Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples

Archaeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection in many organisms. However, most studies to date have ignored the non-random association of genetic variants at different loci (i.e., linkage disequilibrium, LD). This may be in part because basic properties of LD in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: 1) The correlation between the number of pairwise differences observed between time-staggered samples (ΠΔt) in models with and without strict population continuity; 2) The product of the LD coeficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and 3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.

The transition from hunting–gathering to agriculture in Nubia: dental evidence for and against selection, population continuity and discontinuity

Some researchers posit population continuity between Late Palaeolithic hunter–gatherers of the late Pleistocene and Holocene agriculturalists from Lower (northern) Nubia, in northeast Africa. Substantial craniodental differences in these time-successive groups are suggested to result from in situ evolution. Specifically, these populations are considered a model example for subsistence-related selection worldwide in the transition to agriculture. Others question continuity, with findings indicating that the largely homogeneous Holocene populations differ significantly from late Pleistocene Lower Nubians. If the latter are representative of the local populace, post-Pleistocene discontinuity is implied. So who was ancestral to the Holocene agriculturalists? Dental morphological analyses of 18 samples (1075 individuals), including one dated to the 12th millennium BCE from Al Khiday, near the Upper Nubian border, may provide an answer. It is the first Late Palaeolithic sample ( n = 55) recovered within the region in approximately 50 years. Using the Arizona State University Dental Anthropology System to record traits and multivariate statistics to estimate biological affinities, Al Khiday is comparable to several Holocene samples, yet also highly divergent from contemporaneous Lower Nubians. Thus, population continuity is indicated after all, but with late Pleistocene Upper—rather than Lower Nubians as originally suggested—assuming dental traits are adequate proxies for ancient DNA.

The Peopling of the Baraba Forest-Steppe in the Neolithic: Cranial Evidence

On the basis of statistical analysis of craniometric data relating to Mesolithic and Neolithic samples from northern Eurasia, we discuss the peopling of the Baraba forest-steppe in the Early Holocene. This region is represented by samples from Sopka-2/1 (early sixth millennium BC), Protoka (late fifth to early fourth millennia BC), Korchugan (early-mid sixth millennium BC), and Vengerovo-2A (late sixth millennium BC). The results of the principal component analysis are interpreted in the context of debates over the role of autochthonous traditions in the Neolithic. During the Preboreal period (10 ka BP), large parts of the Baraba forest-steppe were flooded by the transgression of lake systems during climatic warming. This may have caused depopulation, lasting for at least a millennium. The Early Holocene people of Baraba were an offshoot of Meso-Neolithic populations of the northwestern Russian Plain. On that basis, the Early Neolithic populations of Baraba were formed. Direct population continuity is traceable only through the Chalcolithic. Since the late sixth millennium BC, however, the local population had incorporated migrants from the Pit-Comb Ware area in the central Russian Plain and, indirectly (via the Neolithic Altai), from the Cis-Baikal area.

Population dynamics in pre-Inca human groups from the Osmore Valley, the Azapa Valley and the coast of the South Central Andes

The present study applies a dental morphological perspective to the understanding of the complex pre-contact population history of the South Central Andes, through the detection of the underlying dynamics, and the assessment of the biological ties among groups. It presents an analysis of 1591 individuals from 66 sites that date from the Archaic to the Late Intermediate phases from Bolivia, Chile and Peru. The results suggest this area is characterized by significant movement of people and cultures and, at the same time, by long standing population continuity, and highlight the need for wider perspectives capable of taking into account both the different micro-regional realities and the region in its entirety.

An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa

Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa—indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.

Effects of mancozeb on the testicular histology of the zebrafish (Danio rerio)

Reproduction is a critical and sensitive process for population continuity of the externally fertilizing aquatic organisms. Environmental pollution may adversely effect the reproductive activities of fish. Pesticides are the mobile chemicals that are known to pollute the aquatic ecosystems. Mancozeb is an ethylene-bis-dithiocarbamate (EBDC) fungicide that is frequently used to protect fruits, vegetables, vineyards and field crops against a wide range of fungal diseases. The aim of the current work was to evaluate the acute toxic effects of mancozeb on the testis tissues of zebrafish (Danio rerio). Zebrafish were exposed to 5 ppm and 7.5 ppm of mancozeb concentrations for five days. Testis tissues were removed and fixed in 10% neutral buffered formalin solution. Specimens were embedded in paraffin and 5 μm serial sections were stained with hematoxylin and eosin. The control and the experimental samples were investigated by light microscopy and histopathological changes were evaluated. Mancozeb gave rise to degenerative spermatogenic cells, seminiferous tubule disorganizations, fibrosis, hemorrhage, vacuolization, hypertrophy of spermatocytes, edema, decreased spermatogenic cell clusters and sperms, pyknotic and karyolytic nuclei. These results showed that mancozeb could interrupt the reproductive activity and decrease the fertilization ratio of zebrafish.

Continuity and Innovations in the Middle Sarmatian and Late Sarmatian Cultures (Based on the Materials of Staritsa Burial Mound)

This article considers the issues of continuity and innovations in the middle and late Sarmatian cultures on the materials of Staritsa burial mound. The burial mound was dug out in the 60s of the 20th century by archaeological expedition under the leadership of V.P. Shilov. To solve this problem the main features of burial complexes and anthropological materials of the 1st – 3rd centuries A.D. were analyzed. The source base of the research includes materials of 30 burial complexes and cranial measurements of 22 skulls. To highlight transition periods the authors used the method of determining sign’s weight during its allocation to the antecedent or subsequent culture, as well as its chronological range. Digital information on anthropological series obtained in the process of measuring skulls was processed by the simple and multivariate statistics methods to identify the population continuity, similarities and differences. As a result of the study, the authors have identified and substantiated partial continuity of the two cultural traditions at the stage of their interaction, which apparently began near the middle of the 2nd century AD, when late Sarmatian culture representatives appeared in the Lower Volga region. The transformation of such middle Sarmatian culture signs as diagonal burials and the appearance of late Sarmatian culture signs such as northern orientation of a buried, cubic incense burners, skulls with traces of artificial deformation may indicate the influence of a new culture on traditions of local people, who continued to dwell in this area and use the burial mound. As for the anthropological material, it shows that in this region the population of the middle and late Sarmatian time partially retains the appearance of its predecessors, the population of the early Sarmatian time. New components, such as long-headed Caucasoid and mixed Caucasoid-Mongoloid, identified on the basis of intragroup analysis, allow to reveal the type of migrants.

Population Continuity and Replacement in the Pre-contact Valley of Mexico

Settlement patterns in the pre-contact period in the Valley of Mexico are often characterized by the collapse and regeneration of civilizations, creating a series of power vacuums over time. How did these abrupt political changes affect population structures throughout the region? Can population structure in the Valley of Mexico be best characterized as population replacement, population continuity, or both? In this chapter, biological distances are compared with distances representing population continuity and replacement models. Biological distances based on dental morphological observations represent samples from Valley of Mexico populations from the Preclassic (1200 BC to AD 200) to the Late Postclassic (AD 1200–1520) periods. The results in this chapter support a population replacement model in the Valley of Mexico, confirming archaeological and ethnohistoric accounts of migration patterns. Population replacement is most evident during the transition from the Classic to Postclassic periods and throughout the Postclassic period.