Biology subjects

Broomandkhoshbacht, N.

Publications and source records attributed to Broomandkhoshbacht, N..

14 recordsLinked to original sources

bioRxiv2023

Social and genetic diversity in first farmers of central Europe

The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of central Europe, settling fertile regions from Ukraine to France during the second half of the 6th millennium BCE. The LBK had a high degree of material culture uniformity, albeit with regional differences in settlement patterns, subsistence, and mortuary practices. To date, ancient DNA data from LBK individuals have been generated for a limited number of locations and often in small sample sizes, making it challenging to study variation within and across sites. We report genome-wide data for 178 LBK individuals, from the Alfold Linearbankeramik Culture (ALPC) eastern LBK site of Polgar-Ferenci-hat in Hungary, the western LBK site of Nitra in Slovakia, and the enclosed western LBK settlement and massacre site of Schletz in Austria, as well as 42 LBK individuals from 18 other sites. We also report genome-wide data for 28 Early Neolithic Koros and Star[c]evo individuals from 13 sites, viewed as the predecessors of the LBK. We observe a higher percentage of western hunter-gatherer (WHG) admixture among individuals in the eastern LBK than in the far more widely distributed western LBK, showing that these two archaeologically distinct cultures also had different genetic trajectories. Most WHG-farmer mixture occurred just before the dawn of the LBK culture and there is no evidence that the WHG ancestry came systematically more from males or females. However, we do find strong genetic evidence for patrilocality among the LBK, extending previous findings based on isotopic analysis, with more genetic structure across sites on the male than on the female line, and a higher rate of within-site relatives for males. At Schletz we detect almost no first-degree relatives despite reporting data from almost every skeleton present at the site, showing that this massacre involved people from a large population, not a small community.

genetics↗

bioRxiv2021

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Nubia has been a corridor for the movement of goods, culture, and people between sub-Saharan Africa, Egypt, and West Eurasia since prehistory, but little is known about the genetic landscape of the region prior to the influence of the Islamic migrations that began in the late 1st millennium CE. We report genome-wide data for 66 individuals from the site of Kulubnarti ([~]650-1000 CE), increasing the number of ancient individuals with genome-level data from the Nile Valley from three to 69. Our results shed light on the genetic ancestry of a Christian Period group and help to address a long-standing question about the relationships among people buried in two neighboring cemeteries who show skeletal evidence of differences in morbidity and mortality that are broadly suggestive of differences in social status. We find that the Kulubnarti Nubians were admixed with [~]43% Nilotic-related ancestry on average (individual proportions varied between [~]36-54%) and the remaining ancestry reflecting a West Eurasian-related gene pool likely introduced into Nubia through Egypt, but ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The admixed ancestry at Kulubnarti reflects interactions between genetically-distinct people in northeast Africa spanning almost a millennium, with West Eurasian ancestry disproportionately associated with females, highlighting the impact of female mobility in this region. We find no significant differences in ancestry among individuals from the two plausibly socially-stratified cemeteries at Kulubnarti, supporting hypotheses that the groups may have been socially divided but were not genetically distinct. We identify seven pairs of inter-cemetery relatives as close as second-degree, suggesting that any social divisions at Kulubnarti did not prevent mixing between groups. Present-day Nubians are not directly descended from the Christian Period people from Kulubnarti without additional admixture, attesting to the dynamic history of interaction that continues to shape the cultural and genetic landscape of Nubia.

genomics↗

bioRxiv2020

A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Ancient DNA sampling methods--although optimized for efficient DNA extraction--are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but standard destructive sampling methods often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and 9 corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

evolutionary biology↗

bioRxiv2020

A genetic history of the pre-contact Caribbean

Humans settled the Caribbean ~6,000 years ago, with intensified agriculture and ceramic use marking a shift from the Archaic Age to the Ceramic Age ~2,500 years ago. To shed new light on the history of Caribbean people, we report genome-wide data from 184 individuals predating European contact from The Bahamas, Cuba, Hispaniola, Puerto Rico, Curacao, and northwestern Venezuela. A largely homogeneous ceramic-using population most likely originating in northeastern South America and related to present-day Arawak-speaking groups moved throughout the Caribbean at least 1,800 years ago, spreading ancestry that is still detected in parts of the region today. These people eventually almost entirely replaced Archaic-related lineages in Hispaniola but not in northwestern Cuba, where unadmixed Archaic-related ancestry persisted into the last millennium. We document high mobility and inter-island connectivity throughout the Ceramic Age as reflected in relatives buried ~75 kilometers apart in Hispaniola and low genetic differentiation across many Caribbean islands, albeit with subtle population structure distinguishing the Bahamian islands we studied from the rest of the Caribbean and from each other, and long-term population continuity in southeastern coastal Hispaniola differentiating this region from the rest of the island. Ceramic-associated people avoided close kin unions despite limited mate pools reflecting low effective population sizes (2Ne=1000-2000) even at sites on the large Caribbean islands. While census population sizes can be an order of magnitude larger than effective population sizes, pan-Caribbean population size estimates of hundreds of thousands are likely too large. Transitions in pottery styles show no evidence of being driven by waves of migration of new people from mainland South America; instead, they more likely reflect the spread of ideas and people within an interconnected Caribbean world.

