scholarly journals Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China

2020 ◽  
Vol 37 (7) ◽  
pp. 2099-2109 ◽  
Author(s):  
Yudong Cai ◽  
Weiwei Fu ◽  
Dawei Cai ◽  
Rasmus Heller ◽  
Zhuqing Zheng ◽  
...  
Keyword(s):  
Iron Age ◽  
Evolutionary History ◽  
De Novo ◽  
Evolutionary Process ◽  
Migration Route ◽  
Neolithic Period ◽  
Late Neolithic ◽  
Standing Variation ◽  
Modern Chinese ◽  
Chalcolithic Period

Abstract Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.

scholarly journals Neolithic to Bronze Age (4850–3450 cal. BP) fire management of the Alpine Lower Engadine landscape (Switzerland) to establish pastures and cereal fields

The Holocene ◽  
2016 ◽  
Vol 27 (2) ◽  
pp. 181-196 ◽  
Author(s):  
Benjamin Dietre ◽  
Christoph Walser ◽  
Werner Kofler ◽  
Katja Kothieringer ◽  
Irka Hajdas ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Cultural Landscape ◽  
Correlation Coefficients ◽  
Continuous Cultivation ◽  
Ice Age ◽  
European Alps ◽  
Neolithic Period ◽  
Late Neolithic ◽  
Coprophilous Fungi

Agro-pastoral activities in the past act as environmental legacy and have shaped the current cultural landscape in the European Alps. This study reports about prehistoric fire incidents and their impact on the flora and vegetation near the village of Ardez in the Lower Engadine Valley (Switzerland) since the Late Neolithic Period. Pollen, charcoal particles and non-pollen palynomorphs preserved in the Saglias and Cutüra peat bog stratigraphies were quantified and the results compared with the regional archaeological evidence. Anthropogenic deforestation using fire started around 4850 cal. BP at Saglias and aimed at establishing first cultivated crop fields (e.g. cereals) and small pastoral areas as implied by the positive correlation coefficients between charcoal particles and cultural and pastoral pollen indicators, as well as spores of coprophilous fungi. Pressure on the natural environment by humans and livestock continued until 3650 cal. BP and was followed by reforestation processes until 3400 cal. BP because of climatic deterioration. Thereafter, a new, continuous cultivation/pastoral phase was recorded for the Middle to Late Bronze Age (3400–2800 cal. BP). After rather minor human impact during the Iron Age and Roman Period, intensive agriculture was recorded for the Medieval Period. The area around Ardez was used for crop cultivation from about 1000 cal. BP until the start of the ‘Little Ice Age’ (600 cal. BP). Despite a land-use reorganisation, the following gradual decrease in agricultural activities led to the extant mixture of a cultivated, grazed and forested landscape in the Lower Engadine. In addition, this study demonstrates the excellent value of the fungus Gelasinospora as a highly local marker of past and today’s fire incidents, as well as of the use of micro-charcoals from pollen slides and macro-charcoals (>150 µm) from pollen sample residues for the reconstruction of short- and long-term fire histories.

An Overview of the 2nd Millennium BC and Iron Age Cultures of the Province of Sinop in Light of New Research

2010 ◽  
Vol 16 (1-2) ◽  
pp. 153-540
Author(s):  
Şevket Dönmez
Keyword(s):  
Bronze Age ◽  
Black Sea ◽  
Iron Age ◽  
City Centre ◽  
Early Bronze Age ◽  
The Black Sea ◽  
Neolithic Period ◽  
Late Chalcolithic ◽  
Chalcolithic Period ◽  
Middle Bronze Age

