scholarly journals Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aaron D. Smith ◽  
Marcin J. Kamiński ◽  
Kojun Kanda ◽  
Andrew D. Sweet ◽  
Julio L. Betancourt ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Essential Components ◽  
History Of ◽  
Species Dynamics ◽  
Reference Sequences ◽  
Past Climate Change ◽  
Potential Inhibitors ◽  
Over Time

AbstractThe study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.

scholarly journals Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Jiekun He ◽  
Siliang Lin ◽  
Jiatang Li ◽  
Jiehua Yu ◽  
Haisheng Jiang
Keyword(s):  
Tibetan Plateau ◽  
Evolutionary History ◽  
The Tibetan Plateau ◽  
Change Over Time ◽  
Deep Time ◽  
Terrestrial Vertebrates ◽  
History Of ◽  
Striking Change ◽  
Time Periods ◽  
Over Time

AbstractThe Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.

scholarly journals Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

2006 ◽  
Vol 2 (3) ◽  
pp. 451-454 ◽  
Author(s):  
Nikos Poulakakis ◽  
Aris Parmakelis ◽  
Petros Lymberakis ◽  
Moysis Mylonas ◽  
Eleftherios Zouros ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Eastern Mediterranean ◽  
Multiple Displacement Amplification ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Mediterranean Islands ◽  
Amplification Method ◽  
History Of

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10 000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cyt b ) DNA fragments from 4200 to 800 000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800 000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas , suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus , seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas .

scholarly journals The past, present and future of ancient bacterial DNA

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Nicolas Arning ◽  
Daniel J. Wilson
Keyword(s):  
Demographic Transition ◽  
Dental Plaque ◽  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Industrial Revolution ◽  
Environmental Isolates ◽  
Bacterial Dna ◽  
Content Type ◽  
The Past ◽  
History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

Ancient DNA Clarifies the Evolutionary History of American Late Pleistocene Equids

2008 ◽  
Vol 66 (5) ◽  
pp. 533-538 ◽  
Author(s):  
Ludovic Orlando ◽  
Dean Male ◽  
Maria Teresa Alberdi ◽  
Jose Luis Prado ◽  
Alfredo Prieto ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Ancient Dna ◽  
Evolutionary History ◽  
History Of

scholarly journals Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
E. Hekkala ◽  
J. Gatesy ◽  
A. Narechania ◽  
R. Meredith ◽  
M. Russello ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Sister Group Relationship ◽  
Molecular Fossil ◽  
Close Relationship ◽  
History Of ◽  
Competing Hypotheses

AbstractAncient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

scholarly journals НОВЫЕ АРХЕОЗООЛОГИЧЕСКИЕ ИССЛЕДОВАНИЯ СРЕДНЕВЕКОВОГО БИЛЯРА

2021 ◽  
pp. 90-95
Author(s):  
Диляра Наилевна Шаймуратова ◽  
Игорь Васильевич Аськеев ◽  
Зуфар Гумарович Шакиров
Keyword(s):  
New York ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Archaeological Sites ◽  
Special Issue ◽  
Middle Volga Region ◽  
Cambridge University ◽  
History Of ◽  
Molecular Assessment ◽  
Middle Volga