genetics↗

bioRxiv2020

The Genomic Formation of Human Populations in East Asia

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE - 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to [~]3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.

genomics↗

bioRxiv2019

Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

genomics↗

bioRxiv2019

The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean

A series of studies have documented how Steppe pastoralist-related ancestry reached central Europe by at least 2500 BCE, while Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BCE. However, the spread of these ancestries into the western Mediterranean where they have contributed to many populations living today remains poorly understood. We generated genome-wide ancient DNA from the Balearic Islands, Sicily, and Sardinia, increasing the number of individuals with reported data from these islands from 3 to 52. We obtained data from the oldest skeleton excavated from the Balearic islands (dating to [~]2400 BCE), and show that this individual had substantial Steppe pastoralist-derived ancestry; however, later Balearic individuals had less Steppe heritage reflecting geographic heterogeneity or immigration from groups with more European first farmer-related ancestry. In Sicily, Steppe pastoralist ancestry arrived by [~]2200 BCE and likely came at least in part from Spain as it was associated with Iberian-specific Y chromosomes. In Sicily, Iranian-related ancestry also arrived by the Middle Bronze Age, thus revealing that this ancestry type, which was ubiquitous in the Aegean by this time, also spread further west prior to the classical period of Greek expansion. In Sardinia, we find no evidence of either eastern ancestry type in the Nuragic Bronze Age, but show that Iranian-related ancestry arrived by at least [~]300 BCE and Steppe ancestry arrived by [~]300 CE, joined at that time or later by North African ancestry. These results falsify the view that the people of Sardinia are isolated descendants of Europes first farmers. Instead, our results show that the islands admixture history since the Bronze Age is as complex as that in many other parts of Europe.

genomics↗

bioRxiv2018

The Genomic Formation of South and Central Asia

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia--consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC--and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.\n\nOne Sentence SummaryGenome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

genomics↗

bioRxiv2018

Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age.

genetics↗

bioRxiv2018

Population Turnover in Remote Oceania Shortly After Initial Settlement

Ancient DNA analysis of three individuals dated to ~3000 years before present (BP) from Vanuatu and one ~2600 BP individual from Tonga has revealed that the first inhabitants of Remote Oceania (\"First Remote Oceanians\") were almost entirely of East Asian ancestry, and thus their ancestors passed New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture with the Papuan groups they encountered [1]. However, all present-day populations in Near and Remote Oceania harbor 25-100% Papuan ancestry, implying that there must have been at least one later stream of migration eastward from Near Oceania. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu ranging from 3,000-150 BP, along with 185 present-day Vanuatu individuals from 18 islands. We show that people of almost entirely Papuan ancestry had arrived in Vanuatu by 2400 BP, an event that coincided with the end of the Lapita cultural period, changes in skeletal morphology, and the cessation of long-distance trade between Near and Remote Oceania [2]. First Remote Oceanian ancestry subsequently increased via admixture but remains at 10-20% in most islands. Through a fine-grained comparison of ancestry profiles in Vanuatu and Polynesia with diverse groups in Near Oceania, we find that Papuan ancestry in Vanuatu is consistent with deriving from the Bismarck Archipelago instead of the geographically closer Solomon Islands. Papuan ancestry in Polynesia also shows connections to the ancestry profiles present in the Bismarck Archipelago but is more similar to Tolai from New Britain and Tutuba from Vanuatu than to the ancient Vanuatu individuals and the great majority of present-day Vanuatu populations. This suggests a third eastward stream of migration from Near to Remote Oceania bringing a different type of Papuan ancestry.

genetics↗

bioRxiv2018

Population Replacement in Early Neolithic Britain

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Anatolian ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers1-9. Neolithic cultures first appear in Britain c. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, the pattern and process of the British Neolithic transition remains unclear10-15. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 10.5-4.5 kBP, a dataset that includes 22 newly reported individuals and the first genomic data from British Mesolithic hunter-gatherers. Our analyses reveals persistent genetic affinities between Mesolithic British and Western European hunter-gatherers over a period spanning Britains separation from continental Europe. We find overwhelming support for agriculture being introduced by incoming continental farmers, with small and geographically structured levels of additional hunter-gatherer introgression. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

evolutionary biology↗

bioRxiv2017

The Genomic History Of Southeastern Europe

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europes population.

genetics↗

bioRxiv2017

The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200-1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britains Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

genomics↗

bioRxiv2017

Parallel ancient genomic transects reveal complex population history of early European farmers

Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date--a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000-2900 BCE, n = 98), Germany (5500-3000 BCE, n = 42), and Spain (5500-2200 BCE, n = 37)--we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ances try among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

genetics↗