Abstract Archaeological research conducted to date has shown that the earliest settlements in the province of Sinop date to the Late Chalcolithic period. However, despite these Late Chalcolithic period cultural strata, identified during the Kocagöz Höyük and Boyabat-Kovuklukaya excavations, the stone bracelet fragments from Maltepe Höyüğü and potsherds supposedly from Kıran Höyük and Kabalı Höyük (but hitherto unpublished) indicate that the settlement process of the region may have started in the Early Chalcolithic or even Late Neolithic period. In the Early Bronze Age, following the Late Chalcolithic period, the number of settlements increased in parallel with the population. A number of settlements identified during the excavations at Kocagöz Höyük and Kovuklukaya, as well as during surveys, indicate that the Early Bronze Age was a very active period in the province of Sinop. Finds from the ensuing Middle Bronze Age, pointing to the fact that the Sinop area was one of the northern extremities of the commercial network of the Assyrian Trade Colonies period, centered at Kültepe/Kaneš, have come to light from the Gerze-Hıdırlı cemetery and its settlement at Keçi Türbesi Höyüğü. As is the case with the neighboring province of Samsun, it is understood that the province of Sinop probably did not host any settlements in the late phases of the Middle Bronze Age. All along the Black Sea coast of Anatolia no centre or even find dating to the Early Iron Age (1190-900 BC) has been identified to date. However, settlements become more frequent in the inland part of the central Black Sea region during the Middle Iron Age (900-650/600 BC), and by the Late Iron Age (650/600-330 BC) they are seen both inland and along the coastline. Evidence to confirm this pattern has been obtained from the city centre of Sinop and Kovuklukaya.

scholarly journals Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hong-Yan Zhao ◽  
Lin Wen ◽  
Yu-Feng Miao ◽  
Yu Du ◽  
Yan Sun ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Evolutionary History ◽  
De Novo ◽  
Venom Gland ◽  
The South China Sea ◽  
Protein Families ◽  
The South ◽  
Widespread Species ◽  
China Sea

Abstract Background A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the venom-transcriptomic and venomic profiles in a same group of spine-bellied sea snakes (Hydrophis curtus) from the South China Sea, where the snake is a widespread species and might generate regionally-specific venom potentially harmful to human activities. The capacity of two heterologous antivenoms to immunocapture the H. curtus venom was determined for an in-depth evaluation of their rationality in treatment of H. curtus envenomation. In addition, a phylogenetic analysis by maximum likelihood was used to detect the adaptive molecular evolution of full-length toxin-coding unigenes. Results A total of 90,909,384 pairs of clean reads were generated via Illumina sequencing from a pooled cDNA library of six specimens, and yielding 148,121 unigenes through de novo assembly. Sequence similarity searching harvested 63,845 valid annotations, including 63,789 non-toxin-coding and 56 toxin-coding unigenes belonging to 22 protein families. Three protein families, three-finger toxins (3-FTx), phospholipase A2 (PLA2), and cysteine-rich secretory protein, were detected in the venom proteome. 3-FTx (27.15% in the transcriptome/41.94% in the proteome) and PLA2 (59.71%/49.36%) were identified as the most abundant families in the venom-gland transcriptome and venom proteome. In addition, 24 unigenes from 11 protein families were shown to have experienced positive selection in their evolutionary history, whereas four were relatively conserved throughout evolution. Commercial Naja atra antivenom exhibited a stronger capacity than Bungarus multicinctus antivenom to immunocapture H. curtus venom components, especially short neurotoxins, with the capacity of both antivenoms to immunocapture short neurotoxins being weaker than that for PLA2s. Conclusions Our study clarified the venom-gland transcriptomic and venomic profiles along with the within-group divergence of a H. curtus population from the South China Sea. Adaptive evolution of most venom components driven by natural selection appeared to occur rapidly during evolutionary history. Notably, the utility of commercial N. atra and B. multicinctus antivenoms against H. curtus toxins was not comprehensive; thus, the development of species-specific antivenom is urgently needed.

