Mitochondrial sequence variation in ancient horses from the Carpathian Basin and possible modern relatives

Movements of human populations leave their traces in the genetic makeup of the areas affected; the same applies to the horses that move with their owners This study is concerned with the mitochondrial control region genotypes of 31 archaeological horse remains, excavated from pre-conquest Avar and post-conquest Hungarian burial sites in the Carpathian Basin dating from the sixth to the tenth century. To investigate relationships to other ancient and recent breeds, modern Hucul and Akhal Teke samples were also collected, and mtDNA control region (CR) sequences from 76 breeds representing 921 individual specimens were combined with our sequence data. Phylogenetic relationships among horse mtDNA CR haplotypes were estimated using both genetic distance and the non-dichotomous network method. Both methods indicated a separation between horses of the Avars and the Hungarians. Our results show that the ethnic changes induced by the Hungarian Conquest were accompanied by a corresponding change in the stables of the Carpathian Basin.     

Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of California

The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small F_ST values (?0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep‐water channel from the coastal sites, however, was significantly divergent (large F_ST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size.     

Low mtDNA variation and shallow population structure of the Chinese pomfret Pampus chinensis along the China coast

In the present study, population genetic structure and genetic diversity of the Chinese pomfret Pampus chinensis, along the China coast were investigated and compared with that from Indonesia using mitochondrial DNA cytochrome b gene sequences. A total of 28 variable sites (including 18 singleton sites and 10 parsimony information sites) were observed and 23 haplotypes were defined in 330 individuals from 11 localities. The haplotype diversity (H_D) of the populations ranged from 0·540 to 0·828, the nucleotide diversity (π) ranged from 0·081 to 0·295%. Pairwise F_ST statistics showed that significant genetic divergence occurred among populations from different geographical regions. The high dispersal capabilities, geographic segregation and ocean currents may be responsible for the present population genetic structure in this species. In addition, a population expansion event during the late Pleistocene period was inferred. The time of population expansion was estimated to occur about 117 000–169 000 years ago.     

Comparison of Avar period anthropological series

This study concerns human skeletal remains recovered from nine Avar period cemeteries from two regions, one in Northern Hungary and the other from Backa in Yugoslavia. Regional differences are compared using Penrose's generalised distance method, Alexeyeva's indices and preauricular facio-cerebral indices.     

Mitochondrial DNA of ancient Cumanians: culturally Asian steppe nomadic immigrants with substantially more western Eurasian mitochondrial DNA lineages

The Cumanians were originally Asian pastoral nomads who in the 13th century migrated to Hungary. We have examined mitochondrial DNA from members of the earliest Cumanian population in Hungary from two archeologically well-documented excavations and from 74 modern Hungarians from different rural locations in Hungary. Haplogroups were defined based on HVS I sequences and examinations of haplogroup-associated polymorphic sites of the protein coding region and of HVS II. To exclude contamination, some ancient DNA samples were cloned. A database was created from previously published mtDNA HVS I sequences (representing 2,615 individuals from different Asian and European populations) and 74 modem Hungarian sequences from the present study. This database was used to determine the relationships between the ancient Cumanians, modern Hungarians, and Eurasian populations and to estimate the genetic distances between these populations. We attempted to deduce the genetic trace of the migration of Cumanians. This study is the first ancient DNA characterization of an eastern pastoral nomad population that migrated into Europe. The results indicate that, while still possessing a Central Asian steppe culture, the Cumanians received a large admixture of maternal genes from more westerly populations before arriving in Hungary. A similar dilution of genetic, but not cultural, factors may have accompanied the settlement of other Asian nomads in Europe.     

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today''s Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth–fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.     