В статье представлено новое исследование остатков рыб и птиц из раскопа XLIV Билярского городища, заложенного с целью изучения крупного кирпичного здания, который располагался в так называемом «Внутреннем городе» – наиболее статусной его части. Целью работы являлся комплексный анализ фаунистических остатков, извлеченных из культурного слоя методом послойного отбора с просеиванием. По костным остаткам и чешуе определено 23 вида рыб с преобладанием остатковкрупноразмерных видов: севрюги, судака, стерляди и белорыбицы. Преобладание крупноразмерных видов указывает на то, что промысел велся на Волге и Каме, и основной состав рыб, употреблявшихся на городище, был привозной. Видовой состав птиц высок и разнообразен – 40 видов диких и 3 вида домашних птиц с доминированием домашней курицы. Среди диких птиц интересны находки элементов скелета хищных птиц из отряда Ястребиных и отряда Соколов, что указывает на наличие соколиной охоты на данном местонахождении и его высокий социальный статус. Библиографические ссылки Аськеев И.В., Галимова Д.Н., Аськеев О.В. Ихтиофауна позднего голоцена Средневолжского бассейна (по материалам археологических раскопок) // Зоологический журнал. 2013а. Т. 92. №. 9. С. 1014−1030. Аськеев И.В., Галимова Д.Н., Аськеев О.В. Птицы Среднего Поволжья в V–XVIII вв. н.э. (по материалам археологических раскопок) // Поволжская археология. 2013б. № 3 (5). С. 116–144. Аськеев И.В., Галимова Д.Н., Аськеев О.В. Домашние и дикие птицы из средневековых археологических памятников Среднего Поволжья // Динамика современных экосистем в голоцене / Материалы Третьей Всероссийской научной конференции (с международным участием). Казань: Отечество, 2013в. С. 72–77. Бадеев Д.Ю., Худяков А.В., Шакиров З.Г. Археологические исследования на территории Билярского комплекса в 2016–2017 гг. // Археологические открытия. 2017 год / Отв. ред. Н.В. Лопатин. М.: ИА РАН, 2019. С. 331–334. Галимова Д.Н., Аськеев И.В., Аськеев О.В. Изучение остатков рыб и птиц из археологических раскопок древних городов Биляр, Болгар и Свияжск // Труды IV (XX) Всероссийского археологического съезда в Казани. Т. V. / Отв. ред. А.П. Деревянко, Н.А. Макаров, А.Г. Ситдиков. Казань: Отечество, 2015. С. 35−37. Худяков А.В., Набиуллин Н.Г., Шакиров З.Г., Шорохов М.В. Археологические Раскопки на территории Билярского городища и Балынгузского кладбища в 2018–2019 гг. // Археологические открытия. 2019 год. (В печати). Хузин Ф.Ш., Шакиров З.Г. Археологические исследования на Билярском городище // Археологические открытия. 2015 год / Отв. ред. Н.В. Лопатин. М.: ИА РАН, 2017. С. 326–328. Шаймуратова Д.Н. Особенности изучения субфоссильных остатков рыб и птиц из археологических памятников Среднего Поволжья и их экологическая интерпретация // Российский журнал прикладной экологии. 2016. № 1. С. 8–13. Galimova D.N., Askeyev I.V. and Askeyev O.V. Bird Remains from 5th – 17th Century AD Archaeological Sites in the Middle Volga Region of Russia // International Journal Osteoarchaeology. Special Issue. 2014. P. 347–357. Honka J., Heino M.T., Kvist L., Askeyev I.V., Shaymuratova D.N., Askeyev O.V., Askeyev A.O.,Heikkinen M.E., Searle J.B., Aspi J. Over a thousand years of evolutionary history of domestic geese from Russian archaeological sites, analysed using ancient DNA. 2018. Genes. №9 (7). P. 367. Lebrasseur O., Shaymuratova D., Askeyev A., Asylgaraeva G., Frantz L., Larson G., Askeyev O., Askeyev I. A zooarchaelogical and molecular assessment of ancient Chicken remains from Russia // Поволжская археология. 2021. №1 (35). С. 216–231. Serjeantson D. Birds. Cambridge Manuals in Archaeology. New York: Cambridge University Press, 2009. 512 р.

scholarly journals Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Guilian Sheng ◽  
Jiaming Hu ◽  
Haowen Tong ◽  
Bastien Llamas ◽  
Junxia Yuan ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Northern China ◽  
Old World ◽  
History Of

scholarly journals Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 367 ◽  
Author(s):  
Johanna Honka ◽  
Matti Heino ◽  
Laura Kvist ◽  
Igor Askeyev ◽  
Dilyara Shaymuratova ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Early Period ◽  
Mitochondrial Control Region ◽  
Archaeological Sites ◽  
Anser Anser ◽  
Bean Goose ◽  
Base Pair Fragment ◽  
History Of ◽  
Greylag Goose

The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th–18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.

scholarly journals Entanglements of Time, Temperature, Technology, and Place in Ancient DNA Research: The Case of the Denisovan Hominin

2019 ◽  
Vol 45 (6) ◽  
pp. 1119-1141
Author(s):  
Venla Oikkonen
Keyword(s):  
Population Genetics ◽  
Ancient Dna ◽  
Science And Technology Studies ◽  
Evolutionary History ◽  
Science And Society ◽  
Hominin Evolution ◽  
The Status ◽  
History Of ◽  
Specific Configuration

The study of ancient DNA (aDNA) has gained increasing attention in science and society as a tool for tracing hominin evolution. While aDNA research overlaps with the history of population genetics, it embodies a specific configuration of technology, temporality, temperature, and place that, this article suggests, cannot be fully unpacked with existing science and technology studies approaches to population genetics. This article explores this configuration through the 2010 discovery of the Denisovan hominin based on aDNA retrieved from a finger bone and tooth in Siberia. The analysis explores how the Denisovan was enacted as a technoscientific object through the cool and even temperatures of Denisova Cave, assumptions about the connection between individual and population, the status of populations as evolutionary entities, and underlying colonialist and imperialist imaginaries of Siberia and Melanesia. The analysis sheds light on how aDNA research is changing the parameters within which evolutionary history is imagined and conceptualized. Through the case study, it also outlines some ways in which the specific technoscientific and cultural entanglements of aDNA can be critically explored.

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