penguin, Pygoscelis adeliae, guano: molecular and morpho‐physiological approaches

The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano was determined during 42 days of decomposition in a location adjacent to the rookery in Admiralty Bay, King George Island, Antarctica. Of the culturable bacteria, 72 randomly selected colonies were described using 49 morpho-physiological tests, 27 of which were subsequently considered significant in characterizing and differentiating the isolates. On the basis of the nucleotide sequence of a fragment of the 16S rRNA gene in each of 72 pure isolates, three major phylogenetic groups were identified, namely the Moraxellaceae/Pseudomonadaceae (29 isolates), the Flavobacteriaceae (14), and the Micrococcaceae (29). Grouping of the isolates on the basis of morpho-physiological tests (whether 49 or 27 parameters) showed similar results to those based on 16S rRNA gene sequences. Clusters were characterized by considerable intra-cluster variation in both 16S rRNA gene sequences and morpho-physiological responses. High diversity in abundance and morphometry of total bacterial communities during penguin guano decomposition was supported by image analysis of epifluorescence micrographs. The results indicate that the bacterial community in penguin guano is not only one of the richest in Antarctica, but is extremely diverse, both phylogenetically and morpho-physiologically.

Studies on Ephelota sp., an epizoic suctorian found on Antarctic krill

Abstract. The anatomy, morphology and life-cycle of ciliates living on Antarctic krill are described. All ciliates found on the bodies of several thousand individual krill belong to one species of the genus Ephelota. Analysis of small subunit rDNA (SS rDNA) sequences from different Ephelota individuals in various stages of their life-cycle confirmed this result and proved that even the cysts found in great numbers in the filtering baskets of krill represent the resting stage of Ephelota. DNA studies have also shown that Antarctic and non-Antarctic species of Ephelota diverged much earlier than Antarctic and non-Antarctic species of krill.

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.

Microsatellite multiplex assay for the analysis of Atlantic sturgeon populations

We have developed a multiplex assay covering 16 microsatellite loci, amplified in four polymerase chain reaction (PCR) assays, and loaded on the ABI DNA Analyzer in two separate panels. The assay was tested on 603 individuals originating from wild populations and hatchery stocks of Atlantic sturgeon. The assay was also tested on 12 individuals of European sturgeon and appeared to be almost equally useful. The multiplex assay designed in this study can be successfully applied in studies requiring high genetic resolution, such as relatedness analysis, selective breeding programs, and stock identification of Atlantic sturgeon.

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

Conservation Genetics of the Capercaillie Tetrao urogallus in Poland — Diversity of Mitochondrial DNA in Remnant and Extinct Populations

Abstract. Human-induced changes in the natural environment impact upon a wide variety of genetic processes at all levels of population structure. Insight into these processes is now achieved by analyses of genetic diversity allowing the past and present condition of populations to be assessed and compared. Given its severe fragmentation and small size, the population of the Capercaillie Tetrao urogallus in Poland can be regarded as especially prone to gene-pool alteration. Moreover, this is a region of Europe in which different genetic lineages of the Capercaillie may be present, ensuring that certain conservation decisions may be even more difficult than they otherwise would be. Bearing the above in mind, we decided to study polymorphism of the mitochondrial DNA Control Region (mtDNA CR) in remnant and extinct populations of the Capercaillie in Poland. The extinct population was represented by samples from birds hunted in the Lower Silesian Forest (SW Poland) between 1951–1962. We compared sequences obtained with data from the large, continuous population present in Russia and Scandinavia. Analysing 331 bp of mtDNA CR for 168 individuals, we identified 24 haplotypes, among which only 6 had not been reported previously in the species according to GenBank. Our data confirmed a previous suggestion regarding the genetic structure of the species in Poland, i.e. that birds from Augustów Forest (NE Poland) are related to Russian and Scandinavian populations, constituting a part of the lowland group within the boreal lineage. The Carpathian population is in turn confirmed as an independent genetic group within the boreal lineage, while specimens from the Solska Forest (SE Poland) prove to be highly differentiated from birds in other Polish populations; most likely because they derive from — or have been connected via gene flow with — birds present in the Balkans. Further genetic analysis is necessary to resolve this evolutionary relationship between Capercaillies from south-eastern Poland and those of the Balkans. Where practice is concerned, the overall advice is that three Conservation Units are to be recognised in Poland. In addition to those, the extinct population from the Lower Silesian Forest has been deemed part of the lowland group within the boreal lineage, albeit a distinctive one, given the possibility of gene exchange with Carpathian birds. We further suggest that some aspect of this extinct populations genetic diversity reflects an uncontrolled process of reintroduction taking place in the past.

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.