Absence of the 9-bp deletion of mitochondrial DNA in pre-Hispanic inhabitants of Argentina

We investigated the incidence of the Region V mitochondrial DNA 9-base-pair (bp) deletion from human remains recovered from several archaeological sites and contexts throughout Argentina. Of the 34 samples analyzed, 24 yielded DNA extractions that gave clear amplification results. All of the individuals carried two repeats of the 9 bp, one of which has been shown to be deleted in some individuals of Asian origin and defines mitochondrial lineage B. Although most of the modern Amerindian groups in the region exhibit the deletion in high frequencies, the absence of the 9-bp deletion among ancient populations of South America seems to be the rule rather than the exception, as was reported by several studies involving extinct populations. The evidence gathered until now suggests that the earliest settlers of this region of South America did not carry mitochondrial lineage B.     

The first archaeobotanical evidence of Dasypyrum villosum in Hungary: an archaeophyte weed or a native grass?

Caryopsis and spikelet fork remains of Dasypyrum villosum (L.) Coss. & Durieu ex P. Candargy have been recovered from a Hallstatt period archaeobotanical assemblage (ca. 900/800–450 cal. bc) in western Hungary (Carpathian basin). The presence of D. villosum has not been reported previously from any Hungarian archaeological sites, however there are accounts of its possible occurrence from the Neolithic, the Bronze and Iron Age in northern Serbia. The exact identification of the species has been hindered by its morphological similarity to wild rye and wheat species, as well as to Secale cereale L. and Triticum timopheevii Zhuk. ssp. timopheevii. D. villosum has been found growing at seven locations in Hungary during the past 100 years. Most of these occurrences do not exist today, and the species is not considered indigenous to the present Hungarian flora. The new finds of this species from an Iron Age feature dated to 702–696 cal. bc in western Hungary leave doubts as to whether it is indigenous or not, and should encourage archaeobotanists to consider the possibility of the occurrence of this species on other sites.     

Population structure of the olive flounder (Paralichthys olivaceus) in Korea inferred from microsatellite marker analysis

The population structure of olive flounder Paralichthys olivaceus was estimated using nine polymorphic microsatellite (MS) loci in 459 individuals collected from eight populations, including five wild and three hatchery populations in Korea. Genetic variation in hatchery (mean number of alleles per locus, A = 10·2–12·1; allelic richness, A_R = 9·3–10·1; observed heterozygosity, H_O = 0·766–0·805) and wild (mean number of alleles per locus, A = 11·8–19·6; allelic richness, A_R = 10·9–16·1; observed heterozygosity, H_O = 0·820–0·888) samples did not differ significantly, suggesting a sufficient level of genetic variation in these well‐managed hatchery populations, which have not lost a substantial amount of genetic diversity. Neighbour‐joining tree and principal component analyses showed that genetic separation between eastern and pooled western and southern wild populations in Korea was probably influenced by restricted gene flow between regional populations due to the barrier effects of sea currents. The pooled western and southern populations are genetically close, perhaps because larval dispersal may depend on warm currents. One wild population (sample from Wando) was genetically divergent from the main distribution, but it was genetically close to hatchery populations, indicating that the genetic composition of the studied populations may be affected by hydrographic conditions and the release of fish stocks. The estimated genetic population structure and potential applications of MS markers may aid in the proper management of P. olivaceus populations.     

Population genetics of Great Basin feral horses

The genetic make-up of Great Basin wild (feral) horses was investigated by blood typing studies. Blood samples of 975 feral horses from seven trap sites in Nevada and Oregon were tested by serological and electrophoretic techniques for genetic markers at 19 polymorphic loci. The average number of variants for the seven feral populations [72·1 ± 3·2 (SEM), range 62–85] was not significantly different from that of 16 domestic breeds (75·0 ± 11·5, range 58–105). The expected average frequency of heterozygotes per locus (average heterozygosity) for the feral populations (0·402 ± 0·009, range 0·368–0·442) was not significantly different from the domestic breeds (0·389 ± 0·045, range 0·295–0·443). Dendrograms constructed using pairwise comparisons of Nei's distance measurements substantiated anecdotal accounts of the origins of Great Basin horses from Iberian, American saddle horse and draft horse breeds.     