Late-glacial and Post-glacial history of the Chalk escarpment near Brook, Kent

1964 ◽  
Vol 248 (745) ◽  
pp. 135-204 ◽  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Late Glacial ◽  
Climatic Conditions ◽  
Valley Floor ◽  
Glacial Period ◽  
Late Neolithic ◽  
Local Conditions ◽  
Arable Farming ◽  
History Of

This paper describes the morphology of a small piece of the Chalk escarpment near Brook in east Kent, and reconstructs its history since the end of the Last Glaciation. The escarpment contains a number of steep-sided valleys, or coombes, with which are associated deposits of chalk debris, filling their bottoms and extending as fans over the Gault Clay plain beyond. Here the fans overlie radiocarbon-dated marsh deposits of zone II (10 000 to 8800 B.C.) of the Late-glacial Period. The debris fans were formed and the coombes were cut very largely during the succeeding zone III (8800 to 8300 B.C.). The fans are the products of frost-shattering, probably transported by a combination of niveo-fluvial action and the release of spring waters; intercalated seams of loess also occur. The molluscs and plants preserved in the Late-glacial deposits give a fairly detailed picture of local conditions. The later history of one of the coombes, the Devil’s Kneadingtrough, is reconstructed. The springs have effected virtually no erosion and have probably always emerged more or less in their present position. In the floor of the coombe the periglacial chalk rubbles of zone III are covered by Postglacial deposits, mainly hillwashes. They are oxidized and yield no pollen, but contain rich faunas of land Mollusca, which are presented in the form of histograms revealing changing local ecological and climatic conditions. During most of the Post-glacial Period, from the end of zone III until about the beginning of zone VIII, very little accumulation took place on the coombe floor. But below the springs there are marsh deposits which span much of this interval. They yield faunas of considerable zoogeographical interest. The approximate beginning of zone VII a (Atlantic Period) is reflected by a calcareous tufa, which overlies a weathering horizon, and represents an increase in spring flow. Two clearance phases are deduced from the molluscan record. The first may have taken place at least as early as the Beaker Period (Late Neolithic/earliest Bronze Age); the second is probably of Iron Age ‘A’ date. In Iron Age times the subsoil was mobilized and a phase of rapid hillwashing began. As a result the valley floor became buried by humic chalk muds. The prime cause of this process was probably the beginning of intensive arable farming on the slopes above the coombe; a possible subsidiary factor may have been the Sub-Atlantic worsening of climate. The muds yield pottery ranging in date from Iron Age ‘Kentish first A’ ( ca . 500 to ca . 300 B.C.) to Romano-British ware of the first or second centuries A.D. Evidence is put forward for a possible climatic oscillation from dry to wet taking place at about the time of Christ. In the later stages of cultivation, possibly in the Roman Era, the valley floor was ploughed and given its present-day form.

scholarly journals The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes

2016 ◽  
Vol 283 (1835) ◽  
pp. 20160942 ◽  
Author(s):  
Jinshui Zheng ◽  
Donghai Peng ◽  
Ling Chen ◽  
Hualin Liu ◽  
Feng Chen ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Process ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Free Living ◽  
C Elegans ◽  
Free Living Nematode ◽  
Plant Nematode ◽  
Ditylenchus Destructor ◽  
Plant Parasitic

Plant-parasitic nematodes were found in 4 of the 12 clades of phylum Nematoda. These nematodes in different clades may have originated independently from their free-living fungivorous ancestors. However, the exact evolutionary process of these parasites is unclear. Here, we sequenced the genome sequence of a migratory plant nematode, Ditylenchus destructor . We performed comparative genomics among the free-living nematode, Caenorhabditis elegans and all the plant nematodes with genome sequences available. We found that, compared with C. elegans , the core developmental control processes underwent heavy reduction, though most signal transduction pathways were conserved. We also found D. destructor contained more homologies of the key genes in the above processes than the other plant nematodes. We suggest that Ditylenchus spp. may be an intermediate evolutionary history stage from free-living nematodes that feed on fungi to obligate plant-parasitic nematodes. Based on the facts that D. destructor can feed on fungi and has a relatively short life cycle, and that it has similar features to both C. elegans and sedentary plant-parasitic nematodes from clade 12, we propose it as a new model to study the biology, biocontrol of plant nematodes and the interaction between nematodes and plants.