Pre‐Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis

Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021–16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre‐Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present‐day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Comparative analysis of morphometric characters of juvenile sterlet Acipenser ruthenus L. from natural population and aquaculture

A comparative analysis was performed on sixteen morphometric characters, in three different juvenile sterlet Acipenser ruthenus L. populations. Specimens were collected from a wild population in the Serbian part of the Danube River (n = 46), from aquaculture stocks in the Czech Republic originating from Russia (n = 40), and aquaculture stocks in the Slovak Republic originating from Slovakian part of the Danube River (n = 28). Average values for total length were 29·9 ± 3·9 cm, 29·1 ± 3·7 cm and 27·3 ± 7·7 cm for Serbia, Czech Republic and Slovak Republic, respectively. Populations were compared using t‐test and sequential Bonferroni correction for multiple comparisons was applied in order to determine significant differences between them. Results of analysis showed that all three populations differed in prebarbel length, interocular distance and maximum head width. Although all these characters are head‐related, head length itself was very uniform among all populations. The natural population from the Serbian part of the Danube River differed from the populations reared in aquaculture in seven morphometric characters. The two populations reared in aquaculture consistently showed lower morphological variability than the wild population, even though they had different genetic backgrounds (Russia and Slovakia). Future genetic studies will show if this tendency is caused by a reduction in genetic variability.     

Ancient mitochondrial DNA analyses of Iberian sturgeons

Today's European sturgeons are relics of erstwhile widely distributed populations, diminished mainly by overfishing and habitat changes over the centuries. While extinct European populations in the Baltic and North seas have been identified as Acipenser oxyrhinchus or A. sturio , a clear species determination on the Iberian Peninsula is still lacking. Plans to conserve existing populations and to re-introduce extinct wild populations in European rivers will benefit from information of historic population/genotype composition. In this study, we used techniques involving ancient DNA as well as morphological comparisons based on bony scutes to identify twelve samples from five archaeological sites (650 bc –1500 ad , one sample dated 10.1–11.8 ky) on the Iberian Peninsula. All amplified PCR products of bony scutes (n = 5) had the mitochondrial DNA haplotypes of European sturgeon. Neither mitochondrial haplotypes of A. naccarii nor mitochondrial haplotypes of A. oxyrinchus were found.     

From small holes to grand narratives: the impact of taphonomy and sample size on the modernity debate in Australia and New Guinea

Our knowledge of early Australasian societies has significantly expanded in recent decades with more than 220 Pleistocene sites reported from a range of environmental zones and depositional contexts. The uniqueness of this dataset has played an increasingly important role in global debates about the origins and expression of complex behaviour among early modern human populations. Nevertheless, discussions of Pleistocene behaviour and cultural innovation are yet to adequately consider the effects of taphonomy and archaeological sampling on the nature and representativeness of the record. Here, we investigate the effects of preservation and sampling on the archaeological record of Sahul, and explore the implications for understanding early cultural diversity and complexity. We find no evidence to support the view that Pleistocene populations of Sahul lacked cognitive modernity or cultural complexity. Instead, we argue that differences in the nature of early modern human populations across the globe were more likely the consequence of differences in population size and density, interaction and historical contingency.     

Something old,something new: do genetic studies of contemporary populations reliably represent prehistoric populations of Pacific Rattus exulans?

Through our research focusing on genetic studies of both ancient and extant commensal animals in the Pacific for addressing issues of population origins and mobility in the region, we have been able to process a large number of archaeological faunal remains that we can compare to modern samples from the same islands. These comparisons shed light on and provide specific evidence for Rattus exulans population change through time. This information may provide a model for understanding human populations in the region and will illustrate the complexities of using data obtained from modern populations to infer prehistoric relationships. Two case studies are presented here-analyses of modern and archaeological populations of R. exulans from both Chatham Island and New Zealand. These two cases provide very different pictures regarding the relationship between the archaeological and the extant populations.     

Palaeopathology of human remains from the Roman Imperial Age

The increasing attention of archaeological and anthropological research towards palaeopathological studies has allowed to focus the examination of many skeletal samples on this aspect and to evaluate the presence of many diseases afflicting ancient populations. This paper describes the most interesting diseases observed in skeletal samples from five necropolises found in urban and suburban areas of Rome during archaeological excavations in the last decades, and dating back to the Imperial Age. The diseases observed were grouped into the following categories: articular diseases, traumas, infections, metabolic or nutritional diseases, congenital diseases and tumors, and some examples are reported for each group. Although extensive epidemiological investigation in ancient skeletal records is impossible, palaeopathology allowed highlighting the spread of numerous illnesses, many of which can be related to the life and health conditions of the Roman population.     

Success of classical biocontrol agent Torymus sinensis within its expanding range in Europe

Torymus sinensis Kamijo (Hymenoptera, Torymidae), a classical biocontrol agent of chestnut gall wasp Dryocosmus kuriphilus (Hymenoptera, Cynipidae), was released in Croatia, Slovenia and Hungary in 2015. Following the introduction, the research of parasitism rates and population genetic indices on 40 different sites was performed to monitor and evaluate the success of establishment. The observed parasitism rates were unexpectedly high and negatively correlated with the distance from westernmost locality, while population genetic indices showed that populations of T. sinensis did not suffer from bottleneck‐induced founder effect phenomenon. Moreover, lack of genetic differentiation demonstrates that all populations share similar genetic structure, which could be shaped only by high levels of gene flow. We conclude that T. sinensis established viable and genetically diverse populations and successfully spread naturally from Italy across Slovenia to Croatia and Hungary.     

Reconstructing the dynamics of ancient human populations from radiocarbon dates: 10 000 years of population growth in Australia

Measuring trends in the size of prehistoric populations is fundamental to our understanding of the demography of ancient people and their responses to environmental change. Archaeologists commonly use the temporal distribution of radiocarbon dates to reconstruct population trends, but this can give a false picture of population growth because of the loss of evidence from older sites. We demonstrate a method for quantifying this bias, and we use it to test for population growth through the Holocene of Australia. We used model simulations to show how turnover of site occupation across an archaeological landscape, interacting with erasure of evidence at abandoned sites, can create an increase in apparent site occupation towards the present when occupation density is actually constant. By estimating the probabilities of abandonment and erasure from archaeological data, we then used the model to show that this effect does not account for the observed increase in occupation through the Holocene in Australia. This is best explained by population growth, which was low for the first part of the Holocene but accelerated about 5000 years ago. Our results provide new evidence for the dynamism of non-agricultural populations through the Holocene.     

Inferring the ancient population structure of the vulnerable albatross Phoebastria albatrus, combining ancient DNA, stable isotope, and morphometric analyses of archaeological samples

The history of population structure is a key to effective wildlife management and conservation. However, inferring the history of population structure using present genetic structures is problematic when the method is applied to species that have experienced severe population bottlenecks. Ancient DNA analysis seemed to be a promising, direct method for inferring ancient population structures. However, the usual methods for inferring modern population structure, i.e. the phylogeographic approach using mitochondrial DNA and the Bayesian approach using microsatellite DNA, are often unsuitable for ancient samples. In this study, we combined ancient DNA obtained from zooarchaeological bones with carbon/nitrogen stable isotope ratios and morphological variations to infer ancient population structure of the short-tailed albatross Phoebastria albatrus. The results showed that the bird existed in two populations, between which the genetic distance was greater than that of distinct sister albatross species, although no subspecies of P. albatrus have been proposed. Our results suggest that the birds at the present two breeding regions (Torishima in the Izu Islands and two islets of the Senkaku Islands) are descended from these two ancient populations, and that reevaluation of the status and conservation strategy for the species is required. Our results also indicate that lineage breeding on the Senkaku Islands has drastically reduced genetic diversity, while that on Torishima has not. The approach proposed in this study would be useful for inferring ancient population structure, using samples of highly mobile animals and/or samples from archaeological sites, and the reconstructed ancient population structure would be useful for conservation and management recommendations.