scholarly journals Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe

2019 ◽  
Author(s):  
Alexander Immel ◽  
Christoph Rinne ◽  
John Meadows ◽  
Rodrigo Barquera ◽  
András Szolek ◽  
...  
Keyword(s):  
Western Europe ◽  
Viral Infections ◽  
Human Leukocyte ◽  
Neolithic Period ◽  
Late Neolithic ◽  
Leukocyte Antigen ◽  
Cultural Transformations ◽  
Farming Community ◽  
Genome Wide ◽  
A Genome

AbstractThe Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.

scholarly journals Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

2021 ◽  
Author(s):  
Julia M. Kreiner ◽  
Amalia Caballero ◽  
Stephen I. Wright ◽  
John R. Stinchcombe
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Sex Differentiation ◽  
Common Garden ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Natural Environments ◽  
Relative Role ◽  
Standing Variation ◽  
Amaranthus Tuberculatus

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated subspecies. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of subspecies divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry-based inference. The transition into agricultural environments has favoured southwestern var. rudis ancestry that leads to higher biomass and environment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation to agricultural habitats independent of ancestry effects, including marginally higher biomass and later flowering in agricultural populations, and a time to germination home advantage. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales—through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.

scholarly journals Understanding the Stability of Early Iron Age folks of South India with Special Reference to Krishna-Tungabhadra- Kaveri, Karnataka; Their Past-Present-Future

2014 ◽  
Vol 13 (4) ◽  
pp. 47
Author(s):  
Arjun R
Keyword(s):  
Iron Age ◽  
Large Scale ◽  
South India ◽  
Early Iron Age ◽  
Late Neolithic ◽  
Early Historic Period ◽  
Indigenous Development ◽  
Iron Smelting ◽  
The Stability ◽  
The Hill

There are about 1933 Early Iron Age Megalithic sites spread across South India. The Early Iron Age of South India is implicit either in the form of burial sites, habitation sites, habitation cum burial sites, Iron Age rock art sites, and isolated iron smelting localities near a habitation or burials. This paper is an attempt to take a rough computation of the potentiality of the labour, technology and quantity of artifact output that this cultural phase might have once had, in micro or in macro level. Considering the emergence of technology and its enormous output in Ceramics, Agriculture, Metallurgy and Building up Burials as industries by themselves, that has economic, ethnographic and socio-technique archaeological imprints. This helps in understanding two aspects: one, whether they were nomadic, semi settled or settled at one location; two, the Diffusion versus Indigenous development. A continuity of late Neolithic phase is seen into Early Iron Age and amalgamation of Early Iron Age with the Early Historic Period as evident in the sites like Maski, Brahmagiri, Sanganakallu, Tekkalakota, T-Narasipur. In few cases, Iron Age folks migrated from one location to the other and settled on the river banks in large scale like that in Hallur and Koppa. In rare cases, they preferred to climb up the hill and stay on the rocky flat surface for example Aihole and Hiere Bekal– sites which are located close to or on the banks of the river or its tributaries of Krishna-Tungabhadra- Kaveri.Keywords: Labour, Industry, Production, Megaliths, Nomadic, Semi Settled, Early Iron Age.

scholarly journals Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jiguang Wang ◽  
Hossein Khiabanian ◽  
Davide Rossi ◽  
Giulia Fabbri ◽  
Valter Gattei ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Evolutionary History ◽  
Directed Graphs ◽  
Evolutionary Process ◽  
Genetic Alterations ◽  
Lymphocytic Leukemia ◽  
Cross Sectional ◽  
History Of ◽  
Evolutionary Paths ◽  
Clonal Replacement

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

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